From 44c03e2d5f0dd544242aadad3b32ddfcbd3933d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 31 Oct 2018 17:39:17 +0100 Subject: [PATCH 001/546] merge bulk into master (#11728) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1  (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN packages lacking license file * Add missing libnetcdf requirement to bioconductor-mzr * Remove r-alakazam (moved to conda-forge) Fix linting issue: ``` recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating ``` * [BULK] Many R 3.5 only packages (#11410) * [BULK] Bulk update 191018b (#11419) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1  (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN packages lacking license file * Add missing libnetcdf requirement to bioconductor-mzr * Remove r-alakazam (moved to conda-forge) Fix linting issue: ``` recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating ``` * [BULK] Many R 3.5 only packages (#11410) * Update pinning to R>=3.5 and a few runtime dependencies. * CSAW is R 3.5 only * Packages using beachmat are 3.5 only * Packages using bioconductor-singlecellexperiment are R 3.5 only * [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452) * Don't use r-base >=3.5, use a conda_build_config.yaml instead * blacklist r-phangorn * Update variancepartition * R 3.5 for packages requiring singlecellexperiment * Update a few packages * Update a number of recipes (#11482) * Update ensemblVEP and derfinder (#11504) * Bulk update 251018 (#11577) * [BULK] various package updates * blacklist bioconductor-mzr * A couple tweaks * [BULK] Update 261018 (#11611) * Apparently the r-rgeos bit works properly now. * Add tissueenrich and try to fix scpipe on Linux * A meaningless change just to trigger an update in bulk. (#11618) * [BULK] update 271018 (#11628) * Bump bioconductor-esetvis * Fix yaqcaffy * Fix more * Another R 3.5 recipe * [BULK] update 281018 (#11689) * Add some files * Fix arrayexpress * Fix another 2 * Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697) * Update blacklist (#11706) * [BULK] fix bioconductor-tissueenrich (#11720) * taxonkit 0.2.5 (#11318) * Update csvtk (#11319) * taxonkit 0.2.5 * csvtk 0.15.0 * bumping GROOT to 0.8.1 (#11323) * HiCMatrix version 3 (#11322) * Correcting dependencies * Version 3 of HiCMatrix, the October release * Update confindr to 0.4.3 (#11330) * Drop-seq_tools: Version 2.0.0 (#11326) * Update meta.yaml * Update build.sh some tool names changed to fit Camel case * Update motus to build only for python3 (#11331) * Update fpa to 0.2 version (#11333) * update taxonkit to 0.3.0 (#11339) * ntcard 1.1.0 (#11338) * Update rgi (#11335) * first commit * update dependencies list * change source to github * change build number * testing circleci * update meta and build * fix build * move build script into meta * remove older recipes * line fix in bootstrap.py * change python & matplotlib versions; add build.sh file * add preprocessing selector to skip python 2.7 * move build script into meta.yaml * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046. * Update gmap to version 2018-07-04. (#11332) MAX_READLENGTH environment variable has been disused since 2016-08-16. * Upgrade r-biodb to 1.2.0a. (#11341) * Upgrade r-biodb to 1.2.0a. * Update meta.yaml * Updated ont-tombo to version 1.5. (#11329) * Updated ont-tombo to version 1.5. * Updated with actual github release version hash. * remove graphicsmagick (#11342) * Build kraken2 for osx (#11343) * First try for a bcalm recipes (#11344) * New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347) - cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig generation and manipulation command line tools including bam to bigwig conversion. - bcbio: fixes for QC on variants and peddy for CWL runs * Try avoid some dependancy (#11349) * Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348) * Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 Also add about:home . * Workaround https://github.com/conda-forge/bison-feedstock/issues/7 * Better bcalm recipes (#11350) * Try avoid some dependancy * Correct mess in build number, sorry * R biodb (#11351) * rebuild r-biodb * trigger build * Add recipe for pypairs (#11356) * Update smoove to 0.2.1. (#11360) * Update duphold to 0.0.9. (#11359) * Update goleft to 0.2.0 (#11361) * Bump slicedimage to 1.0.0 (#11362) * Bump slicedimage to 1.0.1 (#11365) * Added new versions for biopet-sampleconfig (#11268) * perl-velvetoptimiser: update to 2.2.6 (#11369) * update to 2.2.6 * remove unneeded patch * Scanpy upgrade (#11371) * Bump version * Upgrade Scanpy * Bump starfish to 0.0.25 (#11370) * bumping groot to 0.8.2 (#11374) * vep: bump subversion (#11367) * Updated Krocus 1.0.1 (#11355) * Add tiptoft * Fix meta.yaml for tiptoft * Add build script * Updated krocus 1.0.1 * Add tiptoft 0.1.4 (#11352) * Add tiptoft * Fix meta.yaml for tiptoft * Add build script * Kodoja v0.0.9 (#11373) * Add recipe for seer (#11263) * Add recipe for seer * lets try this * Add newer compiler * Using boost-cpp * messed up version string * Attempt building boost * Use c++11 in boost * Use python for boost install * Correct python version spec * try with different python version * Fix b2 command * Fix popd command * build and link boost program options statically * Fix tests * Match dependency order * Link openblas instead of blas * Forcing rebuild with openblas * Don't use armadillo wrapper * Making review changes. Also trying original tests * Previous tests were correct * Add recipe for the translate-gard npm package version 1.0.3 (#11364) * Fix umi tools (#11376) umi_tools: clean up dependencies * add support tools to PATH (#11379) * Bump to v2.2.1 (#11380) * Bump starfish to 0.0.26 (#11378) * Update fpa to 0.3 (#11375) * Update fpa to 0.3 * Correct error in sha256 * Reset build number * Update trial to 2.5.5 (#11386) * Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388) * Update: bioconductor-titancna; 1.19.1 with hg38 support * Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled * Add r-polysat version 1.7-3 (#11384) * Update biomart version so that compatible with r351 (#11366) * Update biomart version so that compatible with r351 * Update meta.yaml reset build number as per https://bioconda.github.io/guidelines.html#buildnum * Update entrez-direct to 10.0.20180927. (#11387) * Added recipe for SonicParanoid 1.0.13 (#11271) * Added recipe for SonicParanoid 1.0.13 * removed 'x.x' for numpy, added basic test * fixed linter related errors * compiler set to cxx and added host section (same build error!) * removed host section * moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md * removed build: noarch * added build and extra sections * set build number to 0; removed skip build; added python3 minimum version; added test for all executables. * restored sh python module as requirement * added Make to run; updated release to latest commit * remove c compiler from meta.yaml * modified build.sh to compile source codel added make in build section * updated to latest commit * updated to latest version with make included in setup.py * reverted build.sh to the simplest version (python setup.py install) * Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389) * Bump IgBLAST to 1.9.0 (#11393) Bump IgBLAST to 1.9.0 Re-package the binary version this time. There are problems building the source version when the configure script reaches this step: "trying to build the NCBI SRA/VDB Toolkit from GitHub" The previous problem about the binaries linking against libbz2.so, for which we had no conda package, is now solved. Also, this saves about 45 minutes compilation time. * Add consan (#11395) * Add consan * Skip osx * Update: vardict, vardict-java 1.5.7 (#11394) * Update: vardict, vardict-java 1.5.7 Latest vardict-java release and corresponding vardict with bug fixes after testing with 1.5.6 * Reduce test output to try and fix build problems * Experiment 2 for build problems: remove r-base from run * Experiment 3 for build problems: add r-base in host * update recipe for 3.9.1 (#11397) * evofold2 (#11396) * evofold2 * wrapper * Update meta.yaml * minor * Update rnastructure to 6.1. (#11400) * Ctat mut (#11401) * updating version number * correct URL * proper hash * Revert "Ctat mut (#11401)" (#11402) This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0. * update version (#11403) * any2fasta 0.4.2 (new formula) (#11407) * W4mclassfilter v0.98.9 (#11385) * Added files to build version 0.98.9 * Update meta.yaml * Update meta.yaml * updated SonicParanoid recipe to version 1.0.14 (#11409) * updated SonicParanoid recipe to version 1.0.14 * Update to version 1.0.2 of PopDel (#11398) * Update to version 1.0.2 of PopDel Update to version 1.0.2. * Reset build number to 0 * PacBio: require Meson 0.48.1 for all recipes (#11090) * Meson 0.47 inserted duplicate RPATHs in macOS binaries, causing `install_name_tool` failures when installing the package. Requiring 0.48.1 ensures we do not run into these issues anymore in the future. * rebuild with latest openmpi (#11411) * Remove kfoots from the blacklist (#11416) * Update gseapy to 0.9.7 (#11417) * Update gseapy to 0.9.7 * remove noarch * Add SC3 as dependency (#11427) * Add recipe for r-poppr (#11418) * Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412) * Update IQ-TREE to 1.6.7.1 (#11429) * Update IQ-TREE to 1.6.7.1 * Change build number * Update: r-deconstructsigs with fixes for hg38 (#11431) The 1.8.0 release, from 2016, has some issues with hg38 and other custom genomes that are fixed in development (raerose01/deconstructSigs#27). There hasn't been a new release pushed so this rolls these into a new sub-version and makes them available. * Update entrez-direct to 10.2.20181018. (#11432) * Add assembly-scan recipe (#11425) * remove python 2.7 skip (#11424) Preparation for rnaQUAST * Add fastq-scan recipe (#11415) * Add patch to fix racon/rampler path in racon_wrapper. (#11434) Fixes #11405. * meme rebuild (#11433) * Update nanocomp to 0.23.1 (#11436) * Update nanocomp to 0.23.1 * remove noarch * Update abricate to 0.8.10 (#11446) * Update angsd to 0.923 (#11445) * Update alfred to 0.1.13 (#11444) * Update alfred to 0.1.13 * Try w/o patch * Update antarna to 2.0.6 (#11442) * Update admixtools to 5.1 (#11443) * Update admixtools to 5.1 * Let makefile choose which bins to install * Update alignstats to 0.5 (#11441) * Update xatlas to 0.2.1 (#11437) * r-gpca (#11428) * r-gpca * r-gpca recipe * Update meta.yaml * Removed All Comments * gseapy bump version 0.9.8 (#11440) * gseapy bump version 0.9.8 * version * titancna: fix for hg38, remove conda build hacks (#11447) * titancna: fix for hg38, remove conda build hacks * Re-add r-base 3.4 pin to avoid 3.5 errors * Hmmlearn older version (#11450) * Adding pygtftk * removed pygtftk from master * add older version of hmmlearn * Add card_trick (#11451) * Add card_trick * Restrict to py3 * Update checkm-genome to 1.0.12 (#11455) * Bump drep (#11457) * Update squid to 1.5 (#11466) * Update ncbi-ngs-sdk to 2.9.3 (#11467) * elprep: bumped major version (#11414) * elprep: bumped major version * fixed hash * fix download link, fixed licence * fixed tests * skip osx build * FRED2 as a conda package (#11469) * Attempt to get FRED2 as a conda package * SHA update * 99 little bugs in the code * Fix things Björn mentioned * add rnaQUAST recipe (#11470) * Update bioconda-utils to 0.14.9 (#11454) * Rapidup (#11474) * Update to v0.7 * Update Buildnumber * rapid: update to v0.6 * rapid: update to v0.6 * update grid (#11478) * Adding biobb_model recipe (#11472) * Updated wtdbg to v2.1 (#11486) * update stream to 0.2.6 (#11483) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * Update meta.yaml (#11487) * Update connectome-workbench to 1.3.2 (#11468) Now needs QT 5.7 * Update deblur to 1.1.0 (#11500) * Update domclust to 1.2.8 (#11498) * WisecondorX: bump version (#11501) * Bump as GitHub wasn't working yesterday (#11502) * Added recipe for Sequenza (#10367) * Added recipe for Sequenza * Removed fn entry in source section * Trying with only one URL * copynumber is a bioconductor package * Added missing requirements section * Removed mailing list address * Added doi * Added license_file * Trying with different license_file path * Fred2 bump (#11503) * Bump as GitHub wasn't working yesterday * Fix licence etc * Scanpy scripts (#11413) Doing squash and merge as requested by @nh3 * Bump version * First implementation of scanpy-scripts bioconda recipe. * fix path in build.sh * Remove "noarch" flag as requested by bioconda recipe checklist * Add a post install notice that post install test needs bats-core. * Add more dependencies * Skip building for python versions other than 3.6 * Target v0.0.2 which has non-ascii characters removed * Lower version requirement for pandas and matplotlib to be the same as scanpy * Requirement matplotlib>=3.0.0, declare noarch * New: hmftools-cobalt; Update: hmftools-purple (#11507) - hmftools-cobalt: Add latest version of PURPLE associated read counter, COBALT, with support for hg38. - hmftools-purple: PURPLE release with hg38 support. * Update Picard to 2.18.15. (#11505) * Genenotebook (#11476) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * dependency versions * v0.1.5 * Update pinning (#11514) * Bump build number for updated dependency (#11510) * Bump build number for updated dependency * Try adding r-base to host requirements * Try adding other requirements to host * Pin to R version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Tweak dependency version syntax * Pin R and package versions correctly * PacBio: Update pbcore to 1.6.5 (#11513) * Bump r seurat scripts version (#11292) * Bump version * Remove noarch * Could wrongly quoted version be causing an issue? * Tweak pinning to try and fix CI error * seqcluster:fix UMI detection. (#11511) * seqcluster:fix UMI detection. * Fix dependency * quast 5.0.1 (#11479) * quast 5.0.1 * quast 5.0.1: remove third-party site packages from the distibution pack * quast 5.0.1: skip Glimmer in test * quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build) * quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build) * quast 5.0.1: Python 2 and 3 compatible code in build.sh * wcX bugfixes (#11508) * wcX bugfixes * fixed shasum * Update fastspar to 0.0.7 (#11515) * Update iqtree to 1.6.7.2 (#11525) * Update illumina-interop to 1.1.6 (#11523) * Update hapbin to 1.3.0 (#11522) * Update hlama to 3.0.1 (#11520) * Update gb_taxonomy_tools to 1.0.1 (#11519) * Update gffcompare to 0.10.5 (#11517) * Update fast5seek to 0.1.1 (#11516) * Update deepbinner to 0.2.0 (#11499) * Update deepbinner to 0.2.0 * Update meta.yaml Try same fix as in #11240 * Update ncbi-vdb to 2.9.3 (#11550) * Update mikado to 1.2.4 (#11549) * Update perl-pcap to 3.5.2 (#11543) * Update python-hyphy-python to 0.1.9 (#11545) * Update mlst to 2.15.2 (#11547) * Update perl-sanger-cgp-vcf to 2.2.1 (#11542) * Update merfishtools to 1.5.0 (#11537) * Update perl-sanger-cgp-vagrent to 3.3.3 (#11536) * Update nonpareil to 3.3.3 (#11535) * Update prophex to 0.1.1 (#11532) * Update krakenuniq to 0.5.3 (#11527) * Update novoplasty to 2.7.2 (#11530) * Update minced to 0.3.2 (#11529) * Update mapdamage2 to 2.0.8 (#11528) * Update perl-sanger-cgp-allelecount to 4.0.0 (#11538) * Update pyvolve to 0.9.0 (#11531) * Genenotebook (#11512) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * add plek (#11554) * Update pyimzml to 1.2.4 (#11534) * Bump shovill (#11555) * PacBio: Update minimum pbcore version (#11556) * We want all users of PacBio tools to be able to use our utilities with pbmm2 alignments. * Add recipe for translate-gard v1.0.4 (#11557) * bioconductor-rnaseqsamplesizedata (#11475) * Adding Recipe for bioconductor-rnaseqsamplesizedata * Updated metadata for RnaSeqSampleSizeData * nextflow 18.10.1 (#11558) * Update raxml to 8.2.12 (#11567) * Update r-fgwas to 0.3.6 (#11566) * Update rapid to 0.7 (#11565) * Update r-spieceasi to 1.0.2 (#11564) * Update rcorrector to 1.0.3.1 (#11562) * Update quicktree to 2.4 (#11560) * Update paladin to 1.4.4 (#11541) * Update paladin to 1.4.4 * delete md5 * Update build.sh * Update build.sh * Fix and unblacklist Tadarida-D (#11568) * Add recipe for rgt * Fix and un-blacklist tadarida-d * Remove RGT * bumping groot (#11575) * update pymzml (#11573) * Add bioconductor-rnaseqsamplesize (#11559) * Add bioconductor-rnaseqsamplesize * Update recipe * Fixing some URLs * Update dependencies missing * Update trumicount to 0.9.11 (#11576) * Update ConFindr to 0.4.4 (#11578) * Added new versions for biopet-scatterregions (#11572) * Added new versions for biopet-bamstats (#11571) * R ggbiplot (#11584) * add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)' * add r-ggbiplot * update meta.yaml * update meta.yaml * update * update * update * update * update * update * update * update * update * fix errors * fix errors number 1 * Update rebaler to 0.1.2 (#11563) * Update rebaler to 0.1.2 * Remove fn * bump graphclust (#11585) * Update seqyclean to 1.10.09 (#11589) * Update stringmlst to 0.5.1 (#11590) * Update snp-dists to 0.6.2 (#11592) * Update snippy to 4.3.3 (#11596) * Update canu to 1.8 (#11600) * Update starfish to 0.0.27 (#11599) * Update womtool to 36 (#11594) * Update telseq to 0.0.2 (#11598) * Update snp-sites to 2.4.1 (#11588) * Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471) * Added recipe for pydemult * Bumped version in favor of py3.5 * bump vcf2db to latest commit (#11601) * bump vcf2db to latest commit * fix shasum * Fixing source url * Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604) * megan (#11046) * megan6: initial commit * megan6: intermediate commit * megan: made tests work * megan: doc improvement * megan: added osx dmg file * megan: add java to build requirements * megan: removed new line * megan: removed osx sources * Update meta.yaml * bumping hulk (#11607) * Update hotspot3d to 1.8.2 (#11521) * Update hotspot3d to 1.8.2 * Add perl-json as dependency * Add perl-archive-extract as dependency * Fqzcomp (#11606) * Added recipe for fqzcomp * There is no configure script * Maybe this works * Added gcc as build requirement * Removed gcc again (lint issue) * Maybe these exports will do the trick * Nope! * Added cxx as host requirement * Compilers are only allowed in build section * There is no need for make install * Copy-paste error... * Add vcf-annotator recipe (#11481) * Add vcf-annotator recipe * added pyvcf dependency * Update meta.yaml * stacks: fix for @ in exe_path (#11580) * stacks: fix for @ in exe_path * stacks: fixed path * New version with bugfix and different progressiveMauve version. (#11613) * Sspupdate (#11614) * New version with bugfix and different progressiveMauve version. * Keeping old version as folder. * Push build number. * Update SVDB to version 1.3.0 (#11506) * new file: recipes/svdb/1.1.2/meta.yaml renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch modified: recipes/svdb/meta.yaml * deleted: 1.1.2/meta.yaml deleted: 1.1.2/svdb.patch * Bump nanosim (#11608) * Bump nanosim * Add scipy as dep * Add recipe for perl-number-range (#11621) * New build for grid (#11620) * update grid * update build num * Recipe for das_tool 1.1.1 (#10528) * recipe for das_tool 1.1.1 * Add recipe for sompy (#11624) * cmake modified to build with NDEBUG (#11328) * cmake modified to build with NDEBUG * Update meta.yaml * new build with fasta test * new build with fasta test * Fix and unblacklist TwoPaCo (#11622) * Add recipe for TwoPaCo * Unblacklist twopaco * Modify and unblacklist recipe for ESTmapper (#11623) * Modify and unblacklist recipe for ESTmapper * Add patch * Modify and unblacklist recipe for Metaseq (#11625) * Fix recipe for metaseq and remove from blacklist * Remove build.sh * nextflow 18.10.1 build 2 (#11630) * Add Clust (#11619) * Add clust * Clean recipe * Add "noarch" * Add DOI * Add build file * Python 2.7 * Fix scikit-learn dependency * Trigger new build * Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631) - PureCN: adds support for specifying cores on command line - PURPLE: adds X library dependencies required for creating plots * scripts/travis-run.sh: added a cleaner method to check for env vars (#11612) * Increase the number of k value usable in bcalm (request by @Malfoy) (#11610) * Increase the number of k value usable in bcalm (request by @Malfoy) * Change compilation parameter to reduce memory impact of compilation * Update anndata to 0.6.11 (#11637) * Update nglview to 1.1.7 (#11643) * Update binsanity to 0.2.7.1 (#11644) * Update cgat-core to 0.5.4 (#11645) * Update nanosv to 1.2.2 (#11673) * Update abeona to 0.36.0 (#11670) * Update pyfaidx to 0.5.5.2 (#11659) * Update agfusion to 1.23 (#11668) * Update iqtree to 1.6.8 (#11686) * update iqtree to 1.6.8 * Trigger rebuild * Update validators to 0.12.2 (#11672) * Update python-edlib to 1.2.3.post1 (#11664) * update for Purge Haplotigs (#11690) * Update loompy to 2.0.16 (#11667) * Update loompy to 2.0.16 * Update meta.yaml * IgBLAST 1.10.0 (#11693) * Update wtforms-alchemy to 0.16.7 (#11679) * Update sickle to 0.6.4 (#11663) * Update sickle to 0.6.4 * Remove fn and libgcc runtime dep * Update confindr to 0.4.5 (#11696) * Batvi (#11695) * batvi initial * Guideline compatibility.. * Dummy test section.. * Missing java dependency.. * use openjdk instead of java-jdk .. * source specified in github .. * trigger build (package did not have batindel directory) .. * update SHA256 .. * update SHA256 .. * Update pythonpy to 0.4.11 (#11661) * Update cortexpy to 0.45.6 (#11660) * Update sevenbridges-python to 0.16.0 (#11674) * Update solvebio to 2.7.0 (#11657) * Update mathstats to 0.2.6.5 (#11656) * Update goatools to 0.8.9 (#11641) * Add gnies (#11627) * Add gnies * noarch python * Update meta.yaml * Add recipe for SKA v1.0 (#11581) * Add recipe for SKA v1.0 * Add lib path for zlib * Older gcc * Correct install dir * Try static linking * Dynamic linking on OS X * ldd command test * correct program * Remove ldd command * Add recipe for transit version 2.3.1 (#11701) * Add recipe for transit version 2.3.1 * Use skip, add spaces. * Update meta.yaml (#11699) * remove pyqi (#11704) * Update python-chado to 2.2.0 (#11714) * update python-chado * 2.2.1 * Update vcfanno to 0.3.1 (#11710) * FGMP-1.0.1 (#11278) * FGMP-1.0.1 recipe * remove unncessary build info * add r-nabor (#11716) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * add r-nabor recipe * update r-nabor recipe * update r-nabor recipe * r-pctgcdata (#11715) * r-pctgcdata * r-pctgcdata - fix * r-pctgcdata - fix * Update meta.yaml * Fix plek by a new branch (#11605) * Modify the PLEK recipe * Start fixing PLEK, though it requires compilation * update build.sh * update yaml * fix build.sh * update build.sh * Update recipe for plek * add bioconductor-chromvar recipe (#11718) * add bioconductor-chromvar recipe * fix bioconductor-tissueenrich * Apparently the popdel recipe didn't get correctly merged * Final merge conflicts --- build-fail-blacklist | 1366 ++--------------- recipes/bcbio-rnaseq/conda_build_config.yaml | 2 + recipes/bioconductor-a4base/meta.yaml | 40 +- recipes/bioconductor-a4core/meta.yaml | 15 +- recipes/bioconductor-a4preproc/meta.yaml | 15 +- recipes/bioconductor-a4reporting/meta.yaml | 12 +- recipes/bioconductor-abadata/meta.yaml | 10 +- recipes/bioconductor-abadata/post-link.sh | 12 +- recipes/bioconductor-abaenrichment/meta.yaml | 19 +- recipes/bioconductor-absseq/meta.yaml | 15 +- 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recipes/bioconductor-webbioc/conda_build_config.yaml create mode 100644 recipes/bioconductor-yapsa/conda_build_config.yaml create mode 100644 recipes/bioconductor-yaqcaffy/conda_build_config.yaml create mode 100644 recipes/bioconductor-zinbwave/conda_build_config.yaml delete mode 100755 recipes/r-alakazam/build.sh delete mode 100644 recipes/r-alakazam/meta.yaml create mode 100644 recipes/r-bcbiornaseq/conda_build_config.yaml create mode 100644 recipes/r-data.table/build.sh create mode 100644 recipes/r-data.table/meta.yaml create mode 100644 recipes/r-msqrob/conda_build_config.yaml create mode 100644 recipes/r-nanostringnorm/conda_build_config.yaml create mode 100755 recipes/seq-seq-pan/1.0.0/build.sh create mode 100644 recipes/seq-seq-pan/1.0.0/meta.yaml diff --git a/build-fail-blacklist b/build-fail-blacklist index bcf90e84a1bd4..b01b60c035c27 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -96,7 +96,8 @@ recipes/r-km.ci recipes/r-kmsurv recipes/r-kriging recipes/r-lsd -#recipes/r-maldiquant +recipes/r-maldiquant +recipes/r-matrixeqtl recipes/r-metarnaseq recipes/r-microseq recipes/r-mixomics @@ -104,9 +105,11 @@ recipes/r-mlgt recipes/r-mqtl recipes/r-pamr recipes/r-patpro +recipes/r-phangorn recipes/r-pinfsc50 recipes/r-plasmidprofiler recipes/r-precrec +recipes/r-propcis recipes/r-purbayes recipes/r-qiimer recipes/r-qtl @@ -152,1254 +155,9 @@ recipes/soapcoverage # download error recipes/soapaligner - -####### -# blacklist r-* packages, we will rebuild in 1 month against R3.5.1 -####### -recipes/r-adegenet -recipes/r-adephylo -recipes/r-alakazam -recipes/r-ampvis -recipes/r-annotables -recipes/r-aptreeshape -recipes/r-argumentcheck -recipes/r-aroma.affymetrix -recipes/r-aroma.core -recipes/r-asics -recipes/r-basejump -recipes/r-bcbiobase -recipes/r-bcbiornaseq -recipes/r-biclust -recipes/r-bio3d -#recipes/r-biodb -recipes/r-biom -recipes/r-biomark -recipes/r-boutroslabplottinggeneral -recipes/r-canopy -recipes/r-chbutils -recipes/r-cimpl 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-recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene -recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene -recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts -recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene -recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene -recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene -recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene -recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene -recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene -recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene -recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene -recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene -recipes/bioconductor-tximport -recipes/bioconductor-undo -recipes/bioconductor-unifiedwmwqpcr -recipes/bioconductor-uniprot.ws -recipes/bioconductor-uniquorn -recipes/bioconductor-vanillaice -recipes/bioconductor-variancepartition -recipes/bioconductor-variantannotation -recipes/bioconductor-variantfiltering -recipes/bioconductor-varianttools -recipes/bioconductor-vbmp -recipes/bioconductor-vega -recipes/bioconductor-vegamc -recipes/bioconductor-viper -recipes/bioconductor-vsn -recipes/bioconductor-watermelon -recipes/bioconductor-wavcluster -recipes/bioconductor-wavetiling -recipes/bioconductor-weaver -recipes/bioconductor-webbioc -recipes/bioconductor-wiggleplotr -recipes/bioconductor-xbseq -recipes/bioconductor-xde -recipes/bioconductor-xmapbridge -recipes/bioconductor-xvector -recipes/bioconductor-yamss -recipes/bioconductor-yapsa -recipes/bioconductor-yaqcaffy -recipes/bioconductor-yarn -recipes/bioconductor-yeastcc -recipes/bioconductor-yeastexpdata -recipes/bioconductor-zfpkm -recipes/bioconductor-zlibbioc - - # unknown recipes/smina + # missing tarball recipes/metagene_annotator recipes/sloika @@ -1643,8 +401,6 @@ recipes/vcftools/0.1.11 # zlib recipes/trimmomatic/0.35 - - # https://github.com/conda-forge/cairo-feedstock/issues/31 recipes/rdkit/2015.09.2 recipes/rdkit/2016.03.3 @@ -1917,6 +673,10 @@ recipes/cap-mirseq ############################################ # OSX related errors, Linux should be fine. # most of the non-perl issues are due to LLVM used as a compiler, GCC should be fine +recipes/cgat-scripts +recipes/shorah +recipes/smalt +recipes/perl-file-homedir recipes/snap recipes/perl-mixin-linewise recipes/perl-pod-coverage-trustpod/0.100003 @@ -1989,3 +749,111 @@ recipes/perl-moosex-app/1.39 ####################### OSX errors above ############### +############### R packages not in CRAN ################# +recipes/r-ampvis +recipes/r-annotables +recipes/r-basejump +recipes/r-bcbiobase +recipes/r-bcbiornaseq +recipes/r-biodb +recipes/r-boutroslabplottinggeneral +recipes/r-chbutils +recipes/r-cimpl +recipes/r-DGEclustering +recipes/r-dpeak +recipes/r-genometricorr +recipes/r-george +recipes/r-histonehmm +recipes/r-ichorcna +recipes/r-intego +recipes/r-lme4qtl +recipes/r-mmgenome +recipes/r-nastiseq +recipes/r-ncbit +recipes/r-ngsplot +recipes/r-ngsplot-hg19 +recipes/r-ngsplot-hg38 +recipes/r-ngsplot-mm10 +recipes/r-peer +recipes/r-phewas +recipes/r-pore +recipes/r-prestor +recipes/r-probmetab +recipes/r-qorts +recipes/r-quorts +recipes/r-raceid3 +recipes/r-rBLAST +recipes/r-rubic +recipes/r-sartools +recipes/r-scimpute +recipes/r-seurat-scripts +recipes/r-sleuth +recipes/r-soap-nmr +recipes/r-spieceasi +recipes/r-wasabi +recipes/r-workflowscriptscommon +recipes/r-xmlrpc +recipes/r-zerone +########### End R packages not in CRAN ################# + +# recipes/bioconductor-dbchip already exists +recipes/r-dbchip + +# Removed from CRAN +recipes/r-asics +recipes/r-biom + +# Deprecated in Bioconductor +recipes/bioconductor-atlasrdf +recipes/bioconductor-jmosaics +recipes/bioconductor-meshsim +recipes/bioconductor-mmdiff +recipes/bioconductor-mmnet +recipes/bioconductor-rcytoscape + +# Old bioconductor version that's no longer available +recipes/bioconductor-edger/3.12.1 +recipes/bioconductor-masigpro/1.49.4 + +# Old package, should we still build it? +recipes/bioconductor-org.dm.eg.db/3.3.0 +recipes/bioconductor-ggbio/1.22.0 + +# Errors with bioconductor-skeleton +recipes/bioconductor-mvgst + +# bioconductor-mzr has compilation problems and the others depend on it +recipes/bioconductor-mzr +recipes/bioconductor-camera +recipes/bioconductor-cosmiq +recipes/bioconductor-faahko +recipes/bioconductor-flagme +recipes/bioconductor-ipo +recipes/bioconductor-lobstahs +recipes/bioconductor-metab +recipes/bioconductor-metams +recipes/bioconductor-msmseda +recipes/bioconductor-msnbase +recipes/bioconductor-msnid +recipes/bioconductor-mspurity +recipes/bioconductor-pbase +recipes/bioconductor-profia +recipes/bioconductor-proloc +recipes/bioconductor-prolocgui +recipes/bioconductor-proteomicsannotationhubdata +recipes/bioconductor-risa +recipes/bioconductor-simat +recipes/bioconductor-synapter +recipes/bioconductor-xcms +recipes/bioconductor-yamss +recipes/r-george +recipes/r-msqrob +recipes/r-probmetab + +# Not actually bioconductor packages +recipes/bioconductor-sc3-scripts +recipes/bioconductor-scater-scripts +recipes/bioconductor-singlecellexperiment-scripts + +# post-link error +recipes/bioconductor-jaspar2018 diff --git a/recipes/bcbio-rnaseq/conda_build_config.yaml b/recipes/bcbio-rnaseq/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bcbio-rnaseq/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index 9c5df4660bd78..fff4e6e9d30ae 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "a4Base" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,35 +10,35 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5a6416fc098d10ad13114b608c251978eef4a43912f35079cb8b1d96ead6404e + sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-a4core - - bioconductor-a4preproc - - bioconductor-annaffy - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-genefilter - - bioconductor-limma - - bioconductor-multtest + - 'bioconductor-a4core >=1.28.0,<1.30.0' + - 'bioconductor-a4preproc >=1.28.0,<1.30.0' + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - bioconductor-a4core - - bioconductor-a4preproc - - bioconductor-annaffy - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-genefilter - - bioconductor-limma - - bioconductor-multtest + - 'bioconductor-a4core >=1.28.0,<1.30.0' + - 'bioconductor-a4preproc >=1.28.0,<1.30.0' + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-glmnet - r-gplots diff --git a/recipes/bioconductor-a4core/meta.yaml b/recipes/bioconductor-a4core/meta.yaml index 06311f2ddf22c..8ec76f661a614 100644 --- a/recipes/bioconductor-a4core/meta.yaml +++ b/recipes/bioconductor-a4core/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "a4Core" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3e14cc7aed4e38c2b4773cb2377c471750ed0e97752ce1031a7cd67c953a6fe9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3e71939ec82a11b5d9be7e28e744903fde2a3e58aa4ecc65138c7e8eaec4ac6b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-glmnet run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-glmnet test: diff --git a/recipes/bioconductor-a4preproc/meta.yaml b/recipes/bioconductor-a4preproc/meta.yaml index 64eb191173b8a..93c0437982550 100644 --- a/recipes/bioconductor-a4preproc/meta.yaml +++ b/recipes/bioconductor-a4preproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "a4Preproc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0b3c3aef87aab8de0a99eb489666f04e08d63f4a5e77394199f5094403970e15 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 84408d2da7e19431824560f1cd9cdd952539550dcfe5607b244220cc88e71042 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4reporting/meta.yaml b/recipes/bioconductor-a4reporting/meta.yaml index 8b3c4e057fbf0..ad23a41ee502c 100644 --- a/recipes/bioconductor-a4reporting/meta.yaml +++ b/recipes/bioconductor-a4reporting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "a4Reporting" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b13ae5accf3f94e5229a603b28e5dcbe3b820596c1319057fb966b122d641ec + sha256: 103e43eaff7834e74c85faf79b7af28a81fb33f148181989d8cf68aea1ccbd43 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annaffy + - 'bioconductor-annaffy >=1.52.0,<1.54.0' - r-base - r-xtable run: - - bioconductor-annaffy + - 'bioconductor-annaffy >=1.52.0,<1.54.0' - r-base - r-xtable test: diff --git a/recipes/bioconductor-abadata/meta.yaml b/recipes/bioconductor-abadata/meta.yaml index bf8295b31dfc7..e1d12b07d83a4 100644 --- a/recipes/bioconductor-abadata/meta.yaml +++ b/recipes/bioconductor-abadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ABAData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06d49593bb20b6a488667c115f85baaff903b616c55a1cc7132d0465b327b00c + sha256: 9fa25de3474c152697a6092a2599d57572c5af84101d861c8737afa1ade46734 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Provides the data for the gene expression enrichment analysis conducted in the package ''ABAEnrichment''. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes.' + + diff --git a/recipes/bioconductor-abadata/post-link.sh b/recipes/bioconductor-abadata/post-link.sh index 5d8e4d85d1db6..c126642788f2f 100644 --- a/recipes/bioconductor-abadata/post-link.sh +++ b/recipes/bioconductor-abadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ABAData_1.8.0.tar.gz" +FN="ABAData_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ABAData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/ABAData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-abadata/bioconductor-abadata_1.8.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ABAData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/ABAData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-abadata/bioconductor-abadata_1.10.0_src_all.tar.gz" ) -MD5="8571736104ead9ebccc282b0dfca0e6e" +MD5="cb4096c89b74d15232d431ffd41485f8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-abaenrichment/meta.yaml b/recipes/bioconductor-abaenrichment/meta.yaml index 2ca9c49c70d2d..7f0fa306cedbf 100644 --- a/recipes/bioconductor-abaenrichment/meta.yaml +++ b/recipes/bioconductor-abaenrichment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ABAEnrichment" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,31 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a17c26cb3ee7b80d577caac9a36ca2c4ca50e28ca6a0f92d0563a98561b15f50 + sha256: dc12cd6e10754bc0f49a84c6d8c4614bb65322009c02db2bdb8d0aaa2d019703 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-abadata >=0.99.2' + - 'bioconductor-abadata >=1.10.0,<1.12.0' - r-base - 'r-data.table >=1.10.4' - 'r-gplots >=2.14.2' - 'r-gtools >=3.5.0' - 'r-rcpp >=0.11.5' run: - - 'bioconductor-abadata >=0.99.2' + - 'bioconductor-abadata >=1.10.0,<1.12.0' - r-base - 'r-data.table >=1.10.4' - 'r-gplots >=2.14.2' - 'r-gtools >=3.5.0' - 'r-rcpp >=0.11.5' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-absseq/meta.yaml b/recipes/bioconductor-absseq/meta.yaml index c6f6de839956f..2e9c8c1182675 100644 --- a/recipes/bioconductor-absseq/meta.yaml +++ b/recipes/bioconductor-absseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.1" %} {% set name = "ABSSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9467de188893affa2ea59769a52f906ab93a7f2e8d6c1d0b628d42398d8254ee + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2ba8585d98a89573cece046d30bf59cc9c9ef8042a68c6d75546f74e6755c156 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-locfit run: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-acde/meta.yaml b/recipes/bioconductor-acde/meta.yaml index 9e1321a166e88..18613c4e27530 100644 --- a/recipes/bioconductor-acde/meta.yaml +++ b/recipes/bioconductor-acde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "acde" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4f629daffd0be79c37d2ea1d8600b4285c652260e41f91c58d40eedddcf1cb41 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: efe908ae1b6f31a719a6de6755dbd1e885d83f9844260d2f0856a9b7a7b889c3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index d1d2b1955dfa0..9b02efde5f943 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "aCGH" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89140e9ca6bd5586e3823482c93d6b2a363924338e710c12bd14d399e395e820 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: be3bb6a3584612c0c51a96b0c2d0847e7d5bcb806f48e2182f2b578c8f955ce1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-cluster - r-survival run: - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-cluster - r-survival + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index f704db53a9d8e..7bac099299623 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "ACME" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2644d22e9892b6e0d7fcecfd9fddbefcfa502306be195ff3559f4e5ab867fad8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 68f30578cc39397ebe5d1d4cd0d46daa4a1d99af0d15b78abb9bd777369a3227 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-adsplit/meta.yaml b/recipes/bioconductor-adsplit/meta.yaml index ccc0510c9cfd1..985d911d24ecb 100644 --- a/recipes/bioconductor-adsplit/meta.yaml +++ b/recipes/bioconductor-adsplit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "adSplit" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,35 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ca161b19138510145ea8c1ebb1129b247764435ae17ac9ef2bbf99360bc57b8d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5886e5d91dfa9c5bd859a0c6d158036a74dc8413f4874bc9fa7bbca46852257e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-biobase >=1.5.12' - - 'bioconductor-go.db >=1.8.1' - - 'bioconductor-kegg.db >=1.8.1' - - 'bioconductor-multtest >=1.6.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - 'r-cluster >=1.9.1' run: - - bioconductor-annotationdbi - - 'bioconductor-biobase >=1.5.12' - - 'bioconductor-go.db >=1.8.1' - - 'bioconductor-kegg.db >=1.8.1' - - 'bioconductor-multtest >=1.6.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - 'r-cluster >=1.9.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,3 +44,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.' + + diff --git a/recipes/bioconductor-affxparser/meta.yaml b/recipes/bioconductor-affxparser/meta.yaml index cb351d35f2c20..18e5489453824 100644 --- a/recipes/bioconductor-affxparser/meta.yaml +++ b/recipes/bioconductor-affxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "affxparser" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c94141d33ca4aafc0ca566d57c6ed65c6bdc4d87f63af2226ee3da7344c9dfdb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: de99cca0efd768fe216b1775b4942d12786d3a630cc2685cef933377f2140ffb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix'' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.' + + diff --git a/recipes/bioconductor-affy/conda_build_config.yaml b/recipes/bioconductor-affy/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affy/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index ed4b825f2158b..92b0d60752a38 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "affy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,35 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 327b0d7ae506632b5c9c0a4f5b527b04fd4bc91be0f63167d3ce15556b9cab4a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 26cef02431581909471bb637ba03c736fde6787699593c9c0ea2bea8cb41b86b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affyio >=1.13.3' - - 'bioconductor-biobase >=2.5.5' - - 'bioconductor-biocgenerics >=0.1.12' - - bioconductor-biocinstaller - - bioconductor-preprocesscore - - bioconductor-zlibbioc + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - 'bioconductor-affyio >=1.13.3' - - 'bioconductor-biobase >=2.5.5' - - 'bioconductor-biocgenerics >=0.1.12' - - bioconductor-biocinstaller - - bioconductor-preprocesscore - - bioconductor-zlibbioc + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. ''affy'' is fully functional without it.' - extra: identifiers: - biotools:affy diff --git a/recipes/bioconductor-affycomp/meta.yaml b/recipes/bioconductor-affycomp/meta.yaml index f6b2c39f2f937..92cdde798083c 100644 --- a/recipes/bioconductor-affycomp/meta.yaml +++ b/recipes/bioconductor-affycomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "affycomp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a093b51ee32c5bdbfa5cef6becf3f3a2fc0f41dbf93ee63363fd815fe2af9389 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 3bd3f4f9ba63776a9549add57b11c74d2126ea1c14793bec6a8b53d9df7b4dc9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.3.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=2.3.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycompatible/meta.yaml b/recipes/bioconductor-affycompatible/meta.yaml index 84943d2640dbf..cb2f1afa4482f 100644 --- a/recipes/bioconductor-affycompatible/meta.yaml +++ b/recipes/bioconductor-affycompatible/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "AffyCompatible" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dabe92e445fd643b3bc148128f4218cb51aff2c50b3a368cb380eafc1abdbdd3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a431003b26362db8565aa83c474cd8b3f8c29a2bab34ca0a85689f520a4cf0cb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - - 'r-rcurl >=0.8_1' - - 'r-xml >=2.8_1' + - 'r-rcurl >=0.8-1' + - 'r-xml >=2.8-1' run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - - 'r-rcurl >=0.8_1' - - 'r-xml >=2.8_1' + - 'r-rcurl >=0.8-1' + - 'r-xml >=2.8-1' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affycontam/conda_build_config.yaml b/recipes/bioconductor-affycontam/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affycontam/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml index 67b7cca2cf8f5..5daf7ca87f605 100644 --- a/recipes/bioconductor-affycontam/meta.yaml +++ b/recipes/bioconductor-affycontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "affyContam" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 68e72b5f5ff1eb8113a9eda1cf4cdcd19315604baf0a42bc10df182f427d529f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: afc3e450d15878232ad906959da83cd71b24516b35b86b718f37f600db78bd29 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-affydata - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affydata >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-affy - - bioconductor-affydata - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affydata >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycoretools/conda_build_config.yaml b/recipes/bioconductor-affycoretools/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affycoretools/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml index 5982b67280f30..caaccedaebb87 100644 --- a/recipes/bioconductor-affycoretools/meta.yaml +++ b/recipes/bioconductor-affycoretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.6" %} +{% set version = "1.52.2" %} {% set name = "affycoretools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: af0aa0483887713cf99cde3a715f84343bcf0815650c599432d5ea6b2999a585 + sha256: 463446ea737148d9273378fb9c0823daebe36a00e3489db7431e7714fd294691 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-edger - - bioconductor-gcrma - - bioconductor-gostats - - bioconductor-limma - - bioconductor-oligoclasses - - bioconductor-reportingtools - - bioconductor-s4vectors + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-reportingtools >=2.20.0,<2.22.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - r-ggplot2 @@ -38,17 +38,17 @@ requirements: - r-rsqlite - r-xtable run: - - bioconductor-affy - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-edger - - bioconductor-gcrma - - bioconductor-gostats - - bioconductor-limma - - bioconductor-oligoclasses - - bioconductor-reportingtools - - bioconductor-s4vectors + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-reportingtools >=2.20.0,<2.22.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - r-ggplot2 diff --git a/recipes/bioconductor-affydata/conda_build_config.yaml b/recipes/bioconductor-affydata/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affydata/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index e2b3e731a7512..87b08e0c5f6e5 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "affydata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3d63aed8f6b9a0f5a9cd07773bacccaf7a9b67f111b8e6b5e589b46126c42d66 + sha256: 70ba50c00b2739b59de4191ec17f4faef9341e53576f7e065a5b4649de966ab0 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.23.4' + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base run: - - 'bioconductor-affy >=1.23.4' + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Example datasets of a slightly large size. They represent ''real world examples'', unlike the artificial examples included in the package affy.' + + diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index 0c3bdab3c30c7..c6919eeb1f0f2 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="affydata_1.26.0.tar.gz" +FN="affydata_1.28.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/affydata_1.26.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.26.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/affydata_1.28.0.tar.gz" + "https://bioarchive.galaxyproject.org/affydata_1.28.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.28.0_src_all.tar.gz" ) -MD5="32d863de539466d38f567ac5289ee873" +MD5="e1e5523f0ee6fd8be2900b693b9bb73d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-affyexpress/conda_build_config.yaml b/recipes/bioconductor-affyexpress/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affyexpress/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affyexpress/meta.yaml b/recipes/bioconductor-affyexpress/meta.yaml index eb363c14a67f5..54d55d3514f9a 100644 --- a/recipes/bioconductor-affyexpress/meta.yaml +++ b/recipes/bioconductor-affyexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "AffyExpress" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dcc52ea4ca32847ced2c85c9c400b84584d2481faf20d8d2532f319be07c9b5b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5e78e275fc2d2bb191f2ce2c6e908ee420050443f89241c205275f20a5a6042c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.23.4' - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - 'bioconductor-affy >=1.23.4' - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base test: commands: diff --git a/recipes/bioconductor-affyilm/conda_build_config.yaml b/recipes/bioconductor-affyilm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affyilm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml index 3c8b6e0d48161..a468e62aee55e 100644 --- a/recipes/bioconductor-affyilm/meta.yaml +++ b/recipes/bioconductor-affyilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "affyILM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8b18e074b4b7c0f1b36e2cf32cf6a192ae4f19136eb1e109c419deba15331f20 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fd28cdbe08eb46ef5258a328621cfd648919d2d9d8f2568682305d9298bdc927 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affxparser >=1.16.0' - - bioconductor-affy - - bioconductor-biobase - - bioconductor-gcrma + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' - r-base run: - - 'bioconductor-affxparser >=1.16.0' - - bioconductor-affy - - bioconductor-biobase - - bioconductor-gcrma + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL version 3' + license: GPL-3 summary: 'affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.' extra: identifiers: diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index db468d33a7c82..857411b39d61e 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "affyio" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 69aa9239db6ab4a0464138c3fdb21996e93bf38d6ec7fdc870beae36dab8ffdf + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 56885f62402c8d68acca2f17fbdb3cd6af2356c50bb26c6cc1d779c8ace5056a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-zlibbioc + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - bioconductor-zlibbioc + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affypdnn/conda_build_config.yaml b/recipes/bioconductor-affypdnn/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affypdnn/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affypdnn/meta.yaml b/recipes/bioconductor-affypdnn/meta.yaml index 603f752456703..a0d5c9ec481a6 100644 --- a/recipes/bioconductor-affypdnn/meta.yaml +++ b/recipes/bioconductor-affypdnn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "affypdnn" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fc8c3e23cf2ec0eac4c1d6ac7b8832ba97bac0ff816679e288d69ae513225a0a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: dbf8564c32f3d21415d3af05fc2aa699aad74ad5b6b7fe228cd657d9b2c185f6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.5' + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base run: - - 'bioconductor-affy >=1.5' + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The package contains functions to perform the PDNN method described by Li Zhang et al.' - extra: identifiers: - biotools:affypdnn diff --git a/recipes/bioconductor-affyplm/conda_build_config.yaml b/recipes/bioconductor-affyplm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affyplm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml index bc70f90f34770..4f33493ff8be3 100644 --- a/recipes/bioconductor-affyplm/meta.yaml +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "affyPLM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 081fae17b4b7a7cef6189a108e61f9e6ab4253ddccf345b9bf7ce2c6fae60712 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 94ca54deabc2b4be06f22e3a4c0a824336dd27853ea275701d2f69f4e66778a3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.11.0' - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-gcrma - - 'bioconductor-preprocesscore >=1.5.1' - - bioconductor-zlibbioc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - 'bioconductor-affy >=1.11.0' - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-gcrma - - 'bioconductor-preprocesscore >=1.5.1' - - bioconductor-zlibbioc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.' - extra: identifiers: - biotools:affyplm diff --git a/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml b/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml index 1bbcd004ef901..1e5469e30d177 100644 --- a/recipes/bioconductor-affyrnadegradation/meta.yaml +++ b/recipes/bioconductor-affyrnadegradation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "AffyRNADegradation" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6b1bea430174466d4756dae7390f6ff7f9291a32b0fe1ebc43d0fada27cdf9a4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fa67369354eb2c3a7675da1c0cdb2780b164f3fff06bdd4d17960f0bfc947960 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base run: - - bioconductor-affy + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3'' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.' - extra: identifiers: - biotools:affyrnadegradation diff --git a/recipes/bioconductor-agdex/meta.yaml b/recipes/bioconductor-agdex/meta.yaml index 0e67e60d1701d..8d4ca0774e088 100644 --- a/recipes/bioconductor-agdex/meta.yaml +++ b/recipes/bioconductor-agdex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "AGDEX" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 11f83e498205485d3e1506091542162484238b8f63720107191f2fd461fcc963 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 31c07d465d469691f644762d42e8d76d3ca1b60c12583184c70a63a657097c30 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-gseabase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base run: - - bioconductor-biobase - - bioconductor-gseabase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base test: commands: diff --git a/recipes/bioconductor-agilp/meta.yaml b/recipes/bioconductor-agilp/meta.yaml index 6306441bfba4c..9be07d3451d13 100644 --- a/recipes/bioconductor-agilp/meta.yaml +++ b/recipes/bioconductor-agilp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "agilp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 43ab496ded8ac54dbcb97787ec3789a5f29507d62ba4ee8e0b4d49d53daddb7b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 4d285b0934d55ae9e523c73f47995d2e5d6f20122b9edfeb14dd4d0f3377d578 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,3 +28,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'More about what it does (maybe more than one line)' + + diff --git a/recipes/bioconductor-aims/meta.yaml b/recipes/bioconductor-aims/meta.yaml index 8b854f73ef039..62de11a8ae348 100644 --- a/recipes/bioconductor-aims/meta.yaml +++ b/recipes/bioconductor-aims/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "AIMS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 627fda89c217307c8c50a9c65f8e922c97ab0364be0c76044fe78454e9c175b0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 633ddb32cd9f751d3cfbaad515cbe5dc69cacec97a5024d8e43dde4f9d1225a6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-e1071 run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml index d65db7ccbb764..a3cf135518c91 100644 --- a/recipes/bioconductor-aldex2/meta.yaml +++ b/recipes/bioconductor-aldex2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ALDEx2" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a3fcadb525906ed3b113a8591c7078c0544f103aa896b2a137dc4052add3c360 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0580de52ddb83195ed5c1938d64ddef3dbbb385677ba96605fa0c122ce244d4e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-multtest - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - bioconductor-biocparallel - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-multtest - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base test: commands: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcox rank test or Welch t-test (via aldex.ttest), or a glm and Kruskal-Wallis test (via aldex.glm). Reports p-values and Benjamini-Hochberg corrected p-values.' - extra: identifiers: - biotools:aldex2 diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index 04a68a8b852ac..7d547d997efba 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ALL" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' - sha256: 5e487b68a15ea8aa83ae2cbd39b88fb41d9708f8e4c1e02efea9aade529ae3cf + sha256: 329fab87700c03b8f82841782f3dbd8f1f578905539144afa128f1e39e71126b build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions)' + + diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index ac11be066b9bd..ddbefaa54c10b 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="ALL_1.20.0.tar.gz" +FN="ALL_1.22.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ALL_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.20.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ALL_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ALL_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.22.0_src_all.tar.gz" ) -MD5="07fe1649ae8facea40fe5e3137fd823f" +MD5="c762f0d3cce828ef717525c45832ab8c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-alpine/meta.yaml b/recipes/bioconductor-alpine/meta.yaml index 7870d9a2d90bb..864d6079e47bb 100644 --- a/recipes/bioconductor-alpine/meta.yaml +++ b/recipes/bioconductor-alpine/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "alpine" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,41 +8,42 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5a2baa08d8ee6b7634edaa7d6e2a0a804ecc633567fc32ad85ebd4deea05379a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 42372a9247cde09da3b466b26a11e73b30f44e555e08210a0dbab67fb33e337a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-graph - - bioconductor-iranges - - bioconductor-rbgl - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-speedglm - r-stringr run: - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-graph - - bioconductor-iranges - - bioconductor-rbgl - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-speedglm - r-stringr @@ -53,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.' - extra: identifiers: - biotools:alpine diff --git a/recipes/bioconductor-altcdfenvs/conda_build_config.yaml b/recipes/bioconductor-altcdfenvs/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-altcdfenvs/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml index 4663aa8c35cc2..36c2babbd3e96 100644 --- a/recipes/bioconductor-altcdfenvs/meta.yaml +++ b/recipes/bioconductor-altcdfenvs/meta.yaml @@ -1,52 +1,47 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "altcdfenvs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f309918895fc512d6f950d6f58f2ab4d3b5374e584d613ea833627fcba0fbe39 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ddba4b59069c284eea7b2ca54a9f1ed0c46dc514e64db4badeb43cdd5a4fea33 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-affy - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-biostrings - - bioconductor-hypergraph - - bioconductor-makecdfenv - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-hypergraph >=1.52.0,<1.54.0' + - 'bioconductor-makecdfenv >=1.56.0,<1.58.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-affy - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-biostrings - - bioconductor-hypergraph - - bioconductor-makecdfenv - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-hypergraph >=1.52.0,<1.54.0' + - 'bioconductor-makecdfenv >=1.56.0,<1.58.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Convenience data structures and functions to handle cdfenvs' - extra: identifiers: - biotools:altcdfenvs diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml index b73d2ac2422e7..cadeb659b66a5 100644 --- a/recipes/bioconductor-amountain/meta.yaml +++ b/recipes/bioconductor-amountain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "AMOUNTAIN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,18 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 39a43c3cc9dbe341b9bbda154403b25393ae35c1115c5df0b3baed85fa21f47d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 94d402f778f446eba3c9a75c6ebb8fb7443153652534e1911f1c761c9a0f2edd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - r-base + - openblas run: - r-base + - openblas + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-annaffy/meta.yaml b/recipes/bioconductor-annaffy/meta.yaml index 0730251989fae..f0365ca0d2535 100644 --- a/recipes/bioconductor-annaffy/meta.yaml +++ b/recipes/bioconductor-annaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "annaffy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1512cdac93a4e6351467094980c45c65570b70034a63ea196f069a82379bf962 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a981787b7c682d2a65ef5001d2417038e401f24e3a8796b05c7ff33fcc376a72 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=0.1.15' - - bioconductor-biobase - - bioconductor-go.db - - bioconductor-kegg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=0.1.15' - - bioconductor-biobase - - bioconductor-go.db - - bioconductor-kegg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-annmap/meta.yaml b/recipes/bioconductor-annmap/meta.yaml index b248ffcf0bb79..42c68a1e87e3a 100644 --- a/recipes/bioconductor-annmap/meta.yaml +++ b/recipes/bioconductor-annmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "annmap" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,33 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7195bb4388a390bded53ecee7c55fb9f3231feb159552eec9565ab2243679460 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 60b56b634842ceafdbb54aa6d89e00fd082ad93a96d0793544fb7e53e14031af build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-dbi - r-digest - r-lattice - 'r-rmysql >=0.6-0' run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index 1c824c0721ef1..5ff04c8078f1f 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "annotate" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 80a22ce4fd2240e70f24b187cd03aff3a47fa26b695c85928e897729f6b89972 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 4e3234694c5f1b2713b64e0e548e1e9a4d21d02d24e638280dea90e0b767b6e2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.27.5' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-dbi - r-rcurl - r-xml - r-xtable run: - - 'bioconductor-annotationdbi >=1.27.5' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index 8fec9cc31a0d6..454a2688e63ec 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.1" %} {% set name = "AnnotationDbi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8c5a98056d4ab3c215d6a01b64953589d127be71940cfd0031f694a382c604b6 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2c2ce448f8512e9b9247dc1f1e2e8da6f53c7e8637e52bb200782310e95fd329 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.17.0' - - 'bioconductor-biocgenerics >=0.23.1' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-biobase >=1.17.0' - - 'bioconductor-biocgenerics >=0.23.1' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-annotationfilter/meta.yaml b/recipes/bioconductor-annotationfilter/meta.yaml index ad4a079bbe159..9b5266d8bf890 100644 --- a/recipes/bioconductor-annotationfilter/meta.yaml +++ b/recipes/bioconductor-annotationfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "AnnotationFilter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9ae92879307a678a85d12e0cf8d988c506e6c0b0ac64e195a26dbbc08841ee13 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2ac95ad4d99b3cdea41a085926b0c791298eea6512da9d1db7fb3cf29bbb1ef1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-lazyeval run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-lazyeval test: @@ -31,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.' + + diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index 92dac17f69d87..bb3c506b132ed 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.2" %} {% set name = "AnnotationForge" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0197cea759e263fac618f263bf8682f6bdce1897b3bbbb0decdbe16d8ecb6b07 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f92570578af4c8b025e696198c58adb5f97c108f4c662f0b37d2fbbbedf1759e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.33.14' - - 'bioconductor-biobase >=1.17.0' - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.33.14' - - 'bioconductor-biobase >=1.17.0' - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-annotationfuncs/meta.yaml b/recipes/bioconductor-annotationfuncs/meta.yaml index 848147366c7a7..df43fc0ca40ed 100644 --- a/recipes/bioconductor-annotationfuncs/meta.yaml +++ b/recipes/bioconductor-annotationfuncs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AnnotationFuncs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2616280b154a12a8115e81ec0922d5a210813b8bb43aa0bd527e9c32f93adebc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3cf31a5ae8258c5734345b65b9f3cc707405ac811c105e6b09d0c61dd999c0a8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-annotationhub/conda_build_config.yaml b/recipes/bioconductor-annotationhub/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-annotationhub/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index 5bf08eecfcd91..21f5b0a0b1e22 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.1" %} +{% set version = "2.12.1" %} {% set name = "AnnotationHub" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 446d0ec8a2973e227ea48c79c499c81ccc040af2a927cbb390e97da308796893 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cf58bade5dd676504108fbad9248dcdf6306e9e613f17d48808ce230d3119a0a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.31.19' - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biocinstaller - - bioconductor-interactivedisplaybase - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-curl - r-httr - r-rsqlite - r-yaml run: - - 'bioconductor-annotationdbi >=1.31.19' - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biocinstaller - - bioconductor-interactivedisplaybase - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-curl - r-httr diff --git a/recipes/bioconductor-annotationhubdata/conda_build_config.yaml b/recipes/bioconductor-annotationhubdata/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-annotationhubdata/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml index ce0ae871a85f0..95bb9f5a7e5e2 100644 --- a/recipes/bioconductor-annotationhubdata/meta.yaml +++ b/recipes/bioconductor-annotationhubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.3" %} {% set name = "AnnotationHubData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 27c56de635b2d3e91771bbf9669e6bc6ae9e5a5b7b4cd23ee3b2b82d148a4adb + sha256: e91b48c7db39456601090dd66e6209023e849a2ccc0d49acab63b066806163f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-annotationforge - - 'bioconductor-annotationhub >=2.9.14' - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocinstaller - - bioconductor-biocviews - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-geoquery - - 'bioconductor-iranges >=2.3.23' - - bioconductor-organismdbi - - bioconductor-rbiopaxparser - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.7.21' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationforge >=1.22.2,<1.24.0' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biocviews >=1.48.3,<1.50.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - 'r-futile.logger >=1.3.0' @@ -44,24 +44,24 @@ requirements: - r-rsqlite - r-xml run: - - bioconductor-annotationdbi - - bioconductor-annotationforge - - 'bioconductor-annotationhub >=2.9.14' - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocinstaller - - bioconductor-biocviews - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-geoquery - - 'bioconductor-iranges >=2.3.23' - - bioconductor-organismdbi - - bioconductor-rbiopaxparser - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.7.21' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationforge >=1.22.2,<1.24.0' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biocviews >=1.48.3,<1.50.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi - 'r-futile.logger >=1.3.0' diff --git a/recipes/bioconductor-annotationtools/meta.yaml b/recipes/bioconductor-annotationtools/meta.yaml index 7959b311dadee..9b20d11433e18 100644 --- a/recipes/bioconductor-annotationtools/meta.yaml +++ b/recipes/bioconductor-annotationtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "annotationTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ed3e91ef9e486aa5d9bb5f04a531c3715179cb8b1c65d240c0ab19b1b47ab0ce + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 48894ee4377fe07205f98b7de47e5e246a5efcc1754a53ee2ea7a2d8c6518342 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).' - extra: identifiers: - biotools:annotationtools diff --git a/recipes/bioconductor-anota/meta.yaml b/recipes/bioconductor-anota/meta.yaml index 4b6172eb07c4f..224b317675b6f 100644 --- a/recipes/bioconductor-anota/meta.yaml +++ b/recipes/bioconductor-anota/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "anota" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7853c2c1885f03d3fbd96967c5d0c1d8873693a8eb2f675ba9a702e7b74f79bb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 275fb5af3c9d8dce6fe1fb2e5b5b402d7ebac2b7e9260fd7b206b96098dbf726 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-multtest - - bioconductor-qvalue + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base run: - - bioconductor-multtest - - bioconductor-qvalue + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base test: commands: diff --git a/recipes/bioconductor-antiprofiles/meta.yaml b/recipes/bioconductor-antiprofiles/meta.yaml index bd9904ef812d2..9aa2c0f3baf78 100644 --- a/recipes/bioconductor-antiprofiles/meta.yaml +++ b/recipes/bioconductor-antiprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "antiProfiles" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cf5b1707a1e050242a3a423e004890d82b4c7fa15a3ef9f9e2df6d0cfc90c60f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d40b1a3f3495b3b1ed59f05253c88b3caa78ad845e16ad5154bfdc1907456d99 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-apcomplex/meta.yaml b/recipes/bioconductor-apcomplex/meta.yaml index 414841e44fd20..f0d24c1cccf1a 100644 --- a/recipes/bioconductor-apcomplex/meta.yaml +++ b/recipes/bioconductor-apcomplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "apComplex" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 41334cdbe0be604a3a9e2617788250d71e183334a6342990aa1a4170ea33528c + sha256: 805d761773a9494b6904c9af82b9246259471fbf24ddb3a16709716673c80610 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-org.sc.sgd.db - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base run: - - bioconductor-graph - - bioconductor-org.sc.sgd.db - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base test: commands: diff --git a/recipes/bioconductor-apeglm/meta.yaml b/recipes/bioconductor-apeglm/meta.yaml index 0fd151ea63112..0328e89e91a41 100644 --- a/recipes/bioconductor-apeglm/meta.yaml +++ b/recipes/bioconductor-apeglm/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.1" %} {% set name = "apeglm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7281d05ec023b38126534f5151661654c2b073419dd15a316229b75ebf46461a - + sha256: ecdf6d18246532d74973ed8eb1262d6451dbd7656710164e9a17b1f3fd5391ca build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-genomicranges - - bioconductor-summarizedexperiment + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-emdbook + - r-rcpp + - r-rcppeigen + - r-rcppnumerical run: - - bioconductor-genomicranges - - bioconductor-summarizedexperiment + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-emdbook - + - r-rcpp + - r-rcppeigen + - r-rcppnumerical + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.' + + diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index f6dc33c3df56f..2fec743665902 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "aroma.light" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4c9b5c791a2c9926be714a472fdbde256ee0d55a4c165a32be9ecb5090993633 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 767638cd7ba45f730052158941d5c7ed29987fbb3bb9718aac09339e358fbab7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - r-base - - 'r-matrixstats >=0.52.1' + - 'r-matrixstats >=0.52.2' - 'r-r.methodss3 >=1.7.1' - 'r-r.oo >=1.21.0' - - 'r-r.utils >=2.5.0' + - 'r-r.utils >=2.6.0' run: - r-base - - 'r-matrixstats >=0.52.1' + - 'r-matrixstats >=0.52.2' - 'r-r.methodss3 >=1.7.1' - 'r-r.oo >=1.21.0' - - 'r-r.utils >=2.5.0' + - 'r-r.utils >=2.6.0' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.' - extra: identifiers: - biotools:aroma.light diff --git a/recipes/bioconductor-arrayexpress/conda_build_config.yaml b/recipes/bioconductor-arrayexpress/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-arrayexpress/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-arrayexpress/meta.yaml b/recipes/bioconductor-arrayexpress/meta.yaml index e2e7caf94c918..68216a6735196 100644 --- a/recipes/bioconductor-arrayexpress/meta.yaml +++ b/recipes/bioconductor-arrayexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ArrayExpress" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ecfc1b7d9635d810d6f8d419ddcd9088f906cf398b3ea3bee189ba2bc4206b06 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 98c8297309653266cfd37d47405222380f45bada6e8e72ae84e801f4653d23b9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.4.0' - - bioconductor-limma - - bioconductor-oligo + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' - r-base - r-xml run: - - 'bioconductor-biobase >=2.4.0' - - bioconductor-limma - - bioconductor-oligo + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' - r-base - r-xml test: @@ -35,3 +36,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet' + + diff --git a/recipes/bioconductor-arrayquality/meta.yaml b/recipes/bioconductor-arrayquality/meta.yaml index 8a06ba3de9024..444d913fb941c 100644 --- a/recipes/bioconductor-arrayquality/meta.yaml +++ b/recipes/bioconductor-arrayquality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "arrayQuality" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 861f16419597d61849054c591471b5b411ce28bd86d0124c10ca0be26b520093 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 437f1d57604f411ab9e55416f30658fef284c795dce682429a5884a028b38680 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-gridbase - r-hexbin - r-rcolorbrewer run: - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-gridbase - r-hexbin diff --git a/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml b/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml index 7fc33092000ed..cbb80e0d3b7e6 100644 --- a/recipes/bioconductor-arrayqualitymetrics/meta.yaml +++ b/recipes/bioconductor-arrayqualitymetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.0" %} +{% set version = "3.36.0" %} {% set name = "arrayQualityMetrics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b6184f04ce46a05b4013aebf0a1d70f2da9fb273e4441cf7db6702e3aa5e3e7 + sha256: d31f0bea123391dd118e7d91e8a8074a40e2ca6c32631062b4ea81dd35ffcd5e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - 'bioconductor-affyplm >=1.27.3' - - bioconductor-beadarray - - bioconductor-biobase - - bioconductor-genefilter - - bioconductor-limma - - 'bioconductor-vsn >=3.23.3' - - 'r-base >=3.4.1' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyplm >=1.56.0,<1.58.0' + - 'bioconductor-beadarray >=2.30.0,<2.32.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' + - r-base - 'r-cairo >=1.4-6' - 'r-gridsvg >=1.4-3' - r-hmisc @@ -35,18 +35,15 @@ requirements: - r-rcolorbrewer - r-setrng - r-xml - - xorg-libxrender - - xorg-libsm - - xorg-libxext run: - - bioconductor-affy - - 'bioconductor-affyplm >=1.27.3' - - bioconductor-beadarray - - bioconductor-biobase - - bioconductor-genefilter - - bioconductor-limma - - 'bioconductor-vsn >=3.23.3' - - 'r-base >=3.4.1' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyplm >=1.56.0,<1.58.0' + - 'bioconductor-beadarray >=2.30.0,<2.32.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' + - r-base - 'r-cairo >=1.4-6' - 'r-gridsvg >=1.4-3' - r-hmisc @@ -56,17 +53,13 @@ requirements: - r-rcolorbrewer - r-setrng - r-xml - - xorg-libxrender - - xorg-libsm - - xorg-libxext test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' - summary: 'This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported. ' - + summary: 'This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.' extra: identifiers: - biotools:arrayqualitymetrics diff --git a/recipes/bioconductor-arraytools/conda_build_config.yaml b/recipes/bioconductor-arraytools/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-arraytools/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-arraytools/meta.yaml b/recipes/bioconductor-arraytools/meta.yaml index a53364b6b7c71..a079e1dbbbbcc 100644 --- a/recipes/bioconductor-arraytools/meta.yaml +++ b/recipes/bioconductor-arraytools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ArrayTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6d52f88a07d8eb0b8471a2f32247e071a90a28fa6a34cc8da94574c0381ecd37 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 109f61ec070ace944b3d7a3fea37aa73f95887a218c908e52e08464a27f14f0c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.23.4' - - 'bioconductor-biobase >=2.5.5' - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-xtable run: - - 'bioconductor-affy >=1.23.4' - - 'bioconductor-biobase >=2.5.5' - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-xtable test: diff --git a/recipes/bioconductor-arrmdata/meta.yaml b/recipes/bioconductor-arrmdata/meta.yaml index e2b6f5fde82e3..f91b2fb0ac509 100644 --- a/recipes/bioconductor-arrmdata/meta.yaml +++ b/recipes/bioconductor-arrmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ARRmData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: de64cedc15fcf58790d10d20da40063bcb746053b3474c4f386cb4ede1dbbc5f + sha256: 2a05e8d5260c51e8fcf9485ac2232aaeee995568d6e7d74dc5a42247e81893f6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays' + + diff --git a/recipes/bioconductor-arrmdata/post-link.sh b/recipes/bioconductor-arrmdata/post-link.sh index 55326dc7757b8..313fe0283fccf 100644 --- a/recipes/bioconductor-arrmdata/post-link.sh +++ b/recipes/bioconductor-arrmdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ARRmData_1.14.0.tar.gz" +FN="ARRmData_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ARRmData_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/ARRmData_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ARRmData_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/ARRmData_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.16.0_src_all.tar.gz" ) -MD5="cc3003990e150c56cc2bd76fd92d6504" +MD5="fce3b1d71d92cf8bf62a52a490543f58" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-arrmnormalization/meta.yaml b/recipes/bioconductor-arrmnormalization/meta.yaml index d1127e2fafb93..e2510d7585ec5 100644 --- a/recipes/bioconductor-arrmnormalization/meta.yaml +++ b/recipes/bioconductor-arrmnormalization/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ARRmNormalization" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 05d900ce9cac4f42819a54b3e450f0efab7173727aa6a216873788370ccac2bf + sha256: 321e66bf19cab82cf9b53f203cfe43f6981c7190a02bb7d8460c069b54bc56f2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-arrmdata + - 'bioconductor-arrmdata >=1.16.0,<1.18.0' - r-base run: - - bioconductor-arrmdata + - 'bioconductor-arrmdata >=1.16.0,<1.18.0' - r-base test: commands: diff --git a/recipes/bioconductor-asafe/meta.yaml b/recipes/bioconductor-asafe/meta.yaml index 766d82c7a58b7..72d8f7f06045f 100644 --- a/recipes/bioconductor-asafe/meta.yaml +++ b/recipes/bioconductor-asafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ASAFE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e7ffdfc0127beafeb655451f671652052261e418efdaaeea841491184cda6d8f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: da61cca0c5d5c1db943b56da27d7e33106888ac476fa1b84dd5478d1d6fb78df build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-aseb/meta.yaml b/recipes/bioconductor-aseb/meta.yaml index cb3d031dec509..44c9feff16d24 100644 --- a/recipes/bioconductor-aseb/meta.yaml +++ b/recipes/bioconductor-aseb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ASEB" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b20b4e7c0fde279b6ecc972360f31b91500a250d98eda3614cfbb33d0f103e5f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b91033ad3ddfae49c55eb1a65287f60d2246530c1e9c278c82736a26e66b3be3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-asgsca/meta.yaml b/recipes/bioconductor-asgsca/meta.yaml index 18d2fdcf6a44e..089210b6f0429 100644 --- a/recipes/bioconductor-asgsca/meta.yaml +++ b/recipes/bioconductor-asgsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ASGSCA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b3df06f538a51e48e57e9a5b3e659fa5a9b1bf02b3581c6c6d656fa93826f1ac + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 49d5d156fd6bc3c159237072b85588c8375bd1edf33ba8e152c2fdd86586c18b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-aspli/meta.yaml b/recipes/bioconductor-aspli/meta.yaml index 271a89a37f121..fb833992085e1 100644 --- a/recipes/bioconductor-aspli/meta.yaml +++ b/recipes/bioconductor-aspli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ASpli" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,39 +8,40 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 47ef32dc216f3da921b7217e56e1cf7ad22c3fc2c1a6726c94f1e79717b969a7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 63987b36701915e6c764aca4f18b52abf3a0ef5087450d0d995de159b4b27abc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biocstyle - - bioconductor-edger - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biocstyle - - bioconductor-edger - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: diff --git a/recipes/bioconductor-atacseqqc/conda_build_config.yaml b/recipes/bioconductor-atacseqqc/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-atacseqqc/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml index c9b09493ea215..f95b249a1d027 100644 --- a/recipes/bioconductor-atacseqqc/meta.yaml +++ b/recipes/bioconductor-atacseqqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.3" %} {% set name = "ATACseqQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,45 +8,52 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5d8e3f4afc4c27e4dc0bff1247f8162963b80a1a487dcd591f718a671c7d1654 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 543e52a8d1fadf2137a9d43ede8aa6f8e2a2959a6b44f64b6c3d19a2034f7e82 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-chippeakanno - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-genomicscores - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-motifstack >=1.24.1,<1.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + - r-kernsmooth + - r-preseqr - r-randomforest run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-chippeakanno - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-genomicscores - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-motifstack >=1.24.1,<1.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + - r-kernsmooth + - r-preseqr - r-randomforest test: commands: @@ -55,3 +62,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.' + + diff --git a/recipes/bioconductor-atlasrdf/meta.yaml b/recipes/bioconductor-atlasrdf/meta.yaml index e3ce042407bb5..53edd1f79410c 100644 --- a/recipes/bioconductor-atlasrdf/meta.yaml +++ b/recipes/bioconductor-atlasrdf/meta.yaml @@ -32,6 +32,9 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Apache License 2.0' summary: 'Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.' + identifiers: + - biotools:atlasrdf + - doi:10.1093/bioinformatics/btt765 extra: identifiers: - biotools:atlasrdf diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml index 2a3d004b75911..8d98cd52e3777 100644 --- a/recipes/bioconductor-baalchip/meta.yaml +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -1,30 +1,28 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "BaalChIP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0313e5862eadbb779a60dab93a6a8ca7d6d17c3f56b9ce33dd17a27016b753fd - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 555c72cf38107f062d1ba406ce62fc8eb7af8b21f512e19a402fc96675a39db9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-coda - r-doby @@ -34,11 +32,11 @@ requirements: - r-reshape2 - r-scales run: - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-coda - r-doby @@ -47,16 +45,13 @@ requirements: - r-ggplot2 - r-reshape2 - r-scales - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.' - extra: identifiers: - biotools:baalchip diff --git a/recipes/bioconductor-bac/meta.yaml b/recipes/bioconductor-bac/meta.yaml index fc9b36058afa2..4633e68afd1da 100644 --- a/recipes/bioconductor-bac/meta.yaml +++ b/recipes/bioconductor-bac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BAC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 51ad5fbb2ca7ed9cde785c000b14718f0668a541971849d5493a9285d6724713 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 29b28af43c62c79a2737c19984c343d5f7b3a0e595417622cd47bbfb665706cf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,9 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index b782319729c29..121ca960209cc 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "bacon" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: be600564444b4ba23ba9fa7aba9d46a8ed383726b83ab86cb165635b5d0bdec4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: adce0d013825084694ad6b4842d6959037a13aa47b267b1ca9ef076caf1f68b0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base - r-ellipse - r-ggplot2 run: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base - r-ellipse - r-ggplot2 + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.' - extra: identifiers: - biotools:bacon diff --git a/recipes/bioconductor-bader/meta.yaml b/recipes/bioconductor-bader/meta.yaml index 6e4d2ea08bbf1..9a7ee53fb8551 100644 --- a/recipes/bioconductor-bader/meta.yaml +++ b/recipes/bioconductor-bader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "BADER" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 855a65d8ac74ef3552910530eaca0ac57aed92ca6ab58754f9db368fb301e016 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3558dfd520aad4fef475918a5101ddfee2e9db855cf99e084b7e32f6c7aeef15 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-badregionfinder/meta.yaml b/recipes/bioconductor-badregionfinder/meta.yaml index a4171c9ac2fb8..8db761c250624 100644 --- a/recipes/bioconductor-badregionfinder/meta.yaml +++ b/recipes/bioconductor-badregionfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BadRegionFinder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d1bc6809c87adb08f74f6140e61a2c66b148d3aadb865e6a6f38446986169413 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 78dab6e99f4fffa8d14b7dff8e50c26b0bbed864eec0a9cdb47891079630a5f2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-genomicranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base run: - - bioconductor-biomart - - bioconductor-genomicranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base test: commands: diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index 12f3840a972c9..e7a8fd184a5d7 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "ballgown" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,35 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3e9d90b9f345d122824260c588d1d36a602a525a9daa1826190193d8c24ba483 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 782a9760d27bb529238b1ecd3fa2f2c0f364ba8f861d7fad54bd127e2935a6d2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.25.0' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.17.25' - - 'bioconductor-iranges >=1.99.22' - - bioconductor-limma - - 'bioconductor-rtracklayer >=1.29.25' - - 'bioconductor-s4vectors >=0.9.39' - - bioconductor-sva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.25.0' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.17.25' - - 'bioconductor-iranges >=1.99.22' - - bioconductor-limma - - 'bioconductor-rtracklayer >=1.29.25' - - 'bioconductor-s4vectors >=0.9.39' - - bioconductor-sva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index 3c8ed0f58fe17..f6ddbff6c0951 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "bamsignals" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,33 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7463b60dbe1c527a28bbfa0e060c55cd537fa4d06e3be5265953972467352d96 + sha256: fb552c89b77193ab47eba93c1cfd03547645100e18c5ee6a9838f24fc91d3890 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rhtslib - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - 'r-rcpp >=0.10.6' run: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rhtslib - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - 'r-rcpp >=0.10.6' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-banocc/meta.yaml b/recipes/bioconductor-banocc/meta.yaml index 594ca2238eae7..9423e5a3a9b36 100644 --- a/recipes/bioconductor-banocc/meta.yaml +++ b/recipes/bioconductor-banocc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "banocc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 70e5afb0d1aae01dfa868c02c962b68a01f7cf91919aeacb7bc1de1a409f8131 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 8e0e0edd7306bf239427155aa4a0ee667ac3f3e01baf8179ab462f8d6304c62e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'r-base >=3.4' + - r-base - 'r-coda >=0.18.1' - r-mvtnorm - 'r-rstan >=2.10.1' - r-stringr run: - - 'r-base >=3.4' + - r-base - 'r-coda >=0.18.1' - r-mvtnorm - 'r-rstan >=2.10.1' @@ -35,3 +36,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.' + + diff --git a/recipes/bioconductor-basecallqc/meta.yaml b/recipes/bioconductor-basecallqc/meta.yaml index d18f1806095b6..8be86eb5b4bc4 100644 --- a/recipes/bioconductor-basecallqc/meta.yaml +++ b/recipes/bioconductor-basecallqc/meta.yaml @@ -1,26 +1,24 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "basecallQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1f6af0dc47a9786557e74c24bb2e29948444bf44c03ec2dc2fb90c0dbeb673cf - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 015a2b6bc9c89997550ba38f500df87350728eafd7d8d44e37631a2daa0c21fd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-shortread + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-data.table - r-dplyr @@ -37,7 +35,7 @@ requirements: - r-xml - r-yaml run: - - bioconductor-shortread + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-data.table - r-dplyr @@ -53,16 +51,13 @@ requirements: - r-tidyr - r-xml - r-yaml - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.' - extra: notes: | 'This package relies on bcl2fastq being available in the system PATH. Due to licensing diff --git a/recipes/bioconductor-basespacer/meta.yaml b/recipes/bioconductor-basespacer/meta.yaml index 27fc5743a7d9a..06123e4e21467 100644 --- a/recipes/bioconductor-basespacer/meta.yaml +++ b/recipes/bioconductor-basespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "BaseSpaceR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 77639724a3f7cc07445aca95b2e1243370ae5e0e2fd98ed0a763c6b46c1593dd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 89e78f2f80d6b18f261ff7ad4c69acb91f437f2c26a7c7c53e50de71c35487ce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index 391b517464765..0a82fcef3e521 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Basic4Cseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 001ed8e1af6b708adf502942294ec8c8e53cf0cb9ec214384b36593e44fad4f7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7a6003173cb26bb7d531b53c6cab9b83f332bc7f782e5187cd3357c325228f21 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-bsgenome.ecoli.ncbi.20080805 - - bioconductor-genomicalignments - - bioconductor-genomicranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.1000,<1.5.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-catools - r-rcircos run: - - bioconductor-biostrings - - bioconductor-bsgenome.ecoli.ncbi.20080805 - - bioconductor-genomicalignments - - bioconductor-genomicranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.1000,<1.5.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-catools - r-rcircos diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml index cfb2382024ea7..f6a7410402b87 100644 --- a/recipes/bioconductor-batchqc/meta.yaml +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.1" %} {% set name = "BatchQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,16 +10,16 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2d5a3bc7a163894681a7135d0242a3697565b829930b177f5ab3ff6764b251ba + sha256: 3d3eb2a68c018066506b2ff4d2c4a94cbca5ebcfac35d68e322cd642893044a0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma - - bioconductor-sva + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-corpcor - r-d3heatmap @@ -35,8 +35,8 @@ requirements: - r-rmarkdown - r-shiny run: - - bioconductor-limma - - bioconductor-sva + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-corpcor - r-d3heatmap @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data, and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs, and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.' - extra: identifiers: - biotools:batchqc diff --git a/recipes/bioconductor-bayespeak/meta.yaml b/recipes/bioconductor-bayespeak/meta.yaml index 64200b6b2062b..19bb10b2bc9a5 100644 --- a/recipes/bioconductor-bayespeak/meta.yaml +++ b/recipes/bioconductor-bayespeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "BayesPeak" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3f41b7a76851519646ec4915622a34eb9b48656e6305895db680c05acf0f19b9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 42592e5fb0dd4629b705679f963b23780ff04f9a8d4500559943bca7eb61ac17 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-iranges + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base run: - - bioconductor-iranges + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.' - extra: identifiers: - biotools:bayespeak diff --git a/recipes/bioconductor-bayseq/meta.yaml b/recipes/bioconductor-bayseq/meta.yaml index 5e3fffbc71536..4782fde701c81 100644 --- a/recipes/bioconductor-bayseq/meta.yaml +++ b/recipes/bioconductor-bayseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "baySeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bf585cdfee8505ca70add124e7d9d36c2f8f7d1fd92fc3e5c9cce2bf6a4621b5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8fcee22b032a24ce2fac943bfbace3597d0ee6b5b3af9a54562b52a402a87541 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-edger - - bioconductor-genomicranges + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-abind - r-base run: - - bioconductor-edger - - bioconductor-genomicranges + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-bbcanalyzer/meta.yaml b/recipes/bioconductor-bbcanalyzer/meta.yaml index 49aa4f17b7dbc..315e37200c9e0 100644 --- a/recipes/bioconductor-bbcanalyzer/meta.yaml +++ b/recipes/bioconductor-bbcanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BBCAnalyzer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b0dfbc0ba57aad797bde9177499f8b603187504b91d1ec691b0980edbe7f653b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0a1dfb72e58e6371d8120df49c3d79a8e1fa94e8fe7531413be03828ec257e5e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base run: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base test: commands: diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index 37a5c86a0f96c..39f4f0fe83af9 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BCRANK" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3c5fc7c5699bcadeb26ceb67dc2822680bba4b3685b0c62b25bb54f8d5d4726d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 98196790877a23218038419beb4f8fc6b977f04ff58ca311998b528349810247 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beachmat/conda_build_config.yaml b/recipes/bioconductor-beachmat/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-beachmat/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index 2b1d4fd176eec..4060272cc7a27 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.1" %} {% set name = "beachmat" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e28ebefe877de87b2b540f58d41dfb1d6a5adb7b2d3338feb937fd4ff785d51e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 26a5233331710cbc57a05586926111718bdfc09ceda5d47f77f9fdd025d820f1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-delayedarray - - bioconductor-hdf5array - - bioconductor-rhdf5 - - bioconductor-rhdf5lib + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-hdf5array >=1.8.1,<1.10.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - r-base - - r-rcpp + - 'r-rcpp >=0.12.14' run: - - bioconductor-delayedarray - - bioconductor-hdf5array - - bioconductor-rhdf5 - - bioconductor-rhdf5lib + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-hdf5array >=1.8.1,<1.10.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - r-base - - r-rcpp + - 'r-rcpp >=0.12.14' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,3 +42,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.' + + diff --git a/recipes/bioconductor-beadarray/meta.yaml b/recipes/bioconductor-beadarray/meta.yaml index 50b56b032624c..accffbdc82565 100644 --- a/recipes/bioconductor-beadarray/meta.yaml +++ b/recipes/bioconductor-beadarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "beadarray" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,42 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 11575596b6b9dd7c7f4c58392cd88c70a441e74f70a3152fa794bdf7bec6ec2b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b62f7771a1a0ae050f5bd983182d57b857428e40c6076d67e6848855a7cbefe5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-beaddatapackr - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-genomicranges - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-limma + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-beaddatapackr >=1.32.0,<1.34.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-ggplot2 - r-reshape2 run: - - bioconductor-annotationdbi - - bioconductor-beaddatapackr - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-genomicranges - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-limma + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-beaddatapackr >=1.32.0,<1.34.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-ggplot2 - r-reshape2 + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +51,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.' - extra: identifiers: - biotools:beadarray diff --git a/recipes/bioconductor-beadarraysnp/meta.yaml b/recipes/bioconductor-beadarraysnp/meta.yaml index 8751fad938058..66e4cb0473639 100644 --- a/recipes/bioconductor-beadarraysnp/meta.yaml +++ b/recipes/bioconductor-beadarraysnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "beadarraySNP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fce4520b18b42218e46f49e69a73e65b776e5413bc5982ff06d442bf55059996 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ee552cb355c5eb34a594c5193ca954e955f934225a1f8ec56fa0479dfcd0e522 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.14' - - bioconductor-quantsmooth + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' - r-base run: - - 'bioconductor-biobase >=2.14' - - bioconductor-quantsmooth + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' - r-base test: commands: diff --git a/recipes/bioconductor-beaddatapackr/meta.yaml b/recipes/bioconductor-beaddatapackr/meta.yaml index 451048cf6cfb2..48bd14c7d71c2 100644 --- a/recipes/bioconductor-beaddatapackr/meta.yaml +++ b/recipes/bioconductor-beaddatapackr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "BeadDataPackR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 157019bcbc231e9c99b1d0d6e0ec03191ee3ca935f6f8e109ded63b896d17394 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8247bcb91a803b6cf95d9595fac032a68c761cf78e6cdc9a949bbd1d9137d7bf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,14 +21,16 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform' - + summary: 'Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.' extra: identifiers: - biotools:beaddatapackr diff --git a/recipes/bioconductor-beat/meta.yaml b/recipes/bioconductor-beat/meta.yaml index 3105b659acd00..56022fba6d895 100644 --- a/recipes/bioconductor-beat/meta.yaml +++ b/recipes/bioconductor-beat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "BEAT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e7997b5d394caa9d407ae8915bdea3ba2825185c5006fc01a866f3ff70219374 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 687556436e352a09f1c1b944d5e783bf30da8ed2badbae4d0401534844e6199d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-shortread + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base run: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-shortread + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base test: commands: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3.0)' summary: 'Model-based analysis of single-cell methylation data' - extra: identifiers: - biotools:beat diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index cf23535172622..567aadbbce56d 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "BEclear" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f65f7af93612186e70c31529e757b11a01146ceda2f947394b9d2604efc773ea + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: aa88a47163ae33af1760be2c82200ba2a9419ab956ac6ba9ce33640a22ad81e9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Provides some functions to detect and correct for batch effects in DNA methylation data. The core function "BEclear" is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' - extra: identifiers: - biotools:beclear diff --git a/recipes/bioconductor-bgafun/meta.yaml b/recipes/bioconductor-bgafun/meta.yaml index b4920b4427412..1ec910c309f3d 100644 --- a/recipes/bioconductor-bgafun/meta.yaml +++ b/recipes/bioconductor-bgafun/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "bgafun" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a425f901dff909dab046bb0710776ca8b4dfef4325ee38e99abdc3e3c71873e8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2edd5d30b472fb64a65b635a28b2a704b1c642693515814f7743bb2a18d43f6b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-made4 + - 'bioconductor-made4 >=1.54.0,<1.56.0' - r-ade4 - r-base - r-seqinr run: - - bioconductor-made4 + - 'bioconductor-made4 >=1.54.0,<1.56.0' - r-ade4 - r-base - r-seqinr @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A method to identify specifity determining residues in protein families using Between Group Analysis' - extra: identifiers: - biotools:bgafun diff --git a/recipes/bioconductor-bgeedb/meta.yaml b/recipes/bioconductor-bgeedb/meta.yaml index 14282868ea588..58641fa86905c 100644 --- a/recipes/bioconductor-bgeedb/meta.yaml +++ b/recipes/bioconductor-bgeedb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.2" %} {% set name = "BgeeDB" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,18 +8,19 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5d906e9b41516b5203efe506084199a06fac8185d1043fadfab2c885a5090aca + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cc65796afb8b77a2b3b88fb80a7b5e9973b00af90321bd790d754f212ed7262e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-topgo + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-data.table - r-digest @@ -27,9 +28,9 @@ requirements: - r-rcurl - r-tidyr run: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-topgo + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-data.table - r-digest @@ -41,9 +42,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + license: GPL-3 summary: 'A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.' - extra: identifiers: - biotools:bgeedb diff --git a/recipes/bioconductor-bgmix/meta.yaml b/recipes/bioconductor-bgmix/meta.yaml index 14628f2777261..09f5188b3f08f 100644 --- a/recipes/bioconductor-bgmix/meta.yaml +++ b/recipes/bioconductor-bgmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BGmix" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d3674143cb270036985e3670f16ec5f0b046dd96a50d0a2c007ca10e435de89c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1b6e97e8efb812e25f02e7a7894220229b459c0ad35681f130a3ea9be53a7f6d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,11 @@ requirements: run: - r-base - r-kernsmooth + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Fully Bayesian mixture models for differential gene expression' - extra: identifiers: - biotools:bgmix diff --git a/recipes/bioconductor-bhc/meta.yaml b/recipes/bioconductor-bhc/meta.yaml index cc40bbc0e56c3..296d82a111e03 100644 --- a/recipes/bioconductor-bhc/meta.yaml +++ b/recipes/bioconductor-bhc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "BHC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1534939f8596d6656df2340ec249d443bbef1352f8879a15dddd0aeca2591a49 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 99668cb1cc2d3caf7609de429c754003d8bb82819861fe4cec2e20741f932c07 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,11 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.' - extra: identifiers: - biotools:bhc diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index 04291ba1418cb..9599a3119a9d8 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "BicARE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 22f6318ae47c7378f5b47848e8733f0367ac90f0e8822a9337f31e19deb572c6 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b9fb578fa611f3cbc4fe26995fd7ffa0d82d2873cc65a895507320179e34863a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-gseabase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-gseabase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Biclustering Analysis and Results Exploration' - extra: identifiers: - biotools:bicare diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index 97942c26c0db2..f1d21e6926c9e 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "Biobase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6fa2f0dc214d42f2d0afcc42d2f4da2223ebe67a2f79ff69fba6dc19940cf5b1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5fa69ab2eac24911ef839055f5046766206b0fa3d6dfd5529849e45894d08dc7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('fortran') }} host: - - 'bioconductor-biocgenerics >=0.3.2' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - 'bioconductor-biocgenerics >=0.3.2' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions that are needed by many other packages or which replace R functions.' - extra: identifiers: - biotools:biobase diff --git a/recipes/bioconductor-biocfilecache/meta.yaml b/recipes/bioconductor-biocfilecache/meta.yaml index 29f4abd7c311a..24bb0a0c4583b 100644 --- a/recipes/bioconductor-biocfilecache/meta.yaml +++ b/recipes/bioconductor-biocfilecache/meta.yaml @@ -1,27 +1,24 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.0" %} {% set name = "BiocFileCache" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 55df35233ca38dcd4a79c22ecb0b2b47c53d4a25f84002f77233393e91045539 - + sha256: 0e8d1f6571795b67d68defdd5501a4983f36c341ee1978c26f8b66b0858aff74 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - r-base >=3.4.0 + - r-base - r-dbi - 'r-dbplyr >=1.0.0' - r-dplyr @@ -29,19 +26,19 @@ requirements: - r-rappdirs - r-rsqlite run: - - r-base >=3.4.0 + - r-base - r-dbi - 'r-dbplyr >=1.0.0' - r-dplyr - r-httr - r-rappdirs - r-rsqlite - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.' + + diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index 4a27b1783f9bb..737dbe586989b 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.24.0" %} +{% set version = "0.26.0" %} {% set name = "BiocGenerics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 517d31c47d7d807170031e116af3ffeba57baca3980ef4d85b37c2ec3bdc9d0f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 571c491d8a103f13be76b30af72f2bc675f5321bb8acf5e19cfe8ec684871da7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'S4 generic functions needed by many Bioconductor packages.' - extra: identifiers: - biotools:biocgenerics diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml index 46cf0225fe566..869b70e51a793 100644 --- a/recipes/bioconductor-biocgraph/meta.yaml +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "biocGraph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d1b7ac11a31e14583093860d1f05db3e0c653610c3921b7d58e176ca1f8f8e86 + sha256: 28b1e9cacd61f633c51c1b48a017e6a3caaa21d9efe660d6fe75cb5e9ea2f902 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-geneplotter - - bioconductor-graph - - bioconductor-rgraphviz + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-geneplotter - - bioconductor-graph - - bioconductor-rgraphviz + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base test: commands: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides examples and code that make use of the different graph related packages produced by Bioconductor.' - extra: identifiers: - biotools:biocgraph diff --git a/recipes/bioconductor-biocinstaller/conda_build_config.yaml b/recipes/bioconductor-biocinstaller/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-biocinstaller/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml index 2b5e5596a2434..d3fa05009189a 100644 --- a/recipes/bioconductor-biocinstaller/meta.yaml +++ b/recipes/bioconductor-biocinstaller/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BiocInstaller" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2d853625dd369d1c7acb6340f1eee6b64245cdf1e4d0786bd9099bbd8e50cfa5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e0395bb6b4d81f7629658730a350bf924d92ab7d414419cea56e1707437ce1f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package is used to install and update Bioconductor, CRAN, and (some) github packages.' - extra: identifiers: - biotools:biocinstaller diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 63611f675d405..6e35ffa466d0a 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.2" %} {% set name = "BiocParallel" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0de25aa5c7a1b1cce8da0d5f42a00eaccc50de1edf4ab30174833ecd851dcf8e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d5c568362f06b36494d54f4134a7ac06b45fe2a10236fcdaed9e58288c2a8bd2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +21,6 @@ requirements: - {{ compiler('fortran') }} host: - r-base - # not specified in DESCRIPTION, but complains during build - r-bh - r-futile.logger - r-snow @@ -29,6 +29,10 @@ requirements: - r-bh - r-futile.logger - r-snow + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -36,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 | GPL-3' summary: 'This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.' - extra: identifiers: - biotools:biocparallel diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 704ecd74f16c5..d2f39629136ec 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.2" %} {% set name = "BiocStyle" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a8877e1a2642ae6059ef6361d839011f3e313ee3864e8c1c81af68d45d92c215 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5750903f26a961b874c66365936da83dfe523608c9156c870a1c804f7d00a99e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.' - extra: identifiers: - biotools:biocstyle diff --git a/recipes/bioconductor-biocviews/meta.yaml b/recipes/bioconductor-biocviews/meta.yaml index df4de093c985c..508ff8266c0e9 100644 --- a/recipes/bioconductor-biocviews/meta.yaml +++ b/recipes/bioconductor-biocviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.3" %} {% set name = "biocViews" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ad868c40c54bbcac5b38776bc56afca95bc514f091ea042b4d08303c83c4fe27 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6582f5a443e33bc33ba584e7021d3564fcd791ff9a7ec5a4ec4fef8867e4bbe7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-graph >=1.9.26' - - 'bioconductor-rbgl >=1.13.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - r-rcurl - r-runit - r-xml run: - - bioconductor-biobase - - 'bioconductor-graph >=1.9.26' - - 'bioconductor-rbgl >=1.13.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - r-rcurl - r-runit @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Infrastructure to support Bioconductor ''views'' used to classify software packages. ''biocViews'' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to ''software'', ''annotation'', and ''experiment data'' packages.' - extra: identifiers: - biotools:biocviews diff --git a/recipes/bioconductor-biocworkflowtools/meta.yaml b/recipes/bioconductor-biocworkflowtools/meta.yaml index bad114a9c0bf1..1fd21e9ffcd68 100644 --- a/recipes/bioconductor-biocworkflowtools/meta.yaml +++ b/recipes/bioconductor-biocworkflowtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.2" %} {% set name = "BiocWorkflowTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6acba24a2c8174efd75b1ca60452fa962d2042ec8ed738e7b719df799a0eb9ea + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c617c971066c904c48c3cdb3b4aedcd991abbf6d9188f418d562c0329b7c9076 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocstyle + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - r-base - r-bookdown + - r-devtools - r-git2r - r-httr - r-knitr - r-rmarkdown + - r-rstudioapi - r-stringr run: - - bioconductor-biocstyle + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - r-base - r-bookdown + - r-devtools - r-git2r - r-httr - r-knitr - r-rmarkdown + - r-rstudioapi - r-stringr test: commands: @@ -41,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.' - extra: identifiers: - biotools:BiocWorkflowTools diff --git a/recipes/bioconductor-biodist/meta.yaml b/recipes/bioconductor-biodist/meta.yaml index c0ad5df050feb..d42dd03291571 100644 --- a/recipes/bioconductor-biodist/meta.yaml +++ b/recipes/bioconductor-biodist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "bioDist" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c9dae5121790396c403c96d55edc8e59bba884f3d813d0c6f13e4bf9266dc80b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5cae25551992991abfdbab65d72e71155e74fefa5b269caa4d2e549a125684c1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-kernsmooth run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-kernsmooth test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of software tools for calculating distance measures.' - extra: identifiers: - biotools:biodist diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index 5a290a2546484..221067c0faacf 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -18,7 +18,7 @@ build: - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-httr - r-progress @@ -26,7 +26,7 @@ requirements: - r-stringr - r-xml run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-httr - r-progress @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.' - extra: identifiers: - biotools:biomaRt diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index fb520eed91caf..7026f64d24cd1 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biomformat" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7aa98827b119f1cac4b49e777d789ab9f387a791596b05a6844db5a39805476b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9cdc0620e70e96b232d12cbb233e2ddcb728ff9469c1ac01960b9cd43f45375b build: - skip: True # [osx] - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-rhdf5 + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' - 'r-plyr >=1.8' run: - - bioconductor-rhdf5 + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.' - extra: identifiers: - biotools:biomformat diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml index 2b101e2d95f97..bdd9d8609b700 100644 --- a/recipes/bioconductor-biomvcclass/meta.yaml +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "BioMVCClass" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ac61875e695c20c666b32c0354d08553efe8e4e628263f6a86ab2e662bfbc821 + sha256: 0fc37d1bb8c04530f42a99d925e9dc4c23bbc877466947b4f1eecc8481f9d9c4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-mvcclass - - bioconductor-rgraphviz + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-mvcclass >=1.54.0,<1.56.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base run: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-mvcclass - - bioconductor-rgraphviz + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-mvcclass >=1.54.0,<1.56.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base test: commands: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Creates classes used in model-view-controller (MVC) design' - extra: identifiers: - biotools:biomvcclass diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index 58ed69ac5f20e..baca54696a37d 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BioNet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 808d977ac8af90e8dbeae65a1e87f537009c88e8532d6d82df0878aa822171dd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6aa91986c4dd4d77f9920e7600c66a1951343e648c4e1f8d31ca48b993d259ab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - 'r-igraph >=1.0.1' run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - 'r-igraph >=1.0.1' test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.' - extra: identifiers: - biotools:bionet diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index 2aac4a8c084c3..c9e4e9a393fa9 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BioQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7abfb656723c874a837c2bad9b3368681c19b02bcbbcf8671406a201bff53bd3 + sha256: ef22544a0fb005c332a14edd802772146cc346a03e229a46b09592423bb2a0ee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rcpp run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rcpp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.' - extra: identifiers: - biotools:bioqc diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index 6ac18410951b1..41fecfe9c5a0e 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biosigner" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a9516501f420b65133267abadccd2ed0a0fad5fbb14480a547e710be7700c834 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9a06b5b98dd98afe127a170415815dfa3aabf65561f7ee01f67c103f2ab632df build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-ropls + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ropls >=1.12.0,<1.14.0' - r-base - r-e1071 - r-randomforest run: - - bioconductor-biobase - - bioconductor-ropls + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ropls >=1.12.0,<1.14.0' - r-base - r-e1071 - r-randomforest @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: CeCILL summary: 'Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding ''restricted'' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.' - extra: identifiers: - biotools:biosigner diff --git a/recipes/bioconductor-biostrings/meta.yaml b/recipes/bioconductor-biostrings/meta.yaml index 5f5c376783889..8d95d5a78488c 100644 --- a/recipes/bioconductor-biostrings/meta.yaml +++ b/recipes/bioconductor-biostrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "Biostrings" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f353f6c1fdbc520a685b880ef05f61245f04397adfcaae4c1395e14e1b06e56d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d244dd2dbe1fdaff293b07d6a9009f7fea49742dc252535f6cfea02941220b85 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.15.6' - - 'bioconductor-iranges >=2.9.18' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-xvector >=0.11.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-biocgenerics >=0.15.6' - - 'bioconductor-iranges >=2.9.18' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-xvector >=0.11.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.' - extra: identifiers: - biotools:biostrings diff --git a/recipes/bioconductor-biosvd/meta.yaml b/recipes/bioconductor-biosvd/meta.yaml index fbb777e9eee10..0ed265a9622c9 100644 --- a/recipes/bioconductor-biosvd/meta.yaml +++ b/recipes/bioconductor-biosvd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "biosvd" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8b023dfcf2004bcfddccefa53f8985a691227687c7685120049a0746be18e076 + sha256: 203134745fde2bde03a835516459261f87bd52bddc055be15b7d6609a488b507 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-nmf run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-nmf test: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The biosvd package contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures. These graphs aid in deciding which eigenfeatures and eigenassays to filter out (i.e., eigenfeatures representing steady state, noise, or experimental artifacts; or when applied to the variance in the data, eigenfeatures representing steady-scale variance). After possible removal of steady state expression, steady-scale variance, noise and experimental artifacts, and after re-applying SVD to the normalized data, a summary html report of the eigensystem is generated, containing among others polar plots of the assays and features, a table with the list of features sortable according to their coordinates, radius and phase in the polar plot, and a visualization of the data sorted according to the two selected eigenfeatures and eigenassays with colored feature/assay annotation information when provided. This gives a global picture of the dynamics of expression/intensity levels, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype.' - extra: identifiers: - biotools:biosvd diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index 3ceb484464cca..e68fc8be366e4 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.2" %} {% set name = "biovizBase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,54 +8,60 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4e44d3ea4c72e00ce5c1bdae821fac8163d22e1effb79f6aca5a130524dc8492 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f82137f3f5c985f567ae65ecc6e65cbfa385ec90b2cfb90889015807872c8471 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-annotationfilter >=0.99.8' - - bioconductor-biocgenerics - - 'bioconductor-biostrings >=2.33.11' - - 'bioconductor-ensembldb >=1.99.13' - - 'bioconductor-genomeinfodb >=1.5.14' - - 'bioconductor-genomicalignments >=1.1.16' - - 'bioconductor-genomicfeatures >=1.21.19' - - 'bioconductor-genomicranges >=1.23.21' - - 'bioconductor-iranges >=1.99.28' - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.11.4' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-dichromat - r-hmisc - r-rcolorbrewer + - r-rlang - r-scales run: - - bioconductor-annotationdbi - - 'bioconductor-annotationfilter >=0.99.8' - - bioconductor-biocgenerics - - 'bioconductor-biostrings >=2.33.11' - - 'bioconductor-ensembldb >=1.99.13' - - 'bioconductor-genomeinfodb >=1.5.14' - - 'bioconductor-genomicalignments >=1.1.16' - - 'bioconductor-genomicfeatures >=1.21.19' - - 'bioconductor-genomicranges >=1.23.21' - - 'bioconductor-iranges >=1.99.28' - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.11.4' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-dichromat - r-hmisc - r-rcolorbrewer + - r-rlang - r-scales + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -63,7 +69,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.' - extra: identifiers: - biotools:biovizbase diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml index 17ca45f511276..2d2946cc97c6f 100644 --- a/recipes/bioconductor-birewire/meta.yaml +++ b/recipes/bioconductor-birewire/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "BiRewire" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f3ba22c1db85f270565c05dc80e6ec4aa0ab0d0efbf32db448a1da805d81e223 + sha256: 05c9329d86695b52a6a550762b5d56529113a48d5fde9b6579340f78bb0dc4b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-igraph @@ -31,7 +29,9 @@ requirements: - r-matrix - r-slam - r-tsne - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs).' - extra: identifiers: - biotools:birewire diff --git a/recipes/bioconductor-birta/meta.yaml b/recipes/bioconductor-birta/meta.yaml index 22a53947bb870..34856df322513 100644 --- a/recipes/bioconductor-birta/meta.yaml +++ b/recipes/bioconductor-birta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "birta" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 904f9543c80b054efe3c5c472b955e86ca2d7eb821cb3fad2d5f20cb5a7c8dff + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 7bb2ddab319fc6d155912eb285acb1258f7842d030965ee2267b2937546cdcc0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-mass run: - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-mass + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.' - extra: identifiers: - biotools:birta diff --git a/recipes/bioconductor-birte/meta.yaml b/recipes/bioconductor-birte/meta.yaml index 360c0670d0ed1..ab032f5eae665 100644 --- a/recipes/bioconductor-birte/meta.yaml +++ b/recipes/bioconductor-birte/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "birte" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fbe939771f26ad59756b3d5a842c3e76a092b5e9c1efe92732ab8ce6800a9ce2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 55af4ce33820be43a9f42fbffca1955321d6ae3af521400b45cf001a990a4bdc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} + - make host: - - bioconductor-biobase - - 'bioconductor-limma >=3.22.0' - - bioconductor-nem + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-nem >=2.54.0,<2.56.0' - r-base - r-glmnet - r-mass - r-rcpp - 'r-rcpparmadillo >=0.3.6.1' - - lapack - openblas run: - - bioconductor-biobase - - 'bioconductor-limma >=3.22.0' - - bioconductor-nem + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-nem >=2.54.0,<2.56.0' - r-base - r-glmnet - r-mass - r-rcpp - - lapack - - openblas - 'r-rcpparmadillo >=0.3.6.1' + - openblas test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. biRte uses regulatory networks of TFs, miRNAs and possibly other factors, together with mRNA, miRNA and other available expression data to predict the relative influence of a regulator on the expression of its target genes. Inference is done in a Bayesian modeling framework using Markov-Chain-Monte-Carlo. A special feature is the possibility for follow-up network reverse engineering between active regulators.' - extra: identifiers: - biotools:birte diff --git a/recipes/bioconductor-biseq/meta.yaml b/recipes/bioconductor-biseq/meta.yaml index 5469c2e63527a..64da5cbc8f06c 100644 --- a/recipes/bioconductor-biseq/meta.yaml +++ b/recipes/bioconductor-biseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: df2a5e88e2a0b5df8bef882f7ab27cbfd16748736ee44d3a8ff60123eda4e708 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b2c2794e56066315ef680cdc513797def0e92651cc1c722af9f6a8b884ca8de0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-globaltest - - 'bioconductor-iranges >=1.17.24' - - bioconductor-rtracklayer - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-betareg - r-formula - r-lokern run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-globaltest - - 'bioconductor-iranges >=1.17.24' - - bioconductor-rtracklayer - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-betareg - r-formula @@ -51,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.' - extra: identifiers: - biotools:biseq diff --git a/recipes/bioconductor-bitseq/meta.yaml b/recipes/bioconductor-bitseq/meta.yaml index a1e00beea8681..1c64a36820da9 100644 --- a/recipes/bioconductor-bitseq/meta.yaml +++ b/recipes/bioconductor-bitseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "BitSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1e769bb9b98435a4ccb04b0e42c2e1089d0f030f82d3ac721d8ab629f6df75f6 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 073667c05fbec52c3eea932a3da68393240ae94fe069a46841b6bc5862060491 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-zlibbioc + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-zlibbioc + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 + file LICENSE' summary: 'The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression.' - extra: identifiers: - biotools:bitseq diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index 100f2fad923ee..a8b10fa28b62d 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "bladderbatch" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f68d9a7b57d20f88e97c306adc5f06a308d6d6890607736a4c2dfed6b7902ee9 + sha256: ecf44aaa06317c9ae9cad015718c889510f7f9b9fb6eb4d46ef23f0150ab0005 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package.' + + diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index 5f3461273e2f8..c1c628daf295c 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="bladderbatch_1.14.0.tar.gz" +FN="bladderbatch_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.5/data/experiment/src/contrib/bladderbatch_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/bladderbatch_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/bladderbatch_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.18.0_src_all.tar.gz" ) -MD5="e78d20742c18d7a526aefed891ee12b5" +MD5="c9baea96a9d50fadbbdfcf319c76b717" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-blima/meta.yaml b/recipes/bioconductor-blima/meta.yaml index 236eed077ce26..c14ed977ef371 100644 --- a/recipes/bioconductor-blima/meta.yaml +++ b/recipes/bioconductor-blima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "blima" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5d83e9c62a578a3005d4b5768522f8733ebb4c0f6a40243b1719279ab49b8301 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9548736beec21598bc8496f0d56fbeee88ad9d8fecf16c38c47950d629163935 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-beadarray >=2.0.0' - - 'bioconductor-biobase >=2.0.0' - - bioconductor-biocgenerics + - 'bioconductor-beadarray >=2.30.0,<2.32.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - 'r-rcpp >=0.12.8' run: - - 'bioconductor-beadarray >=2.0.0' - - 'bioconductor-biobase >=2.0.0' - - bioconductor-biocgenerics + - 'bioconductor-beadarray >=2.30.0,<2.32.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - 'r-rcpp >=0.12.8' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.' - extra: identifiers: - biotools:blima diff --git a/recipes/bioconductor-brain/meta.yaml b/recipes/bioconductor-brain/meta.yaml index 339f6dfded9f3..2fd2a9d8c0cb6 100644 --- a/recipes/bioconductor-brain/meta.yaml +++ b/recipes/bioconductor-brain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BRAIN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 950a19ee7a466d52323010f48c3a9c6be8c1ae4f0433d337ca287d4fd988ac33 + sha256: bf56e42ac4f497e66c020436a80fc24768b8f733b63ab8bef3e3ee8cbc0a40a6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-lattice - r-polynomf run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-lattice - r-polynomf @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg.' - extra: identifiers: - biotools:brain diff --git a/recipes/bioconductor-brainstars/meta.yaml b/recipes/bioconductor-brainstars/meta.yaml index 4f0aa6c8bc194..47e34564b4a36 100644 --- a/recipes/bioconductor-brainstars/meta.yaml +++ b/recipes/bioconductor-brainstars/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "BrainStars" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 726fb8fc0b1aefee7a35aa846fa6c07a13c5b4b7996ded7413865c7de5b5373a + sha256: b54f910a8fd645a46cfafe218f2f0c9e005d5b14cc168b4024dc32443c464a70 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rcurl - r-rjsonio run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rcurl - r-rjsonio @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package can search and get gene expression data and plots from BrainStars (B*). BrainStars is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.' - extra: identifiers: - biotools:brainstars diff --git a/recipes/bioconductor-bridge/meta.yaml b/recipes/bioconductor-bridge/meta.yaml index 39c2ac2f01909..83a437aea9c0a 100644 --- a/recipes/bioconductor-bridge/meta.yaml +++ b/recipes/bioconductor-bridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "bridge" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 537acf2edd96df67a1c19fa0f5114b60a2d205a10094f829879f6f86c498ac2b + sha256: 69562d8824201c4ac2c6874e78665a9fa35b04b9dd8dcd86a324f09d5558ffaf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-rama + - 'bioconductor-rama >=1.54.0,<1.56.0' - r-base run: - - bioconductor-rama + - 'bioconductor-rama >=1.54.0,<1.56.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.' - extra: identifiers: - biotools:bridge diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml index 8feee422ad474..88bf9e6d4bba0 100644 --- a/recipes/bioconductor-browserviz/meta.yaml +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "2.2.0" %} {% set name = "BrowserViz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ac0f17636dcb0bb2c060bdd76181626fba2cdf116d05ee3ea1c015209d066dec + sha256: d84c9f4238491950ab72087e14981819e0c08654deddad5f7b6e0e793bde178e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - - 'r-httpuv >=1.3.2' - - 'r-jsonlite >=0.9.15' + - 'r-httpuv >=1.4.0' + - 'r-jsonlite >=1.5' run: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - - 'r-httpuv >=1.3.2' - - 'r-jsonlite >=0.9.15' + - 'r-httpuv >=1.4.0' + - 'r-jsonlite >=1.5' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Interactvive graphics in a web browser from R, using websockets and JSON.' - extra: identifiers: - biotools:browserviz diff --git a/recipes/bioconductor-browservizdemo/meta.yaml b/recipes/bioconductor-browservizdemo/meta.yaml index 8232209837928..63441fde1d90d 100644 --- a/recipes/bioconductor-browservizdemo/meta.yaml +++ b/recipes/bioconductor-browservizdemo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} {% set name = "BrowserVizDemo" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1d3d43e647083d9ffcdd389e066cdf58c9fc2eb8b5de3ad2029884162845fa7a + sha256: 0d5ea637eccefd4e57e3ab55f7c77cc0b40a422a9f1e6963cbb37826673ab9c5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-browserviz + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-browserviz >=2.2.0,<2.4.0' - r-base - 'r-httpuv >=1.3.2' - 'r-jsonlite >=0.9.15' - 'r-rcpp >=0.11.5' run: - - bioconductor-biocgenerics - - bioconductor-browserviz + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-browserviz >=2.2.0,<2.4.0' - r-base - 'r-httpuv >=1.3.2' - 'r-jsonlite >=0.9.15' - 'r-rcpp >=0.11.5' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A BrowserViz subclassing example, xy plotting in the browser using d3.' - extra: identifiers: - biotools:browservizdemo diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index e92789448aa50..1faba25a90d7e 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce10" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3337ffc0b59ee6d4f74e790cfd7aea9f54b8b3f87cbb48c2ecd792294faa5efd build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct. 2010) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh index 4551f810ac8bc..3149d7232e3db 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz" ) MD5="98a8ca836d6db23e46674552669d7942" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index b1521233c2a2e..2e0bb0533e53e 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce6" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6997709c5f9eca77a1b7d3367bee676f765b672b61acb9471d4cec3eca581f57 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh index 46142280cf217..a5a5ba9805914 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz" ) MD5="cb86ff861d8f660c2abd8fc1907d84a6" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index d6a9c9113bd80..826cc2be08604 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 68ebdefa8c99330f320d1928673ac89601e842102990cbed1b4f4d08271d75a5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh index 100d8dae8565d..729fbf774928a 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz" ) MD5="b7ceebf7bfee766596f602f9e808d069" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml index 2e984bf8943b0..02b00c0b64861 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer7" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: ef2e7e27508d7dbfc63e09ae36f96d2578590af1f12b82912fe029898084a39f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh index 98a91893e6427..b699f31ab28dc 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" ) MD5="766b407a46f20d69a143eab0809eb10a" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index ff31490956269..77b37aa5e4963 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Ecoli.NCBI.20080805" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4740ebd81b56e9a990e7bbf3eb799011346db8af4a2615572558cda0bd97f5d0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh index c61a2059674e4..619361318f646 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz" ) MD5="c653e9cbee3faeb6fd5759b7575f234d" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml index 8ce1d64cbb76e..c6e28bb8804f0 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 26fa81bfdb16269d76299aae1f352ddd3c56bec30da7259785fe3e3d8985a7ad build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index c67fcee743f05..573fe27c5f850 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh index 816f5921c3773..1fa4558fa5741 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.0_src_all.tar.gz" ) MD5="672a988b28d8602afb2bd5595db7303b" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index 47fbbed21e03e..0eda5d3a25b9e 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 71d7e4557666e2ff76ffc6c637331bfab0c0b59f4963f2b6f5606f12f74580e2 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.35.16' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.35.16' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh index a46efc1b95a8f..3cf524720b090 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.1_src_all.tar.gz" ) MD5="1b95bfdc9763351b04611666cd624b30" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index fc0cc25872f7f..95af0c8d1bfff 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, Dec. 2011) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index 30148e3da3a6c..6d718bd04865a 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3110745e93ae7c470b826921efc308fd5805efacdf497b7b8d5f890706c739ae build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base run: - - 'bioconductor-bsgenome >=1.33.5' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.' + + diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh index 42cf78ad7df07..46e2c221f96b6 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash -FN="BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" +FN="bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" ) MD5="5a30ba2b4481a17e8e6979eb69eabf78" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 00e6ba40dadd4..a13a0c56f047b 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "BSgenome" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 98126e5cb970b113a8ca158c8cdf6e2e4da0f5b4ddc525ac54524551e9c17fc9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e815eb2def62b70e9aade10094f0cee3d9d3c44179581a4a9bf7b68271bc62e6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.13.8' - - 'bioconductor-biostrings >=2.35.3' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - bioconductor-rsamtools - - 'bioconductor-rtracklayer >=1.25.8' - - 'bioconductor-s4vectors >=0.9.36' - - bioconductor-xvector + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-biocgenerics >=0.13.8' - - 'bioconductor-biostrings >=2.35.3' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - bioconductor-rsamtools - - 'bioconductor-rtracklayer >=1.25.8' - - 'bioconductor-s4vectors >=0.9.36' - - bioconductor-xvector + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base test: commands: @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Infrastructure shared by all the Biostrings-based genome data packages.' - extra: identifiers: - biotools:bsgenome diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml index 63d089a2a7d5e..90046ca92c9e6 100644 --- a/recipes/bioconductor-bsseq/meta.yaml +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -1,72 +1,67 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "bsseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 244f58c0f58d41c1c5888ddbf33a9c073fe5dd5e15e9a3d3f3b541afcdcad648 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a5463893c12ab9cf479ecc3d32113d2e436b657c02def951dcc56d748c1ab064 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-delayedarray - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.14' - - bioconductor-hdf5array - - 'bioconductor-iranges >=2.11.16' - - bioconductor-limma - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.7.8' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-hdf5array >=1.8.1,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-gtools - r-locfit - - 'r-matrixstats >=0.50.0' - r-permute - 'r-r.utils >=2.0.0' - r-scales run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-delayedarray - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.14' - - bioconductor-hdf5array - - 'bioconductor-iranges >=2.11.16' - - bioconductor-limma - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.7.8' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-hdf5array >=1.8.1,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-gtools - r-locfit - - 'r-matrixstats >=0.50.0' - r-permute - 'r-r.utils >=2.0.0' - r-scales - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of tools for analyzing and visualizing bisulfite sequencing data.' - extra: identifiers: - biotools:bsseq diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index b6b92cf29e919..0ee695d98fbac 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "BubbleTree" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 218d2c332c8b861af538cf4e5a2b470b7fdb76602cc2f8766b72aad8ac3e0eda + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 966e8e59ae9ac9ae950faf6559eb395cd42d1853d12504bea1065308fffdd83c build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-biocstyle - - bioconductor-biovizbase - - 'bioconductor-genomeinfodb >=1.14.0' - - 'bioconductor-genomeinfodbdata >=1.0.0' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dplyr - r-e1071 @@ -38,15 +37,13 @@ requirements: - r-rcolorbrewer - r-writexls run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-biocstyle - - bioconductor-biovizbase - - 'bioconductor-genomeinfodb >=1.14.0' - - 'bioconductor-genomeinfodbdata >=1.0.0' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dplyr - r-e1071 @@ -65,7 +62,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'CNV analysis in groups of tumor samples.' - extra: identifiers: - biotools:bubbletree diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml index 14d6419672b90..3639dca003a4e 100644 --- a/recipes/bioconductor-bufferedmatrix/meta.yaml +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "BufferedMatrix" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 07f8c652593aa9ae7495a8e698672463807b70dc4a6b563e5f75b1687b48b9ef + sha256: f366c3b558e925f14d600bbedc23ac17afe7541d8b4e18d73fe3287b57db4036 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.' - extra: identifiers: - biotools:bufferedmatrix diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml index 4016afff919e7..d2f016af7a0fc 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "BufferedMatrixMethods" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2550805761d33f47a2e32c8e4cc613645a252a2968b1dabb434d25c99215ecd + sha256: b0824c8216f969d722c055ef0c38421f38533bd83c0f67c435f835de40a0a02b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-bufferedmatrix >=1.3.0' + - 'bioconductor-bufferedmatrix >=1.44.0,<1.46.0' - r-base run: - - 'bioconductor-bufferedmatrix >=1.3.0' + - 'bioconductor-bufferedmatrix >=1.44.0,<1.46.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Microarray analysis methods that use BufferedMatrix objects' - extra: identifiers: - biotools:bufferedmatrixmethods diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index 93c1b56897815..68ff1af08260b 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "bumphunter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 906a119be54151901d3bd266be33da512052d92a0f8ad26cf4ce28f93a80e029 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: bedff4dc62c5274ac835c877de825f959d1f40e0779d356d42117847efcd4b34 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.3.23' - - bioconductor-limma - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dorng - r-foreach @@ -32,14 +33,14 @@ requirements: - r-locfit - r-matrixstats run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.3.23' - - bioconductor-limma - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dorng - r-foreach @@ -53,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for finding bumps in genomic data' - extra: identifiers: - biotools:bumphunter diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index 08e3a657e7865..b269e37a0d528 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "BUS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 76c764307fb9baa5781b0804fd7fc3eeb4bc1ae0433a9d584f40ac863029151e + sha256: dc2262578a875ff3a5a17100c11dc110977847a742f96138ff6cfaec05dc85cf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-minet + - 'bioconductor-minet >=3.38.0,<3.40.0' - r-base - r-infotheo run: - - bioconductor-minet + - 'bioconductor-minet >=3.38.0,<3.40.0' - r-base - r-infotheo - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).' - extra: identifiers: - biotools:bus diff --git a/recipes/bioconductor-cager/conda_build_config.yaml b/recipes/bioconductor-cager/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-cager/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml index e75322b020424..dc985ba8818b5 100644 --- a/recipes/bioconductor-cager/meta.yaml +++ b/recipes/bioconductor-cager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.3" %} {% set name = "CAGEr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,70 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 76f40d4c2d6f74f2fa6628b093ba5f22b74d8c0b5d24e146a90fb915f9cd5b3d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c4651de70deada80715d6013a52f3818aa7fee025d558584edc416d1606a8d57 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bsgenome - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-beanplot - r-data.table + - 'r-ggplot2 >=2.2.0' + - r-gtools + - r-kernsmooth + - r-memoise + - r-plyr + - r-reshape - r-som + - r-stringdist + - r-stringi + - r-vegan - r-vgam run: - - bioconductor-bsgenome - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-beanplot - r-data.table + - 'r-ggplot2 >=2.2.0' + - r-gtools + - r-kernsmooth + - r-memoise + - r-plyr + - r-reshape - r-som + - r-stringdist + - r-stringi + - r-vegan - r-vgam test: commands: @@ -45,7 +80,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).' - extra: identifiers: - biotools:cager diff --git a/recipes/bioconductor-calib/meta.yaml b/recipes/bioconductor-calib/meta.yaml index 68e8fe3b5d43c..48e9d343f46b0 100644 --- a/recipes/bioconductor-calib/meta.yaml +++ b/recipes/bioconductor-calib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "CALIB" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e5d5ee39cd065928595f94f5e580c71ab0cbf978f511a0186a9e01d500a7d6d8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5cf0010419dda41f2ea4e5e04b9edee580d491275d709ff0476febb4e2d693e2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.' - extra: identifiers: - biotools:calib diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index 2d5bff896ee07..bc0b25f3b60c6 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -1,53 +1,48 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "CAMERA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - - source: - url: https://depot.galaxyproject.org/software/bioconductor-camera/bioconductor-camera_1.34.0_src_all.tar.gz - sha256: 714ba1f5a4e0e97c0704dacfa5a7150c4c5ac39dcb95eba140b0cd108c3e7ac5 - + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a009b4b5ba0e30ae9eed3962e7a81228eaaffc5e768355b3e4e68bfcb6c170ad build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} host: - - bioconductor-biobase - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-hmisc - r-igraph run: - - bioconductor-biobase - - libgfortran-ng - - bioconductor-graph - - bioconductor-rbgl - - 'bioconductor-xcms >=1.13.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-hmisc - r-igraph - + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments' - extra: identifiers: - biotools:camera diff --git a/recipes/bioconductor-cancerinsilico/meta.yaml b/recipes/bioconductor-cancerinsilico/meta.yaml index a7ab151fa0df6..fcfd0f1d11951 100644 --- a/recipes/bioconductor-cancerinsilico/meta.yaml +++ b/recipes/bioconductor-cancerinsilico/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "2.0.0" %} {% set name = "CancerInSilico" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 30f18ce1520f522638f1b3fb1a84ca9fbb164e479a6eff599f9ea4d40512f7a6 + sha256: c35f23004342562d43e5aa42da890d446eeaf9703eaa353a76356a08eba29caa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-bh - r-rcpp - - r-testthat run: - r-base - r-bh - r-rcpp - - r-testthat - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'The CancerInSilico package provides an R interface for running mathematical models of tumor progresson. This package has the underlying models implemented in C++ and the output and analysis features implemented in R.' - + license: GPL-2 + summary: 'The CancerInSilico package provides an R interface for running mathematical models of tumor progresson and generating gene expression data from the results. This package has the underlying models implemented in C++ and the output and analysis features implemented in R.' extra: identifiers: - biotools:cancerinsilico diff --git a/recipes/bioconductor-cancermutationanalysis/meta.yaml b/recipes/bioconductor-cancermutationanalysis/meta.yaml index c503d21b761f7..f2fb1ea998c10 100644 --- a/recipes/bioconductor-cancermutationanalysis/meta.yaml +++ b/recipes/bioconductor-cancermutationanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CancerMutationAnalysis" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1cbcaf6efc42c526e07694778dce88f0af15e45cb0d4080b7b36f78d8c719a99 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 749165ff107d99e4b7d5ad341ce1411e25349f25e70c3b9e3e090b141231d3a4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.' - extra: identifiers: - biotools:cancermutationanalysis diff --git a/recipes/bioconductor-cancersubtypes/meta.yaml b/recipes/bioconductor-cancersubtypes/meta.yaml index 39973805eb71e..97da03742dbc3 100644 --- a/recipes/bioconductor-cancersubtypes/meta.yaml +++ b/recipes/bioconductor-cancersubtypes/meta.yaml @@ -1,28 +1,26 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CancerSubtypes" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ece51c69ed73b60b79b7c6bbe19754cde3318c079fecdb56b5635ea043517458 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e365e26d253616dfdcf85a146a79bafbefa3c91604c35beac9807c9bc9e774bf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-consensusclusterplus - - bioconductor-impute - - bioconductor-limma + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-cluster - r-icluster @@ -31,9 +29,9 @@ requirements: - r-snftool - r-survival run: - - bioconductor-consensusclusterplus - - bioconductor-impute - - bioconductor-limma + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-cluster - r-icluster @@ -41,16 +39,13 @@ requirements: - r-sigclust - r-snftool - r-survival - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'CancerSubtypes integrates the current common computational biology methods for cancer subtypes identification and provides a standardized framework for cancer subtype analysis based multi-omics data, such as gene expression, miRNA expression, DNA methylation and others.' - extra: identifiers: - biotools:cancersubtypes diff --git a/recipes/bioconductor-cand/meta.yaml b/recipes/bioconductor-cand/meta.yaml index cba3e27a3aac7..58a366017a00f 100644 --- a/recipes/bioconductor-cand/meta.yaml +++ b/recipes/bioconductor-cand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CAnD" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e7fca582632d0f9540c365e0ad6da7e702f12bb77f1952ea870db5f4e9a5df9e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 59d74d2e70ccd062c5ad282d12fbd4229d5dde90dbd3dc9db15132a4f8b17ab5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions to perform the CAnD test on a set of ancestry proportions. For a particular ancestral subpopulation, a user will supply the estimated ancestry proportion for each sample, and each chromosome or chromosomal segment of interest. A p-value for each chromosome as well as an overall CAnD p-value will be returned for each test. Plotting functions are also available.' - extra: identifiers: - biotools:cand diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index 7e2e974def6df..23a28227f9e38 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -6,36 +6,41 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: d72bb63d15040fcc46b97022a45a92bb3c1ecb2cafc1b9806f746e1e8d12a1f7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-matter >=1.6 - - bioconductor-protgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-matter >=1.6.0,<1.8.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - r-base - r-irlba - r-lattice - r-signal - r-sp run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-matter >=1.6 - - bioconductor-protgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-matter >=1.6.0,<1.8.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - r-base - r-irlba - r-lattice - r-signal - r-sp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,11 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.' - extra: identifiers: - biotools:cardinal - skip-lints: - - bioconductor_37 - - diff --git a/recipes/bioconductor-casper/meta.yaml b/recipes/bioconductor-casper/meta.yaml index 72926067d70e9..d6bbe54976ed4 100644 --- a/recipes/bioconductor-casper/meta.yaml +++ b/recipes/bioconductor-casper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "casper" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f5ec65097a0d3fe9c35fc11e4d0b3fe0f8fdf20dcc333da9bd68fa4725ecb887 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ceada9d23d5da7e0f65bd6355722ba1d25f979318b0c7e0e0242149b44e68a37 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-ebarrays - - bioconductor-gaga - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-ebarrays >=2.44.0,<2.46.0' + - 'bioconductor-gaga >=2.26.0,<2.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-coda - r-gtools @@ -37,18 +38,18 @@ requirements: - r-survival - r-vgam run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-ebarrays - - bioconductor-gaga - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-ebarrays >=2.44.0,<2.46.0' + - 'bioconductor-gaga >=2.26.0,<2.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-coda - r-gtools @@ -56,6 +57,10 @@ requirements: - r-sqldf - r-survival - r-vgam + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -63,7 +68,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.' - extra: identifiers: - biotools:casper diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index 7d8bcc05f135d..4de199737bb1e 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "Category" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 28028f6a1b12161c8ba3b30f14bb4ea86899416b5deb0694eb40d1b509d86a56 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a0bf452fcfd0513f3e46a98880e1af03b783e7ad82fe2346d5fcb5d090c28e0f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-graph - - bioconductor-gseabase - - bioconductor-rbgl + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - r-dbi - r-matrix run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-graph - - bioconductor-gseabase - - bioconductor-rbgl + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - r-dbi - r-matrix @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of tools for performing category (gene set enrichment) analysis.' - extra: identifiers: - biotools:category diff --git a/recipes/bioconductor-causalr/meta.yaml b/recipes/bioconductor-causalr/meta.yaml index 1120ba38e542b..fce4bd7e61c80 100644 --- a/recipes/bioconductor-causalr/meta.yaml +++ b/recipes/bioconductor-causalr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CausalR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 225969a6fdf129629b6cdbbcde73555620f25a52f2d6678fd626a3f372b3463a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1f542a9ffc79fe02f79892d9161db85b8c782e011d1f16790c58699e0a3521bf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.' - extra: identifiers: - biotools:causalr diff --git a/recipes/bioconductor-cellgrowth/meta.yaml b/recipes/bioconductor-cellgrowth/meta.yaml index 0204f26f605a1..bd9def2beeb8f 100644 --- a/recipes/bioconductor-cellgrowth/meta.yaml +++ b/recipes/bioconductor-cellgrowth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "cellGrowth" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 756a22a541663e9f6877b6634fa5c792fe75de446bc027af18dfa3a506109811 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 641735000edf3981d23ebf871b2617e20576151411509d1e02af1d973b17400f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides functionalities for the fitting of cell population growth models on experimental OD curves.' - extra: identifiers: - biotools:cellgrowth diff --git a/recipes/bioconductor-cellhts2/conda_build_config.yaml b/recipes/bioconductor-cellhts2/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-cellhts2/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-cellhts2/meta.yaml b/recipes/bioconductor-cellhts2/meta.yaml index a328246eeba49..58c4173232b2b 100644 --- a/recipes/bioconductor-cellhts2/meta.yaml +++ b/recipes/bioconductor-cellhts2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "cellHTS2" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7d7e8d25fe33417abb529c1bffde28151fa1d2c766e1d8f7e94095bfe3230030 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 90c46478b3a0e3e3b812b20c311cf41899bb94965e30820bb174e15904548a4a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-category - - bioconductor-genefilter - - bioconductor-gseabase - - bioconductor-prada - - bioconductor-splots - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-prada >=1.56.0,<1.58.0' + - 'bioconductor-splots >=1.46.0,<1.48.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-hwriter - r-locfit - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-category - - bioconductor-genefilter - - bioconductor-gseabase - - bioconductor-prada - - bioconductor-splots - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-prada >=1.56.0,<1.58.0' + - 'bioconductor-splots >=1.46.0,<1.48.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-hwriter - r-locfit @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.' - extra: identifiers: - biotools:cellhts2 diff --git a/recipes/bioconductor-cellmapper/meta.yaml b/recipes/bioconductor-cellmapper/meta.yaml index fd5fcf45000b5..84d978dd1996b 100644 --- a/recipes/bioconductor-cellmapper/meta.yaml +++ b/recipes/bioconductor-cellmapper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CellMapper" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ab0062c4c584d57be8089314ecaf33e8c15f635c32928c2e4ae3d1b30440ea9a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d01348fa8b262193fbe2277418931e9440ae460a2bd257f279034b36db78967a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-s4vectors + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-s4vectors + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.' - extra: identifiers: - biotools:cellmapper diff --git a/recipes/bioconductor-cellnoptr/meta.yaml b/recipes/bioconductor-cellnoptr/meta.yaml index 4e2bd50a72260..b799b0ae99c3d 100644 --- a/recipes/bioconductor-cellnoptr/meta.yaml +++ b/recipes/bioconductor-cellnoptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "CellNOptR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6af85d48faf045458607be91b7f8fceb6cb85929074e578192ab16689e9ecf5c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1eb26216d20f4a4a6824b4bea4c328c794143280c51a5eb4e5251033d708776f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-ggplot2 - r-hash - r-rcurl - r-xml run: - - bioconductor-graph - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-ggplot2 - r-hash - r-rcurl - r-xml + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.' - extra: identifiers: - biotools:cellnoptr diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index ecc06532ad9b9..6304de1badf34 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CexoR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,33 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e6ebe512c1e56c529c486583cb520352aa1bf91c1a690a23682f5eda062d72d8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b337039bb3db90dc74f1367868ba39379cc752eb5bc546ce9efbbea2e91cfba0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomation - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-genomation >=1.12.0,<1.14.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-idr - r-rcolorbrewer run: - - bioconductor-genomation - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-genomation >=1.12.0,<1.14.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-idr - r-rcolorbrewer @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | GPL-2 + file LICENSE' summary: 'Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package ''skellam'') is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package ''idr''.' - extra: identifiers: - biotools:cexor diff --git a/recipes/bioconductor-cfassay/meta.yaml b/recipes/bioconductor-cfassay/meta.yaml index 30b76f82c6352..6494e124400a1 100644 --- a/recipes/bioconductor-cfassay/meta.yaml +++ b/recipes/bioconductor-cfassay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CFAssay" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 48c82f112cd05c12536f59a6cb8e3f3fc6471a46309b91460083e875679eca07 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5187e9a3b990f447d7b84e274051e9ea44be03b574127c53fdde1d8c6ad6baca build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.' - extra: identifiers: - biotools:cfassay diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index 92868c9824ce2..d70a282bf1e2d 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CGHbase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9562f906d128261bd2b2239799fa0c0b6654a2452c770b6232f7ad2635dbd63b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 58f12ed6f5ebb38d996d355465b15c486d35bbdb5f2f3983c9fccda1ea26c4c1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Contains functions and classes that are needed by arrayCGH packages.' - extra: identifiers: - biotools:cghbase diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index 1b8a36ba7bdff..84df548d0f8bd 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "CGHcall" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 90515a55d93af4e828798148459ab9afe9cae670787ca0c9f2a8a0f1b932f186 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: bf89e06a9600c589e70ebdc126923ff52c5652f64094bdfba80af4b4bbdbe178 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-cghbase >=1.15.1' - - 'bioconductor-dnacopy >=1.6.0' - - 'bioconductor-impute >=1.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-base - r-snowfall run: - - bioconductor-biobase - - 'bioconductor-cghbase >=1.15.1' - - 'bioconductor-dnacopy >=1.6.0' - - 'bioconductor-impute >=1.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-base - r-snowfall test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (http://www.gnu.org/copyleft/gpl.html)' summary: 'Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.' - extra: identifiers: - biotools:cghcall diff --git a/recipes/bioconductor-cghmcr/meta.yaml b/recipes/bioconductor-cghmcr/meta.yaml index f518e8c13a996..f8c377c1c6d6e 100644 --- a/recipes/bioconductor-cghmcr/meta.yaml +++ b/recipes/bioconductor-cghmcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "cghMCR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9aa166fbb0f6b924be95e7f51a95e949fe0539ed613b3ac77ae02d2caa658681 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7a483c8f37fe841e4029634ffaa9a9fc502cd16824e98b037ad77ea60d057a75 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.1.6' - - bioconductor-cntools - - bioconductor-dnacopy - - bioconductor-limma + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-cntools >=1.36.0,<1.38.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - 'bioconductor-biocgenerics >=0.1.6' - - bioconductor-cntools - - bioconductor-dnacopy - - bioconductor-limma + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-cntools >=1.36.0,<1.38.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base test: commands: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.' - extra: identifiers: - biotools:cghmcr diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml index f9852195e09d8..3e1343cb97f8b 100644 --- a/recipes/bioconductor-cghnormaliter/meta.yaml +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CGHnormaliter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8c7c974157467ec4ac24fcc55424bcfe2e60fe5c96e9aa2cc65e0c473cf523af + sha256: 3c36826990685373baaf34836520e28c8b8425dc19a6870b6473baa80680d4dd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-cghbase >=1.15.0' - - 'bioconductor-cghcall >=2.17.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-cghcall >=2.42.0,<2.44.0' - r-base run: - - bioconductor-biobase - - 'bioconductor-cghbase >=1.15.0' - - 'bioconductor-cghcall >=2.17.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-cghcall >=2.42.0,<2.44.0' - r-base test: commands: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).' - extra: identifiers: - biotools:cghnormaliter diff --git a/recipes/bioconductor-cghregions/meta.yaml b/recipes/bioconductor-cghregions/meta.yaml index 88c084fe29001..0fc4628de0594 100644 --- a/recipes/bioconductor-cghregions/meta.yaml +++ b/recipes/bioconductor-cghregions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CGHregions" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5827279763ee9f00bab54cc0a2e315343e25daef473932604a688298ae9d8405 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7ab10d41625ea1b4004bc0cb4d3a7ada2964b5bfd29cb5f8f9f242ba991c5b79 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-cghbase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' - r-base run: - - bioconductor-biobase - - bioconductor-cghbase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (http://www.gnu.org/copyleft/gpl.html)' summary: 'Dimension Reduction for Array CGH Data with Minimal Information Loss' - extra: identifiers: - biotools:cghregions diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index b710b2c8fe6e1..be8af210f3cc8 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "3.32.1" %} {% set name = "ChemmineR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,42 +8,49 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 54b99549687ddebab04144c6321a595e66ec0161e7d52626b8d7d4f6d55e09e1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1cd0a789ea9e1da73f40ca0fc585b370044447507731eef6cc95df666145ef87 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - - r-bh # not in DESCRIPTION + - r-base64enc + - r-bh - r-dbi - r-digest + - r-dt - r-ggplot2 - r-gridextra - r-png - 'r-rcpp >=0.11.0' - r-rcurl - r-rjson - - r-bh # not specified in DESCRIBTION + - r-rsvg run: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - - r-bh # not in DESCRIPTION + - r-base64enc + - r-bh - r-dbi - r-digest + - r-dt - r-ggplot2 - r-gridextra - r-png - 'r-rcpp >=0.11.0' - r-rcurl - r-rjson - - r-bh # not specified in DESCRIBTION + - r-rsvg + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.' - extra: identifiers: - biotools:chemminer diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index 2d670fd1e8f2b..971813f3c899e 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Chicago" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fc19bcadfd08325d9e568d157e989db9ad4900acd97b2ce7b2c3b685cfcf58e8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0d938792567088e2458762df32ef40c845cc9070a8932c7e5a7fb9517f9e2954 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A pipeline for analysing Capture Hi-C data.' - extra: identifiers: - biotools:chicago diff --git a/recipes/bioconductor-chimera/meta.yaml b/recipes/bioconductor-chimera/meta.yaml index b7c8932a1005f..4fae5141f57f2 100644 --- a/recipes/bioconductor-chimera/meta.yaml +++ b/recipes/bioconductor-chimera/meta.yaml @@ -1,52 +1,52 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "chimera" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a473b0db84efef737782dc07f784eef7acc62133fcac140c7ba2fb6d3dbfa07c - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b24054dd8cfccd9fcb5ae546a8b220c91eac68a8e965ddd1bd224ec3dfc16ccf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomicalignments - - 'bioconductor-genomicranges >=1.13.3' - - bioconductor-homo.sapiens - - 'bioconductor-rsamtools >=1.13.1' - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomicalignments - - 'bioconductor-genomicranges >=1.13.3' - - bioconductor-homo.sapiens - - 'bioconductor-rsamtools >=1.13.1' - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base - + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package facilitates the characterisation of fusion products events. It allows to import - fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, - FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.' + summary: 'This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.' + + diff --git a/recipes/bioconductor-chimeraviz/build.sh b/recipes/bioconductor-chimeraviz/build.sh index be092347e8f41..da43ce2168312 100644 --- a/recipes/bioconductor-chimeraviz/build.sh +++ b/recipes/bioconductor-chimeraviz/build.sh @@ -1,17 +1,4 @@ - #!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# -$R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chimeraviz/meta.yaml b/recipes/bioconductor-chimeraviz/meta.yaml index 4c802c7c92a19..6cf8b6199ec0a 100644 --- a/recipes/bioconductor-chimeraviz/meta.yaml +++ b/recipes/bioconductor-chimeraviz/meta.yaml @@ -1,84 +1,80 @@ -{% set version="1.0.4" %} +{% set version = "1.6.2" %} +{% set name = "chimeraviz" %} +{% set bioc = "3.7" %} + package: - name: bioconductor-chimeraviz - version: {{ version }} + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' source: - url: https://github.com/Bioconductor-mirror/chimeraviz/archive/release-3.5.zip - md5: 129446e46040fa2cdb34854bbf837fd1 - + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 72155e7a9e6ae51f6ad588d6ee0d98cbcda3710d9794eb6c6f03d3d502f1d5a9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-gviz - - bioconductor-s4vectors - - bioconductor-ensembldb - - bioconductor-annotationfilter - - bioconductor-rsamtools - - bioconductor-genomeinfodb - - bioconductor-genomeinfodbdata - - bioconductor-genomicalignments - - bioconductor-annotationdbi - - bioconductor-org.hs.eg.db - - bioconductor-graph - - bioconductor-rgraphviz - - bioconductor-biocstyle - - r-readr - - r-gridbase - - r-gridextra - - r-rcolorbrewer - - r-rcircos - - r-rmarkdown + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - r-argumentcheck + - r-base + - r-data.table + - r-dplyr - r-dt - r-plyr - - r-argumentcheck - - r-base >=3.4 - - pandoc - - run: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-gviz - - bioconductor-s4vectors - - bioconductor-ensembldb - - bioconductor-annotationfilter - - bioconductor-rsamtools - - bioconductor-genomeinfodb - - bioconductor-genomeinfodbdata - - bioconductor-genomicalignments - - bioconductor-annotationdbi - - bioconductor-org.hs.eg.db - - bioconductor-graph - - bioconductor-rgraphviz - - bioconductor-biocstyle - - r-readr - - r-gridbase - - r-gridextra - - r-rcolorbrewer - r-rcircos + - r-rcolorbrewer - r-rmarkdown + run: + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - r-argumentcheck + - r-base + - r-data.table + - r-dplyr - r-dt - r-plyr - - r-argumentcheck - - r-base >=3.4 - - pandoc - + - r-rcircos + - r-rcolorbrewer + - r-rmarkdown test: commands: - - '$R -e "library(''chimeraviz'')"' + - '$R -e "library(''{{ name }}'')"' about: - home: https://bioconductor.org/packages/release/bioc/html/chimeraviz.html - license: 'Artistic-2.0' + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 summary: 'chimeraviz manages data from fusion gene finders and provides useful visualization tools.' + + diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index abcbaa0644df4..fb74682688bdd 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ChIPComp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,42 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 80fc73580189dcba21b763cdf88b28783d3b1177ebd42ccd36274668074843da + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1a43058202e3fbf2e0e8265d9113d0187d0885513ce54386eb0d8ff18f8b3649 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-bsgenome.mmusculus.ucsc.mm9 - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-bsgenome.mmusculus.ucsc.mm9 - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +51,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.' - extra: identifiers: - biotools:chipcomp diff --git a/recipes/bioconductor-chippeakanno/conda_build_config.yaml b/recipes/bioconductor-chippeakanno/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-chippeakanno/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml index a772c8b72a493..6a77f5238d575 100644 --- a/recipes/bioconductor-chippeakanno/meta.yaml +++ b/recipes/bioconductor-chippeakanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.2" %} {% set name = "ChIPpeakAnno" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fd189e557e7534e4cf7cb6dffbc5910ded2b655fd722cc93bc0a4f308b41762e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4c73984fc86297346ade9747fe408ce5feb77f3790aa1702f7bf775a0cd3338f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-biocinstaller - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-delayedarray - - bioconductor-ensembldb - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.29.14' - - bioconductor-go.db - - bioconductor-graph - - 'bioconductor-iranges >=2.11.16' - - bioconductor-limma - - bioconductor-multtest - - bioconductor-rbgl - - bioconductor-regioner - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-regioner >=1.12.0,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dbi - r-idr @@ -47,29 +48,29 @@ requirements: - r-seqinr - r-venndiagram run: - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-biocinstaller - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-delayedarray - - bioconductor-ensembldb - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.29.14' - - bioconductor-go.db - - bioconductor-graph - - 'bioconductor-iranges >=2.11.16' - - bioconductor-limma - - bioconductor-multtest - - bioconductor-rbgl - - bioconductor-regioner - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-regioner >=1.12.0,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dbi - r-idr @@ -83,7 +84,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.' - extra: identifiers: - biotools:chippeakanno diff --git a/recipes/bioconductor-chipqc/conda_build_config.yaml b/recipes/bioconductor-chipqc/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-chipqc/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-chipqc/meta.yaml b/recipes/bioconductor-chipqc/meta.yaml index c690443dfce97..9cd63a962e5d9 100644 --- a/recipes/bioconductor-chipqc/meta.yaml +++ b/recipes/bioconductor-chipqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "ChIPQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,57 +8,58 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 20b6d2ac3410cbd4cc1ee95b05b7c12368e4764f8e9cf16b6efecfd3d47fd5da + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fdebb0fdc165e292b0141a2f540f6bb24c112202b0b8a6a4bed41394e9687abc build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.38.0' - - 'bioconductor-biocgenerics >=0.11.3' - - bioconductor-biocparallel - - 'bioconductor-chipseq >=1.12.0' - - 'bioconductor-diffbind >=2.6.6' - - 'bioconductor-genomicalignments >=1.14.1' - - 'bioconductor-genomicfeatures >=1.30.3' - - 'bioconductor-genomicranges >=1.17.19' - - 'bioconductor-iranges >=1.99.17' - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-s4vectors >=0.1.0' - - bioconductor-txdb.celegans.ucsc.ce6.ensgene - - bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene - - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene - - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene - - bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-diffbind >=2.8.0,<2.10.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.6.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.2,<3.4.0' - r-base - r-ggplot2 - r-gtools - r-nozzle.r1 - r-reshape2 run: - - 'bioconductor-biobase >=2.38.0' - - 'bioconductor-biocgenerics >=0.11.3' - - bioconductor-biocparallel - - 'bioconductor-chipseq >=1.12.0' - - 'bioconductor-diffbind >=2.6.6' - - 'bioconductor-genomicalignments >=1.14.1' - - 'bioconductor-genomicfeatures >=1.30.3' - - 'bioconductor-genomicranges >=1.17.19' - - 'bioconductor-iranges >=1.99.17' - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-s4vectors >=0.1.0' - - bioconductor-txdb.celegans.ucsc.ce6.ensgene - - bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene - - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene - - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene - - bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-diffbind >=2.8.0,<2.10.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.6.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.2,<3.4.0' - r-base - r-ggplot2 - r-gtools @@ -71,7 +72,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Quality metrics for ChIPseq data.' - extra: identifiers: - biotools:chipqc diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index f1cb4a597b729..f593667c36008 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.2" %} +{% set version = "1.16.1" %} {% set name = "ChIPseeker" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3ed20e2c848b3f5d640bcf33a5a13fd07de8bf3051d2eea84438e50ce49962b5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fe358c80a1a5f2d4ccbadcca59a23074aa5f81b681384fc1106066defa3581d6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - 'bioconductor-dose >=3.0.0' - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base - r-boot - r-dplyr @@ -39,16 +40,16 @@ requirements: - r-rcolorbrewer - r-upsetr run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - 'bioconductor-dose >=3.0.0' - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base - r-boot - r-dplyr @@ -67,7 +68,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.' - extra: identifiers: - biotools:chipseeker diff --git a/recipes/bioconductor-chipseq/meta.yaml b/recipes/bioconductor-chipseq/meta.yaml index 8eef5238325f7..c4ce3c4dea605 100644 --- a/recipes/bioconductor-chipseq/meta.yaml +++ b/recipes/bioconductor-chipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "chipseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d869dd1e0c68e6bc3f4fbf1c03d851785696404af170f6ffcc5ff23ccfc1acfa + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a767466f1511d1d3682a7a8ed5c9a6f7e63832bf776f7bdcc4e5445be86bc825 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-genomicranges >=1.17.7' - - 'bioconductor-iranges >=1.99.1' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-shortread + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-lattice run: - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-genomicranges >=1.17.7' - - 'bioconductor-iranges >=1.99.1' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-shortread + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-lattice + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for helping process short read data for chipseq experiments' - extra: identifiers: - biotools:chipseq diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml index cb80acf33542f..c3db1989f8772 100644 --- a/recipes/bioconductor-chipsim/meta.yaml +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ChIPsim" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ea914c481d7d809ce2088efd6ff56dc5d1da66ce3dd5e67bda035cbbfd877506 + sha256: 2d0d5fb309ed681962dba1698158df8f4612316d5adf8570c94c46c3a17c676e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.29.2' - - bioconductor-iranges - - bioconductor-shortread - - bioconductor-xvector + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-biostrings >=2.29.2' - - bioconductor-iranges - - bioconductor-shortread - - bioconductor-xvector + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base test: commands: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.' - extra: identifiers: - biotools:chipsim diff --git a/recipes/bioconductor-chipxpress/conda_build_config.yaml b/recipes/bioconductor-chipxpress/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-chipxpress/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml index d06935a4c65f0..4c177ebc4fa06 100644 --- a/recipes/bioconductor-chipxpress/meta.yaml +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ChIPXpress" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2b1b1056cbe87817593200a7fd0b91346c3e516649a2485c986bbf09f83b9a71 + sha256: b64b509939b988973f09aaf715529d8a5e9eb84f83d2aefd88cc3ea633ae53a1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-chipxpressdata - - bioconductor-frma - - bioconductor-geoquery + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-chipxpressdata >=1.18.0,<1.20.0' + - 'bioconductor-frma >=1.32.0,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' - r-base - r-biganalytics - r-bigmemory run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-chipxpressdata - - bioconductor-frma - - bioconductor-geoquery + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-chipxpressdata >=1.18.0,<1.20.0' + - 'bioconductor-frma >=1.32.0,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' - r-base - r-biganalytics - r-bigmemory @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.' - extra: identifiers: - biotools:chipxpress diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml index 6774f654682c1..a1bb8c58862ba 100644 --- a/recipes/bioconductor-chipxpressdata/meta.yaml +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ChIPXpressData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 84e4e096c947ace46402ed962a7936b9d08d1db5adeb900ff2df60fcb191472e + sha256: 2fc3ca28b77347bddde703816a892f8874d855d146245452cd6230d05df1e6a4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking.' + + diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh index c89d30841ac54..def21373b1b00 100644 --- a/recipes/bioconductor-chipxpressdata/post-link.sh +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChIPXpressData_1.16.0.tar.gz" +FN="ChIPXpressData_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ChIPXpressData_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChIPXpressData_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ChIPXpressData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIPXpressData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.18.0_src_all.tar.gz" ) -MD5="020fc315cf29fb563d2c78b750ad4765" +MD5="5c2695c0ef69ef1d8c5702a478667047" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml index dc84ecaa246a7..d98e5c8c1922a 100644 --- a/recipes/bioconductor-chopsticks/meta.yaml +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "chopsticks" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8d599d1afd587b9f7c3df6892623d0c0c65b6115f5041603034cdb7d269a9c2b + sha256: d9573d3caa31c7a200802b0a87070838531ff4a3c7c04fd8130f32dabd868c26 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-survival run: - r-base - r-survival - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Implements classes and methods for large-scale SNP association studies' - extra: identifiers: - biotools:chopsticks diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index 0cbe28c3b788a..d4b4ded0a93f8 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "chromDraw" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4eb3d62f7c6037a25dc04612d6abd313ff154131bc22034abf7d0a31dcba19d3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8429d9c00418d6cd63180ee5763c8ef907cf8aa5855140553143830c47af59e7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-genomicranges >=1.17.46' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - 'r-rcpp >=0.11.1' run: - - 'bioconductor-genomicranges >=1.17.46' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - 'r-rcpp >=0.11.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.' - extra: identifiers: - biotools:chromdraw diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml index 64d72bff62a52..80d100aea51a0 100644 --- a/recipes/bioconductor-chromheatmap/meta.yaml +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ChromHeatMap" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5976d27fe6b43359658b2875943afb4cfa29eb29aeba68dbd3939c1073f2504f + sha256: dbfd69528bb77da0fa85cb53b9feab831077f96e421f5ce75694b8fdb9bdca01 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotate >=1.20.0' - - 'bioconductor-annotationdbi >=1.4.0' - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base run: - - 'bioconductor-annotate >=1.20.0' - - 'bioconductor-annotationdbi >=1.4.0' - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base test: commands: @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.' - extra: identifiers: - biotools:chromheatmap diff --git a/recipes/bioconductor-chromplot/meta.yaml b/recipes/bioconductor-chromplot/meta.yaml index dad5db8ccc494..0438822e3d6b7 100644 --- a/recipes/bioconductor-chromplot/meta.yaml +++ b/recipes/bioconductor-chromplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "chromPlot" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 87aca7fe1d474f939797e2ad4da6f8ace46d67464e86d566bb8275caf10f1e9b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3f164cbb4f23dafec6352e6df2cd8bc5057a13553dcef0dcfc4d111efae6b5fc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-genomicranges + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-biomart - - bioconductor-genomicranges + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.' - extra: identifiers: - biotools:chromplot diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml index 28973ed438439..6732eae31181b 100644 --- a/recipes/bioconductor-chromstar/meta.yaml +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.2" %} {% set name = "chromstaR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5f329f313dfcad93b97fe08452dfb4a81f5d984acfa244dafe8ff36776fac2cf + sha256: 14a2d48db46c858ee773b18c2bc72fb132a7438d9f66bb761074683d503fdf6d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-bamsignals - - bioconductor-chromstardata - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-bamsignals >=1.12.1,<1.14.0' + - 'bioconductor-chromstardata >=1.6.0,<1.8.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-doparallel - r-foreach @@ -35,21 +33,24 @@ requirements: - r-mvtnorm - r-reshape2 run: - - bioconductor-bamsignals - - bioconductor-chromstardata - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-bamsignals >=1.12.1,<1.14.0' + - 'bioconductor-chromstardata >=1.6.0,<1.8.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-doparallel - r-foreach - r-ggplot2 - r-mvtnorm - r-reshape2 - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -57,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.' - extra: identifiers: - biotools:chromstar diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml index 5aef67ca2074d..6b53f576bf9ff 100644 --- a/recipes/bioconductor-chromstardata/meta.yaml +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "chromstaRData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f1b64e4dd6d3627321dfe65f00e47889db86210df11d96b7cc392416a1ce8d82 + sha256: df7d487f0d792f3b22df14408855b6c6b32b6c9185e4d0b171c341b726e97f24 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'ChIP-seq data for demonstration purposes in the chromstaR package.' + + diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh index 874ca52e5cb2b..9b4e472efcd0a 100644 --- a/recipes/bioconductor-chromstardata/post-link.sh +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="chromstaRData_1.4.0.tar.gz" +FN="chromstaRData_1.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/chromstaRData_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/chromstaRData_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.4.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/chromstaRData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/chromstaRData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.6.0_src_all.tar.gz" ) -MD5="bb4511694d5906d4677e84e44e6374b2" +MD5="eda1145219cebb5688aa0043391b0270" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-chronos/conda_build_config.yaml b/recipes/bioconductor-chronos/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-chronos/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-chronos/meta.yaml b/recipes/bioconductor-chronos/meta.yaml index 89bd6cad1f28f..dd70faff781e5 100644 --- a/recipes/bioconductor-chronos/meta.yaml +++ b/recipes/bioconductor-chronos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "CHRONOS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,18 +8,19 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: df913f00b6cc912fb7da5ec10c8e53d5278f3bc19e131dbe745376529f2fe42b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 75c03fbb73ce2c2561005feeb65c757798be41cabe7742a8eb00c8932cdf1234 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - r-circlize - r-doparallel @@ -28,9 +29,9 @@ requirements: - r-rcurl - r-xml run: - - bioconductor-biomart - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - r-circlize - r-doparallel @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.' - extra: identifiers: - biotools:CHRONOS diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml index 72e90602763bf..ee7a3ad0edd0f 100644 --- a/recipes/bioconductor-cindex/meta.yaml +++ b/recipes/bioconductor-cindex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CINdex" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 26e5c2dfac363255139738ddceac61afb7de3d84835fd0e55653395331762053 + sha256: 5d482deea03bc6ef5b1813448c69bc2e027014c4b7dfa53cc06e64f6ae868a9d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-bitops - r-dplyr @@ -31,10 +31,10 @@ requirements: - r-som - r-stringr run: - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-bitops - r-dplyr @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.' - extra: identifiers: - biotools:cindex diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml index 04a27eca314bf..b6aa04e645bfb 100644 --- a/recipes/bioconductor-cispath/meta.yaml +++ b/recipes/bioconductor-cispath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cisPath" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9044abda3d71c0e4a5a4685b09a309dff8a390d16a368f33614368f8f69c4179 + sha256: bd458092836f93f9995167f1aa8816efefc3e215191fc88c11481b1514c48ef4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks.' - extra: identifiers: - biotools:cispath diff --git a/recipes/bioconductor-classifyr/conda_build_config.yaml b/recipes/bioconductor-classifyr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-classifyr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml index a8bb9b0963b47..043c5d728078e 100644 --- a/recipes/bioconductor-classifyr/meta.yaml +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "2.0.10" %} {% set name = "ClassifyR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5c32745f0c94df16dc20a31cb84a9faef95060ef3cfcb3407f8dc442e0d66cf9 + sha256: 7b313c24b6825c35f0b90957fb2eec6d79ce12b95a6cb79a17273128871eb0c1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-locfit - - r-rocr + - r-plyr run: - - bioconductor-biobase - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-locfit - - r-rocr + - r-plyr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -36,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The software formalises a framework for classification in R. There are four stages; Data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, but specialised variables for functions can also be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.' - extra: identifiers: - biotools:classifyr diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml index 786e470e78192..48b07865b1386 100644 --- a/recipes/bioconductor-cleanupdtseq/meta.yaml +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "cleanUpdTSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7bcb94f2c58a9831a71092e3152d0961a8375f3c5121cf330b9dca9cbdc591e4 + sha256: d055b4e455bd9be214baa9229a03c6a73f1f00a39cdeddfd61e93020fbb1d42f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-bsgenome - - bioconductor-bsgenome.drerio.ucsc.danrer7 - - bioconductor-genomicranges + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-e1071 - r-seqinr run: - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-bsgenome - - bioconductor-bsgenome.drerio.ucsc.danrer7 - - bioconductor-genomicranges + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-e1071 - r-seqinr @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.' - extra: identifiers: - biotools:cleanupdtseq diff --git a/recipes/bioconductor-cleaver/meta.yaml b/recipes/bioconductor-cleaver/meta.yaml index 5a451491a975a..2c5770c9e6735 100644 --- a/recipes/bioconductor-cleaver/meta.yaml +++ b/recipes/bioconductor-cleaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "cleaver" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9769e6a0fd86855106736816b0d2255296a01ad72733a0300c3df62002aef4ff + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2d7a222959268fc5cc7d9048267d5993d0c97a3c60e5b4c23db7640eacfad764 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=1.29.8' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - 'bioconductor-biostrings >=1.29.8' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html' - extra: identifiers: - biotools:cleaver diff --git a/recipes/bioconductor-clomial/meta.yaml b/recipes/bioconductor-clomial/meta.yaml index 47fa6cd0edeb0..6338f492c1240 100644 --- a/recipes/bioconductor-clomial/meta.yaml +++ b/recipes/bioconductor-clomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Clomial" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 98d5ef8ef69f27aad4e2607aeb431b74658b831b6b24dec27b5617cd6e19a1c1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 011379922782078d02cb3ead86de0b2d0d1ebd93565a2b5ddcc424a41f6eb0cd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.' - extra: identifiers: - biotools:clomial diff --git a/recipes/bioconductor-clonality/meta.yaml b/recipes/bioconductor-clonality/meta.yaml index a6ef7589fc0ef..07411cc14794b 100644 --- a/recipes/bioconductor-clonality/meta.yaml +++ b/recipes/bioconductor-clonality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Clonality" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c1a08fe2a81047f4ca3193a246e50393424aa9a47e57c15af93df46cedfd29d0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e18af28e399c47a7c66649ef4f6555184537a979b5ac5aae365dae5549c95bf5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-dnacopy + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - r-base run: - - bioconductor-dnacopy + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles' - extra: identifiers: - biotools:clonality diff --git a/recipes/bioconductor-clonotyper/meta.yaml b/recipes/bioconductor-clonotyper/meta.yaml index 95c219b4d175f..f0b4899f601ac 100644 --- a/recipes/bioconductor-clonotyper/meta.yaml +++ b/recipes/bioconductor-clonotyper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "clonotypeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: eb0e1340641964178e664fbd7e16e556c2b4773f18f649d24439fe97af7d381d + sha256: f4d1afd969aa4b632be5b7ae702e0d55ece6ea2ba38fcf468f04c08e1307de31 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop. The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.' - extra: identifiers: - biotools:clonotyper diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml index f6552824bf8d9..e7ce5e0a1d3ca 100644 --- a/recipes/bioconductor-clst/meta.yaml +++ b/recipes/bioconductor-clst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "clst" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dc8ec394358db8b6a13d9b19d70d48f3887dd870ad1dd75ec9a79e2948f32dc0 + sha256: 632521ce98e86024424a14ddca80ac0959056b40db8419ddc90340a7d31ee25d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-roc + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - r-lattice run: - - bioconductor-roc + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - r-lattice test: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.' - extra: identifiers: - biotools:clst diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml index 638f5d51ff9b8..c2f9616d1c622 100644 --- a/recipes/bioconductor-clstutils/meta.yaml +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "clstutils" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e60dc6b3f500cc39876e26bf3b2895cf5e370673640195127ec3d94ea8cae0a6 + sha256: 628bc1297b326e4fc0c71280028726dfc1f4e7e921867d6539937d8ca8755136 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-clst + - 'bioconductor-clst >=1.28.0,<1.30.0' - r-ape - r-base - r-lattice - r-rjson - r-rsqlite run: - - bioconductor-clst + - 'bioconductor-clst >=1.28.0,<1.30.0' - r-ape - r-base - r-lattice @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.' - extra: identifiers: - biotools:clstutils diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml index 95bffa2090f76..a2b12bab794df 100644 --- a/recipes/bioconductor-clustcomp/meta.yaml +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "clustComp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 63dd6f1232875068f708a00a141aaf7227f060295382b3c4232b0edbb26acd3d + sha256: f5e149b4bc931123d81416f289bb6454817e87648fa43bd2da12473521eaafad build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.' - extra: identifiers: - biotools:clustcomp diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index b5c30ef077cbe..ef7f762596ed7 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.6.0" %} +{% set version = "3.8.1" %} {% set name = "clusterProfiler" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: daf8e5d39b60b7f54a27598d8cd216775f537e88d3c2f9cc422cb09e0e99c718 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1583d5fb93df68d8ae3e998138bd01d4287a1753ca0a558832fd9c660bc4a789 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-dose >=3.3.2' - - bioconductor-go.db - - 'bioconductor-gosemsim >=2.0.0' - - bioconductor-qvalue + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-ggplot2 - r-magrittr @@ -29,11 +31,12 @@ requirements: - r-rvcheck - r-tidyr run: - - bioconductor-annotationdbi - - 'bioconductor-dose >=3.3.2' - - bioconductor-go.db - - 'bioconductor-gosemsim >=2.0.0' - - bioconductor-qvalue + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-ggplot2 - r-magrittr @@ -47,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.' - extra: identifiers: - biotools:clusterprofiler diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml index 6dd58759b89d6..23df69c895170 100644 --- a/recipes/bioconductor-clustersignificance/meta.yaml +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.2" %} {% set name = "ClusterSignificance" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 61db4b25f4298f396441f3def371a11b37e30997a97bbf019d931a27f69792a7 + sha256: 54c6d9c4a36ea55066761ceeb6c277e2c8e94e3890a29e97af12cdf68d8793d7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,13 +20,13 @@ requirements: host: - r-base - r-pracma - - r-princurve + - 'r-princurve >=2.0.5' - r-rcolorbrewer - r-scatterplot3d run: - r-base - r-pracma - - r-princurve + - 'r-princurve >=2.0.5' - r-rcolorbrewer - r-scatterplot3d test: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.' - extra: identifiers: - biotools:clustersignificance diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml index d01d650cfd670..396aced2ff824 100644 --- a/recipes/bioconductor-clusterstab/meta.yaml +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "clusterStab" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 68c80c7bf92a75a0c610457f6a8174bd4c1c5a66b1ced229126876f610ee3f67 + sha256: 503836113b24f67107e42d1f9b05be501267f6f93edc8d75a377ffbb21e67528 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.4.22' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=1.4.22' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.' - extra: identifiers: - biotools:clusterstab diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml index b7ce79ee1f57e..7dc01d2803e9f 100644 --- a/recipes/bioconductor-cma/meta.yaml +++ b/recipes/bioconductor-cma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CMA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6d32caeda1e5de598010bfa561a21d59cb3a7e133f88a53b29c0dfe6b69cb150 + sha256: 30cb1696be1ec077327992d7127cb08097be00ade8d3229205af383aafd73272 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.' - extra: identifiers: - biotools:cma diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml index 84ad7b4f0a8ca..44b824176dcb4 100644 --- a/recipes/bioconductor-cmap/meta.yaml +++ b/recipes/bioconductor-cmap/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.1" %} {% set name = "cMAP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3bf24aca1ce63ebff4ac0172467ecd8acbb0c1f8a240cd0f8b8abd7c44fdf15f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: LGPL summary: 'Annotation data file for cMAP assembled using data from public data repositories' + + diff --git a/recipes/bioconductor-cmap/post-link.sh b/recipes/bioconductor-cmap/post-link.sh index 525ebbdb1b149..4c76f2a85875d 100644 --- a/recipes/bioconductor-cmap/post-link.sh +++ b/recipes/bioconductor-cmap/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="cMAP_1.15.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" "https://bioarchive.galaxyproject.org/cMAP_1.15.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" ) MD5="dbf8df4d4540151936884e1c5d747bcf" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml index a5adc65787d71..bc5ae3c2da5cc 100644 --- a/recipes/bioconductor-cmap2data/meta.yaml +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "cMap2data" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3fcb5f5f82dfa60faece83b593b7fcca50eca3a03b97a1a1798c0cc1742c5400 + sha256: 4158c38925a807da44c0c3aaee568f39d64d1647589d1455fd06234cfaf3c05a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.' + + diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh index 1587bebb6a63a..f7b1a1e98a746 100644 --- a/recipes/bioconductor-cmap2data/post-link.sh +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="cMap2data_1.14.0.tar.gz" +FN="cMap2data_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/cMap2data_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/cMap2data_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/cMap2data_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/cMap2data_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.16.0_src_all.tar.gz" ) -MD5="c24b3dfa3c8cdaca2457b9795345a26a" +MD5="07ed9ef43caf12a0f4250f7c6e2848ff" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-cn.farms/conda_build_config.yaml b/recipes/bioconductor-cn.farms/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-cn.farms/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml index faaef939968a4..f979c43c8c3ab 100644 --- a/recipes/bioconductor-cn.farms/meta.yaml +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "cn.farms" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,41 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4f728d1c22ec367ece919276a370910b69cf13a372a025d0dec89458b3f53600 + sha256: ec995fc0d1a2cdd177db01916ab9a161b3fd8e08dcbe967313b58addfe022d7d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affxparser - - bioconductor-biobase - - bioconductor-dnacopy - - bioconductor-oligo - - bioconductor-oligoclasses - - bioconductor-preprocesscore + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - r-ff - r-lattice - r-snow run: - - bioconductor-affxparser - - bioconductor-biobase - - bioconductor-dnacopy - - bioconductor-oligo - - bioconductor-oligoclasses - - bioconductor-preprocesscore + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - r-ff - r-lattice - r-snow - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.' - extra: identifiers: - biotools:cn.farms diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index dbfd18f3dbfd4..5166cb6d90c14 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cn.mops" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9f92a9f3522eb1de68066e8cc372d25fc0b7bd3fa2d836c3459b8f5e5c29e394 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b9b0be3df2a0ebe6f77d2bfd6087b8f1fd03dc0327ea5e7066a97e64dca68cf5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-exomecopy - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-exomecopy - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.' - extra: identifiers: - biotools:cn.mops diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index 37fcda7062129..f89c4ee933323 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CNAnorm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7ae5748c85ec0b22be029b481c50671575b0d1156088b505f536f5f22e23a38d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d7be2b7579a6a3885bc1c01f287c43c4669235407827ec3576cbcb3e7430bdfe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-dnacopy + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - r-base run: - - bioconductor-dnacopy + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.' - extra: identifiers: - biotools:cnanorm diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index 5e44c3e27e66c..30cc28e7d2160 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "CNEr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6c510e8aa2667658ef62c52c30f39132f8d8c9fda1d13965763b5c5cfcfdc0f9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 431f04c9915af270b60e628737c53a0b3550d23c214f09eba6f172b456cbc425 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotate >=1.50.0' - - bioconductor-biocgenerics - - 'bioconductor-biostrings >=2.33.4' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicalignments >=1.1.9' - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-go.db >=3.3.0' - - 'bioconductor-iranges >=2.5.27' - - 'bioconductor-keggrest >=1.14.0' - - 'bioconductor-rtracklayer >=1.25.5' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-xvector >=0.5.4' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -38,18 +39,18 @@ requirements: - 'r-reshape2 >=1.4.1' - 'r-rsqlite >=0.11.4' run: - - 'bioconductor-annotate >=1.50.0' - - bioconductor-biocgenerics - - 'bioconductor-biostrings >=2.33.4' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicalignments >=1.1.9' - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-go.db >=3.3.0' - - 'bioconductor-iranges >=2.5.27' - - 'bioconductor-keggrest >=1.14.0' - - 'bioconductor-rtracklayer >=1.25.5' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-xvector >=0.5.4' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -58,6 +59,9 @@ requirements: - 'r-readr >=0.2.2' - 'r-reshape2 >=1.4.1' - 'r-rsqlite >=0.11.4' + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -65,7 +69,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 | file LICENSE' summary: 'Large-scale identification and advanced visualization of sets of conserved noncoding elements.' - extra: identifiers: - biotools:cner diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml index e7fabd06e47e4..d1f1ce716354c 100644 --- a/recipes/bioconductor-cnorfuzzy/meta.yaml +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CNORfuzzy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d7baf1e59c9f845d6ff3a5f970a83246bfbb2f7a77a66a04f21b61075722319c + sha256: a8fe42cbf825457625445bfaad7586b9757b98c1faa44016a34d4033e4c7a735 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-cellnoptr >=1.4.0' + - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' - r-base - 'r-nloptr >=0.8.5' run: - - 'bioconductor-cellnoptr >=1.4.0' + - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' - r-base - 'r-nloptr >=0.8.5' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).' - extra: identifiers: - biotools:cnorfuzzy diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml index 3542c18a12eee..b05e515831b16 100644 --- a/recipes/bioconductor-cnorode/meta.yaml +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CNORode" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1e3f779adf086b3fe63ec66420ba425b5d49496f8f2c6c2c485083eadee3ddf0 + sha256: c7b64bbe51cc9ad24a4eaceb1e12ff459817da059abaec683f60d16a50db016d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-cellnoptr >=1.5.14' + - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' - r-base - r-genalg run: - - 'bioconductor-cellnoptr >=1.5.14' + - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' - r-base - r-genalg - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'ODE add-on to CellNOptR' - extra: identifiers: - biotools:cnorode diff --git a/recipes/bioconductor-cntools/meta.yaml b/recipes/bioconductor-cntools/meta.yaml index 3c7d94ab57f7b..0d0048d00d995 100644 --- a/recipes/bioconductor-cntools/meta.yaml +++ b/recipes/bioconductor-cntools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "CNTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6a92715248751f434b454276fe5b93fcacfe58fb9186482ac9cf015de0e8ad5b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8b22ddb405bec464ede7b63cce655ddf4de3d93260de91b8ebb1a7a711e24375 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genefilter + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base run: - - bioconductor-genefilter + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data' - extra: identifiers: - biotools:cntools diff --git a/recipes/bioconductor-cnvgsa/meta.yaml b/recipes/bioconductor-cnvgsa/meta.yaml index 6782f8587b7cb..ae882721e81f3 100644 --- a/recipes/bioconductor-cnvgsa/meta.yaml +++ b/recipes/bioconductor-cnvgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "cnvGSA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 984804bbd703dde15fe80b7e45d0758e339c1ff9bad0fbaafe93181e9e82fd48 + sha256: 6236cc65e337f5d84ef3f52b511b28ba0522f9261fdcb7c1521dcd35275cc5ec build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-brglm - r-doparallel @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package is intended to facilitate gene-set association with rare CNVs in case-control studies.' - extra: identifiers: - biotools:cnvgsa diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml index 813a263b29ae9..5e41d7ea4e44a 100644 --- a/recipes/bioconductor-cnvpanelizer/meta.yaml +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "CNVPanelizer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,53 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b1671257e010d318aafaa7054c0d162c212135f3fd5bbd963fdf70e64e16f520 + sha256: 36dd57265e65fae10b9339cd9671d60bcf148d96508dbbff8e9af41e2ce3d5cf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-exomecopy - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-noiseq - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-noiseq >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-foreach - r-ggplot2 + - r-gplots - r-openxlsx - r-plyr + - r-reshape2 + - r-shiny + - r-shinyfiles + - r-shinyjs + - r-stringr + - r-testthat run: - - bioconductor-exomecopy - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-noiseq - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-noiseq >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-foreach - r-ggplot2 + - r-gplots - r-openxlsx - r-plyr + - r-reshape2 + - r-shiny + - r-shinyfiles + - r-shinyjs + - r-stringr + - r-testthat test: commands: - '$R -e "library(''{{ name }}'')"' @@ -48,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.' - extra: identifiers: - biotools:cnvpanelizer diff --git a/recipes/bioconductor-cnvtools/meta.yaml b/recipes/bioconductor-cnvtools/meta.yaml index 75d8fbf7ec2c7..037b2a1a1856a 100644 --- a/recipes/bioconductor-cnvtools/meta.yaml +++ b/recipes/bioconductor-cnvtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "CNVtools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 65e185c1e4c33064d53219fd4dc0e10c66e60a3a4b8e23c083fe5ce0ca7b1546 + sha256: d129df72861ec507dd4670fe8596b1378d4eba83631c1626fe354d3e24f2babc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-survival run: - r-base - r-survival - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.' - extra: identifiers: - biotools:cnvtools diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml index 81a3a5a4bc2b5..7623bbcc4fc07 100644 --- a/recipes/bioconductor-codelink/meta.yaml +++ b/recipes/bioconductor-codelink/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "codelink" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: baa1c3553ee9d870698d8ca9548cdefae59c58c57596cd31cec045b8c22a9348 + sha256: 3455f089ce1063d6882a766752ee007a7e062082c77003155393073342338a4c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-limma + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - bioconductor-annotate - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-limma + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base test: commands: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.' - extra: identifiers: - biotools:codelink diff --git a/recipes/bioconductor-codex/meta.yaml b/recipes/bioconductor-codex/meta.yaml index 778472972ac76..d243dd27f1573 100644 --- a/recipes/bioconductor-codex/meta.yaml +++ b/recipes/bioconductor-codex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CODEX" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d83685a70122cf8beeb9795b2d601c69ce2edc997a2a3308b1f9210b627ccece + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: facca69dfd7a7bf32333eab374c82dac6178da13408a19cfcbc3dd0a0c02c65b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomeinfodb - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biostrings - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomeinfodb - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.' - extra: identifiers: - biotools:codex diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml index 7bf65b84f8019..0c42794065a59 100644 --- a/recipes/bioconductor-cogena/meta.yaml +++ b/recipes/bioconductor-cogena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cogena" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8fdd3d4744c7e960598d1186761d277e0b1dc255d6a2ed2448b15fb970c9f3d9 + sha256: eb1d08e4601eef63e125212b63a93ecf156ff2bc4298056f407aabc212e60534 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-amap - r-apcluster - r-base @@ -37,7 +37,7 @@ requirements: - r-mclust - r-reshape2 run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-amap - r-apcluster - r-base @@ -62,7 +62,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.' - extra: identifiers: - biotools:cogena diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml index fbe1df5e1a333..7ea1346b245cd 100644 --- a/recipes/bioconductor-cogps/meta.yaml +++ b/recipes/bioconductor-cogps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "coGPS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 858563852d92cc8427fce8779a7fb88cf0d4ff01f56fcfa76a79d237944b9d40 + sha256: 5f558092a19cbbc6ec45da9be8a691615b7e73a4fb100caa8b0419fbcbba7c16 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies' - extra: identifiers: - biotools:cogps diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml index 0e5ac966aaaf8..fb4cf9b923726 100644 --- a/recipes/bioconductor-cohcap/meta.yaml +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "COHCAP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,35 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f2d5a888f29619fd4bcda97a3e8a0d6fe17681b3b1db95c3249db808cbb0fdbd + sha256: 3d6ceaf99409025c1483957c229e42c149bc9e6f41d8618e928667038ab2cdf5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cohcapanno + - 'bioconductor-cohcapanno >=1.16.0,<1.18.0' - r-base + - r-bh - r-gplots - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo - r-writexls run: - - bioconductor-cohcapanno + - 'bioconductor-cohcapanno >=1.16.0,<1.18.0' - r-base + - r-bh - r-gplots - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo - r-writexls + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -36,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options.' - extra: identifiers: - biotools:cohcap diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml index 0800384a9539f..951aadb003e70 100644 --- a/recipes/bioconductor-cohcapanno/meta.yaml +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "COHCAPanno" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5064f4260e289012e333b0edbd3e93d55c567a1c4cd89b06d5010efc7de34c20 + sha256: d5a74932f43dba6f89346f3e490642911d3fa4d9e885af76fb99b8d1d3b27e22 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms' + + diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh index e6fef36de3dc2..47ca84f9d718b 100644 --- a/recipes/bioconductor-cohcapanno/post-link.sh +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="COHCAPanno_1.14.0.tar.gz" +FN="COHCAPanno_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/COHCAPanno_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/COHCAPanno_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/COHCAPanno_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/COHCAPanno_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.16.0_src_all.tar.gz" ) -MD5="dd8fcfcf7aeba72f5d4cfb6594eae522" +MD5="9b88358fffd88f0ff80cd3892e4d3604" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index ea96006c5dcf6..658e44863a54b 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "COMPASS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,16 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 560fa4df6e37df0db5f9bb4fd6b3067d3d52ccf3507d844b6795647b86653bf4 + sha256: a25c213a31ea4c63c54793cc448cb841d2dfda9e45e4db70b6c8a131cdd0b114 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - r-abind - r-base - r-clue @@ -33,9 +32,11 @@ requirements: - 'r-rcpp >=0.11.0' - r-reshape2 - r-rlang + - r-rmarkdown - r-scales - r-tidyr run: + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - r-abind - r-base - r-clue @@ -49,9 +50,13 @@ requirements: - 'r-rcpp >=0.11.0' - r-reshape2 - r-rlang + - r-rmarkdown - r-scales - r-tidyr - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -59,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject''s immune response to external stimuli such as infection or vaccination.' - extra: identifiers: - biotools:compass diff --git a/recipes/bioconductor-compepitools/meta.yaml b/recipes/bioconductor-compepitools/meta.yaml index 3a1e46fbe2efb..dd8b10e0394a7 100644 --- a/recipes/bioconductor-compepitools/meta.yaml +++ b/recipes/bioconductor-compepitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "compEpiTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,44 +8,45 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: af14f9db33d310e768de6de9be4645282f00c25e6c1ee4f906b897f29314e055 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 745c5f30b63520ac68a9d88aa78bbc7ca71ad0c0d5db6094f8de1cabbe1bce15 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-iranges - - bioconductor-methylpipe - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-topgo - - bioconductor-xvector + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-methylpipe >=1.14.0,<1.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-gplots run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-iranges - - bioconductor-methylpipe - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-topgo - - bioconductor-xvector + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-methylpipe >=1.14.0,<1.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-gplots test: @@ -55,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.' - extra: identifiers: - biotools:compepitools diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index 6885e28bceb9d..793bd5dd7d076 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.17.1" %} +{% set version = "1.18.1" %} {% set name = "ComplexHeatmap" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9e71eec1020eed2075e87aad460df1c247674b820c0fdae0424d631c4bb9d3f4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1661fa2af0cdf77bbe94cdfd81c58950836cdd8c53da182548cccafb61f85c62 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -35,9 +36,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'MIT + file LICENSE' summary: 'Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.' - extra: identifiers: - biotools:complexheatmap diff --git a/recipes/bioconductor-consensusclusterplus/meta.yaml b/recipes/bioconductor-consensusclusterplus/meta.yaml index 68fcc7238c6e1..6e92bb502872a 100644 --- a/recipes/bioconductor-consensusclusterplus/meta.yaml +++ b/recipes/bioconductor-consensusclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ConsensusClusterPlus" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a102168b8deb9048cd1ff6f3fc71f3244dad9e96a8a8ddb6fcc7a0d4493e5cde + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ce09181763cfcb03a650d3b3c378b6e84533efd37e5693786255ead94dcb7a52 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-all - - bioconductor-biobase + - 'bioconductor-all >=1.22.0,<1.24.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster run: - - bioconductor-all - - bioconductor-biobase + - 'bioconductor-all >=1.22.0,<1.24.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL version 2' summary: 'algorithm for determining cluster count and membership by stability evidence in unsupervised analysis' - extra: identifiers: - biotools:consensusclusterplus diff --git a/recipes/bioconductor-consensusov/meta.yaml b/recipes/bioconductor-consensusov/meta.yaml index fb82fe2cd52cf..886bce7b48afb 100644 --- a/recipes/bioconductor-consensusov/meta.yaml +++ b/recipes/bioconductor-consensusov/meta.yaml @@ -1,49 +1,46 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "consensusOV" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: be3c9a9772217ff573b17963c59b24a045484270cccc57fccf09cbb2c410eb5f - + sha256: 487c6acf505fdcc2394a98ee88427fbbbb5a77ccd1f7d16f53763cc7d291cd5f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-genefu - - bioconductor-gsva - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefu >=2.12.0,<2.14.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-gdata - r-matrixstats - r-randomforest run: - - bioconductor-biobase - - bioconductor-genefu - - bioconductor-gsva - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefu >=2.12.0,<2.14.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-gdata - r-matrixstats - r-randomforest - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.' + + diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml index 2ec2b32469a30..cbe4cee1ad67c 100644 --- a/recipes/bioconductor-consensusseeker/meta.yaml +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "consensusSeekeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ed47acb8c7aad1643b39770711cb396020413a7e36aabc7d60ab1a53fe57c594 + sha256: 286721522fcec4124beb0f7b0c2830589109a68828019b43a904ca1c36b7805b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-stringr run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-stringr test: @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region.' - extra: identifiers: - biotools:consensusseeker diff --git a/recipes/bioconductor-contibait/meta.yaml b/recipes/bioconductor-contibait/meta.yaml index 732f86154273d..56173c2c6fbb1 100644 --- a/recipes/bioconductor-contibait/meta.yaml +++ b/recipes/bioconductor-contibait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "contiBAIT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9ae1ecf3219a276e00e36816a7ba78a0e866ea292a3a0265ab4043226bc3c62f + sha256: 58bf2ef2c66036bbd356257334ec557be6af06ed791c94986e907d857f2ce3e3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocparallel - - bioconductor-dnacopy - - bioconductor-exomecopy - - bioconductor-genomicalignments - - bioconductor-genomicfiles - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.21' - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-bh >=1.51.0-3' - r-clue - r-cluster - r-colorspace + - r-data.table - r-diagram - r-ggplot2 - r-gplots @@ -43,21 +42,22 @@ requirements: - r-reshape2 - r-tsp run: - - bioconductor-biocparallel - - bioconductor-dnacopy - - bioconductor-exomecopy - - bioconductor-genomicalignments - - bioconductor-genomicfiles - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.21' - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-bh >=1.51.0-3' - r-clue - r-cluster - r-colorspace + - r-data.table - r-diagram - r-ggplot2 - r-gplots @@ -65,7 +65,10 @@ requirements: - r-rcpp - r-reshape2 - r-tsp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -73,7 +76,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.' - extra: identifiers: - biotools:contibait diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml index ebf0923d3409c..d4953f0a129d7 100644 --- a/recipes/bioconductor-convert/meta.yaml +++ b/recipes/bioconductor-convert/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "convert" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 24427569b5775d5293acec4f1ed13d00e74d47b2c40b90321c6d1ed4bc5fe440 + sha256: 344208d1cf513bcb9a66b8b34c51274faf24e05d03f06362c833adf4391ac62b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.15.33' - - 'bioconductor-limma >=1.7.0' - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base run: - - 'bioconductor-biobase >=1.15.33' - - 'bioconductor-limma >=1.7.0' - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base test: commands: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Define coerce methods for microarray data objects.' - extra: identifiers: - biotools:convert diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml index 880a292bb172b..a33dcae4461ca 100644 --- a/recipes/bioconductor-copyhelper/meta.yaml +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CopyhelpeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 479e75da8c815952a3bd402b8d44a8983ef7cc191cf93c48e0a42b36c5987bbd + sha256: 2927de1db24986129406c4d8e8699675dfb1b48b1c906e7bc4406670264494c7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.' + + diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh index 01c1168fcbf6b..e4c9f44df41a3 100644 --- a/recipes/bioconductor-copyhelper/post-link.sh +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CopyhelpeR_1.10.0.tar.gz" +FN="CopyhelpeR_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/CopyhelpeR_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/CopyhelpeR_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.10.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/CopyhelpeR_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/CopyhelpeR_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.12.0_src_all.tar.gz" ) -MD5="03e42db6682fe395328a0ef01505833b" +MD5="5a1d068158d3fb73abaf6ca93ee994b0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-copynumber/meta.yaml b/recipes/bioconductor-copynumber/meta.yaml index 0d315202f6a72..f924933fd6a8c 100644 --- a/recipes/bioconductor-copynumber/meta.yaml +++ b/recipes/bioconductor-copynumber/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "copynumber" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dd57c9be2b4d4fe2fa5a0467b381d6a7241ac33a21a0e7dfccd21744e8e76c06 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: bad6db743ca26a2f12e2a538fb4b2e24bff291139223d4e3b8f0ea0b16b73679 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.' - extra: identifiers: - biotools:copynumber diff --git a/recipes/bioconductor-copywriter/meta.yaml b/recipes/bioconductor-copywriter/meta.yaml index 2a66e20c175a1..2e5895a0fce82 100644 --- a/recipes/bioconductor-copywriter/meta.yaml +++ b/recipes/bioconductor-copywriter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "CopywriteR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,40 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8ad12b68c6516e40f3a78014f1311c46d851e0417b9e03b68176385f1815de9d + sha256: e383b2bdf215962f4792035e9aa1d891e05a6f2cec0047caa2ec0bb503e6fd2c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-chipseq - - bioconductor-copyhelper - - bioconductor-dnacopy - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-copyhelper >=1.12.0,<1.14.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-futile.logger - r-gtools - r-matrixstats run: - - bioconductor-biocparallel - - bioconductor-chipseq - - bioconductor-copyhelper - - bioconductor-dnacopy - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-copyhelper >=1.12.0,<1.14.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-futile.logger @@ -56,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.' - extra: identifiers: - biotools:copywriter diff --git a/recipes/bioconductor-cormotif/conda_build_config.yaml b/recipes/bioconductor-cormotif/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-cormotif/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml index e88617b10da64..70d3c05b263c1 100644 --- a/recipes/bioconductor-cormotif/meta.yaml +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "Cormotif" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dba86a067d7e11c9b263f03f90ef654ee9938c1042cafd5b95e2364b0d6addc6 + sha256: ee273daa7997a0249f0a07dfe4317656adbfeee07152af7199d46e190c4066be build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - bioconductor-affy - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'It fits correlation motif model to multiple studies to detect study specific differential expression patterns.' - extra: identifiers: - biotools:cormotif diff --git a/recipes/bioconductor-correp/meta.yaml b/recipes/bioconductor-correp/meta.yaml index 6ccf653268472..c3184599801bb 100644 --- a/recipes/bioconductor-correp/meta.yaml +++ b/recipes/bioconductor-correp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "CORREP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2a27a6b8948154ef56bd3ef4e61ff80768a14feb6bebe5a4b2ea77d105d87281 + sha256: e3b3e907709ff15c337e14444c7125f7b0ede1449fbc4587653afeb759a8da3e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Multivariate correlation estimation and statistical inference. See package vignette.' - extra: identifiers: - biotools:correp diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml index 7a5e226488542..675a5aa9dbc36 100644 --- a/recipes/bioconductor-cosmiq/meta.yaml +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.13.0" %} {% set name = "cosmiq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,31 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b593e317cebeded863c21674d57860b4cf21828b8644c59415acc271e2faa1bc + sha256: 76e57b7368920cef01e28bfeed4ddf25735f43e4b5e71f83170836575b568ac7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-faahko - - bioconductor-massspecwavelet - - bioconductor-xcms + - 'bioconductor-faahko >=1.20.0,<1.22.0' + - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-pracma - r-rcpp run: - - bioconductor-faahko - - bioconductor-massspecwavelet - - bioconductor-xcms + - 'bioconductor-faahko >=1.20.0,<1.22.0' + - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-pracma - r-rcpp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.' - extra: identifiers: - biotools:cosmiq diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml index 4dfa162dc1edd..96d14fb357596 100644 --- a/recipes/bioconductor-covrna/meta.yaml +++ b/recipes/bioconductor-covrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "covRNA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fb7c7931cb0ba7db5bcb082b53cf6dfa6e6dd8d94a741a6e2eca93ecc9722320 + sha256: 6dfee06f3b3722dfa39cac96574c073ca91e6b6ee494961eee2a669b05542da9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-genefilter + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-ade4 - r-base run: - - bioconductor-biobase - - bioconductor-genefilter + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-ade4 - r-base test: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.' - extra: identifiers: - biotools:covrna diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml index 08a62e19c9103..045d362ef57ac 100644 --- a/recipes/bioconductor-cpvsnp/meta.yaml +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "cpvSNP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a8713080c1e637d35cace162d8661bdd6daa06e119b1e07452da44df5cba7eaa + sha256: dd9d5369cc78395f7860b5ecb276c04e6f385bc437611e178cf84b486dcababb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-genomicfeatures - - 'bioconductor-gseabase >=1.24.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base - r-corpcor - r-ggplot2 - r-plyr run: - - bioconductor-biocparallel - - bioconductor-genomicfeatures - - 'bioconductor-gseabase >=1.24.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base - r-corpcor - r-ggplot2 @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.' - extra: identifiers: - biotools:cpvsnp diff --git a/recipes/bioconductor-cqn/meta.yaml b/recipes/bioconductor-cqn/meta.yaml index c21a51634f158..e408f1b58ad65 100644 --- a/recipes/bioconductor-cqn/meta.yaml +++ b/recipes/bioconductor-cqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cqn" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 36841a614baf7e17018e19349ffd4e32034cdff644904de3834b7b38dc5084c7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d8ce94ce508dea2284fc121f00dba4ee64b2ddd65c1ef0f2309a65d7cf20db6f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-preprocesscore + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-mclust - r-nor1mix - r-quantreg run: - - bioconductor-preprocesscore + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-mclust - r-nor1mix @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.' - extra: identifiers: - biotools:cqn diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml index bc0c82270a974..f10163c9c7dc1 100644 --- a/recipes/bioconductor-crimage/meta.yaml +++ b/recipes/bioconductor-crimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CRImage" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 480d924f4daf01ad88315b8bdce066a469a5f5be4365568d6a2472fdd4d03df8 + sha256: 945b1bd9a5287e961857412ac742b9c881161e4c4b235e67bac15767edcbd9dc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-acgh - - bioconductor-dnacopy - - bioconductor-ebimage + - 'bioconductor-acgh >=1.58.0,<1.60.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat run: - - bioconductor-acgh - - bioconductor-dnacopy - - bioconductor-ebimage + - 'bioconductor-acgh >=1.58.0,<1.60.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' - r-base - r-e1071 - r-foreach @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.' - extra: identifiers: - biotools:crimage diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml index d19a1b2c3349d..0303d6fd3dd36 100644 --- a/recipes/bioconductor-crisprseek/meta.yaml +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CRISPRseek" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 80f9df6dae1f2da23d2c2cc7408f37f16596c0546f26008e72b206af9ae47a63 + sha256: cc8e9cfdef9a66734b8207dbb38345a725bd4dc0b08399505b7bf64c2abc73b1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-hash - r-seqinr run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-hash @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.' - extra: identifiers: - biotools:crisprseek diff --git a/recipes/bioconductor-crisprseekplus/conda_build_config.yaml b/recipes/bioconductor-crisprseekplus/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-crisprseekplus/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-crisprseekplus/meta.yaml b/recipes/bioconductor-crisprseekplus/meta.yaml index 6196721da2033..a99bf1d94d729 100644 --- a/recipes/bioconductor-crisprseekplus/meta.yaml +++ b/recipes/bioconductor-crisprseekplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "crisprseekplus" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,34 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ac7822fcab662a8bfa1f8bb3697d4bb15b25d74bdca95529679be27b02a139d9 + sha256: ef0a05e770b745512ace4e0b3c56aae299cde00372490ecc75fbf86d674608e0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocinstaller - - bioconductor-bsgenome - - bioconductor-crisprseek - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-guideseq + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-crisprseek >=1.20.0,<1.22.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-guideseq >=1.10.0,<1.12.0' - r-base - r-dt - r-hash - r-shiny - r-shinyjs run: - - bioconductor-annotationdbi - - bioconductor-biocinstaller - - bioconductor-bsgenome - - bioconductor-crisprseek - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-guideseq + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-crisprseek >=1.20.0,<1.22.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-guideseq >=1.10.0,<1.12.0' - r-base - r-dt - r-hash @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.' - extra: identifiers: - biotools:crisprseekplus diff --git a/recipes/bioconductor-crisprvariants/conda_build_config.yaml b/recipes/bioconductor-crisprvariants/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-crisprvariants/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml index 1d06a7999bdd4..7b58deaf33cde 100644 --- a/recipes/bioconductor-crisprvariants/meta.yaml +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CrispRVariants" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,37 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8b0dd8425ba6747c5d46ae062fd8968219cee7c877c12670acdc496bb537ea97 + sha256: 00e161bb5614820fbaad0753439b2453a8c96fa909ed918ff23da72abb22a332 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra - r-reshape2 run: - - bioconductor-annotationdbi - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra @@ -52,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.' - extra: identifiers: - biotools:crisprvariants diff --git a/recipes/bioconductor-crlmm/conda_build_config.yaml b/recipes/bioconductor-crlmm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-crlmm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml index f89c079b12cc8..329219b07dd8e 100644 --- a/recipes/bioconductor-crlmm/meta.yaml +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "crlmm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3ab9d0a8b0dbfc59afd08a69ce282cd4ef5b1dd662fb8d651b6ff63d27492045 + sha256: ce2821228fc573b1bc4dc36d783e74a9500601e13feb89cce877616d152e083a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-affyio >=1.23.2' - - 'bioconductor-biobase >=2.15.4' - - bioconductor-biocgenerics - - bioconductor-illuminaio - - bioconductor-limma - - 'bioconductor-oligoclasses >=1.21.12' - - 'bioconductor-preprocesscore >=1.17.7' - - bioconductor-snpchip + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-snpchip >=2.26.0,<2.28.0' - r-base - r-beanplot - r-ellipse @@ -39,14 +37,14 @@ requirements: - 'r-rcppeigen >=0.3.1.2.1' - r-vgam run: - - 'bioconductor-affyio >=1.23.2' - - 'bioconductor-biobase >=2.15.4' - - bioconductor-biocgenerics - - bioconductor-illuminaio - - bioconductor-limma - - 'bioconductor-oligoclasses >=1.21.12' - - 'bioconductor-preprocesscore >=1.17.7' - - bioconductor-snpchip + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-snpchip >=2.26.0,<2.28.0' - r-base - r-beanplot - r-ellipse @@ -57,7 +55,9 @@ requirements: - r-mvtnorm - 'r-rcppeigen >=0.3.1.2.1' - r-vgam - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -65,7 +65,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.' - extra: identifiers: - biotools:crlmm diff --git a/recipes/bioconductor-csaw/conda_build_config.yaml b/recipes/bioconductor-csaw/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-csaw/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index 343a16dc54cb5..6675885ee89c7 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "csaw" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,48 +8,51 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 894cf793f221c0cc2564f1f1c43ca899a7ca6f925e0ba7cd7365388e996d844b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 718a6ce380ae8d7f72b1da2434705a459b373bb5fb1eb824823947949c6935ba build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rhtslib - - bioconductor-rsamtools - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.2.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-rcpp run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rhtslib - - bioconductor-rsamtools - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.2.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -57,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.' - extra: identifiers: - biotools:csaw diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml index c7ecb36f9d970..0f5a66b82713b 100644 --- a/recipes/bioconductor-ctc/meta.yaml +++ b/recipes/bioconductor-ctc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "ctc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6f8e18a8f0074a8f2346f04851defd70cd2ae21a30d74ad219f1480f2a82382f + sha256: 694e669972363fef4a07e0402c29a590e4854d1bded86aa3f9c3264b2abd4d69 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Tools for export and import classification trees and clusters to other programs' - extra: identifiers: - biotools:ctc diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml index 77df63dbc2c3b..44972efff7f72 100644 --- a/recipes/bioconductor-ctsge/meta.yaml +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "ctsGE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9bff2a7c108a277922f4359fe9a787405033d1f7ac8e73017242619a4a81afc3 + sha256: 0460482b3575ca441698824da239d230295f71599df7502f6d6426cd37136afb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-ccapp - r-ggplot2 @@ -26,7 +26,7 @@ requirements: - r-shiny - r-stringr run: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-ccapp - r-ggplot2 @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.' - extra: identifiers: - biotools:ctsge diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index 3db6177b525a5..dbdd23afde242 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "cummeRbund" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8034f5509d507057d3ba491ae51b93ee9be303ce51a977ecc5561b7d1d106907 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: edc8d4c2e0b1cf6b8096ba69d84aecb083dea9a135a72d5b511d37ebb2e61596 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-gviz - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fastcluster - r-ggplot2 @@ -29,11 +30,11 @@ requirements: - r-reshape2 - r-rsqlite run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-gviz - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fastcluster - r-ggplot2 @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.' - extra: identifiers: - biotools:cummerbund diff --git a/recipes/bioconductor-curatedmetagenomicdata/conda_build_config.yaml b/recipes/bioconductor-curatedmetagenomicdata/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-curatedmetagenomicdata/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml index fc9811bdc99d3..b44a073ec828d 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml +++ b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.2" %} {% set name = "curatedMetagenomicData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 256186f7112c3d992874951c361aa128abd2804d89f33f6478fd646a36d8e9c6 + sha256: 873352867c5af358425f497c95e5a51834a73b808d28ab4319d9e5b1a5fa036a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationhub >=2.9.0' - - 'bioconductor-biobase >=2.37.0' - - 'bioconductor-experimenthub >=1.3.0' - - bioconductor-s4vectors + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-experimenthub >=1.6.1,<1.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-dplyr >=0.5.0' - r-magrittr - r-tidyr run: - - 'bioconductor-annotationhub >=2.9.0' - - 'bioconductor-biobase >=2.37.0' - - 'bioconductor-experimenthub >=1.3.0' - - bioconductor-s4vectors + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-experimenthub >=1.6.1,<1.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-dplyr >=0.5.0' - r-magrittr diff --git a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh index 330d28b798385..406f8735b1e59 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh +++ b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedMetagenomicData_1.8.1.tar.gz" +FN="curatedMetagenomicData_1.10.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/curatedMetagenomicData_1.8.1.tar.gz" - "https://bioarchive.galaxyproject.org/curatedMetagenomicData_1.8.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_1.8.1_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/curatedMetagenomicData_1.10.2.tar.gz" + "https://bioarchive.galaxyproject.org/curatedMetagenomicData_1.10.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_1.10.2_src_all.tar.gz" ) -MD5="e50a410a98cf2943d53e42f29c9a5da5" +MD5="36b9a395b479a4024fbf376e3009dc02" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-curatedovariandata/conda_build_config.yaml b/recipes/bioconductor-curatedovariandata/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-curatedovariandata/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index 0db931a52f37f..652fd76d63ed4 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "curatedOvarianData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 68443c35ca13b271eea69771fb3b8b868a7d3ea6a2f8fc188278c36bf579a395 + sha256: b7663661c156fd6b616562850c49fd98dddb7dd32f9a04ba7eb5abe87809f3d9 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biocgenerics + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - bioconductor-affy - - bioconductor-biocgenerics + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - wget test: diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index ed6767d1006e5..e7a730f612358 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="curatedOvarianData_1.16.0.tar.gz" +FN="curatedOvarianData_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/curatedOvarianData_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/curatedOvarianData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedOvarianData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.18.0_src_all.tar.gz" ) -MD5="ce3b7806e9a24e289454db0df74fbc75" +MD5="0fd49d3ff3764702e6324e8e03af2a0a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-cve/meta.yaml b/recipes/bioconductor-cve/meta.yaml index 460ac82168c55..8c11ef9a582da 100644 --- a/recipes/bioconductor-cve/meta.yaml +++ b/recipes/bioconductor-cve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CVE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9719ea5105e639eb698518eab9ed205163db4fb488a1ae723ae457a5ec621d41 + sha256: ea637575e5524138da65c50e14b02e41873927bb3b916404cd8d514c694d8d22 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-consensusclusterplus + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - r-ape - r-base - r-ggplot2 @@ -29,7 +29,7 @@ requirements: - r-shiny - r-wgcna run: - - bioconductor-consensusclusterplus + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - r-ape - r-base - r-ggplot2 @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Shiny app for interactive variant prioritisation in precision oncology. The input file for CVE is the output file of the recently released Oncotator Variant Annotation tool summarising variant-centric information from 14 different publicly available resources relevant for cancer researches. Interactive priortisation in CVE is based on known germline and cancer variants, DNA repair genes and functional prediction scores. An optional feature of CVE is the exploration of the tumour-specific pathway context that is facilitated using co-expression modules generated from publicly available transcriptome data. Finally druggability of prioritised variants is assessed using the Drug Gene Interaction Database (DGIdb).' - extra: identifiers: - biotools:cve diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index 7fd440405e72c..2136b887eb320 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "cytolib" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f16c070427f352a9611da81629cfa54f87f19d4b3ce33ba2c654e3635c81d9fb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b348fb0dbe1b53484807e9a94fc14654afccdefab039ddd19037fa5cb94ca865 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: + - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' - r-base - - r-bh # not in DESCRIPTION - - bioconductor-rprotobuflib # not in DESCRIPTION + - 'r-bh >=1.62.0-1' run: + - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' - r-base - - r-bh # not in DESCRIPTION - - bioconductor-rprotobuflib # not in DESCRIPTION + - 'r-bh >=1.62.0-1' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides the core data structure and API to represent and interact with the gated cytometry data.' + + diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index 72f769dd3b234..34ad7daa6c6b9 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "dada2" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 79b65f611f7a4da5b08c9d258ab69540139d8159b24481bbbc2e786604e48e51 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0444f3cbe52037a25d80052f081e2e7c4ad2167faab76d1b3d3f036186e3d824 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-biostrings >=2.42.1' - - 'bioconductor-shortread >=1.32.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-data.table >=1.9.4' - 'r-ggplot2 >=2.1.0' @@ -28,14 +30,21 @@ requirements: - 'r-rcppparallel >=4.3.0' - 'r-reshape2 >=1.4.1' run: - - 'bioconductor-biostrings >=2.42.1' - - 'bioconductor-shortread >=1.32.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-data.table >=1.9.4' - 'r-ggplot2 >=2.1.0' - 'r-rcpp >=0.11.2' - 'r-rcppparallel >=4.3.0' - 'r-reshape2 >=1.4.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and genus-species assignment by exact matching.' - extra: identifiers: - biotools:dada2 diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml index f0ee08a4da5eb..21354013ac775 100644 --- a/recipes/bioconductor-dama/meta.yaml +++ b/recipes/bioconductor-dama/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "daMA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e6e03b6ccf4580b8c061086632d20ce712012b502440dc26d8bd188e3aa918c3 + sha256: b202d97c77ea55125f56cd048a20a3e7c08a23f48d3c54ddcb17f501bdb92aff build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)' - extra: identifiers: - biotools:dama diff --git a/recipes/bioconductor-dbchip/meta.yaml b/recipes/bioconductor-dbchip/meta.yaml index 54338e05b4f2e..a706e46279277 100644 --- a/recipes/bioconductor-dbchip/meta.yaml +++ b/recipes/bioconductor-dbchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DBChIP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dd1414b409ab6677cfa094550e690ca2cc3d5a4e8db1194e2d99d0c676adfa1e + sha256: 1730dedbabacbeb22181dda8d9929e185a478721b7eb51204f8d2655f7c2c3c9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-deseq - - bioconductor-edger + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base run: - - bioconductor-deseq - - bioconductor-edger + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base test: commands: @@ -32,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.' + + diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml index b40849c70a166..0acb71ec61caa 100644 --- a/recipes/bioconductor-dcgsa/meta.yaml +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "dcGSA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06cc6ca1033c2093b566db1c31fbe49921d5333bf352e61d3367b465408723f6 + sha256: 3719cf082f6fb781bb157b156692cabb538e8ba101bdaccfc230c6b633d3b0a7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base - r-matrix run: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base - r-matrix test: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The dcGSA package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.' - extra: identifiers: - biotools:dcgsa diff --git a/recipes/bioconductor-dchiprep/conda_build_config.yaml b/recipes/bioconductor-dchiprep/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-dchiprep/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-dchiprep/meta.yaml b/recipes/bioconductor-dchiprep/meta.yaml index 7cc9a54ac3ac6..f55d5b0bd57f4 100644 --- a/recipes/bioconductor-dchiprep/meta.yaml +++ b/recipes/bioconductor-dchiprep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DChIPRep" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 959b5598fff357d15c27913674cc89353f21236865f4e4e9786f4c7c6fab27c6 + sha256: 8220ab43aa87cb6963cd69bc4680e6f21c9f9e022e0a9d32f6f9e52252dd67a9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-chippeakanno - - bioconductor-deseq2 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-soggi - - bioconductor-summarizedexperiment + - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-soggi >=1.12.0,<1.14.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-assertthat - r-base - r-fdrtool @@ -34,12 +34,12 @@ requirements: - r-smoothmest - r-tidyr run: - - bioconductor-chippeakanno - - bioconductor-deseq2 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-soggi - - bioconductor-summarizedexperiment + - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-soggi >=1.12.0,<1.14.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-assertthat - r-base - r-fdrtool @@ -56,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENCE' summary: 'The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776. A detailed description of the method is given in the software paper at https://doi.org/10.7717/peerj.1981' - extra: identifiers: - biotools:dchiprep diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml index ae0ecdc159133..01341c8b08727 100644 --- a/recipes/bioconductor-ddct/meta.yaml +++ b/recipes/bioconductor-ddct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ddCt" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aded934154e743047010037c1cdb6ef7603fa6c660df51ccddb616d55317da40 + sha256: ad7eee57cd0e2e392d2d3f468ec1b050de62efc748bb6ee55105023d625f3805 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.10.0' - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' - r-xtable run: - - 'bioconductor-biobase >=1.10.0' - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.' - extra: identifiers: - biotools:ddct diff --git a/recipes/bioconductor-deds/meta.yaml b/recipes/bioconductor-deds/meta.yaml index d092e00eca814..778578d918dd9 100644 --- a/recipes/bioconductor-deds/meta.yaml +++ b/recipes/bioconductor-deds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "DEDS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: da08370a847214ab71c1317d341399c0158aee661b6844cac6d1af327b91f7a1 + sha256: dc6dd316e1214f61bf58c9b6a14836726ed6f57a1c72b299687ec8f0b17bbc8b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.' - extra: identifiers: - biotools:deds diff --git a/recipes/bioconductor-deepbluer/meta.yaml b/recipes/bioconductor-deepbluer/meta.yaml index 99306356823ad..dbe5cc5d63e0b 100644 --- a/recipes/bioconductor-deepbluer/meta.yaml +++ b/recipes/bioconductor-deepbluer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "DeepBlueR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2cc33c6407d3fb784f8ba330c3b7c0bb1aa8ccf71a0d9f890d944558ab150f8f + sha256: 459af8d672d68aa498b5babd16be29c91fe90cf00320421734dd7c7cdc850334 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-rtracklayer + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-data.table - r-diffr @@ -35,9 +35,9 @@ requirements: - r-withr - r-xml run: - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-rtracklayer + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-data.table - r-diffr @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'Accessing the DeepBlue Epigenetics Data Server through R.' - extra: identifiers: - biotools:deepbluer diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index f8e1c4a926f48..b79fbf2f734a9 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.1" %} {% set name = "deepSNV" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,38 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 76d7c6ba83aebaf0adffc2673af19220ddb956528d6cdb03c6a5bb92c8e6689a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 55036b553920826aeead816e48a8760b756bca513de09a247521b36788aaa01d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rhtslib - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.13.44' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-vgam run: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rhtslib - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.13.44' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-vgam + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +47,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.' - extra: identifiers: - biotools:deepsnv diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml index c86f3d9299231..115af25add325 100644 --- a/recipes/bioconductor-deformats/meta.yaml +++ b/recipes/bioconductor-deformats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "DEFormats" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a9dcdcdeb8fa6ec107c17abf0eebe18c74297fd68f09f3b549080d628e2d3df2 + sha256: 29c1f463f5afda69be011c4d23549838c5f30571c3015d5a30d5b60c97115723 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-deseq2 - - 'bioconductor-edger >=3.13.4' - - bioconductor-genomicranges - - bioconductor-summarizedexperiment + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-checkmate - r-data.table run: - - bioconductor-deseq2 - - 'bioconductor-edger >=3.13.4' - - bioconductor-genomicranges - - bioconductor-summarizedexperiment + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-checkmate - r-data.table @@ -40,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Convert between different data formats used by differential gene expression analysis tools.' - extra: identifiers: - biotools:deformats diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml index 7fac84f24d5d8..e261c6255683f 100644 --- a/recipes/bioconductor-degraph/meta.yaml +++ b/recipes/bioconductor-degraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DEGraph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 118e3be5f578b0cc7153f81e7cf54ba6b610dd006d541c7e9c7d6870f30e7c20 + sha256: fd70e69c20e39e93ee0a53705191d9d9e94f1b6ac11ba373e15517c2fb9a6023 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-ncigraph - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-ncigraph >=1.28.0,<1.30.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-lattice - r-mvtnorm @@ -30,11 +30,11 @@ requirements: - r-r.utils - r-rrcov run: - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-ncigraph - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-ncigraph >=1.28.0,<1.30.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-lattice - r-mvtnorm @@ -48,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.' - extra: identifiers: - biotools:degraph diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index 7a909d2ac70a2..d50bd1444ef76 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "DEGreport" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 47875412771c12cb55a65a3f517275a162348b0e4e2a48c30eb1f6f24129add1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9c837442bf21031bc88fb6fec9ef30abd01fcb56fa45ee6f39b62701b8ee89e5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-complexheatmap - - bioconductor-consensusclusterplus - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base + - r-circlize - r-cluster - r-cowplot - r-dplyr @@ -40,18 +42,20 @@ requirements: - r-reshape - r-rlang - r-scales + - r-stringr - r-tibble - r-tidyr run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-complexheatmap - - bioconductor-consensusclusterplus - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base + - r-circlize - r-cluster - r-cowplot - r-dplyr @@ -66,6 +70,7 @@ requirements: - r-reshape - r-rlang - r-scales + - r-stringr - r-tibble - r-tidyr test: @@ -75,7 +80,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.' - extra: identifiers: - biotools:degreport diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index ace37e53657c8..923a2bf646bf5 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.1" %} {% set name = "DEGseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f2b0c26cdb89b3e159f32a2fee1b50b5a9396b44c469559103ae0e69d18b0136 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0512b751635a51e9123ebdcbc6bf1e1a6440524d06ecdc1efc6a93738f01ad18 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-qvalue + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - - r-samr run: - - bioconductor-qvalue + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - - r-samr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>=2)' summary: 'DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.' - extra: identifiers: - biotools:degseq diff --git a/recipes/bioconductor-delayedarray/meta.yaml b/recipes/bioconductor-delayedarray/meta.yaml index 4d4471ab5b8c2..84020fb5ece73 100644 --- a/recipes/bioconductor-delayedarray/meta.yaml +++ b/recipes/bioconductor-delayedarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.4.1" %} +{% set version = "0.6.6" %} {% set name = "DelayedArray" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8b7ca552d391c58c5899480bbab5bdb975c8ef5f6b2222cc6304fcede313f068 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c25d2c41c18f37930ad94ccea9d18f1c2c45481cb0253456b48e0fac5d057766 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - 'bioconductor-iranges >=2.11.17' - - 'bioconductor-s4vectors >=0.15.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-matrixstats run: - - bioconductor-biocgenerics - - 'bioconductor-iranges >=2.11.17' - - 'bioconductor-s4vectors >=0.15.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-matrixstats test: @@ -35,3 +38,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.' + + diff --git a/recipes/bioconductor-delayedmatrixstats/build.sh b/recipes/bioconductor-delayedmatrixstats/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-delayedmatrixstats/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-delayedmatrixstats/meta.yaml b/recipes/bioconductor-delayedmatrixstats/meta.yaml new file mode 100644 index 0000000000000..76fddf0acb794 --- /dev/null +++ b/recipes/bioconductor-delayedmatrixstats/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "DelayedMatrixStats" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7ef0c42d1fb2810202bb90500dd9eabdbfc02a79ea45d0eaff4774e41d7c5ab5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - r-base + - r-matrix + - 'r-matrixstats >=0.53.1' + run: + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - r-base + - r-matrix + - 'r-matrixstats >=0.53.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A port of the ''matrixStats'' API for use with DelayedMatrix objects from the ''DelayedArray'' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.' + + + diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml index c268b8eb71bf2..5c26c8af2e28c 100644 --- a/recipes/bioconductor-demand/meta.yaml +++ b/recipes/bioconductor-demand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DeMAND" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 03c0a71c8c77e68753539225a16eb540ba19d0c17123cac3bff17109ea60c5bd + sha256: 932af6daf6014d8ab650d900b2d0ed0eae2e1fff5d23041270395eed6d54bfc7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.' - extra: identifiers: - biotools:demand diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml index 8d9b4fa609a5c..af3228b812d69 100644 --- a/recipes/bioconductor-derfinder/meta.yaml +++ b/recipes/bioconductor-derfinder/meta.yaml @@ -1,71 +1,69 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "derfinder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b4c510bca06699d1490ff860ea726c214c6a4c5aa4a8e3e18e2848e45cff1d42 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2a9311b86a201ae0b7953733420f2f1175c578c3f98d7a776be3bec21c24f837 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - 'bioconductor-annotationdbi >=1.27.9' - - bioconductor-biocparallel - - 'bioconductor-bumphunter >=1.9.2' - - 'bioconductor-derfinderhelper >=1.1.0' - - 'bioconductor-genomeinfodb >=1.3.3' - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicfiles - - 'bioconductor-genomicranges >=1.17.40' - - 'bioconductor-iranges >=2.3.23' - - 'bioconductor-qvalue >=1.99.0' - - 'bioconductor-rsamtools >=1.25.0' - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-bumphunter >=1.22.0,<1.24.0' + - 'bioconductor-derfinderhelper >=1.14.0,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-hmisc run: - - 'bioconductor-annotationdbi >=1.27.9' - - bioconductor-biocparallel - - 'bioconductor-bumphunter >=1.9.2' - - 'bioconductor-derfinderhelper >=1.1.0' - - 'bioconductor-genomeinfodb >=1.3.3' - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicfiles - - 'bioconductor-genomicranges >=1.17.40' - - 'bioconductor-iranges >=2.3.23' - - 'bioconductor-qvalue >=1.99.0' - - 'bioconductor-rsamtools >=1.25.0' - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-bumphunter >=1.22.0,<1.24.0' + - 'bioconductor-derfinderhelper >=1.14.0,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-hmisc - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package provides functions for annotation-agnostic differential expression analysis of - RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single - base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder + summary: 'This package provides functions for annotation-agnostic differential + expression analysis of RNA-seq data. Two implementations of the DER Finder + approach are included in this package (1) single base-level F-statistics + and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.' - extra: identifiers: - biotools:derfinder diff --git a/recipes/bioconductor-derfinderhelper/meta.yaml b/recipes/bioconductor-derfinderhelper/meta.yaml index d2b22b01a7efc..e32dbc5f84218 100644 --- a/recipes/bioconductor-derfinderhelper/meta.yaml +++ b/recipes/bioconductor-derfinderhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "derfinderHelper" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2b4ca09478fa851e1c6a290bcab429a7760ebbbc27764503bb47d48d12145219 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 25eda535a4442aa581aa6ae28a98584d43ac0a948f86269f31be82910b8ee475 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-iranges >=1.99.27' - - 'bioconductor-s4vectors >=0.2.2' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=1.99.27' - - 'bioconductor-s4vectors >=0.2.2' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-matrix test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Helper package for speeding up the derfinder package when using multiple cores.' - extra: identifiers: - biotools:derfinderhelper diff --git a/recipes/bioconductor-derfinderplot/conda_build_config.yaml b/recipes/bioconductor-derfinderplot/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-derfinderplot/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-derfinderplot/meta.yaml b/recipes/bioconductor-derfinderplot/meta.yaml index a7fe34036ec2e..a2ec90694cb52 100644 --- a/recipes/bioconductor-derfinderplot/meta.yaml +++ b/recipes/bioconductor-derfinderplot/meta.yaml @@ -1,64 +1,61 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "derfinderPlot" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d77e828f9446280414c4fc7582ff4cec62488e77744a7bcbe578cc111f821dae - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 59bc73fcb16331910b0cecaa8ff418d31afad9bd093c850a166e8e597beed8f8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - 'bioconductor-derfinder >=1.1.0' - - 'bioconductor-genomeinfodb >=1.3.3' - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.17.40' - - 'bioconductor-ggbio >=1.13.13' - - 'bioconductor-iranges >=1.99.28' - - bioconductor-limma - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-derfinder >=1.14.0,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-plyr - r-rcolorbrewer + - r-refmanager - r-reshape2 - r-scales run: - - 'bioconductor-derfinder >=1.1.0' - - 'bioconductor-genomeinfodb >=1.3.3' - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.17.40' - - 'bioconductor-ggbio >=1.13.13' - - 'bioconductor-iranges >=1.99.28' - - bioconductor-limma - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-derfinder >=1.14.0,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-plyr - r-rcolorbrewer + - r-refmanager - r-reshape2 - r-scales - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides plotting functions for results from the derfinder package.' - extra: identifiers: - biotools:derfinderplot diff --git a/recipes/bioconductor-deseq/meta.yaml b/recipes/bioconductor-deseq/meta.yaml index f8904933a8f41..83acb09e9a992 100644 --- a/recipes/bioconductor-deseq/meta.yaml +++ b/recipes/bioconductor-deseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DESeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,38 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 693b7b5af137c05fda2fe4815f8e62d932a39451ffe8fed1e43c9ae0d9e0c556 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d5d29792e1ecdd29dd63b04eac4c0937eba68504a5f3227c3702b8a827e27d7a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.21.7' - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-genefilter - - bioconductor-geneplotter + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - r-base - r-lattice - r-locfit - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.21.7' - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-genefilter - - bioconductor-geneplotter + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - r-base - r-lattice - r-locfit - r-mass - r-rcolorbrewer + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +47,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution' - extra: identifiers: - biotools:deseq diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index f9c26a0ba1c77..820855ff60a7a 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "DESeq2" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,58 +8,51 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bb6a175217f3aea72003457f092df029800d20d2087444776db774a0c3abd1c7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 33e214e9f9f9bb5d6c0dacdd0d4a8ba4857ce0277f09a192ab35a940d67556f2 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - 'bioconductor-biocparallel >=1.12.0' - - bioconductor-genefilter - - bioconductor-geneplotter - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-summarizedexperiment >=1.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-hmisc - - 'r-lazyeval >=0.2.0' - r-locfit - 'r-rcpp >=0.11.0' - r-rcpparmadillo run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - 'bioconductor-biocparallel >=1.12.0' - - bioconductor-genefilter - - bioconductor-geneplotter - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-summarizedexperiment >=1.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-hmisc - - 'r-lazyeval >=0.2.0' - r-locfit - 'r-rcpp >=0.11.0' - r-rcpparmadillo - # optional dependencies - - bioconductor-tximport - - bioconductor-rhdf5 - - r-rjson - - r-hmisc - - r-getopt - - r-gplots - + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -67,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.' - extra: identifiers: - biotools:deseq2 diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index 353db15e7dd15..da43ce2168312 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -1,21 +1,4 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . - -python_scripts=$PREFIX/lib/R/library/DEXSeq/python_scripts - -sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_count.py -sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_prepare_annotation.py - -if [ "$PY3K" == 1 ]; then - 2to3 -w $python_scripts/dexseq_count.py - 2to3 -w $python_scripts/dexseq_prepare_annotation.py -fi - -chmod +x $python_scripts/dexseq_count.py -chmod +x $python_scripts/dexseq_prepare_annotation.py - -mkdir -p $PREFIX/bin -ln -s $python_scripts/dexseq_count.py $PREFIX/bin/dexseq_count.py -ln -s $python_scripts/dexseq_prepare_annotation.py $PREFIX/bin/dexseq_prepare_annotation.py +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index c9e1d8d3e2c18..110aae2fd7724 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -1,70 +1,67 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "DEXSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2db4e0ef43c0d14b4a08fcd012474cea3b6680982501cba84e5b41e7c4b7bc63 + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e1e9026c07fc26e1eaee06a0dd63d2f765bcd711f350fdb2a2236ad65b1d0bd7 build: - noarch: python - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biomart - - 'bioconductor-deseq2 >=1.9.11' - - bioconductor-genefilter - - bioconductor-geneplotter - - 'bioconductor-genomicranges >=1.23.7' - - 'bioconductor-iranges >=2.5.17' - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biomart - - 'bioconductor-deseq2 >=1.9.11' - - bioconductor-genefilter - - bioconductor-geneplotter - - 'bioconductor-genomicranges >=1.23.7' - - 'bioconductor-iranges >=2.5.17' - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr - - libgfortran-ng - - python <3 test: commands: - '$R -e "library(''{{ name }}'')"' - - dexseq_count.py --help - - dexseq_prepare_annotation.py --help about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.' - extra: identifiers: - biotools:dexseq diff --git a/recipes/bioconductor-dexus/meta.yaml b/recipes/bioconductor-dexus/meta.yaml index 82b7af4de8202..b52dbaf9616f1 100644 --- a/recipes/bioconductor-dexus/meta.yaml +++ b/recipes/bioconductor-dexus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "dexus" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2f566e4a6c91dcecc2554c013462d4618bb532e295513d0adc1f151c78283dd1 + sha256: 06d27f602a1bed95b7b14481901db2b5b78e04c357a2739a8fb9ca1dff324bb3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. DEXUS works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.' - extra: identifiers: - biotools:dexus diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml index 32522ea4bcc4f..f44bb1c7e66f5 100644 --- a/recipes/bioconductor-dfp/meta.yaml +++ b/recipes/bioconductor-dfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DFP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 337cda573c495f334387156617b437a74d95293f358377164f99a7fcd8afef84 + sha256: cd8b0d9abb19314173743430d6c47ea3d21f2d142733d96a33c3529bac51eb8f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.' - extra: identifiers: - biotools:dfp diff --git a/recipes/bioconductor-diffbind/conda_build_config.yaml b/recipes/bioconductor-diffbind/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-diffbind/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index 466f832daca4c..3683be1c17e62 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.6" %} +{% set version = "2.8.0" %} {% set name = "DiffBind" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 77ee6153d3756247bb230cdfd70efaee75f6a3c736e4697474129e83ad81a5ea + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 50478712ff5b0fe9dd47a9879ddde81a611a1dcf117e84c7634c8cd3fef230f0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocparallel - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-systempiper - - bioconductor-zlibbioc + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-systempiper >=1.14.0,<1.16.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-amap - r-base - r-dplyr @@ -42,18 +41,18 @@ requirements: - r-rcolorbrewer - r-rcpp run: - - bioconductor-biocparallel - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-systempiper - - bioconductor-zlibbioc + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-systempiper >=1.14.0,<1.16.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-amap - r-base - r-dplyr @@ -64,7 +63,10 @@ requirements: - r-locfit - r-rcolorbrewer - r-rcpp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -72,7 +74,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.' - extra: identifiers: - biotools:diffbind diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml index 5438ef4fa05ee..e7121679e2049 100644 --- a/recipes/bioconductor-diffgeneanalysis/meta.yaml +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "diffGeneAnalysis" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e38295ee0f2bdf73ec4c9e5a5572236c17d709b5f3cec7003644b1cc921dda2d + sha256: 41cb78d5a2afaa71a324598ed8fcca613fd71c88f97b8dd2598d286123d4979d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Analyze microarray data' - extra: identifiers: - biotools:diffgeneanalysis diff --git a/recipes/bioconductor-diffloop/meta.yaml b/recipes/bioconductor-diffloop/meta.yaml index 6b41c2c51b463..bbe0fd37af806 100644 --- a/recipes/bioconductor-diffloop/meta.yaml +++ b/recipes/bioconductor-diffloop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "diffloop" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cc9a352e8b6c5393adf8b36a75947a98e1a88d5348960622fecbbac66ae4663f + sha256: 9aa3941c0740a604c427570611a9fd9defc9475170ba707af0de57ee64557bf9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-sushi + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-sushi >=1.18.0,<1.20.0' - r-base - r-data.table - r-dplyr @@ -41,16 +41,16 @@ requirements: - r-reshape2 - r-statmod run: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-sushi + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-sushi >=1.18.0,<1.20.0' - r-base - r-data.table - r-dplyr @@ -70,7 +70,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.' - extra: identifiers: - biotools:diffloop diff --git a/recipes/bioconductor-diffustats/meta.yaml b/recipes/bioconductor-diffustats/meta.yaml index dc41c7221aa50..22bb914de41ba 100644 --- a/recipes/bioconductor-diffustats/meta.yaml +++ b/recipes/bioconductor-diffustats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.102.0" %} +{% set version = "0.104.0" %} {% set name = "diffuStats" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,16 +8,15 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 80132d6cffc4ab623cc0e03b55b96cdfb3969beb396f91d1fa276754fcf3b021 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 82b116d961ffb346635336e18ae1ea646457f757ca0e994cd1b2e07277b0baf0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-expm @@ -40,6 +39,10 @@ requirements: - r-rcpp - r-rcpparmadillo - r-rcppparallel + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation and benchmarking.' - extra: identifiers: - biotools:diffuStats diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml index 77bd238720dcb..18d2f5893ab1e 100644 --- a/recipes/bioconductor-director/meta.yaml +++ b/recipes/bioconductor-director/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Director" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6876551f960cda6a2458e22edd9ce05f0d8f188134a4dc9e43263cea785504fb + sha256: 95b739eeb2ab5864dafa4b557ca25214dc205b365003981221ec9c2ca50cd368 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Director is an R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view. This enables a straightforward approach for scientists to interpret the data produced, and bioinformatics developers an alternative means to present relevant data.' - extra: identifiers: - biotools:director diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index b60af0ce06077..6f51b6b8feaa2 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DirichletMultinomial" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a193f836368f71aa2a39242aa5d5fdd4de3993f63d34969f2905888a41379ab0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: da7972706c671159b08b5891949b57e909ce8c614d2d5b34253682b402ba9e6d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: build: - {{ compiler('c') }} + - make host: - - bioconductor-biocgenerics - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + - openblas run: - - bioconductor-biocgenerics - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + - openblas test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.' - extra: identifiers: - biotools:dirichletmultinomial diff --git a/recipes/bioconductor-dmrcate/meta.yaml b/recipes/bioconductor-dmrcate/meta.yaml index 24fddc9ef9d52..ded67f87b14ca 100644 --- a/recipes/bioconductor-dmrcate/meta.yaml +++ b/recipes/bioconductor-dmrcate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "DMRcate" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,35 +10,35 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06aee8d8584a8d035e044e0a190b7cb629d153fdf9732e35dac9a4111535ebcf + sha256: aaa612d617c617b313aa6ffa4ef80c33efe3c5dcc36f573cc02442d18bfab04a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-dmrcatedata - - bioconductor-dss - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-limma - - bioconductor-minfi - - bioconductor-missmethyl - - bioconductor-s4vectors + - 'bioconductor-dmrcatedata >=1.16.0,<1.18.0' + - 'bioconductor-dss >=2.28.0,<2.30.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-missmethyl >=1.14.0,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-plyr run: - - bioconductor-dmrcatedata - - bioconductor-dss - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-limma - - bioconductor-minfi - - bioconductor-missmethyl - - bioconductor-s4vectors + - 'bioconductor-dmrcatedata >=1.16.0,<1.18.0' + - 'bioconductor-dss >=2.28.0,<2.30.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-missmethyl >=1.14.0,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-plyr test: @@ -48,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.' - extra: identifiers: - biotools:dmrcate diff --git a/recipes/bioconductor-dmrcatedata/meta.yaml b/recipes/bioconductor-dmrcatedata/meta.yaml index cdda586f6c6a6..710399ea52776 100644 --- a/recipes/bioconductor-dmrcatedata/meta.yaml +++ b/recipes/bioconductor-dmrcatedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "DMRcatedata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c3e8f207901a4e8df2e406d15ab73bc428476f7d27c8a937cbd9e0ba15712cc4 + sha256: aeb119417a23374f8d39e0a86b914258455c1446ff3f5b930eea1d18b378b701 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'This package contains 8 data objects supporting functionality and examples of the Bioconductor package DMRcate.' + + diff --git a/recipes/bioconductor-dmrcatedata/post-link.sh b/recipes/bioconductor-dmrcatedata/post-link.sh index 04f057935fc70..af9780e1d5bd9 100644 --- a/recipes/bioconductor-dmrcatedata/post-link.sh +++ b/recipes/bioconductor-dmrcatedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DMRcatedata_1.14.0.tar.gz" +FN="DMRcatedata_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/DMRcatedata_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/DMRcatedata_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/DMRcatedata_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/DMRcatedata_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_1.16.0_src_all.tar.gz" ) -MD5="715c907d263668bf5a210ed8cd4d89a4" +MD5="9ab81fc10aecb5a0ee56ecd7374c093e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml index 7a8a55f3823d6..61ad5970eceae 100644 --- a/recipes/bioconductor-dnabarcodes/meta.yaml +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DNABarcodes" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 57e8d2375709e7402437b560f78270c55f88cec1d0e43e0b01fc948d2ce57774 + sha256: bdac77417ac37bc37dec8e3aa88bc9ada67a4a2c2a2b8ea1b8f7e409dc511676 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-bh @@ -29,7 +27,10 @@ requirements: - r-bh - r-matrix - 'r-rcpp >=0.11.2' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.' - extra: identifiers: - biotools:dnabarcodes diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index aa0921080aa36..79b0a5d3d2e61 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "DNAcopy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 51f192baca80ba98965893a5760306e0a250ede8c468c821951f864773a1f188 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 163510992ff6e204c75da992434b08129fec043f66d4c79ec8c0f8c26a850e0e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.' - extra: identifiers: - biotools:dnacopy diff --git a/recipes/bioconductor-dnashaper/meta.yaml b/recipes/bioconductor-dnashaper/meta.yaml index 3e9d96465afed..d8fcaf3456511 100644 --- a/recipes/bioconductor-dnashaper/meta.yaml +++ b/recipes/bioconductor-dnashaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "DNAshapeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5ba3cfb15f6b312a5941e55a666740107b828bef30ff61f8252c6b7f4b5c84dc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3ce868aa1189c396f1a20822fef9ca1768bddfaf1467e17d9a5a79bed3fa2fbc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biostrings - - bioconductor-genomicranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-fields - 'r-rcpp >=0.12.1' run: - - bioconductor-biostrings - - bioconductor-genomicranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-fields - 'r-rcpp >=0.12.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.' - extra: identifiers: - biotools:dnashaper diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index 0d97e95d76d1b..e8b505e99a533 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.9" %} {% set name = "DO.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.9.7' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.9.7' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire Disease Ontology assembled using data from DO' + + diff --git a/recipes/bioconductor-do.db/post-link.sh b/recipes/bioconductor-do.db/post-link.sh index 0a652c03612cd..2a87d86b99b54 100644 --- a/recipes/bioconductor-do.db/post-link.sh +++ b/recipes/bioconductor-do.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="DO.db_2.9.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/DO.db_2.9.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/DO.db_2.9.tar.gz" + "https://bioarchive.galaxyproject.org/DO.db_2.9.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz" ) MD5="63dda6d46d2fe40c52a2e79260a7fb9d" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-doppelgangr/meta.yaml b/recipes/bioconductor-doppelgangr/meta.yaml index 336a5804beb15..bb11543e3796d 100644 --- a/recipes/bioconductor-doppelgangr/meta.yaml +++ b/recipes/bioconductor-doppelgangr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "doppelgangR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0e055570573d59491c06a43d3dd7645b397c9bd6ea4d644e6f115bec950e6042 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8a74bd7904a0ec830ad5f48dc17aee2e8c7433e33bb64a20a02a25ab6a14ea6a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocparallel - - bioconductor-impute - - bioconductor-sva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-digest - r-mnormt run: - - bioconductor-biobase - - bioconductor-biocparallel - - bioconductor-impute - - bioconductor-sva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-digest - r-mnormt @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).' - extra: identifiers: - biotools:doppelgangr diff --git a/recipes/bioconductor-doqtl/meta.yaml b/recipes/bioconductor-doqtl/meta.yaml index 38112c092aada..0a3ae09f40b52 100644 --- a/recipes/bioconductor-doqtl/meta.yaml +++ b/recipes/bioconductor-doqtl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.2" %} {% set name = "DOQTL" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e5fe9820a6a02d54a25206dbb37d0b033861728519069668a9291e450982fb42 + sha256: a44668e9af9dfea9d82e85ba2e83d6034e526b6fc95ab60612f4ae8aeae08fe1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-annotate - - bioconductor-annotationtools - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-bsgenome.mmusculus.ucsc.mm10 - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rhdf5 - - bioconductor-rsamtools - - bioconductor-variantannotation + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationtools >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-corpcor - r-doparallel @@ -44,17 +42,17 @@ requirements: - r-runit - r-xml run: - - bioconductor-annotate - - bioconductor-annotationtools - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-bsgenome.mmusculus.ucsc.mm10 - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rhdf5 - - bioconductor-rsamtools - - bioconductor-variantannotation + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationtools >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-corpcor - r-doparallel @@ -67,7 +65,9 @@ requirements: - r-regress - r-runit - r-xml - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -75,7 +75,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.' - extra: identifiers: - biotools:doqtl diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 3b644edaf4f28..fe8a7e52e4727 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.0" %} +{% set version = "3.6.1" %} {% set name = "DOSE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,42 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ba950ca991ef2ce89281b0656bb468480dfe4285af0916e908719bac9840bc81 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7b38aa2e548912f8ec2e471841e83346d240ff5dd1d6c2620d2fe209ca8cc9df build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocparallel - - bioconductor-do.db - - bioconductor-fgsea - - 'bioconductor-gosemsim >=2.0.0' - - bioconductor-qvalue - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-do.db >=2.9,<2.11.0' + - 'bioconductor-fgsea >=1.6.0,<1.8.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - - r-igraph - r-reshape2 - - r-rvcheck - - r-scales run: - - bioconductor-annotationdbi - - bioconductor-biocparallel - - bioconductor-do.db - - bioconductor-fgsea - - 'bioconductor-gosemsim >=2.0.0' - - bioconductor-qvalue - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-do.db >=2.9,<2.11.0' + - 'bioconductor-fgsea >=1.6.0,<1.8.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - - r-igraph - r-reshape2 - - r-rvcheck - - r-scales test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.' - extra: identifiers: - biotools:dose diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml index 72a92b0624ab7..8929577128c11 100644 --- a/recipes/bioconductor-drimseq/meta.yaml +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -1,58 +1,53 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "DRIMSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 96e954c3cbddb2cd39186ca942b0e1e1e8ea411dd285171a9bf6d9b23475e89f - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 336b05fcd2047fb41185437373557d3719e18b76bbf9bf0aade043f5473576d8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-mass - r-reshape2 run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-mass - r-reshape2 - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.' - extra: identifiers: - biotools:drimseq diff --git a/recipes/bioconductor-drivernet/meta.yaml b/recipes/bioconductor-drivernet/meta.yaml index cb743d5e7142c..10ecef010cb53 100644 --- a/recipes/bioconductor-drivernet/meta.yaml +++ b/recipes/bioconductor-drivernet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DriverNet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4baf65a59e95413353baef788b20c6bb97d3bdcc907dda9783ae141a73d01719 + sha256: 95c7c3ab5eb4f3b4837542fd58d2a8d7e9e7bd39df355482b1c139be8d622d55 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.' - extra: identifiers: - biotools:drivernet diff --git a/recipes/bioconductor-drugvsdisease/conda_build_config.yaml b/recipes/bioconductor-drugvsdisease/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-drugvsdisease/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml index ce9fad30e1e85..b393e73ff0ce7 100644 --- a/recipes/bioconductor-drugvsdisease/meta.yaml +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.1" %} +{% set version = "2.22.0" %} {% set name = "DrugVsDisease" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,44 +10,44 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 53c2cb62af1cdd4e636aced0387f589e0cafed2f3918daa8fd355da6385f892f + sha256: cd1554211afe42f7f75549bdc331ff8a80a26d52acf4e4e3afde1d328f0c2d38 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-annotate - - bioconductor-arrayexpress - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-cmap2data - - bioconductor-drugvsdiseasedata - - bioconductor-geoquery - - bioconductor-hgu133a.db - - bioconductor-hgu133a2.db - - bioconductor-hgu133plus2.db - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-arrayexpress >=1.40.0,<1.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-cmap2data >=1.16.0,<1.18.0' + - 'bioconductor-drugvsdiseasedata >=1.16.0,<1.18.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' + - 'bioconductor-hgu133a2.db >=3.2.3,<3.4.0' + - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-runit - r-xtable run: - - bioconductor-affy - - bioconductor-annotate - - bioconductor-arrayexpress - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-cmap2data - - bioconductor-drugvsdiseasedata - - bioconductor-geoquery - - bioconductor-hgu133a.db - - bioconductor-hgu133a2.db - - bioconductor-hgu133plus2.db - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-arrayexpress >=1.40.0,<1.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-cmap2data >=1.16.0,<1.18.0' + - 'bioconductor-drugvsdiseasedata >=1.16.0,<1.18.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' + - 'bioconductor-hgu133a2.db >=3.2.3,<3.4.0' + - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-runit - r-xtable @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.' - extra: identifiers: - biotools:drugvsdisease diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml index 213ff9b92a9f7..b69986483ab11 100644 --- a/recipes/bioconductor-drugvsdiseasedata/meta.yaml +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "DrugVsDiseasedata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7a1e7f9d3dc3000b388cbab04ba6adc49104065a225359c428c96a87d89a250c + sha256: 24f6371b471a2478dab6d1c0a4ddf227f2074e5f6d06571b1f7a1d4173a984f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package.' + + diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh index c992173b13b77..d464527fba155 100644 --- a/recipes/bioconductor-drugvsdiseasedata/post-link.sh +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DrugVsDiseasedata_1.14.0.tar.gz" +FN="DrugVsDiseasedata_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/DrugVsDiseasedata_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/DrugVsDiseasedata_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.16.0_src_all.tar.gz" ) -MD5="6623685264db20d9ab1ec5bd51989e50" +MD5="3cc03987897e80f8eb7ddfc821ed1ac1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-dsimer/meta.yaml b/recipes/bioconductor-dsimer/meta.yaml index 7387616ca0d54..92f353b96566f 100644 --- a/recipes/bioconductor-dsimer/meta.yaml +++ b/recipes/bioconductor-dsimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "dSimer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,35 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ce419fc58d2654fc760acc9f0178c87714d6d87fa3fdaf03bc8d6f84096bf5e5 + sha256: 6775ba21090a335eaeed343f75c997c94222a0f80514af09c019de1d1e959179 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-annotationdbi - - bioconductor-go.db - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-ggplot2 - 'r-igraph >=1.0.1' - 'r-rcpp >=0.11.3' - r-reshape2 run: - - bioconductor-annotationdbi - - bioconductor-go.db - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-ggplot2 - 'r-igraph >=1.0.1' - 'r-rcpp >=0.11.3' - r-reshape2 - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'dSimer is an R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided by dSimer.' - extra: identifiers: - biotools:dsimer diff --git a/recipes/bioconductor-dss/meta.yaml b/recipes/bioconductor-dss/meta.yaml index 62e8c9c9480a4..87a4da0f5f85e 100644 --- a/recipes/bioconductor-dss/meta.yaml +++ b/recipes/bioconductor-dss/meta.yaml @@ -1,47 +1,42 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "DSS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1fecdae846e3ced49b1569fada4d6b452c61be91978248ab4eda10474cb6c02a - + sha256: ae607b625c4451e6c7b91be226e6daeb5207ba97290812a989846298d80fa291 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - bioconductor-bsseq - - bioconductor-delayedarray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-bsseq >=1.16.1,<1.18.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - r-base run: - - bioconductor-biobase - - bioconductor-bsseq - - bioconductor-delayedarray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-bsseq >=1.16.1,<1.18.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - r-base - + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.' - extra: identifiers: - biotools:dss diff --git a/recipes/bioconductor-dta/meta.yaml b/recipes/bioconductor-dta/meta.yaml index 26b260554c698..67a58ac37129b 100644 --- a/recipes/bioconductor-dta/meta.yaml +++ b/recipes/bioconductor-dta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "DTA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9c424b89ca2a76dd7ff428e674136e646b47782f3f7ee2581e935b363fe0491c + sha256: 5bdf6c45717e63d88bbfaa48975b00b983d54d9815c5ca24c7de656670e1c2c4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.' - extra: identifiers: - biotools:dta diff --git a/recipes/bioconductor-dupchecker/meta.yaml b/recipes/bioconductor-dupchecker/meta.yaml index 5c116c5ff8bd9..dbf7b66579f74 100644 --- a/recipes/bioconductor-dupchecker/meta.yaml +++ b/recipes/bioconductor-dupchecker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DupChecker" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e581f36582cff53cc6865086e2db7f816c1333bab876717182595c49b7d0acbb + sha256: e668197c0e0c4d560de03365a28e7bcbd7ca17a112e78596e2df95879054e13e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: ' Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data. Not removing duplicates would make study results questionable. We developed a Bioconductor package DupChecker that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.' - extra: identifiers: - biotools:dupchecker diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index c8a0e1dff70ee..317339bce97e4 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "dupRadar" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f6b605828f02480259adc6a692a0a90e96387457d4bb5cd4a2b0daa65b03609d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e845aa9c135b741990e27a307fbb834ffacdd350ae5254920fa816f5145099ac build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-rsubread >=1.14.1' + - 'bioconductor-rsubread >=1.30.8,<1.32.0' - r-base run: - - 'bioconductor-rsubread >=1.14.1' + - 'bioconductor-rsubread >=1.30.8,<1.32.0' - r-base - - r-kernsmooth # loaded when running duprateExpDensPlot test: commands: - '$R -e "library(''{{ name }}'')"' @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Duplication rate quality control for RNA-Seq datasets.' - extra: identifiers: - biotools:dupradar diff --git a/recipes/bioconductor-dyebias/meta.yaml b/recipes/bioconductor-dyebias/meta.yaml index 83a0b568290dd..9aee4da8a9595 100644 --- a/recipes/bioconductor-dyebias/meta.yaml +++ b/recipes/bioconductor-dyebias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "dyebias" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5312f64b9c710e61581d7af49fe4325cde10b313457b5051a0ad0625138eb4a2 + sha256: 68ea39bc0ae6d4f8693a1ac8473559e4a7498f403d657085c51da3688412151e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base run: - - bioconductor-biobase - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)' - extra: identifiers: - biotools:dyebias diff --git a/recipes/bioconductor-dyndoc/meta.yaml b/recipes/bioconductor-dyndoc/meta.yaml index 209f8ea901a07..986b176048adb 100644 --- a/recipes/bioconductor-dyndoc/meta.yaml +++ b/recipes/bioconductor-dyndoc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "DynDoc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: acef52631ac134ebd2b2cb155fcac5da1505960c477dc0a82604e2b3851b84fd + sha256: 78572bbef190ba20cfa7c9a23f62570aebe35b73e83e18c590875c6fc49c4dd2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of functions to create and interact with dynamic documents and vignettes.' - extra: identifiers: - biotools:dyndoc diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml index 77e09fc0f79f7..606cfc2a8fcc6 100644 --- a/recipes/bioconductor-easyrnaseq/meta.yaml +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "easyRNASeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,50 +10,50 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7d9d71012c9dce33cd7938e3639ba394858438b14d016c8b02b35cc6935c8086 + sha256: 08fda441093ae8770cab7e4378fdcf6b5823e3689b9bbf5121acc0c6201d25c0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.31.3' - - 'bioconductor-biocgenerics >=0.17.2' - - 'bioconductor-biocparallel >=1.5.1' - - 'bioconductor-biomart >=2.27.2' - - 'bioconductor-biostrings >=2.39.3' - - 'bioconductor-deseq >=1.23.0' - - 'bioconductor-edger >=3.13.4' - - 'bioconductor-genomeinfodb >=1.7.3' - - 'bioconductor-genomeintervals >=1.27.0' - - 'bioconductor-genomicalignments >=1.7.3' - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - 'bioconductor-rsamtools >=1.23.1' - - 'bioconductor-s4vectors >=0.9.38' - - 'bioconductor-shortread >=1.29.1' - - 'bioconductor-summarizedexperiment >=1.1.11' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-locfit - 'r-lsd >=3.0' run: - - 'bioconductor-biobase >=2.31.3' - - 'bioconductor-biocgenerics >=0.17.2' - - 'bioconductor-biocparallel >=1.5.1' - - 'bioconductor-biomart >=2.27.2' - - 'bioconductor-biostrings >=2.39.3' - - 'bioconductor-deseq >=1.23.0' - - 'bioconductor-edger >=3.13.4' - - 'bioconductor-genomeinfodb >=1.7.3' - - 'bioconductor-genomeintervals >=1.27.0' - - 'bioconductor-genomicalignments >=1.7.3' - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - 'bioconductor-rsamtools >=1.23.1' - - 'bioconductor-s4vectors >=0.9.38' - - 'bioconductor-shortread >=1.29.1' - - 'bioconductor-summarizedexperiment >=1.1.11' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-locfit - 'r-lsd >=3.0' @@ -64,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.' - extra: identifiers: - biotools:easyrnaseq diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index 0b0b0a93c605c..c9f1e3e19f3f2 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "EBarrays" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 35442736d1f0feacb709081872678f6fcfe381658dd95fef9d6e5cdfd449a241 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d7e3ff110be38d9276adfb7e331eabf84d77282156a1d26df8b49b686aedaae1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster - r-lattice run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster - r-lattice + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'EBarrays provides tools for the analysis of replicated/unreplicated microarray data.' - extra: identifiers: - biotools:ebarrays diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index 1a42514126ee4..24511d0f2d276 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.20.0" %} +{% set version = "4.22.1" %} {% set name = "EBImage" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 18331f7380b0f89ee6e02a07c4ba7fc9fb69d36b5daf8c48520287b30e70f220 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 497bb6a34edc39023339173c92d65ed4f558c6ab7eaa00459cc9684d612a5755 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.7.1' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-abind - r-base - - 'r-fftwtools >=0.9_7' + - 'r-fftwtools >=0.9-7' - r-htmltools - r-htmlwidgets - r-jpeg @@ -29,10 +30,10 @@ requirements: - r-rcurl - r-tiff run: - - 'bioconductor-biocgenerics >=0.7.1' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-abind - r-base - - 'r-fftwtools >=0.9_7' + - 'r-fftwtools >=0.9-7' - r-htmltools - r-htmlwidgets - r-jpeg @@ -40,6 +41,10 @@ requirements: - r-png - r-rcurl - r-tiff + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.' - extra: identifiers: - biotools:ebimage diff --git a/recipes/bioconductor-ebsea/meta.yaml b/recipes/bioconductor-ebsea/meta.yaml index 9927acb2c51ea..f2ba8c88c7adb 100644 --- a/recipes/bioconductor-ebsea/meta.yaml +++ b/recipes/bioconductor-ebsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "EBSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: df2e5dece0e9238a7113dca104d17016cec901d6c961aad4fb062cb239ab0f8f + sha256: 22f601ca51ef5365f8f0a9dcd830c66aed9d847bc29f3bb2590bdadc7763f5c5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - - r-gtools + - r-plyr run: - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - - r-gtools + - r-plyr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data.' - extra: identifiers: - biotools:ebsea diff --git a/recipes/bioconductor-ebseq/meta.yaml b/recipes/bioconductor-ebseq/meta.yaml index d1fe9d9896fcc..82e0879550416 100644 --- a/recipes/bioconductor-ebseq/meta.yaml +++ b/recipes/bioconductor-ebseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "EBSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bc9eeeeb1ac825d74d9f325d8c10fee39e7bf76958655486cfc372629cea275f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9b39642a70e606d85ca5d17716fd48aa82e5459f85d44af592e9050eeb2fd5cd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Differential Expression analysis at both gene and isoform level using RNA-seq data' - extra: identifiers: - biotools:ebseq diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index 5de93dfcd2195..1fa2529b83a28 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.1" %} {% set name = "EDASeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,41 +8,42 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9b5f79f6cdae393b9d6f09a63c052251224f2bce2f61158c10d6efc87e42f51f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e8695f6701f4b9f1af7d5cb622d366151ad8678bcd298c3b0e1cb7565ae2e024 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-aroma.light - - 'bioconductor-biobase >=2.15.1' - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-deseq - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-iranges >=1.13.9' - - 'bioconductor-rsamtools >=1.5.75' - - 'bioconductor-shortread >=1.11.42' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-aroma.light >=3.10.0,<3.12.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-aroma.light - - 'bioconductor-biobase >=2.15.1' - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-deseq - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-iranges >=1.13.9' - - 'bioconductor-rsamtools >=1.5.75' - - 'bioconductor-shortread >=1.11.42' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-aroma.light >=3.10.0,<3.12.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base test: commands: @@ -51,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).' - extra: identifiers: - biotools:edaseq diff --git a/recipes/bioconductor-edda/meta.yaml b/recipes/bioconductor-edda/meta.yaml index e8f174d26086f..8e5d87f68cb87 100644 --- a/recipes/bioconductor-edda/meta.yaml +++ b/recipes/bioconductor-edda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "EDDA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,33 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 602823ecbfd955f6437928048711c863672ee743143fd2d262b659380fb81300 + sha256: bc1918bad514dd8e18c62d74dfe5cb719626d0378509529748e231aaeae687b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-bayseq - - bioconductor-deseq - - bioconductor-edger + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - 'r-rcpp >=0.10.4' - r-rocr - r-snow run: - - bioconductor-bayseq - - bioconductor-deseq - - bioconductor-edger + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - 'r-rcpp >=0.10.4' - r-rocr - r-snow - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. This work was published on 3 December 2014 at Genome Biology under the title "The importance of study design for detecting differentially abundant features in high-throughput experiments" (http://genomebiology.com/2014/15/12/527).' - extra: identifiers: - biotools:edda diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index 598dce1f7b6d6..36f927a7ce8cb 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.20.7" %} +{% set version = "3.22.5" %} {% set name = "edgeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5c4286fd0d80ae0696c4ef65111366152cc071c3e8fd446b2d0fce6d75b235dc + sha256: 47d2234f29a4717e4f7079f23ef300d910e81adf4721d58d62aaf18ae06c6c5e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-limma >=3.34.5' + - 'bioconductor-limma >=3.36.0,<3.38.0' - r-base - r-locfit - r-rcpp run: - - 'bioconductor-limma >=3.34.5' + - 'bioconductor-limma >=3.36.0,<3.38.0' - r-base - r-locfit - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -36,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.' - extra: identifiers: - biotools:edger diff --git a/recipes/bioconductor-egsea/meta.yaml b/recipes/bioconductor-egsea/meta.yaml index 3f778bfc40a0a..56e32af05b484 100644 --- a/recipes/bioconductor-egsea/meta.yaml +++ b/recipes/bioconductor-egsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "EGSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8e60d394094703e402dcb98781807ed42825f2e4e895dfea58d074fb7ca51fef + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 72b0b4dcb8d1a799cbec3f65df9d7a75fd91084c06fe75beeb81fa4946769dab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-edger >=3.6.8' - - 'bioconductor-egseadata >=1.3.1' - - 'bioconductor-gage >=2.14.4' - - 'bioconductor-glimma >=1.4.0' - - 'bioconductor-globaltest >=5.18.0' - - 'bioconductor-gsva >=1.12.0' - - 'bioconductor-limma >=3.20.9' - - bioconductor-org.hs.eg.db - - bioconductor-org.mm.eg.db - - bioconductor-org.rn.eg.db - - 'bioconductor-padog >=1.6.0' - - 'bioconductor-pathview >=1.4.2' - - 'bioconductor-safe >=3.4.0' - - 'bioconductor-topgo >=2.16.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-egseadata >=1.8.0,<1.10.0' + - 'bioconductor-gage >=2.30.0,<2.32.0' + - 'bioconductor-glimma >=1.8.2,<1.10.0' + - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-padog >=1.22.0,<1.24.0' + - 'bioconductor-pathview >=1.20.0,<1.22.0' + - 'bioconductor-safe >=3.20.0,<3.22.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-dt - 'r-ggplot2 >=1.0.0' @@ -45,22 +46,22 @@ requirements: - r-rcolorbrewer - 'r-stringi >=0.5.0' run: - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-edger >=3.6.8' - - 'bioconductor-egseadata >=1.3.1' - - 'bioconductor-gage >=2.14.4' - - 'bioconductor-glimma >=1.4.0' - - 'bioconductor-globaltest >=5.18.0' - - 'bioconductor-gsva >=1.12.0' - - 'bioconductor-limma >=3.20.9' - - bioconductor-org.hs.eg.db - - bioconductor-org.mm.eg.db - - bioconductor-org.rn.eg.db - - 'bioconductor-padog >=1.6.0' - - 'bioconductor-pathview >=1.4.2' - - 'bioconductor-safe >=3.4.0' - - 'bioconductor-topgo >=2.16.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-egseadata >=1.8.0,<1.10.0' + - 'bioconductor-gage >=2.30.0,<2.32.0' + - 'bioconductor-glimma >=1.8.2,<1.10.0' + - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-padog >=1.22.0,<1.24.0' + - 'bioconductor-pathview >=1.20.0,<1.22.0' + - 'bioconductor-safe >=3.20.0,<3.22.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-dt - 'r-ggplot2 >=1.0.0' @@ -79,7 +80,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.' - extra: identifiers: - biotools:egsea diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index 918f839aa1b97..e1b2091037528 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "EGSEAdata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1d266debcc106ad05ed63413a49ebdfa4dfc597f444235b5f82e106717d26ebb + sha256: 128219a76de39e2e0f00ec6c485d1c8608b3107221a1a810a77c5d1e8f1b927a build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'file LICENSE' summary: 'This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections.' + + diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index 90d4a539fd212..2f6b1c5a7517f 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="EGSEAdata_1.6.0.tar.gz" +FN="EGSEAdata_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/EGSEAdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.6.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/EGSEAdata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/EGSEAdata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.8.0_src_all.tar.gz" ) -MD5="899eb37b2b0cd33ba2566c5197f602bf" +MD5="bc854d47778e6ee4fa029d65eda9134b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-elmer.data/meta.yaml b/recipes/bioconductor-elmer.data/meta.yaml index e81908a66d020..e52bdd780efb2 100644 --- a/recipes/bioconductor-elmer.data/meta.yaml +++ b/recipes/bioconductor-elmer.data/meta.yaml @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - wget test: @@ -32,6 +32,4 @@ about: license: GPL-3 summary: ' Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily' -extra: - skip-lints: - - bioconductor_37 + diff --git a/recipes/bioconductor-elmer/conda_build_config.yaml b/recipes/bioconductor-elmer/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-elmer/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-elmer/meta.yaml b/recipes/bioconductor-elmer/meta.yaml index 06039a0698e4c..c983ca8b8e4b2 100644 --- a/recipes/bioconductor-elmer/meta.yaml +++ b/recipes/bioconductor-elmer/meta.yaml @@ -12,24 +12,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 81c6f4ab69313670441f329ff2c6e9d13b8d93f7acc8e0b567287cff2042ec50 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-complexheatmap - - bioconductor-elmer.data - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-multiassayexperiment - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - 'bioconductor-tcgabiolinks >=2.5.5' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-elmer.data >=2.4.2,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' - r-base - r-circlize - r-doparallel @@ -50,18 +50,18 @@ requirements: - r-stringr - r-xml2 run: - - bioconductor-biomart - - bioconductor-complexheatmap - - bioconductor-elmer.data - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-multiassayexperiment - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - 'bioconductor-tcgabiolinks >=2.5.5' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-elmer.data >=2.4.2,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' - r-base - r-circlize - r-doparallel @@ -88,8 +88,3 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.' - -extra: - skip-lints: - - bioconductor_37 - diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml index 0190b84dab244..14251732b18b7 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "EmpiricalBrownsMethod" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1ebd334bac4be2e562ae4aecc03637f8041ee832c0629a229ea2f245aa5561f3 + sha256: 8f77f71f7ff1942f6d1f76fc6cb46ad10053f2d0843a199f085072f748b48931 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.' - extra: identifiers: - biotools:empiricalbrownsmethod diff --git a/recipes/bioconductor-encodexplorer/meta.yaml b/recipes/bioconductor-encodexplorer/meta.yaml index 766d60af2ce6a..e4d9725a79e2f 100644 --- a/recipes/bioconductor-encodexplorer/meta.yaml +++ b/recipes/bioconductor-encodexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "ENCODExplorer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: de8ff9650f33ccf3befbdc2f527f802f26dede14f38ec5fe93008779d7bb8357 + sha256: f0da70176e0eede01132fbe727e60d0640b4c40c59618a0ffcb9df0377521d24 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -48,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.' - extra: identifiers: - biotools:encodexplorer diff --git a/recipes/bioconductor-enrichmentbrowser/conda_build_config.yaml b/recipes/bioconductor-enrichmentbrowser/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-enrichmentbrowser/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml index bf0db513554bb..6e46048b42106 100644 --- a/recipes/bioconductor-enrichmentbrowser/meta.yaml +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.5" %} +{% set version = "2.10.11" %} {% set name = "EnrichmentBrowser" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,63 +10,69 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f2b2e6ca297338e0a78e7627bd7d1f49d8686f10ea52e9a117db52de6b38b7ab + sha256: 3bd9d31cd2a7514ce13db33011a27f703257617bd0f4e0a04734295358d9acee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgraph - - bioconductor-complexheatmap - - bioconductor-deseq2 - - bioconductor-edaseq - - bioconductor-edger - - bioconductor-geneplotter - - bioconductor-go.db - - bioconductor-graph - - bioconductor-gseabase - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-limma - - bioconductor-pathview - - bioconductor-reportingtools - - bioconductor-rgraphviz - - bioconductor-s4vectors - - bioconductor-safe - - bioconductor-spia - - bioconductor-summarizedexperiment - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' + - 'bioconductor-biocgraph >=1.42.0,<1.44.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edaseq >=2.14.1,<2.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graphite >=1.26.1,<1.28.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-pathview >=1.20.0,<1.22.0' + - 'bioconductor-reportingtools >=2.20.0,<2.22.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-safe >=3.20.0,<3.22.0' + - 'bioconductor-spia >=2.32.0,<2.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-hwriter - r-mass + - r-rappdirs run: - - bioconductor-annotationdbi - - bioconductor-biocgraph - - bioconductor-complexheatmap - - bioconductor-deseq2 - - bioconductor-edaseq - - bioconductor-edger - - bioconductor-geneplotter - - bioconductor-go.db - - bioconductor-graph - - bioconductor-gseabase - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-limma - - bioconductor-pathview - - bioconductor-reportingtools - - bioconductor-rgraphviz - - bioconductor-s4vectors - - bioconductor-safe - - bioconductor-spia - - bioconductor-summarizedexperiment - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' + - 'bioconductor-biocgraph >=1.42.0,<1.44.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edaseq >=2.14.1,<2.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graphite >=1.26.1,<1.28.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-pathview >=1.20.0,<1.22.0' + - 'bioconductor-reportingtools >=2.20.0,<2.22.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-safe >=3.20.0,<3.22.0' + - 'bioconductor-spia >=2.32.0,<2.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-hwriter - r-mass + - r-rappdirs test: commands: - '$R -e "library(''{{ name }}'')"' @@ -74,3 +80,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.' + + diff --git a/recipes/bioconductor-enrichplot/build.sh b/recipes/bioconductor-enrichplot/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-enrichplot/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichplot/meta.yaml b/recipes/bioconductor-enrichplot/meta.yaml new file mode 100644 index 0000000000000..5980b210fbb3a --- /dev/null +++ b/recipes/bioconductor-enrichplot/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.2" %} +{% set name = "enrichplot" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: eff2bd856c5e14cca9b7af6f8fc853dd22dac2ee057acbed0f248da604b4dbbf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - r-base + - r-cowplot + - r-ggplot2 + - r-ggraph + - r-ggridges + - r-igraph + - r-reshape2 + - r-upsetr + run: + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - r-base + - r-cowplot + - r-ggplot2 + - r-ggraph + - r-ggridges + - r-igraph + - r-reshape2 + - r-upsetr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The ''enrichplot'' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. All the visualization methods are developed based on ''ggplot2'' graphics.' + + + diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml index f388d922965bf..7655d071d9588 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v75" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 2c59f95959f344b2a3eaa65a00086b01a420823e30b0810fc81e49b08dcba64b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-ensembldb + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - r-base run: - - bioconductor-ensembldb + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from Ensembl.' + + diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh index cf84267028182..948e9a99d7114 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh +++ b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="EnsDb.Hsapiens.v75_2.99.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v75_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" ) MD5="6c896475252903972bfc6c0eb0d8f334" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 342ebc9d0dd63..d08f8fccd9664 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.2" %} +{% set version = "2.4.1" %} {% set name = "ensembldb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,47 +10,45 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7360ac20fc3551d08fb8617753a532e20e41dedc4e28f043fa0895e166b3cffa + sha256: 86a3df73a98d820149084c5f0114d433e5533a6cc3914f7e2d60331f3b234bd0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.31.19' - - 'bioconductor-annotationfilter >=1.1.9' - - bioconductor-annotationhub - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biostrings - - bioconductor-genomeinfodb - - 'bioconductor-genomicfeatures >=1.29.10' - - 'bioconductor-genomicranges >=1.23.21' - - 'bioconductor-iranges >=2.11.16' - - bioconductor-protgenerics - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-curl - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-annotationdbi >=1.31.19' - - 'bioconductor-annotationfilter >=1.1.9' - - bioconductor-annotationhub - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biostrings - - bioconductor-genomeinfodb - - 'bioconductor-genomicfeatures >=1.29.10' - - 'bioconductor-genomicranges >=1.23.21' - - 'bioconductor-iranges >=2.11.16' - - bioconductor-protgenerics - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-curl - r-dbi @@ -61,8 +59,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL - summary: 'The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.' - + summary: 'The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.' extra: identifiers: - biotools:ensembldb diff --git a/recipes/bioconductor-ensemblvep/meta.yaml b/recipes/bioconductor-ensemblvep/meta.yaml index f528e3b78dd39..81483edf1f1dc 100644 --- a/recipes/bioconductor-ensemblvep/meta.yaml +++ b/recipes/bioconductor-ensemblvep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "ensemblVEP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c26480895abfdab4e6763aaab35b8eb69c60beaeea4694d88c1d5dec9d39eaf7 + sha256: f2f3fcd2a74c01c898a2e2e543a808c3f9c9051bd6c6343d6764cc54bdb94306 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base test: commands: @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Query the Ensembl Variant Effect Predictor via the perl API.' - extra: identifiers: - biotools:ensemblvep diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml index 7e60613274dd5..5b5af43287577 100644 --- a/recipes/bioconductor-epigenomix/meta.yaml +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "epigenomix" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,35 +10,35 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 973b9a3fe5c2ddba3be21c2d177a802faa80c631a50f0d8b7f168da9ba3ba674 + sha256: fa526d60cae35c4ff89fa4e1124e746c196d691176af8a5ccfba04554b883203 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-beadarray - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-beadarray >=2.30.0,<2.32.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-mcmcpack run: - - bioconductor-beadarray - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-beadarray >=2.30.0,<2.32.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-mcmcpack test: @@ -48,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.' - extra: identifiers: - biotools:epigenomix diff --git a/recipes/bioconductor-epivizr/conda_build_config.yaml b/recipes/bioconductor-epivizr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-epivizr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml index 79f48d906e9de..f8a241a1652a5 100644 --- a/recipes/bioconductor-epivizr/meta.yaml +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "epivizr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7cb7bae00b0cea5a2db5b4e03581cb4cf3eb64c7e24269c02d5c70a625120e21 + sha256: a243a05d22a20567ba00e31498bdfc27e046e1e0d066f4ace32f84b5655b8a20 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-epivizrdata >=1.3.4' - - 'bioconductor-epivizrserver >=1.1.1' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-epivizrdata >=1.8.0,<1.10.0' + - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - 'bioconductor-epivizrdata >=1.3.4' - - 'bioconductor-epivizrserver >=1.1.1' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-epivizrdata >=1.8.0,<1.10.0' + - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.' - extra: identifiers: - biotools:epivizr diff --git a/recipes/bioconductor-epivizrdata/conda_build_config.yaml b/recipes/bioconductor-epivizrdata/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-epivizrdata/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml index 7201b45385534..0cdd89356bbc3 100644 --- a/recipes/bioconductor-epivizrdata/meta.yaml +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "epivizrData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,36 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a4840fe556800430b75e34e7a0bfb7c453546f185e4e248bb5ed046c535f3180 + sha256: 82701cbf197744d711c5f62274c56ce1b2d23d966bbd6443c20a890bf3f16d7d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-ensembldb - - 'bioconductor-epivizrserver >=1.1.1' - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-organismdbi - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - bioconductor-biobase - - bioconductor-ensembldb - - 'bioconductor-epivizrserver >=1.1.1' - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-organismdbi - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base test: commands: @@ -48,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Serve data from Bioconductor Objects through a WebSocket connection.' - extra: identifiers: - biotools:epivizrdata diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml index 7825a1fea8737..2581dbc5d1cce 100644 --- a/recipes/bioconductor-epivizrserver/meta.yaml +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "epivizrServer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2b84e5bbddf18ce04e0d79617b330aefb1830030b16e61431d8afb84b71f4161 + sha256: 249216e081abc9788c738f59e75abefdcab4db7ebef41a7a8563e11304b02df8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.' - extra: identifiers: - biotools:epivizrserver diff --git a/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml b/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml index aaae317e8ee4b..8b3231fa8e107 100644 --- a/recipes/bioconductor-epivizrstandalone/meta.yaml +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "epivizrStandalone" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 12fdcf19c658dba96ad9ecad30c38b8eea93f4486f3e717a3dc983d8ea146d65 + sha256: ebd600132569c5c391c33f593379fc3cc5aff9c3a46cb256adda1d4a0a5eb47e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - 'bioconductor-epivizr >=2.3.6' - - bioconductor-epivizrserver - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-epivizr >=2.10.0,<2.12.0' + - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-git2r run: - - bioconductor-biocgenerics - - 'bioconductor-epivizr >=2.3.6' - - bioconductor-epivizrserver - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-epivizr >=2.10.0,<2.12.0' + - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-git2r test: @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The ''epivizrServer'' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.' - extra: identifiers: - biotools:epivizrstandalone diff --git a/recipes/bioconductor-esetvis/conda_build_config.yaml b/recipes/bioconductor-esetvis/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-esetvis/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml index a56e852e677f9..69d1027f6964a 100644 --- a/recipes/bioconductor-esetvis/meta.yaml +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.3" %} {% set name = "esetVis" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c1c28bf08e5c2819a974aeed222efa9709626e2ea2fd5163af5823df291a62f9 + sha256: defb62207facbad84b2d420d50833c9cee8ba17dfd943c024dcc9422b3c9733c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-mlp + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-mlp >=1.28.0,<1.30.0' - r-base - r-hexbin - r-mass - r-mpm - r-rtsne run: - - bioconductor-biobase - - bioconductor-mlp + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-mlp >=1.28.0,<1.30.0' - r-base - r-hexbin - r-mass @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.' - extra: identifiers: - biotools:esetvis diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml index 41ee2e966cde2..8eb9719d27212 100644 --- a/recipes/bioconductor-eudysbiome/meta.yaml +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "eudysbiome" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 69480f65354e411a7b387edd7e99f39bfd6af2392e5535ac32b014ff5fcc5e8d + sha256: 1f6f59838e0b54b8d40b30cc6408cc1aac192bd72fd75e84d10fbf082fcc1370 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-rsamtools + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-plyr - r-r.utils run: - - bioconductor-biostrings - - bioconductor-rsamtools + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-plyr - r-r.utils @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.' - extra: identifiers: - biotools:eudysbiome diff --git a/recipes/bioconductor-eximir/conda_build_config.yaml b/recipes/bioconductor-eximir/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-eximir/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml index 68ca2be20f606..3ddee083dae78 100644 --- a/recipes/bioconductor-eximir/meta.yaml +++ b/recipes/bioconductor-eximir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "ExiMiR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b93675e6e6567bff038092f4121029bb33eeb5a2f60636b13270164bce25d69 + sha256: 8db4a380e83229f0c0604eca519026a9744e64b89aa01080a9349f1cec553c68 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.26.1' - - 'bioconductor-affyio >=1.13.3' - - 'bioconductor-biobase >=2.5.5' - - bioconductor-limma - - 'bioconductor-preprocesscore >=1.10.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base run: - - 'bioconductor-affy >=1.26.1' - - 'bioconductor-affyio >=1.13.3' - - 'bioconductor-biobase >=2.5.5' - - bioconductor-limma - - 'bioconductor-preprocesscore >=1.10.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base test: commands: @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.' - extra: identifiers: - biotools:eximir diff --git a/recipes/bioconductor-exomecopy/meta.yaml b/recipes/bioconductor-exomecopy/meta.yaml index 1977da977b86f..4242b30f949a1 100644 --- a/recipes/bioconductor-exomecopy/meta.yaml +++ b/recipes/bioconductor-exomecopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "exomeCopy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2ef2b446e11612d98a35f0af86763a9b24b0962213efb2f38e398bc9ea51379f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1cff39c955f7c20aaa429cea83cfb8fd831ed4d36500157521e831f20c6a7aab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base run: - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.' - extra: identifiers: - biotools:exomecopy diff --git a/recipes/bioconductor-exomepeak/meta.yaml b/recipes/bioconductor-exomepeak/meta.yaml index cffca8f587c99..0a0eccb015c51 100644 --- a/recipes/bioconductor-exomepeak/meta.yaml +++ b/recipes/bioconductor-exomepeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.13.2" %} +{% set version = "2.14.0" %} {% set name = "exomePeak" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 87562bfc22436c8d4cee85fa9dffeb16546732ac1b1c40375d1f605e591cdf05 + sha256: 53444fe6488672d2fa8d19530ba737e9ccd13e32b6b0c38625180aec4ff7b3ba build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicalignments - - 'bioconductor-genomicfeatures >=1.14.5' - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base run: - - bioconductor-genomicalignments - - 'bioconductor-genomicfeatures >=1.14.5' - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base test: commands: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng if you have any questions.' - extra: identifiers: - biotools:exomepeak diff --git a/recipes/bioconductor-experimenthub/conda_build_config.yaml b/recipes/bioconductor-experimenthub/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-experimenthub/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-experimenthub/meta.yaml b/recipes/bioconductor-experimenthub/meta.yaml index 5a521aa9529f0..9b6030e6595f8 100644 --- a/recipes/bioconductor-experimenthub/meta.yaml +++ b/recipes/bioconductor-experimenthub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "ExperimentHub" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 43820b5fdecdb07462cdbc6f3afc210622576cd9dbf885b6c4b451924d1fefc1 + sha256: db4e6cc33e53dd3de0b6bd413f1679fed043dfe5d487229484d3c5172d9e58eb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationhub >=2.9.11' - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biocinstaller - - bioconductor-s4vectors + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-curl run: - - 'bioconductor-annotationhub >=2.9.11' - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biocinstaller - - bioconductor-s4vectors + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-curl test: diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml index 8effc14d2aa1f..786051a31cc65 100644 --- a/recipes/bioconductor-faahko/meta.yaml +++ b/recipes/bioconductor-faahko/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "faahKO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3097c03851eb054c4beec9ca0b655ffaf328839d6d012e3d2e1f590df6e18328 + sha256: f156932d08ab79f0607ce6b3584b868bd161615ea6f427af12e718ff41846923 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-xcms + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base run: - - bioconductor-xcms + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL summary: 'Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet.' + + diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh index 7e6fa81bfebad..c5af208cb421f 100644 --- a/recipes/bioconductor-faahko/post-link.sh +++ b/recipes/bioconductor-faahko/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="faahKO_1.18.0.tar.gz" +FN="faahKO_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/faahKO_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/faahKO_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.18.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/faahKO_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/faahKO_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.20.0_src_all.tar.gz" ) -MD5="9fe453baeee61b8b070704e8738174b8" +MD5="5cfa6b1656efb3167d8fbccbc99b97d4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-fabia/build.sh b/recipes/bioconductor-fabia/build.sh index 26dbe349a5be9..da43ce2168312 100644 --- a/recipes/bioconductor-fabia/build.sh +++ b/recipes/bioconductor-fabia/build.sh @@ -1,13 +1,4 @@ #!/bin/bash - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -if [[ "$(uname)" == "Darwin" ]]; then - export CC=clang - export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" - export LDFLAGS="${LDFLAGS} -Wl,-rpath,$PREFIX/lib" -fi -autoconf - -$R CMD INSTALL --build . || (echo "error code: $?" ; cat config.log ; exit 1) +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml index 511b8a5c24a1a..ccd1535733846 100644 --- a/recipes/bioconductor-fabia/meta.yaml +++ b/recipes/bioconductor-fabia/meta.yaml @@ -1,46 +1,39 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "fabia" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 073c3529e4812745fb69dfca6b32c498d02be65b586fe7af17e7f1f6847593b0 - patches: - - non-destructive-compile-link-flags.patch - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 40e0d6731dd6764a85176646d1b38e4ec34ea565e691b56ea7185df21a5ac04f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} host: - - autoconf - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - - libgfortran # [osx] - + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.1)' summary: 'Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.' - extra: identifiers: - biotools:fabia diff --git a/recipes/bioconductor-farms/conda_build_config.yaml b/recipes/bioconductor-farms/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-farms/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-farms/meta.yaml b/recipes/bioconductor-farms/meta.yaml index ead153f42059f..da392428ee9da 100644 --- a/recipes/bioconductor-farms/meta.yaml +++ b/recipes/bioconductor-farms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "farms" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 62cffbde26ce184a06b5f3964c0e7056e905d509c4762410c768c8c6d4f3b64c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9b6425ac3540e59ad7b06bf8c160fc2be63ac7f3c5e715ace54be25a635bed13 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.20.0' - - 'bioconductor-biobase >=1.13.41' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass run: - - 'bioconductor-affy >=1.20.0' - - 'bioconductor-biobase >=1.13.41' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.1)' summary: 'The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization (FARMS) and a novel unsupervised feature selection criterion called "I/NI-calls"' - extra: identifiers: - biotools:farms diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index caf451d0ff4a0..c5a3de89d271b 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "fastseg" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 578a6ea22769dd17879346deb53e5a9c0ad3a0f5cb42cd6954e9733a47b6a735 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 33be8adf3cd52a4d12906d22b3fe48fe1368aecb8ed436d5f1182d68a28286fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments'' first and higher order moments.' - extra: identifiers: - biotools:fastseg diff --git a/recipes/bioconductor-fccac/meta.yaml b/recipes/bioconductor-fccac/meta.yaml index 10f89166d5d60..cbc30b34887c4 100644 --- a/recipes/bioconductor-fccac/meta.yaml +++ b/recipes/bioconductor-fccac/meta.yaml @@ -1,56 +1,49 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "fCCAC" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e940b09c32140fdb217a3c8d24f91811b18ad9f44be3556ff6b128f235c6a158 - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: dbe5368f2130730abd567026a029f1343bbbb7da7ee75d195590506d9c5bfb1f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-complexheatmap - - bioconductor-genomation - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-genomation >=1.12.0,<1.14.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fda - r-ggplot2 - r-rcolorbrewer run: - - bioconductor-complexheatmap - - bioconductor-genomation - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-genomation >=1.12.0,<1.14.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fda - r-ggplot2 - r-rcolorbrewer - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://www.bioconductor.org/packages/release/bioc/html/fCCAC.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'An application of functional canonical correlation analysis to assess covariance of nucleic - acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).' - + summary: 'An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).' extra: identifiers: - biotools:fccac diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index 4cb77867324da..4ee7d049e0ae4 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biostrings - - 'bioconductor-genomicfeatures >=1.7.22' - - bioconductor-org.hs.eg.db - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-biostrings - - 'bioconductor-genomicfeatures >=1.7.22' - - bioconductor-org.hs.eg.db - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base - wget test: @@ -38,3 +39,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Compiled HumanMethylation27 and HumanMethylation450 annotations' + + diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh index 5889410296302..75afe3b912650 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz" ) MD5="b8b1abc599b9556b9fe9c6e824cb2697" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-ffpe/conda_build_config.yaml b/recipes/bioconductor-ffpe/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-ffpe/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml index bc8050ab0a11b..d11d5a2433cb6 100644 --- a/recipes/bioconductor-ffpe/meta.yaml +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -1,55 +1,47 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ffpe" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0400831fc0451f4847ad511452ab4868b77264da0bbcdd5a36bf374f160f1430 - + sha256: efaabc3e9c8582c5827793c6c232679c4d62a96812fa996a0aeb8796e7b66fb5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-lumi - - bioconductor-methylumi + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' - r-base - r-sfsmisc - r-ttr run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-lumi - - bioconductor-methylumi + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' - r-base - r-sfsmisc - r-ttr - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>2)' summary: 'Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).' - extra: identifiers: - biotools:ffpe diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index 7d0dbfa7315cc..81558a5499645 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "fgsea" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 580602aa630e80cc8c0c3f5ea27df0c4192fec826a988a9bca3822ac31143711 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9ac57aceebf752f287ec94ed663d383ddf8ea1e7beb419c277b3f7f2d7d5c6c0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base - r-data.table - r-fastmatch - 'r-ggplot2 >=2.2.0' - r-gridextra + - r-matrix - r-rcpp run: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base - r-data.table - r-fastmatch - 'r-ggplot2 >=2.2.0' - r-gridextra + - r-matrix - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENCE' summary: 'The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.' - extra: identifiers: - biotools:fgsea diff --git a/recipes/bioconductor-findmyfriends/meta.yaml b/recipes/bioconductor-findmyfriends/meta.yaml index cbcee0e4767a2..a07a763899a12 100644 --- a/recipes/bioconductor-findmyfriends/meta.yaml +++ b/recipes/bioconductor-findmyfriends/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FindMyFriends" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 66a8f49d01f2770d8d7417bb70bc4695f5cffe5d4ae0a95b76bd50626583c68d + sha256: f207cfb4e8836357b9acafb1c8d578a57fa5530498230568e931fa1a138f979b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-iranges - - bioconductor-kebabs - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-kebabs >=1.14.0,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-digest - r-dplyr @@ -39,13 +37,13 @@ requirements: - r-rcpp - r-reshape2 run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-iranges - - bioconductor-kebabs - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-kebabs >=1.14.0,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-digest - r-dplyr @@ -57,7 +55,10 @@ requirements: - r-matrix - r-rcpp - r-reshape2 - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -65,7 +66,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.' - extra: identifiers: - biotools:findmyfriends diff --git a/recipes/bioconductor-fis/meta.yaml b/recipes/bioconductor-fis/meta.yaml index 6ad4a075fdbcc..e09b570e040c1 100644 --- a/recipes/bioconductor-fis/meta.yaml +++ b/recipes/bioconductor-fis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FIs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8996fb9c1d674b3ce0b734b111b8bc3e9053bbb5d28ba4ff4ef8b227e9dfccac + sha256: 5079ed505952460d83859eb8c8c028cfff8abe25ab5dd645f5a2e7be08f1ddb4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases.' + + diff --git a/recipes/bioconductor-fis/post-link.sh b/recipes/bioconductor-fis/post-link.sh index 28bd468b3f77c..da643cb8bc422 100644 --- a/recipes/bioconductor-fis/post-link.sh +++ b/recipes/bioconductor-fis/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FIs_1.6.0.tar.gz" +FN="FIs_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/FIs_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/FIs_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.6.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/FIs_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/FIs_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.8.0_src_all.tar.gz" ) -MD5="91486b16361f9aae8baeecd8fae06fc1" +MD5="2724d2e77ed0d6583fc3cdb03586df39" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-fishalyser/meta.yaml b/recipes/bioconductor-fishalyser/meta.yaml index 43bb9a45ce9ae..5706d907f07a1 100644 --- a/recipes/bioconductor-fishalyser/meta.yaml +++ b/recipes/bioconductor-fishalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "FISHalyseR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0b0d162336ebc9475814321331c573b3f89629c6877a7e02c6882f7fbdba051f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7d9538726a00d4a4659ca6bd01e7a74d977169355b796b7b21ae5143a9064ae4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-ebimage + - 'bioconductor-ebimage >=4.22.1,<4.24.0' - r-abind - r-base run: - - bioconductor-ebimage + - 'bioconductor-ebimage >=4.22.1,<4.24.0' - r-abind - r-base test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.' - extra: identifiers: - biotools:fishalyser diff --git a/recipes/bioconductor-fithic/meta.yaml b/recipes/bioconductor-fithic/meta.yaml index 9dc1600075b80..8c235eefe57a0 100644 --- a/recipes/bioconductor-fithic/meta.yaml +++ b/recipes/bioconductor-fithic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "FitHiC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,16 +8,15 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d6b0d32fe50a4b564a74ff8348c6ad3cbdd4fe2c093f8deda9a180786f86d48b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cd573c41219a8ed0d49be732f4e4ed90dc92c9864fe940d7dc35c46506c2841b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-data.table @@ -28,6 +27,10 @@ requirements: - r-data.table - r-fdrtool - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.' - extra: identifiers: - biotools:fithic diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml index 400fb7d1d87d0..2b996f7691338 100644 --- a/recipes/bioconductor-flagme/meta.yaml +++ b/recipes/bioconductor-flagme/meta.yaml @@ -1,50 +1,48 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "flagme" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7e05cd321bedca9a0c8526703a4f08758d690af887ce69744d4f5621b6812b97 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c60206b52cbe07a4442c39bf7a2ffe3d5f1cfec1cd1c24975460f2f8af429a7f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-camera - - bioconductor-gcspikelite - - bioconductor-xcms + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-gcspikelite >=1.18.0,<1.20.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-gplots - r-mass - r-sparsem run: - - bioconductor-camera - - bioconductor-gcspikelite - - bioconductor-xcms + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-gcspikelite >=1.18.0,<1.20.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-gplots - r-mass - r-sparsem - + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data' - extra: identifiers: - biotools:flagme diff --git a/recipes/bioconductor-flipflop/meta.yaml b/recipes/bioconductor-flipflop/meta.yaml index fb6cabd20b4c4..7e0acb4c786d9 100644 --- a/recipes/bioconductor-flipflop/meta.yaml +++ b/recipes/bioconductor-flipflop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "flipflop" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1abeb14cff8f7046bb58b9b7d3ac27ce0a8f9288aeb2c921a3b710f7a4739bbb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ddc865bf10511537392a46a5c50735007deb20b55f0e647dce502b8364592084 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-matrix run: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-matrix + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. It takes an alignment file in SAM format as input. It can also discover transcripts from several samples simultaneously, increasing statistical power.' - extra: identifiers: - biotools:flipflop diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index 31e55b1d90200..b386b634a2b93 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.10.1" %} {% set name = "flowAI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,16 +8,17 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a3c4b4152fadd0aa6fd812d4dbb888700aee141dc7b5a26fe81cb408c58abdfe + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7cfd063a85442eac9ebfc5a1aa5b8b8ee7687a36c42e59f519f884d5dec54e1d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-flowcore + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-changepoint - r-ggplot2 @@ -25,9 +26,10 @@ requirements: - r-plyr - r-rcolorbrewer - r-reshape2 + - r-rmarkdown - r-scales run: - - bioconductor-flowcore + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-changepoint - r-ggplot2 @@ -35,6 +37,7 @@ requirements: - r-plyr - r-rcolorbrewer - r-reshape2 + - r-rmarkdown - r-scales test: commands: @@ -43,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.' - extra: identifiers: - biotools:flowai diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml index 3ddeb5a899972..85a8415836f4e 100644 --- a/recipes/bioconductor-flowbeads/meta.yaml +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -1,48 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "flowBeads" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 250cf0d32568a4f2767580015ca2c7d0843d1288ab6f01e5472ed5d52a754c1a - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 347e01ce4a32b3c1e91583912e9b5ec1e3dc4eaab7f4d7e9d360f6ff3e8cbef2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-flowcore + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-knitr - r-rrcov - r-xtable run: - - bioconductor-biobase - - bioconductor-flowcore + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-knitr - r-rrcov - r-xtable - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.' - extra: identifiers: - biotools:flowbeads diff --git a/recipes/bioconductor-flowcl/meta.yaml b/recipes/bioconductor-flowcl/meta.yaml index 861b47ede21a2..f2053dc36aabc 100644 --- a/recipes/bioconductor-flowcl/meta.yaml +++ b/recipes/bioconductor-flowcl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "flowCL" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2946890c0db5cef68a27a654082b0ee2dadb3e2998a5471a795594237d470f62 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0b650e3bbca75e53a42f5933aa8f0cf9720ae1747d62479c11422cc8ba0f2a5e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-sparql run: - - bioconductor-graph - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-sparql test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Semantic labelling of flow cytometric cell populations.' - extra: identifiers: - biotools:flowcl diff --git a/recipes/bioconductor-flowclean/meta.yaml b/recipes/bioconductor-flowclean/meta.yaml index a5b29cef25e4c..cd94777c540c8 100644 --- a/recipes/bioconductor-flowclean/meta.yaml +++ b/recipes/bioconductor-flowclean/meta.yaml @@ -1,46 +1,41 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "flowClean" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 64787000903720d2b26c7b3f6151c149cdafb30681c6dc5bb60e4bbe8b68bfa2 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 17dec0e2f27dd8e54c4d7e8777404824b89ff330fe5e4c2d2de395fc83cab488 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-flowcore + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-bit - r-changepoint - r-sfsmisc run: - - bioconductor-flowcore + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-bit - r-changepoint - r-sfsmisc - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/flowClean.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A quality control tool for flow cytometry data based on compositional data analysis.' - extra: identifiers: - biotools:flowclean diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index c74b81ddc7d56..7f59ce7fae3f6 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.2" %} {% set name = "flowCore" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,37 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 46903d63fd36a8b0a7ab04ba5328811405613e94c78448b0d33f9ea52b99bc6a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1430325fa5da6c57735b7b7a085868fe269d28dca7a7980ce20d21babdfa3403 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.14' - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - - r-bh # not included in original DESCRIPTION + - 'r-bh >=1.65.0.1' - r-corpcor - r-matrixstats - r-rcpp - r-rrcov - run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.14' - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - - r-bh # not included in original DESCRIPTION + - 'r-bh >=1.65.0.1' - r-corpcor - r-matrixstats - r-rcpp - r-rrcov + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -46,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides S4 data structures and basic functions to deal with flow cytometry data.' - extra: identifiers: - biotools:flowcore diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index 2877aa1ab61ca..35669c7cb48c6 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "flowDensity" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f362235594a58651dc75e5f1c212c05a3861447b5b4abf1de5b61e4c6340c1b5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0519b8fa0530cdc533f8443697c47afbda2854325a9b0bbba18c6e13feadfd0a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ +# The geos dependency gets around an incompatible dependency somewhere requirements: host: - - bioconductor-flowcore - - 'bioconductor-flowworkspace >=3.21.5' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' - r-base - r-car - - r-geomap - r-gplots - - r-nloptr # not in DESCRIPTION - r-rfoc - r-rgeos - r-sp + - geos 3.6.2 run: - - bioconductor-flowcore - - 'bioconductor-flowworkspace >=3.21.5' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' - r-base - r-car - - r-geomap - r-gplots - - r-nloptr # not in DESCRIPTION - r-rfoc - r-rgeos - r-sp + - geos 3.6.2 test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.' - extra: identifiers: - biotools:flowdensity diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 6d5add8d56316..2bc030de362b9 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowFP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0ea942db120bf59f09c43cc407c5c3845d6628da12bb16571dff5ed52f48fc4e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 13eb62a9485c55e63c4fa957c86046872957cbcc8e01224f26c9165ebe2a5533 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.6' - - bioconductor-flowcore - - bioconductor-flowviz + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' - r-base run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.6' - - bioconductor-flowcore - - bioconductor-flowviz + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.' - extra: identifiers: - biotools:flowfp diff --git a/recipes/bioconductor-flowmap/meta.yaml b/recipes/bioconductor-flowmap/meta.yaml index 9fe59bd670250..7f860ad0d1a86 100644 --- a/recipes/bioconductor-flowmap/meta.yaml +++ b/recipes/bioconductor-flowmap/meta.yaml @@ -1,55 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "flowMap" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bcc27a0fcfc028857c7cdd715288e92954e578562048ae74bba0fc9fb9fa0d53 - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0b7c51d7d4c2570f0d54ad6b761bae25b6a7ab75d8807d53d10ef0b8aabd813a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - r-abind >=1.4.0 - - r-ade4 >=1.5-2 + - 'r-abind >=1.4.0' + - 'r-ade4 >=1.5-2' - r-base - - r-doparallel >=1.0.3 - - r-matrix >=1.1-4 - - r-reshape2 >=1.2.2 - - r-scales >=0.2.3 + - 'r-doparallel >=1.0.3' + - 'r-matrix >=1.1-4' + - 'r-reshape2 >=1.2.2' + - 'r-scales >=0.2.3' run: - - r-abind >=1.4.0 - - r-ade4 >=1.5-2 + - 'r-abind >=1.4.0' + - 'r-ade4 >=1.5-2' - r-base - - r-doparallel >=1.0.3 - - r-matrix >=1.1-4 - - r-reshape2 >=1.2.2 - - r-scales >=0.2.3 - + - 'r-doparallel >=1.0.3' + - 'r-matrix >=1.1-4' + - 'r-reshape2 >=1.2.2' + - 'r-scales >=0.2.3' test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/flowMap.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' - summary: 'flowMap quantifies the similarity of cell populations across multiple flow cytometry samples - using a nonparametric multivariate statistical test. The method is able to map cell populations of - different size, shape, and proportion across multiple flow cytometry samples. The algorithm can be - incorporated in any flow cytometry work flow that requires accurate quantification of similarity - between cell populations.' - + summary: 'flowMap quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The method is able to map cell populations of different size, shape, and proportion across multiple flow cytometry samples. The algorithm can be incorporate in any flow cytometry work flow that requires accurat quantification of similarity between cell populations.' extra: identifiers: - biotools:flowmap diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index 163f1ed1834c6..a577f7b177d5f 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "flowMatch" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c33a4fec14fc5069a6da5756991b3531623edcf6f08413c74e5b9019780a0774 + sha256: 85065fbe032498519f789fe5dc82422de595e720ff99c01124875d772f96ced7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-flowcore + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - 'r-rcpp >=0.11.0' run: - - bioconductor-biobase - - bioconductor-flowcore + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - 'r-rcpp >=0.11.0' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Matching cell populations and building meta-clusters and templates from a collection of FC samples.' - extra: identifiers: - biotools:flowmatch diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml index 9d0cc04603427..81c17bbd5261a 100644 --- a/recipes/bioconductor-flowpeaks/meta.yaml +++ b/recipes/bioconductor-flowpeaks/meta.yaml @@ -1,40 +1,39 @@ -{% set version = "1.20.0" %} +{% set version = "1.26.0" %} {% set name = "flowPeaks" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 968ecda70b1a7187214ef0c503bf728172c92351030227572706ac2c4e7d2dd0 - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8db483f53772b770a424b7d570a6b13aa468b70170463f1b9aae7e3c96628e81 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base + - openblas run: - r-base - + - openblas test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/flowPeaks.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-1.0 - summary: 'A fast and automatic clustering to classify the cells into subpopulations based on - finding the peaks from the overall density function generated by K-means.' - + summary: 'A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.' extra: identifiers: - biotools:flowpeaks diff --git a/recipes/bioconductor-flowploidy/meta.yaml b/recipes/bioconductor-flowploidy/meta.yaml index 663acd92a0f7f..edb3ec45ca667 100644 --- a/recipes/bioconductor-flowploidy/meta.yaml +++ b/recipes/bioconductor-flowploidy/meta.yaml @@ -1,26 +1,24 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "flowPloidy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 05e77dbc9fdd5cea9ab80b855777cfcf74c27a5c91ccd849a6425c8a96611ec7 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8e821b2d364401915e86ba3cfdced6f65373b7e1edd8e5a6aa6e08f211e1dcb3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-flowcore + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-car - r-catools @@ -29,7 +27,7 @@ requirements: - r-rmarkdown - r-shiny run: - - bioconductor-flowcore + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-car - r-catools @@ -37,16 +35,13 @@ requirements: - r-minpack.lm - r-rmarkdown - r-shiny - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.' - extra: identifiers: - biotools:flowploidy diff --git a/recipes/bioconductor-flowq/build.sh b/recipes/bioconductor-flowq/build.sh index b58dbca4d229f..da43ce2168312 100644 --- a/recipes/bioconductor-flowq/build.sh +++ b/recipes/bioconductor-flowq/build.sh @@ -1,4 +1,4 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowq/meta.yaml b/recipes/bioconductor-flowq/meta.yaml index d3d0ffa49746f..4cea4ec5b447a 100644 --- a/recipes/bioconductor-flowq/meta.yaml +++ b/recipes/bioconductor-flowq/meta.yaml @@ -1,33 +1,30 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "flowQ" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: edafded694551f5bd706ca99e61b69a5859fba0d026d0bb688a71f72ac3bacef - + sha256: dd8c8464e300c02001e731140d3c86f828e4acdf2aab7dd58f8abbd3f52d0ac4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biocgenerics - - bioconductor-biodist - - bioconductor-flowcore - - bioconductor-flowviz - - bioconductor-geneplotter - - bioconductor-iranges - - bioconductor-parody + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biodist >=1.52.0,<1.54.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-parody >=1.38.0,<1.40.0' - r-base - r-lattice - r-latticeextra @@ -36,13 +33,13 @@ requirements: - r-rcolorbrewer - imagemagick run: - - bioconductor-biocgenerics - - bioconductor-biodist - - bioconductor-flowcore - - bioconductor-flowviz - - bioconductor-geneplotter - - bioconductor-iranges - - bioconductor-parody + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biodist >=1.52.0,<1.54.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-parody >=1.38.0,<1.40.0' - r-base - r-lattice - r-latticeextra @@ -50,16 +47,13 @@ requirements: - r-outliers - r-rcolorbrewer - imagemagick - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides quality control and quality assessment tools for flow cytometry data.' - extra: identifiers: - biotools:flowq diff --git a/recipes/bioconductor-flowrepositoryr/meta.yaml b/recipes/bioconductor-flowrepositoryr/meta.yaml index 680c2bf2cd1b5..549b4e6b3d21d 100644 --- a/recipes/bioconductor-flowrepositoryr/meta.yaml +++ b/recipes/bioconductor-flowrepositoryr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FlowRepositoryR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6a68fc49feaeb7a9ddbb30c737f920d57edb9f5c49a0f0fe8cc85f6c7fb5f855 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 085c20352fb3f41454cc211d377dfce3dc0f898b46c00a794db6e187a3d543bf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides an interface to search and download data and annotations from FlowRepository (flowrepository.org). It uses the FlowRepository programming interface to communicate with a FlowRepository server.' - extra: identifiers: - biotools:flowrepositoryr diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index 0c757f6b61176..4c7a1e5e8175e 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FlowSOM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 32ce4f207c90c44261b91e1d7875bc9af0410a00171097f5e39f9b519ff5ff4d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 93f5ca235048ae643078ac61b56bc5cbe84628806847f40188178b094f2e4efe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-consensusclusterplus - - bioconductor-flowcore - - bioconductor-flowutils + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowutils >=1.44.0,<1.46.0' - r-base - r-igraph - r-tsne - r-xml run: - - bioconductor-biocgenerics - - bioconductor-consensusclusterplus - - bioconductor-flowcore - - bioconductor-flowutils + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowutils >=1.44.0,<1.46.0' - r-base - r-igraph - r-tsne - r-xml + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.' - extra: identifiers: - biotools:flowsom diff --git a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml index 33cf840775ddd..36a4db41c6c9d 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "FlowSorted.Blood.450k" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bb18474f38684aa94b90f2a2760360a2b556c81dde46af2495f1a46ddb314b27 + sha256: c7c9d339d7e17f0569d7ea8dfefc4936f2506308c52e9516b35a57db6588ac75 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-minfi >=1.21.2' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - 'bioconductor-minfi >=1.21.2' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type.' + + diff --git a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh index 8bf3415e78bc2..5894150841ea4 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.Blood.450k_1.16.0.tar.gz" +FN="FlowSorted.Blood.450k_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/FlowSorted.Blood.450k_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/FlowSorted.Blood.450k_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.18.0_src_all.tar.gz" ) -MD5="2aa3d6e5445cdcbcbe0079480afbcba5" +MD5="1d76f19de113f7b3fe1c12b0f7e63c39" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-flowutils/meta.yaml b/recipes/bioconductor-flowutils/meta.yaml index 8e50334ac2f72..8a849f5f815df 100644 --- a/recipes/bioconductor-flowutils/meta.yaml +++ b/recipes/bioconductor-flowutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "flowUtils" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 78c6bf00d9461a2687c3ca955f8c6fe7e3f091e4059db85582429cdbc1588a34 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a8ad6718efcdf2eebef99632f0815eb9c58f2afef169edacde4416e301f4eba2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-flowcore >=1.32.0' - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-corpcor - r-runit - r-xml run: - - bioconductor-biobase - - 'bioconductor-flowcore >=1.32.0' - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-corpcor - r-runit @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides utilities for flow cytometry data.' - extra: identifiers: - biotools:flowutils diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index 7e31db58ffecd..d2a05ed07f30a 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "flowViz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d447e334e6a856bd8fc920918c6e31c42643e6e4ad2c3d46586fa716ad0679b9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 82dae08a9eb73f4468e6303627764f1a6b616f8a17d166ae9b75ada1f1459bca build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-flowcore >=1.41.9' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-hexbin - r-idpmisc @@ -28,8 +29,8 @@ requirements: - r-mass - r-rcolorbrewer run: - - bioconductor-biobase - - 'bioconductor-flowcore >=1.41.9' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' - r-base - r-hexbin - r-idpmisc @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides visualization tools for flow cytometry data.' - extra: identifiers: - biotools:flowviz diff --git a/recipes/bioconductor-flowworkspace/meta.yaml b/recipes/bioconductor-flowworkspace/meta.yaml index 7f25a08651037..5429d35930cff 100644 --- a/recipes/bioconductor-flowworkspace/meta.yaml +++ b/recipes/bioconductor-flowworkspace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.26.2" %} +{% set version = "3.28.2" %} {% set name = "flowWorkspace" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,60 +8,68 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dfbb69608507bba6d29a9c1143343593b25f1b95523624ca2f7a2fade08343a5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 64f60df146a17b9ef0f4935a3db3fcabc31820aa4da61fc7408fb1c0d19a46a8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-flowcore >=1.39.9' - - bioconductor-flowviz - - bioconductor-graph - - 'bioconductor-ncdfflow >=2.19.5' - - bioconductor-rbgl - - bioconductor-rgraphviz - - bioconductor-cytolib # not specified - - bioconductor-rprotobuflib # not specified + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-cytolib >=1.2.0,<1.4.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' - r-base + - 'r-bh >=1.62.0-1' - r-data.table - r-dplyr - r-gridextra - r-lattice - r-latticeextra + - r-matrixstats - r-rcolorbrewer - r-rcpp - r-scales - r-stringr - r-xml run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-flowcore >=1.39.9' - - bioconductor-flowviz - - bioconductor-graph - - 'bioconductor-ncdfflow >=2.19.5' - - bioconductor-rbgl - - bioconductor-rgraphviz - - bioconductor-cytolib # not specified - - bioconductor-rprotobuflib # not specified + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-cytolib >=1.2.0,<1.4.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' - r-base + - 'r-bh >=1.62.0-1' - r-data.table - r-dplyr - r-gridextra - r-lattice - r-latticeextra + - r-matrixstats - r-rcolorbrewer - r-rcpp - r-scales - r-stringr - r-xml + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -69,7 +77,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.' - extra: identifiers: - biotools:flowworkspace diff --git a/recipes/bioconductor-focalcall/meta.yaml b/recipes/bioconductor-focalcall/meta.yaml index a1faf2fee5823..64a3a08bae4b7 100644 --- a/recipes/bioconductor-focalcall/meta.yaml +++ b/recipes/bioconductor-focalcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "focalCall" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d442447ee5c8e2416472360f1bcf0ac2a53bd2b8cf95db5b18cd67dd64048b1e + sha256: db49bbc1b715ca304f5dfa2429c1e736d410d9193735d2d91f79be220bcd96aa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cghcall + - 'bioconductor-cghcall >=2.42.0,<2.44.0' - r-base run: - - bioconductor-cghcall + - 'bioconductor-cghcall >=2.42.0,<2.44.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Detection of genomic focal aberrations in high-resolution DNA copy number data' - extra: identifiers: - biotools:focalcall diff --git a/recipes/bioconductor-fourcseq/conda_build_config.yaml b/recipes/bioconductor-fourcseq/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-fourcseq/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-fourcseq/meta.yaml b/recipes/bioconductor-fourcseq/meta.yaml index 71544f137b716..297d31995c898 100644 --- a/recipes/bioconductor-fourcseq/meta.yaml +++ b/recipes/bioconductor-fourcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "FourCSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 10936a5fd3b0b02d9cc7c4827a7fb6ee7e830bc12fc09b757dee3c541312d821 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 662cc98cd7609dfbd5a27abb608a0b9e860d3a255bb70657ce1bce8f5167802c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biostrings - - 'bioconductor-deseq2 >=1.9.11' - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-fda - r-ggplot2 @@ -34,15 +35,15 @@ requirements: - r-matrix - r-reshape2 run: - - bioconductor-biobase - - bioconductor-biostrings - - 'bioconductor-deseq2 >=1.9.11' - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-fda - r-ggplot2 @@ -57,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script (extdata/python/demultiplex.py) to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.' - extra: identifiers: - biotools:fourcseq diff --git a/recipes/bioconductor-frma/conda_build_config.yaml b/recipes/bioconductor-frma/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-frma/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-frma/meta.yaml b/recipes/bioconductor-frma/meta.yaml index 0f2654ef8b149..8266a972793cd 100644 --- a/recipes/bioconductor-frma/meta.yaml +++ b/recipes/bioconductor-frma/meta.yaml @@ -1,55 +1,49 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "frma" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 810e6a090b1e97b82a0830d5bdf1d988e4a81aab60ae7ab8bbc09059e8901c7d - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5ef83662a1d9afb45cd41edb14628b89f6d6daf14f33c4406ee22beb1c6231dd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-affy - - bioconductor-biobase >=2.6.0 - - bioconductor-biocgenerics - - bioconductor-oligo - - bioconductor-oligoclasses - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - r-mass run: - - bioconductor-affy - - bioconductor-biobase >=2.6.0 - - bioconductor-biocgenerics - - bioconductor-oligo - - bioconductor-oligoclasses - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - r-mass - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://www.bioconductor.org/packages/3.5/bioc/html/frma.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Preprocessing and analysis for single microarrays and microarray batches.' - extra: identifiers: - biotools:frma diff --git a/recipes/bioconductor-frmatools/conda_build_config.yaml b/recipes/bioconductor-frmatools/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-frmatools/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-frmatools/meta.yaml b/recipes/bioconductor-frmatools/meta.yaml index fd4296a0629e2..4a3a1adf39c31 100644 --- a/recipes/bioconductor-frmatools/meta.yaml +++ b/recipes/bioconductor-frmatools/meta.yaml @@ -1,47 +1,41 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "frmaTools" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f5c394e29524ee247c5fb4a7cc5cba5c17bf99a44f80513e96c12e99076ce58c - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 83a5daa041637f4d20320f9950e9ff063196ba18d477c7bd529e769b25c3bfac build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://www.bioconductor.org/packages/release/bioc/html/frmaTools.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Tools for advanced use of the frma microarray package.' - + summary: 'Tools for advanced use of the frma package.' extra: identifiers: - biotools:frmatools diff --git a/recipes/bioconductor-funchip/meta.yaml b/recipes/bioconductor-funchip/meta.yaml index 8089447cb984a..c6d062d583772 100644 --- a/recipes/bioconductor-funchip/meta.yaml +++ b/recipes/bioconductor-funchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "FunChIP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4ba53b8c8cff85329eb8046e17833e666422f15643a084dcc1e91ed2a2f4a23f + sha256: 70dd6f3e1087b69c47731a95805791f6bfba7cef2e786ab43efb0986fc284b16 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-rsamtools + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-doparallel - r-fda @@ -32,10 +30,10 @@ requirements: - r-rcpp - r-shiny run: - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-rsamtools + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-doparallel - r-fda @@ -43,7 +41,10 @@ requirements: - r-rcolorbrewer - r-rcpp - r-shiny - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.' - extra: identifiers: - biotools:funchip diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index 54de32b1a068a..b93ff17147b05 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "gaga" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fdcac2a7425d3e74774c2531251939664161e88b01b5bf3be4510463891bf3bb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 4e2b1eb0cbb1b5ea9310c67acb4d117563fafb49a6e691ac9cc7a4c770bdd66e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-ebarrays + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ebarrays >=2.44.0,<2.46.0' - r-base - r-coda - r-mgcv run: - - bioconductor-biobase - - bioconductor-ebarrays + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ebarrays >=2.44.0,<2.46.0' - r-base - r-coda - r-mgcv + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).' - extra: identifiers: - biotools:gaga diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index 8738f82bbb67c..a39f359a1fcc1 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "gage" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f3076fe52c663792d99075c7d787efc1ff185c8ded928ae735e3f88111ba24e4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c288e3e38d470edc6fe1e6c2dd7f65f101641256aed5c90d09eed2937cc76c48 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-keggrest + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-keggrest + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.' - extra: identifiers: - biotools:gage diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index f63d50d6815ea..3379e18da789f 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "gageData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: acbc5dc445845acc73579d71096180fc87401c57d445277db355c88055e385a3 + sha256: 324e57f4d685af00eb7892ecc418ce4e6cae3254e9d42d91639d57b28dc5ad1d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.' + + diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index 5e855f11da36a..957670c2d0e97 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="gageData_2.16.0.tar.gz" +FN="gageData_2.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/gageData_2.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/gageData_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/gageData_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.18.0_src_all.tar.gz" ) -MD5="e79551bd0b5a52f5befe0fae21e5eb35" +MD5="1a08b3bb2a8944fa982488f998659c65" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml index eec1ef703ee00..a83ba8454edec 100644 --- a/recipes/bioconductor-gaprediction/meta.yaml +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "GAprediction" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 21954a61055d6264f87fa17a94e04f3da68b0cbd060618d997ff6e37a7b61382 + sha256: 59d07415ce04e694aa7fdf9c870679f9d8a077efc306860d6c05ef68fe95922d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,8 +31,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' - summary: '[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data.' - + summary: "[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data." extra: identifiers: - biotools:gaprediction diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml index 6090c1913ad9b..b37a68867b7eb 100644 --- a/recipes/bioconductor-gcatest/meta.yaml +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "gcatest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d65e011a9e04b585c0a05d714e572242763b6e1f418a80b6afd14647a4eaec6a + sha256: 086839540cad6878c3bd874e3010f92f4f6b3d6348cb142c035f61f1f686f0ea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-lfa + - 'bioconductor-lfa >=1.10.0,<1.12.0' - r-base run: - - bioconductor-lfa + - 'bioconductor-lfa >=1.10.0,<1.12.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait. models.' - extra: identifiers: - biotools:gcatest diff --git a/recipes/bioconductor-gcrisprtools/meta.yaml b/recipes/bioconductor-gcrisprtools/meta.yaml index d06b9c63d4cb7..2a31cf0e06783 100644 --- a/recipes/bioconductor-gcrisprtools/meta.yaml +++ b/recipes/bioconductor-gcrisprtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "gCrisprTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0f183031c730558239e542a21b4b1fc8bbc615d51ee53ea7ab91e3a1a1d5eb74 + sha256: 0f7c1b5244d9b0aa5ef83d791ca2f6d2d1f03b26e54f42178df4a2460c9d7430 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-panther.db + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-panther.db >=1.0.4,<1.2.0' - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg run: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-panther.db + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-panther.db >=1.0.4,<1.2.0' - r-base - r-ggplot2 - r-rmarkdown @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting.' - extra: identifiers: - biotools:gcrisprtools diff --git a/recipes/bioconductor-gcrma/conda_build_config.yaml b/recipes/bioconductor-gcrma/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-gcrma/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-gcrma/meta.yaml b/recipes/bioconductor-gcrma/meta.yaml index 6b8d15d42efc2..7a84db87751a7 100644 --- a/recipes/bioconductor-gcrma/meta.yaml +++ b/recipes/bioconductor-gcrma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "gcrma" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 906793fd29916fdb9c46737dc846788c4c4813f9c101a11e8f3a55bc999456e8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e1310d019392319f8d4384653deab6122d1db1c0d8594b8e10c874e7ba2f8291 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.23.2' - - 'bioconductor-affyio >=1.13.3' - - bioconductor-biobase - - bioconductor-biocinstaller - - 'bioconductor-biostrings >=2.11.32' - - bioconductor-xvector + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-affy >=1.23.2' - - 'bioconductor-affyio >=1.13.3' - - bioconductor-biobase - - bioconductor-biocinstaller - - 'bioconductor-biostrings >=2.11.32' - - bioconductor-xvector + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Background adjustment using sequence information' - extra: identifiers: - biotools:gcrma diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index fcc21abc3bac2..0d30edceea609 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "gcspikelite" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f78f714cde33026c18f7e79873bb1899419a9a719dfb0ef566d07a1253ed1e5c + sha256: 2c0c76a8b6682fc9d49fcea473d01c64a7183c83fd08c02d567f10f74308db2c build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL summary: 'Spike-in data for GC/MS data and methods within flagme' + + diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index 457c0e7a60b9b..7799e2a3fabf4 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="gcspikelite_1.16.0.tar.gz" +FN="gcspikelite_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/gcspikelite_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/gcspikelite_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/gcspikelite_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.18.0_src_all.tar.gz" ) -MD5="b7806c37e0bfa69530c0387c7ab21a11" +MD5="27f20c8a5b7e2f9e68fef3bac7813225" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-gdsfmt/meta.yaml b/recipes/bioconductor-gdsfmt/meta.yaml index a79e7da991552..f23f4c9b51073 100644 --- a/recipes/bioconductor-gdsfmt/meta.yaml +++ b/recipes/bioconductor-gdsfmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "gdsfmt" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e183b9b979512e61dea13bfbb63279d4f018faff5effbca614dccf526591fe34 + sha256: ead9c16e1b3089eaca20a9509cd273e414fec10baeda10188954e37c849bef03 build: - number: 1 - skip: True # [osx] + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.' + + diff --git a/recipes/bioconductor-genbankr/meta.yaml b/recipes/bioconductor-genbankr/meta.yaml index 1ff76a6e6b483..2751ef4abd9df 100644 --- a/recipes/bioconductor-genbankr/meta.yaml +++ b/recipes/bioconductor-genbankr/meta.yaml @@ -1,58 +1,53 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "genbankr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ae680df37d00ed5e9d1ab64620d4544af6740006a0e771f83b8f94d198acc97b - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: bea0a9dbf0c5cccd4668fc1cbee3a45d447604d304a339e17a5bc97eb0458160 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.23.24' - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.23.24' - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Reads Genbank files.' - extra: identifiers: - biotools:genbankr diff --git a/recipes/bioconductor-geneattribution/meta.yaml b/recipes/bioconductor-geneattribution/meta.yaml index 7e2dc5f176e9f..1e943bea91893 100644 --- a/recipes/bioconductor-geneattribution/meta.yaml +++ b/recipes/bioconductor-geneattribution/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "geneAttribution" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9da7be2a6624ea2ecbdc6ba85c8dac4aab95d19ea54a6f1da08c39562bfee886 + sha256: 656c60c15d52ba20403c2811de777a4b5c2d37531bb0f29547ed6a962b85a317 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-org.hs.eg.db - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-org.hs.eg.db - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base test: commands: @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.' - extra: identifiers: - biotools:geneattribution diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index 81388c779a57f..07f0b3bffcf30 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GeneBreak" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8b26a47384d09f7e9d20792ab601972e97002f116a9c64728e6f30116466a784 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f22d56049037084772dca16d73619d9773a96fdef44f1eab716cd772281ec511 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cghbase - - bioconductor-cghcall - - bioconductor-genomicranges - - bioconductor-qdnaseq + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' - r-base run: - - bioconductor-cghbase - - bioconductor-cghcall - - bioconductor-genomicranges - - bioconductor-qdnaseq + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' - r-base test: commands: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Recurrent breakpoint gene detection on copy number aberration profiles.' - extra: identifiers: - biotools:genebreak diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index c3ff6fa355501..f40d24026656e 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "genefilter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e78d58043cf6f746b6a6b4e2cb298f9dadf75ae1d16fbc286d93c8671ee57a9c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 11ab26d789c6ee644545d5b371a263fc4dbacb839f850a64e7b25e2d80738092 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-s4vectors >=0.9.42' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-survival run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-s4vectors >=0.9.42' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-survival + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Some basic functions for filtering genes' - extra: identifiers: - biotools:genefilter diff --git a/recipes/bioconductor-genefu/meta.yaml b/recipes/bioconductor-genefu/meta.yaml index 1140e0b93e256..42fb3fa96a70d 100644 --- a/recipes/bioconductor-genefu/meta.yaml +++ b/recipes/bioconductor-genefu/meta.yaml @@ -1,52 +1,47 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "genefu" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8ef9c99fe003b6f14598d30cd917f61d89643428a09510f75bd446f08b20e95d - + sha256: c18c62048f4038d94a2fc15cbce8decfb3ac3791e64d72668344429f3aa7c7d2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-aims - - bioconductor-biomart - - bioconductor-limma - - bioconductor-survcomp + - 'bioconductor-aims >=1.12.0,<1.14.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-survcomp >=1.30.0,<1.32.0' - r-amap - r-base - r-ic10 - r-mclust run: - - bioconductor-aims - - bioconductor-biomart - - bioconductor-limma - - bioconductor-survcomp + - 'bioconductor-aims >=1.12.0,<1.14.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-survcomp >=1.30.0,<1.32.0' - r-amap - r-base - r-ic10 - r-mclust - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Description: This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.' - extra: identifiers: - biotools:genefu diff --git a/recipes/bioconductor-genega/meta.yaml b/recipes/bioconductor-genega/meta.yaml index 355f101d43e53..4a4eedfa2b2f1 100644 --- a/recipes/bioconductor-genega/meta.yaml +++ b/recipes/bioconductor-genega/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GeneGA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cd7d0773ec36580030594c1fcde9fda3cae058ead36655d5be44fe906ee7509c + sha256: 79f1b800ee88be9a9c6b337d4a965d54c7b2c84c942ea1e52f5e7331de84b48e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL version 2' summary: 'R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.' - extra: identifiers: - biotools:genega diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index 722e0eeea440d..ff1aa1ae1cec9 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "geneLenDataBase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 66613729237ea033d8e65fd8e49adafa0ca30e6fdd97bd2329480ac0fbdf7118 + sha256: 454972055f675858c2cc2ec2ccf85e5ac387ead26d04a62b09fbac398aadb51e build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-genomicfeatures >=1.3.15' - - bioconductor-rtracklayer + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base run: - - 'bioconductor-genomicfeatures >=1.3.15' - - bioconductor-rtracklayer + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser' + + diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index a0c468dafd534..8616f3b604c0b 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="geneLenDataBase_1.14.0.tar.gz" +FN="geneLenDataBase_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/geneLenDataBase_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/geneLenDataBase_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/geneLenDataBase_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.16.0_src_all.tar.gz" ) -MD5="f1466f1d89f074c7a084f08ca3df7781" +MD5="aa23db3bc55f6d20e42e66a47a99f065" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-genemeta/meta.yaml b/recipes/bioconductor-genemeta/meta.yaml index 9fab500c9ff7c..bdf8e20884154 100644 --- a/recipes/bioconductor-genemeta/meta.yaml +++ b/recipes/bioconductor-genemeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "GeneMeta" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 42a7578c553b8b268c4a4a49385dca2f2f51fa94353ae48e0f1afae4b9f9c8b1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a7f42a9e65043449c0c877bb133bff9ff23bf932e750480af135bc5c9f64ee02 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-genefilter + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-genefilter + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of meta-analysis tools for analysing high throughput experimental data' - extra: identifiers: - biotools:genemeta diff --git a/recipes/bioconductor-geneoverlap/meta.yaml b/recipes/bioconductor-geneoverlap/meta.yaml index 412a373db28f9..d75a3c55a161b 100644 --- a/recipes/bioconductor-geneoverlap/meta.yaml +++ b/recipes/bioconductor-geneoverlap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GeneOverlap" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6840ea40cb79d3a567020ed1aee37ac65d8f48403b0a3c060087a81ba6675b0b + sha256: 3f753a59517641e56586e0c19d6657ecdc07b446cb5fa9a21e361c2a83c6b092 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Test two sets of gene lists and visualize the results.' - extra: identifiers: - biotools:geneoverlap diff --git a/recipes/bioconductor-geneplast/meta.yaml b/recipes/bioconductor-geneplast/meta.yaml index 3bb7d8a6d51cd..804e6c7c6633b 100644 --- a/recipes/bioconductor-geneplast/meta.yaml +++ b/recipes/bioconductor-geneplast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.2" %} {% set name = "geneplast" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3818d9538f412c09fc8d51117320fb96ddfb1efc7f65c25be5356c7b7372cc8a + sha256: cf9d190319d5ca34aa62075a92ba53c6b173b0903557741c91b6737d56fbdccf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,10 +20,12 @@ requirements: host: - r-ape - r-base + - r-igraph - r-snow run: - r-ape - r-base + - r-igraph - r-snow test: commands: @@ -32,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.' - extra: identifiers: - biotools:geneplast diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index 6b2b5b49c2251..ca8f864c45e34 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "geneplotter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aa728e2c1520d8ee3c4203a84d604106b0b9b1259536b175e671c7c0b23b6ffc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0f74be95c4a699b654e0db4b39992f8e183dab8a1dbdf90025f4abf83a12af14 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-lattice - r-rcolorbrewer run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-lattice - r-rcolorbrewer @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions for plotting genomic data' - extra: identifiers: - biotools:geneplotter diff --git a/recipes/bioconductor-generecommender/meta.yaml b/recipes/bioconductor-generecommender/meta.yaml index 0eae0da4b79f7..35698131bc27d 100644 --- a/recipes/bioconductor-generecommender/meta.yaml +++ b/recipes/bioconductor-generecommender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "geneRecommender" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c90fffeb45118492bca96670c801e9135cc3d964649d0aa9c8ad3a27e7178e99 + sha256: 61cce313de9cdd28769654e1e289c6d1975679246889bfc9fa6209120c097372 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.4.22' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=1.4.22' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.' - extra: identifiers: - biotools:generecommender diff --git a/recipes/bioconductor-generegionscan/meta.yaml b/recipes/bioconductor-generegionscan/meta.yaml index 42826df0f38dc..ddbfea66ea8a8 100644 --- a/recipes/bioconductor-generegionscan/meta.yaml +++ b/recipes/bioconductor-generegionscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GeneRegionScan" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f756aa9a35a2e4b7d8cecf451a8b08d4dd219b44d91892b99950672a6d989d79 + sha256: faaf1a6202015008281ba459467a914897fd7766485e1a329bf192314cbec9a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affxparser - - 'bioconductor-biobase >=2.5.5' - - bioconductor-biostrings - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-rcolorbrewer run: - - bioconductor-affxparser - - 'bioconductor-biobase >=2.5.5' - - bioconductor-biostrings - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-rcolorbrewer test: @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.' - extra: identifiers: - biotools:generegionscan diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml index c5c9230b4636e..0a25d52005350 100644 --- a/recipes/bioconductor-generxcluster/meta.yaml +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "geneRxCluster" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f7497e687420ac412036ed4ec5064e0df497c1a76298832e6981e3141cb41464 + sha256: 574b94248242e36998d7c5aaa9e6cb33cd361dbf8074ed0ae94d977d0f099f05 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base run: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.' - extra: identifiers: - biotools:generxcluster diff --git a/recipes/bioconductor-geneselector/meta.yaml b/recipes/bioconductor-geneselector/meta.yaml index 9693473c57e1e..1b340eefe96c5 100644 --- a/recipes/bioconductor-geneselector/meta.yaml +++ b/recipes/bioconductor-geneselector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "GeneSelector" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3a292ef0236ad9004a98636379ce85636d8a325a148158dfd3836bfeac168139 + sha256: 2ed67f869d7835022929e2ce13173833340f7b4a1930e8acdb9cb69350f7a124 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-multtest - - bioconductor-siggenes + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' - r-base - r-samr run: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-multtest - - bioconductor-siggenes + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' - r-base - r-samr - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The term ''GeneSelector'' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. ''Selected'' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.' - extra: identifiers: - biotools:geneselector diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml index 9c6bfe03fa4e9..bd899a425720a 100644 --- a/recipes/bioconductor-genetclassifier/meta.yaml +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "geNetClassifier" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 88384956517f1c6e638eabb5a576709493c7eff16344ecbe1217cfcd96cc1b93 + sha256: d620749f5f4e436bce373d0b1832e6ca8dc95708644549a8f8b6530078179dd3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-ebarrays - - bioconductor-minet + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ebarrays >=2.44.0,<2.46.0' + - 'bioconductor-minet >=3.38.0,<3.40.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-ebarrays - - bioconductor-minet + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ebarrays >=2.44.0,<2.46.0' + - 'bioconductor-minet >=3.38.0,<3.40.0' - r-base - r-e1071 test: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.' - extra: identifiers: - biotools:genetclassifier diff --git a/recipes/bioconductor-geneticsdesign/meta.yaml b/recipes/bioconductor-geneticsdesign/meta.yaml index 951e38f745fbf..6d65fa8ef6d79 100644 --- a/recipes/bioconductor-geneticsdesign/meta.yaml +++ b/recipes/bioconductor-geneticsdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "GeneticsDesign" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 16d14fc331ee2c55b67e278c4c59a72c7a1adf4728040bb5e837c9d0b7e79a9c + sha256: d49bf0c3bcb0840eca83f74b21d521467cfdfae96c7f0d665cb48e9d66a1dbc3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package contains functions useful for designing genetics studies, including power and sample-size calculations.' - extra: identifiers: - biotools:geneticsdesign diff --git a/recipes/bioconductor-genogam/meta.yaml b/recipes/bioconductor-genogam/meta.yaml index d58631b95c57d..d0893db772164 100644 --- a/recipes/bioconductor-genogam/meta.yaml +++ b/recipes/bioconductor-genogam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GenoGAM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,40 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 031ae9656882d0525ada94f7f6f48185d504e56a10c761e2b0ef6665e3556ab7 + sha256: dac8591de7ba5396e9c2461df9aeea1c4172a15b9d92509b28c9760e7cf89981 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocparallel >=1.5.17' - - 'bioconductor-biostrings >=2.39.14' - - 'bioconductor-deseq2 >=1.11.23' - - 'bioconductor-genomeinfodb >=1.7.6' - - 'bioconductor-genomicalignments >=1.7.17' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-rsamtools >=1.18.2' - - 'bioconductor-s4vectors >=0.9.34' - - 'bioconductor-summarizedexperiment >=1.1.19' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - 'r-data.table >=1.9.4' - 'r-futile.logger >=1.4.1' - 'r-mgcv >=1.8' - 'r-reshape2 >=1.4.1' run: - - 'bioconductor-biocparallel >=1.5.17' - - 'bioconductor-biostrings >=2.39.14' - - 'bioconductor-deseq2 >=1.11.23' - - 'bioconductor-genomeinfodb >=1.7.6' - - 'bioconductor-genomicalignments >=1.7.17' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-rsamtools >=1.18.2' - - 'bioconductor-s4vectors >=0.9.34' - - 'bioconductor-summarizedexperiment >=1.1.19' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - 'r-data.table >=1.9.4' - 'r-futile.logger >=1.4.1' @@ -56,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package ''mgcv''. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.' - extra: identifiers: - biotools:genogam diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index fb069d55d4b7d..e7c3b4b1a49d3 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "genomation" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8a850f3ff151f9bbd090a4f70659d05ce98c588c7cdd9cd40b31b8c01343adb5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 3747df788cc3535f593bcf11fa535b2cb30ccf062509bf1972f75880b36fb5ed build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - 'bioconductor-genomicranges >=1.23.26' - - bioconductor-impute - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.25.2' - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-seqpattern + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqpattern >=1.12.0,<1.14.0' - r-base - r-data.table - r-ggplot2 @@ -37,22 +36,22 @@ requirements: - r-matrixstats - r-plotrix - r-plyr - - 'r-rcpp >=0.12.11' + - 'r-rcpp >=0.12.14' - r-readr - r-reshape2 - r-runit run: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - 'bioconductor-genomicranges >=1.23.26' - - bioconductor-impute - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.25.2' - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-seqpattern + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqpattern >=1.12.0,<1.14.0' - r-base - r-data.table - r-ggplot2 @@ -60,10 +59,14 @@ requirements: - r-matrixstats - r-plotrix - r-plyr - - 'r-rcpp >=0.12.11' + - 'r-rcpp >=0.12.14' - r-readr - r-reshape2 - r-runit + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -71,7 +74,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.' - extra: identifiers: - biotools:genomation diff --git a/recipes/bioconductor-genomegraphs/meta.yaml b/recipes/bioconductor-genomegraphs/meta.yaml index 500b1b9a6b415..8c64faecc630c 100644 --- a/recipes/bioconductor-genomegraphs/meta.yaml +++ b/recipes/bioconductor-genomegraphs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "GenomeGraphs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 95c45054085145774b404e8d7333a8d18744a09a5c6dcfd560ecf1b7162be796 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8d5ed29b87f30da2d4d03fc31606500e3734f020e647d986fb40234a0cc5b73b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart + - 'bioconductor-biomart >=2.36.1,<2.38.0' - r-base run: - - bioconductor-biomart + - 'bioconductor-biomart >=2.36.1,<2.38.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.' - extra: identifiers: - biotools:genomegraphs diff --git a/recipes/bioconductor-genomeinfodb/meta.yaml b/recipes/bioconductor-genomeinfodb/meta.yaml index 531c3359dee46..397ebb2c160d8 100644 --- a/recipes/bioconductor-genomeinfodb/meta.yaml +++ b/recipes/bioconductor-genomeinfodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GenomeInfoDb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d7db65fe2a494c3a1a0a087a2776eb69cca914024476b920db8f30356b0415ca + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4d3cfacef3abf26241cb180b3a52ba053b45a85a794858613cb8d6e615c4167a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-genomeinfodbdata - - 'bioconductor-iranges >=1.99.26' - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodbdata >=1.1.0,<1.3.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-rcurl run: - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-genomeinfodbdata - - 'bioconductor-iranges >=1.99.26' - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodbdata >=1.1.0,<1.3.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-rcurl test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.' - extra: identifiers: - biotools:genomeinfodb diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index e4dabaa049555..88b7f5bf80d78 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,17 +1,18 @@ -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} {% set name = "GenomeInfoDbData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d7bb73db4a76960e65c5f6d8ccdcb9480a48cea529a30ea2399f8e4c9887e876 + sha256: 6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -25,6 +26,8 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.' + + diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index 597a96bf604cc..1c0228a1c3abe 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="GenomeInfoDbData_1.0.0.tar.gz" +FN="GenomeInfoDbData_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.0.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz" + "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.1.0_src_all.tar.gz" ) -MD5="3926f72117c49fbee36ab8e9c0b34885" +MD5="e7fe0694dc065ebe8a7474d9b7afca63" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-genomeintervals/meta.yaml b/recipes/bioconductor-genomeintervals/meta.yaml index 6b086a05d64cc..9f96fdf864682 100644 --- a/recipes/bioconductor-genomeintervals/meta.yaml +++ b/recipes/bioconductor-genomeintervals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "genomeIntervals" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 39899dff3d7532df236b7d45c1cbcdd3e1bc914ee4b169d7d0858888bcab5486 + sha256: d4d500f022255abd214723f690d278ce00b3c4582b694d4452f61c350259420f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.15.2' - - 'bioconductor-genomeinfodb >=1.5.8' - - 'bioconductor-genomicranges >=1.21.16' - - 'bioconductor-iranges >=2.3.14' - - 'bioconductor-s4vectors >=0.7.10' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-intervals >=0.14.0' run: - - 'bioconductor-biocgenerics >=0.15.2' - - 'bioconductor-genomeinfodb >=1.5.8' - - 'bioconductor-genomicranges >=1.21.16' - - 'bioconductor-iranges >=2.3.14' - - 'bioconductor-s4vectors >=0.7.10' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-intervals >=0.14.0' test: @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: ' This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package ''girafe''.' - extra: identifiers: - biotools:genomeintervals diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index fa9d0089a6752..da770863630f3 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "GenomicAlignments" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,38 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 697c17e3a8d4f5480280df6c0b2803c34dcb705a9604ebbde0c76a43b833770c + sha256: 5c31ea7deaf17c3ea3a66fe41dfce754b5495f65a28be7860042ae392d13f102 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.37.1' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-rsamtools >=1.21.4' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.5.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.37.1' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-rsamtools >=1.21.4' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.5.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -48,7 +49,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.' - extra: identifiers: - biotools:genomicalignments diff --git a/recipes/bioconductor-genomicdatacommons/meta.yaml b/recipes/bioconductor-genomicdatacommons/meta.yaml index fa1a7a84313cd..8e1c5df614f8c 100644 --- a/recipes/bioconductor-genomicdatacommons/meta.yaml +++ b/recipes/bioconductor-genomicdatacommons/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.3" %} {% set name = "GenomicDataCommons" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,41 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4d72679d98321d82a0830d4f3dac2219c2373bf9b703322d1a7dc51bf3bfbf59 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2b4259874fc3507fb81712e750c5aba8311abf913a78125ba39defee883aae7b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - - r-data.table + - r-dplyr - r-httr - r-jsonlite - r-lazyeval - r-magrittr + - r-rappdirs - r-readr - r-xml2 run: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - - r-data.table + - r-dplyr - r-httr - r-jsonlite - r-lazyeval - r-magrittr + - r-rappdirs - r-readr - r-xml2 test: @@ -45,3 +52,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Programmatically access the NIH / NCI Genomic Data Commons RESTful service.' + + diff --git a/recipes/bioconductor-genomicfeatures/meta.yaml b/recipes/bioconductor-genomicfeatures/meta.yaml index 71fd4544d3eea..fd2ebffc05029 100644 --- a/recipes/bioconductor-genomicfeatures/meta.yaml +++ b/recipes/bioconductor-genomicfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.3" %} +{% set version = "1.32.3" %} {% set name = "GenomicFeatures" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,47 +8,46 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7f587b3d263761b97251eb9d523aefe37a11aad917b5d0ae08dc2e4e21b21b04 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 081592aee639cbc730fc10e309d41012b97193a0ee5100f0d3dc0f186391f91a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.33.15' - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-biomart >=2.17.1' - - 'bioconductor-biostrings >=2.23.3' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-rtracklayer >=1.29.24' - - 'bioconductor-s4vectors >=0.9.47' - - bioconductor-xvector + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-dbi - r-rcurl - - r-rmysql - 'r-rsqlite >=2.0' run: - - 'bioconductor-annotationdbi >=1.33.15' - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-biomart >=2.17.1' - - 'bioconductor-biostrings >=2.23.3' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-rtracklayer >=1.29.24' - - 'bioconductor-s4vectors >=0.9.47' - - bioconductor-xvector + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-dbi - r-rcurl - - r-rmysql - 'r-rsqlite >=2.0' test: commands: @@ -57,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.' - extra: identifiers: - biotools:genomicfeatures diff --git a/recipes/bioconductor-genomicfiles/meta.yaml b/recipes/bioconductor-genomicfiles/meta.yaml index 5d724a3e2001e..06890911958dc 100644 --- a/recipes/bioconductor-genomicfiles/meta.yaml +++ b/recipes/bioconductor-genomicfiles/meta.yaml @@ -1,62 +1,55 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GenomicFiles" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3669d0da57f3d4eac35a7736c968d6668c5be5d3825938d90c8e795974ae1c64 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b8ebf3927dafb3d9144042a357981aeb9841efbc53acf912f532bff859c11a2e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - 'bioconductor-biocgenerics >=0.11.2' - - 'bioconductor-biocparallel >=1.1.0' - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=1.7.7' - - 'bioconductor-genomicranges >=1.29.6' - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.17.29' - - 'bioconductor-rtracklayer >=1.25.3' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base run: - - 'bioconductor-biocgenerics >=0.11.2' - - 'bioconductor-biocparallel >=1.1.0' - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=1.7.7' - - 'bioconductor-genomicranges >=1.29.6' - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.17.29' - - 'bioconductor-rtracklayer >=1.25.3' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package provides infrastructure for parallel computations distributed ''by file'' - or ''by range''. User defined MAPPER and REDUCER functions provide added flexibility for data - combination and manipulation.' - + summary: 'This package provides infrastructure for parallel computations distributed ''by file'' or ''by range''. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.' extra: identifiers: - biotools:genomicfiles diff --git a/recipes/bioconductor-genomicinteractions/conda_build_config.yaml b/recipes/bioconductor-genomicinteractions/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-genomicinteractions/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-genomicinteractions/meta.yaml b/recipes/bioconductor-genomicinteractions/meta.yaml index 4a59a3d2e0b0b..c62c5de64acb3 100644 --- a/recipes/bioconductor-genomicinteractions/meta.yaml +++ b/recipes/bioconductor-genomicinteractions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "GenomicInteractions" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f6db0af7691271cb367067a91f34d0754b533bf4af1f923171e675a5bf881338 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 58e0ba4203e9d0481bf1a2c8570eccf5c1233bc7d0c724b4b96701d9f37dca32 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.6' - - bioconductor-gviz - - bioconductor-interactionset - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.13.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-interactionset >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-dplyr @@ -35,16 +36,16 @@ requirements: - r-igraph - r-stringr run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.6' - - bioconductor-gviz - - bioconductor-interactionset - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.13.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-interactionset >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-dplyr @@ -59,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics.' - extra: identifiers: - biotools:genomicinteractions diff --git a/recipes/bioconductor-genomicranges/meta.yaml b/recipes/bioconductor-genomicranges/meta.yaml index e6371cc1277f7..3a8088ebe24ed 100644 --- a/recipes/bioconductor-genomicranges/meta.yaml +++ b/recipes/bioconductor-genomicranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.3" %} +{% set version = "1.32.7" %} {% set name = "GenomicRanges" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,37 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c122cfdf18733682c1b23bff6c21bb06c64384d4963bd7c8fc96a49813fb9a1d + sha256: 3dfb5943567056c4e4908b85113b9fea3b36c3bd5b9961044ab3e6a5b42205d2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-biocgenerics >=0.21.2' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-s4vectors >=0.9.47' - - bioconductor-xvector + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-biocgenerics >=0.21.2' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-iranges >=2.11.16' - - 'bioconductor-s4vectors >=0.9.47' - - bioconductor-xvector + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure.' - + summary: 'The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.' extra: identifiers: - biotools:genomicranges diff --git a/recipes/bioconductor-genomicscores/conda_build_config.yaml b/recipes/bioconductor-genomicscores/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-genomicscores/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-genomicscores/meta.yaml b/recipes/bioconductor-genomicscores/meta.yaml index f82460fa21f9c..0d7251ab91405 100644 --- a/recipes/bioconductor-genomicscores/meta.yaml +++ b/recipes/bioconductor-genomicscores/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.1" %} {% set name = "GenomicScores" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4aeefe1d96dfd0f9e32b374952a782994626c1dedc3498f2c1cdb162d991c92e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: db91e995ca16bc45bb36987eed0e2eb921c4190d272061fbbf454d5c61836575 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationhub - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.3.23' - - 'bioconductor-s4vectors >=0.7.21' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-xml run: - - bioconductor-annotationhub - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.3.23' - - 'bioconductor-s4vectors >=0.7.21' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-genomictuples/meta.yaml b/recipes/bioconductor-genomictuples/meta.yaml index 68820592d03f4..b58fdef4e38ad 100644 --- a/recipes/bioconductor-genomictuples/meta.yaml +++ b/recipes/bioconductor-genomictuples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "GenomicTuples" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3e604fbaa5e940fc841191e0f5c9e59f3548d7a39b7eccf6e9a56e0244a2c224 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 95f5e2e9be0502a57e524894089027f5061bbb2a408fc78288ddf71d7faab5f0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-biocgenerics >=0.17.0' - - 'bioconductor-genomeinfodb >=1.7.2' - - 'bioconductor-genomicranges >=1.23.15' - - 'bioconductor-iranges >=2.5.26' - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biocgenerics >=0.17.0' - - 'bioconductor-genomeinfodb >=1.7.2' - - 'bioconductor-genomicranges >=1.23.15' - - 'bioconductor-iranges >=2.5.26' - - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.' - extra: identifiers: - biotools:genomictuples diff --git a/recipes/bioconductor-genominator/meta.yaml b/recipes/bioconductor-genominator/meta.yaml index e361c32f40b28..cc94c665012fd 100644 --- a/recipes/bioconductor-genominator/meta.yaml +++ b/recipes/bioconductor-genominator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "Genominator" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0ac624d72dc6b2e8f478f3d9e1b0882c6001d19bfb2e0e5646aef4e77c3705be + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b1e8f89947dee843d4194acdf4e614277ef415aebfe350a5a2a71e25e70130b2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-genomegraphs - - 'bioconductor-iranges >=2.5.27' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - - 'r-dbi >=0.2_5' + - 'r-dbi >=0.2-5' - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-genomegraphs - - 'bioconductor-iranges >=2.5.27' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - - 'r-dbi >=0.2_5' + - 'r-dbi >=0.2-5' - r-rsqlite test: commands: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for storing, accessing, analyzing and visualizing genomic data.' - extra: identifiers: - biotools:genominator diff --git a/recipes/bioconductor-genoset/meta.yaml b/recipes/bioconductor-genoset/meta.yaml index 8ed00bb63655f..7b8afb9c06159 100644 --- a/recipes/bioconductor-genoset/meta.yaml +++ b/recipes/bioconductor-genoset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "genoset" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e0e79c4cec94a7b9a44ea23c150e9c29fcdfe634d669b92aa67d0c3b327a86b3 + sha256: 6313ba101617a192ffc7066b3fccf4b564760f918838c5b53cb53e3faf3d33b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-biocgenerics >=0.11.3' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicranges >=1.17.19' - - 'bioconductor-iranges >=2.5.12' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.1.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - 'bioconductor-biocgenerics >=0.11.3' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicranges >=1.17.19' - - 'bioconductor-iranges >=2.5.12' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.1.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'GenoSet provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).' - extra: identifiers: - biotools:genoset diff --git a/recipes/bioconductor-genrank/meta.yaml b/recipes/bioconductor-genrank/meta.yaml index ff8c707c3a734..08fefa82c49eb 100644 --- a/recipes/bioconductor-genrank/meta.yaml +++ b/recipes/bioconductor-genrank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GenRank" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9faf025ae5802305165115f117a110b2d77ac0ad4cc8254437a45d3bf110331c + sha256: 9a61a6085c797dc11682740c9b98583709058facdd0048a2a97c4347e80252f0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-survcomp + - 'bioconductor-survcomp >=1.30.0,<1.32.0' - r-base - r-matrixstats - r-reshape2 run: - - bioconductor-survcomp + - 'bioconductor-survcomp >=1.30.0,<1.32.0' - r-base - r-matrixstats - r-reshape2 @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Methods for ranking genes based on convergent evidence obtained from multiple independent evidence layers. This package adapts three methods that are popular for meta-analysis.' - extra: identifiers: - biotools:genrank diff --git a/recipes/bioconductor-genvisr/meta.yaml b/recipes/bioconductor-genvisr/meta.yaml index 3f0142beb6678..bdf4932acea4c 100644 --- a/recipes/bioconductor-genvisr/meta.yaml +++ b/recipes/bioconductor-genvisr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.1" %} {% set name = "GenVisR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2617e027c272db14bb5189bd57330b4283f3ce8a452f8c285d17bb1e3e2e4c0e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 575d7f8a0c316661b6ff290c36a37006e62c20f1393675e85f93b86a1327b7b4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.25.4' - - 'bioconductor-iranges >=2.7.5' - - bioconductor-rsamtools + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base + - r-data.table - r-dbi - r-ffield - 'r-ggplot2 >=2.1.0' - - r-gridextra + - 'r-gridextra >=2.0.0' - r-gtable - r-gtools - 'r-plyr >=1.8.3' @@ -37,19 +42,23 @@ requirements: - r-scales - r-viridis run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.25.4' - - 'bioconductor-iranges >=2.7.5' - - bioconductor-rsamtools + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base + - r-data.table - r-dbi - r-ffield - 'r-ggplot2 >=2.1.0' - - r-gridextra + - 'r-gridextra >=2.0.0' - r-gtable - r-gtools - 'r-plyr >=1.8.3' @@ -63,7 +72,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.' - extra: identifiers: - biotools:genvisr diff --git a/recipes/bioconductor-geometadb/meta.yaml b/recipes/bioconductor-geometadb/meta.yaml index ae6cea42b9ecb..71c7503258e56 100644 --- a/recipes/bioconductor-geometadb/meta.yaml +++ b/recipes/bioconductor-geometadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "GEOmetadb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0a34f652c2d1426c9299a882d9fab0f2e521b94d00904e61544d4e8c2ab77100 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6aa42745ede4b84d337454db584ff0c8881edc288d9efe55b6f23d372be03656 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-geoquery + - 'bioconductor-geoquery >=2.48.0,<2.50.0' - r-base - r-rsqlite run: - - bioconductor-geoquery + - 'bioconductor-geoquery >=2.48.0,<2.50.0' - r-base - r-rsqlite test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .' - extra: identifiers: - biotools:geometadb diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index 610c15bb119e2..e067c3fd6cb43 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.3" %} +{% set version = "2.48.0" %} {% set name = "GEOquery" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 96575bd699c63cb61eb8bc03c6262b5ad068bc832be048dd5e1620546b7606d6 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8a1edf0e93f9da2561210bb709807cb8d848c1f68603b7cccc6c2c21161fb622 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dplyr - r-httr - r-magrittr - - r-rcurl - r-readr - r-tidyr - - r-xml - r-xml2 run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dplyr - r-httr - r-magrittr - - r-rcurl - r-readr - r-tidyr - - r-xml - r-xml2 test: commands: @@ -45,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.' - extra: identifiers: - biotools:geoquery diff --git a/recipes/bioconductor-geosubmission/conda_build_config.yaml b/recipes/bioconductor-geosubmission/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-geosubmission/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml index 62bd68501d1e5..eca6a270fbc16 100644 --- a/recipes/bioconductor-geosubmission/meta.yaml +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GEOsubmission" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e8a640fe21bbf931bf652d4aae532b46872dc4b01e140b1dbb9fc933e9a9896a + sha256: 14e7be69f386b0f7b97d0b36fe275cd13379363a1324e48d28e9ef2242509170 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-affy - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).' - extra: identifiers: - biotools:geosubmission diff --git a/recipes/bioconductor-gewist/meta.yaml b/recipes/bioconductor-gewist/meta.yaml index 7b9b48ac848b0..33795f86de50a 100644 --- a/recipes/bioconductor-gewist/meta.yaml +++ b/recipes/bioconductor-gewist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "GEWIST" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d372c1d9acad459e36d6767de158013726f01bce4739f82ffc47964f740ad551 + sha256: 20f0beb921758bdcfa4b1accbb9d7cca053082ff2622e46568377937e7d3a58e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This ''GEWIST'' package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions.' - extra: identifiers: - biotools:gewist diff --git a/recipes/bioconductor-ggbase/meta.yaml b/recipes/bioconductor-ggbase/meta.yaml index 0ffbb00786dca..0b6e9b1988f3c 100644 --- a/recipes/bioconductor-ggbase/meta.yaml +++ b/recipes/bioconductor-ggbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.40.0" %} +{% set version = "3.42.0" %} {% set name = "GGBase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,38 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ea6b6cda20978d7efabb23575c540e94486ad5307d1d46f0453696beddaa5b45 + sha256: 7cb06de6feb0dcbda0dc2a2f9f03a54344777ac7c981359edaae7c359006bfdf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-snpstats - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-snpstats >=1.30.0,<1.32.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-digest - r-matrix run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-snpstats - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-snpstats >=1.30.0,<1.32.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-digest - r-matrix @@ -52,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: infrastructure - extra: identifiers: - biotools:ggbase diff --git a/recipes/bioconductor-ggbio/conda_build_config.yaml b/recipes/bioconductor-ggbio/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-ggbio/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index fb9abb369a425..0718a0b3635fd 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.5" %} {% set name = "ggbio" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,35 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a9e609c61525d6366933f55fd4cfcfcd06f0e572947c91ba3ac839083c761daf + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 4d901925bc46118cc1135883b18ee1bf97617c48a7d2411d218e33ef00d942a7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-annotationfilter - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - 'bioconductor-biovizbase >=1.23.3' - - bioconductor-bsgenome - - 'bioconductor-ensembldb >=1.99.13' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicalignments >=1.1.16' - - 'bioconductor-genomicfeatures >=1.29.11' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - bioconductor-organismdbi - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-rtracklayer >=1.25.16' - - 'bioconductor-s4vectors >=0.13.13' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.11.4' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -43,27 +44,28 @@ requirements: - r-gtable - r-hmisc - r-reshape2 + - r-rlang - r-scales run: - - bioconductor-annotationdbi - - bioconductor-annotationfilter - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - 'bioconductor-biovizbase >=1.23.3' - - bioconductor-bsgenome - - 'bioconductor-ensembldb >=1.99.13' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicalignments >=1.1.16' - - 'bioconductor-genomicfeatures >=1.29.11' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.16' - - bioconductor-organismdbi - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-rtracklayer >=1.25.16' - - 'bioconductor-s4vectors >=0.13.13' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.11.4' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -71,6 +73,7 @@ requirements: - r-gtable - r-hmisc - r-reshape2 + - r-rlang - r-scales test: commands: @@ -79,7 +82,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.' - extra: identifiers: - biotools:ggbio diff --git a/recipes/bioconductor-ggcyto/meta.yaml b/recipes/bioconductor-ggcyto/meta.yaml index affdfe87807f3..60eeaf4190f1f 100644 --- a/recipes/bioconductor-ggcyto/meta.yaml +++ b/recipes/bioconductor-ggcyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.2" %} {% set name = "ggcyto" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,38 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3ee149bfc6183a372a853078fc025edc376fe2e066621e3237e59f7f7327e3ea + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 481774bcc1f99f4dfb3feb4083829c1ce5acebd2fd5670e316f17b4625a0edd9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-flowcore >=1.41.5' - - 'bioconductor-flowworkspace >=3.17.24' - - 'bioconductor-ncdfflow >=2.17.1' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' + - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' - r-base - r-data.table - - 'r-ggplot2 >=2.0.0' + - 'r-ggplot2 >=2.2.1.9000' - r-gridextra - r-plyr - r-rcolorbrewer + - r-rlang - r-scales run: - - 'bioconductor-flowcore >=1.41.5' - - 'bioconductor-flowworkspace >=3.17.24' - - 'bioconductor-ncdfflow >=2.17.1' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' + - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' - r-base - r-data.table - - 'r-ggplot2 >=2.0.0' + - 'r-ggplot2 >=2.2.1.9000' - r-gridextra - r-plyr - r-rcolorbrewer + - r-rlang - r-scales test: commands: @@ -44,8 +47,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'With the dedicated fority method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.' - + summary: 'With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.' extra: identifiers: - biotools:ggcyto diff --git a/recipes/bioconductor-ggtools/meta.yaml b/recipes/bioconductor-ggtools/meta.yaml index cb404c8cf3ae3..81989860e2995 100644 --- a/recipes/bioconductor-ggtools/meta.yaml +++ b/recipes/bioconductor-ggtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "5.14.0" %} +{% set version = "5.16.0" %} {% set name = "GGtools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f1dce53285c7d8fa8d41c9013ff2a73c1c9c5bdee0aa118767effc61c6673440 + sha256: e86780b6d4583bf5f31f2b6063120f4c75b461b2807063293b161397a0d25a3c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.6' - - 'bioconductor-ggbase >=3.19.7' - - bioconductor-gviz - - bioconductor-homo.sapiens - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-snpstats - - bioconductor-variantannotation + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbase >=3.42.0,<3.44.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-snpstats >=1.30.0,<1.32.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-biglm - r-bit @@ -44,21 +44,21 @@ requirements: - r-reshape2 - r-rocr run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.6' - - 'bioconductor-ggbase >=3.19.7' - - bioconductor-gviz - - bioconductor-homo.sapiens - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-snpstats - - bioconductor-variantannotation + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbase >=3.42.0,<3.44.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-snpstats >=1.30.0,<1.32.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-biglm - r-bit @@ -76,7 +76,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'software and data for analyses in genetics of gene expression and/or DNA methylation' - extra: identifiers: - biotools:ggtools diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 0f53cfa5d7188..3bd216026ac5d 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.7" %} {% set name = "ggtree" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,43 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1c1dcfec5359867d6e6ed0ad3dab701a8b68cf65d976aebc2a3e680523472064 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 901344970ebb84e50b43d41c167fbdf1045ed92e52378fa60a4a11fc4ab0c685 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-treeio + - 'bioconductor-treeio >=1.4.3,<1.6.0' - r-ape - r-base - - 'r-ggplot2 >=2.2.0' + - r-dplyr + - 'r-ggplot2 >=2.2.1.9000' - r-magrittr - - r-rvcheck + - r-purrr + - r-rlang + - 'r-rvcheck >=0.1.0' - r-scales + - r-tibble - r-tidyr + - 'r-tidytree >=0.1.5' run: - - bioconductor-treeio + - 'bioconductor-treeio >=1.4.3,<1.6.0' - r-ape - r-base - - 'r-ggplot2 >=2.2.0' + - r-dplyr + - 'r-ggplot2 >=2.2.1.9000' - r-magrittr - - r-rvcheck + - r-purrr + - r-rlang + - 'r-rvcheck >=0.1.0' - r-scales + - r-tibble - r-tidyr + - 'r-tidytree >=0.1.5' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: '''ggtree'' extends the ''ggplot2'' plotting system which implemented the grammar of graphics. ''ggtree'' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.' - extra: identifiers: - biotools:ggtree diff --git a/recipes/bioconductor-girafe/meta.yaml b/recipes/bioconductor-girafe/meta.yaml index 2085b8a0f38db..16b845f951eb4 100644 --- a/recipes/bioconductor-girafe/meta.yaml +++ b/recipes/bioconductor-girafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "girafe" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,39 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bb1c67a233cd464664e21e4e664f44048053d83e9e72bf818dbcc3d08e950e4d + sha256: 18090a1f196e19f69fdb4ec9404a8e54bc5c8613ed6bb5d5047413ebe330d4b2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-biostrings - - 'bioconductor-genomeintervals >=1.25.1' - - 'bioconductor-iranges >=2.3.23' - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.7.21' - - 'bioconductor-shortread >=1.3.21' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - 'r-intervals >=0.13.1' run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-biostrings - - 'bioconductor-genomeintervals >=1.25.1' - - 'bioconductor-iranges >=2.3.23' - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.7.21' - - 'bioconductor-shortread >=1.3.21' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - 'r-intervals >=0.13.1' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package ''girafe'' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.' - extra: identifiers: - biotools:girafe diff --git a/recipes/bioconductor-glimma/meta.yaml b/recipes/bioconductor-glimma/meta.yaml index e28e1d4550b6b..316a8488e7643 100644 --- a/recipes/bioconductor-glimma/meta.yaml +++ b/recipes/bioconductor-glimma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.2" %} {% set name = "Glimma" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f82f75d4b3ce484624b52e011c4b2ba0fc942915624eb523553b5ee23203c4a4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ba88b72acce876fd192c164b67cff27c2e1e03e8b141d6aa32dad3bc8151d14d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-edger - - bioconductor-s4vectors + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-jsonlite run: - - bioconductor-biobase - - bioconductor-edger - - bioconductor-s4vectors + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-jsonlite test: @@ -35,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | file LICENSE' summary: 'This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.' - extra: identifiers: - biotools:glimma diff --git a/recipes/bioconductor-globalancova/meta.yaml b/recipes/bioconductor-globalancova/meta.yaml index bedfcbbec8973..952cf0df0eeef 100644 --- a/recipes/bioconductor-globalancova/meta.yaml +++ b/recipes/bioconductor-globalancova/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.46.0" %} +{% set version = "3.48.0" %} {% set name = "GlobalAncova" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3c6d28cae6faf08b586db96d3ca6a2fd853f08d8b1137fc1ee1c12f1f3cc7099 + sha256: 7ee0cec93d5a5bd6ebe1a23a531ad6b447ac852586586d5f82fa0adcec018eee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-globaltest + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-globaltest >=5.34.1,<5.36.0' - r-base - r-corpcor run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-globaltest + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-globaltest >=5.34.1,<5.36.0' - r-base - r-corpcor + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -38,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.' - extra: identifiers: - biotools:globalancova diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml index 081e75ee8df41..498bb6e4f23df 100644 --- a/recipes/bioconductor-globalseq/meta.yaml +++ b/recipes/bioconductor-globalseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "globalSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8ee431e9320695e382f73dff8a459cf1a25b018bcfd56e7eeefc950c50d05ca5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d1e0e01cbeef11aaf9ca37ea633e764d7d1d26eb84743e8d67629d190d90bc4b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size.' - extra: identifiers: - biotools:globalseq diff --git a/recipes/bioconductor-globaltest/meta.yaml b/recipes/bioconductor-globaltest/meta.yaml index bcf9692a2354d..f17524b12c940 100644 --- a/recipes/bioconductor-globaltest/meta.yaml +++ b/recipes/bioconductor-globaltest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "5.32.0" %} +{% set version = "5.34.1" %} {% set name = "globaltest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b942923511c12f6db6e7e1ae27875dad4ab3ac044bffe2297b11ab61cdf469ba + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: aac458fc1d896b2c317cd23b038e8646eccb92d6073f65702cfdf42991317ad0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-survival run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-survival test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.' - extra: identifiers: - biotools:globaltest diff --git a/recipes/bioconductor-gmrp/meta.yaml b/recipes/bioconductor-gmrp/meta.yaml index 9ede2d1305a1c..237db368a834b 100644 --- a/recipes/bioconductor-gmrp/meta.yaml +++ b/recipes/bioconductor-gmrp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.5.0" %} +{% set version = "1.8.1" %} {% set name = "GMRP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b7aeb2045b56d988058c868f5aeb949c2d6c012e07366b6e7381210fdafd9288 + sha256: 6cdeebee72275c1200c303f14482a1f1f44175df29960985374d0ff30ad822a0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-diagram - r-plotrix run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-diagram - r-plotrix @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.' - extra: identifiers: - biotools:gmrp diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index b3c48c9792372..4de79974e8eff 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "GO.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 656055d3e43f9b31c44ea895e831e0917092d5c899fad0e1c6070faa82ada109 + sha256: 120d1485f17a118b4d3145f40e5b26dbe6b70cc6093bec382defaa94b9c7223a build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire Gene Ontology assembled using data from GO' + + diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index 6ae59038da5cb..8b3e6288ac725 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="GO.db_3.5.0.tar.gz" +FN="GO.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/GO.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/GO.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/GO.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.6.0_src_all.tar.gz" ) -MD5="58b59a93504a33b29652d25b00f212ea" +MD5="5ae3316dcda13d46c8cdfd18cf29dfcc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-gofunction/meta.yaml b/recipes/bioconductor-gofunction/meta.yaml index 219525b824f92..7dc23884b2a26 100644 --- a/recipes/bioconductor-gofunction/meta.yaml +++ b/recipes/bioconductor-gofunction/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GOFunction" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7d4bf3360d7d3a525db0974ee846dbdb6e7aa95507591c8b5b52673a497b6a7a + sha256: 578464fffe8f97854ac3d3f6a61a4d77ed2591c75e791ab6a9eaf546634e3b2f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.10.2' - - 'bioconductor-biobase >=2.8.0' - - 'bioconductor-go.db >=2.4.1' - - 'bioconductor-graph >=1.26.0' - - 'bioconductor-rgraphviz >=1.26.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-dbi - 'r-sparsem >=0.85' run: - - 'bioconductor-annotationdbi >=1.10.2' - - 'bioconductor-biobase >=2.8.0' - - 'bioconductor-go.db >=2.4.1' - - 'bioconductor-graph >=1.26.0' - - 'bioconductor-rgraphviz >=1.26.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-dbi - 'r-sparsem >=0.85' @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The GO-function package provides a tool to address the redundancy that result from the GO structure or multiple annotation genes and derive biologically relevant functions from the statistically significant functions based on some intuitive assumption and statistical testing.' - extra: identifiers: - biotools:gofunction diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml index 6e65651c43447..d0e7e6dc04e18 100644 --- a/recipes/bioconductor-golubesets/meta.yaml +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "golubEsets" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e533ab15f3f28722dcc62a7105caa76fcc63617daa925c9a6d2dd11ad8a35e7f + sha256: b0fc7482331f9d890133cb367bd25442c75a7b9266e336d810d3b2e9121c677d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL summary: 'representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format' + + diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh index 6a112d488d76d..af62f26d5c339 100644 --- a/recipes/bioconductor-golubesets/post-link.sh +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="golubEsets_1.20.0.tar.gz" +FN="golubEsets_1.22.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/golubEsets_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/golubEsets_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.20.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/golubEsets_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/golubEsets_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.22.0_src_all.tar.gz" ) -MD5="318b22688927ad8baa67775e6b77b0c1" +MD5="fbc8881356c1f9aa83c081c32093dda0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index 1d919eddbe81b..0191380606cd5 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.2" %} {% set name = "GOSemSim" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e4438305b6c2531eae5a2e8ecaebb20506f8968f5e51702255cc0389a2d8d797 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3a606ece278c4658186f022488e7cedcebe5345166c753782f0b83f3c51d04fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base + - r-rcpp run: - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.' - extra: identifiers: - biotools:gosemsim diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index 6a603095d4eba..82bf30a0dde48 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "goseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6e4e344fe6048cc91576b4411ae8360221250ed5b3b8650444fa930d08a4d606 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 54f464d3cb096722138bd3771cb123f8eaf9c8f00265109077998aa12a5aab76 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - 'bioconductor-genelendatabase >=1.9.2' - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base - r-biasedurn - r-mgcv run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - 'bioconductor-genelendatabase >=1.9.2' - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base - r-biasedurn - r-mgcv @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data' - extra: identifiers: - biotools:goseq diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index a2472582608aa..aed5b6401a37e 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "GOstats" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 31b81be4d20570155df911a3b28d05816eac14e94850e0f049aebbd46973f811 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 00b769e3bee17a76d9962461594a8b82da55610032658cc414bca4567ef3b5c4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotate >=1.13.2' - - 'bioconductor-annotationdbi >=0.0.89' - - bioconductor-annotationforge - - 'bioconductor-biobase >=1.15.29' - - 'bioconductor-category >=2.43.2' - - 'bioconductor-go.db >=1.13.0' - - bioconductor-graph - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationforge >=1.22.2,<1.24.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base run: - - 'bioconductor-annotate >=1.13.2' - - 'bioconductor-annotationdbi >=0.0.89' - - bioconductor-annotationforge - - 'bioconductor-biobase >=1.15.29' - - 'bioconductor-category >=2.43.2' - - 'bioconductor-go.db >=1.13.0' - - bioconductor-graph - - bioconductor-rbgl - - bioconductor-rgraphviz + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationforge >=1.22.2,<1.24.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base test: commands: @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.' - extra: identifiers: - biotools:gostats diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index f4851d2000499..de7454473a17a 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GOTHiC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,37 +8,38 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4a4eceaa315ac4b327b6eba3c080bfdf35cb2bde96c7cccb0da9391f32b5c962 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: dfeeed7502bc4339e3da803968eb00a37e917945a283ec39935dedbcb20d36be build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.38' - - bioconductor-shortread + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-data.table - r-ggplot2 run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.38' - - bioconductor-shortread + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-data.table - r-ggplot2 @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.' - extra: identifiers: - biotools:gothic diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml index 1dd96cbd95023..2b9f807b4b2c2 100644 --- a/recipes/bioconductor-gotools/meta.yaml +++ b/recipes/bioconductor-gotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "goTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 59cc09b98200c2c0185453a9df3737bda396254b009ca31f57989f790d108a1f + sha256: c5d490d2c7f7e7eeef7565e40e005287b12e59aabeb83ae544053165e534c450 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Wraper functions for description/comparison of oligo ID list using Gene Ontology database' - extra: identifiers: - biotools:gotools diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml index be1bb6610e174..9fc6bedded97d 100644 --- a/recipes/bioconductor-gpls/meta.yaml +++ b/recipes/bioconductor-gpls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "gpls" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6f5442b8922a4b411f931e73b11429f4f996034804637fc61bef753ed061e36a + sha256: e1ddd66e585cc2d18d26127c068e31b2c906c5cfabe3a8e547cb0846be0ecaf4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.' - extra: identifiers: - biotools:gpls diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index 1f7179d118f27..355a795610134 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.2" %} {% set name = "graph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c12a519e9984ca2e134a8bef75aac63be59a33691e2206d025e10b88ae944a95 - patches: - - Makevars.patch + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ea81f17367f1e15616bfdd60d14d974567f0740f28bc22482ef982c1c65a551f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.13.11' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - 'bioconductor-biocgenerics >=0.13.11' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base test: commands: @@ -31,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package that implements some simple graph handling capabilities.' - extra: identifiers: - biotools:graph diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml index 3029da8053c82..3f7d5dca394a9 100644 --- a/recipes/bioconductor-graphat/meta.yaml +++ b/recipes/bioconductor-graphat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "GraphAT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d97e35562cd3e9f1c7c65cef91368dc68dfc3ab73fcdff239ae181495af82c43 + sha256: a2feaff6c04b3c3941b94dab2834c013fa7bc3390746c024fd08de9ab195cecf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-mcmcpack run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-mcmcpack test: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions and data used in Balasubramanian, et al. (2004)' - extra: identifiers: - biotools:graphat diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index 52f6f943e00c0..a5aa5cf05f400 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.3" %} {% set name = "graphite" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e1cfa2a960d06ac233250dad18f07a4df6f38654f94c184bc0f45a5f098cf4f1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a6a62e225b31c37082624f90e15d1da30323fba35e6bef5b8c7e4f0ce342f2a0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-graph + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-checkmate - r-httr - r-rappdirs run: - - bioconductor-annotationdbi - - bioconductor-graph + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-checkmate - r-httr @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.' - extra: identifiers: - biotools:graphite diff --git a/recipes/bioconductor-graphpac/meta.yaml b/recipes/bioconductor-graphpac/meta.yaml index fe1cac0d2c0e2..8ab3d16db68da 100644 --- a/recipes/bioconductor-graphpac/meta.yaml +++ b/recipes/bioconductor-graphpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "GraphPAC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: eda3df7b7cf3917ff242655cda24e6433095e09af83dfe0aae6a8146c231193c + sha256: fd75feff6524bfd48fa5cca73ecd317ccca661f28b6df510c06c5696cb028239 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-ipac + - 'bioconductor-ipac >=1.24.2,<1.26.0' - r-base - r-igraph - r-rmallow - r-tsp run: - - bioconductor-ipac + - 'bioconductor-ipac >=1.24.2,<1.26.0' - r-base - r-igraph - r-rmallow @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model.' - extra: identifiers: - biotools:graphpac diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml index 21bb17edfbbf0..6ed27aeda54a9 100644 --- a/recipes/bioconductor-grmetrics/meta.yaml +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "GRmetrics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6f80e19b7cbe10c698393e90e79bcf39647f22d04ee9b2c5bbf1c7adc2e22e86 + sha256: 778a0930864c40b88337d9188bf20e4c3bc20d519fc3d9e38ebf5369d79955f9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-drc - r-ggplot2 - r-plotly run: - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-drc - r-ggplot2 @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Functions for calculating and visualizing growth-rate inhibition (GR) metrics.' - extra: identifiers: - biotools:grmetrics diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml index 72bb006129fa8..a90fc3f946be0 100644 --- a/recipes/bioconductor-gsalightning/meta.yaml +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GSALightning" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5dd38e6dcef36728fc7fb7ea4c100b95d56ba97cf706f4b74f906a0755612dd9 + sha256: 9ff71cd1c042d01e0faffb7927c43d5a9072bc052a246ffd4bd5e31f070c5c75 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.' - extra: identifiers: - biotools:gsalightning diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml index 6791b6584a9d3..4967d25469ba8 100644 --- a/recipes/bioconductor-gsca/meta.yaml +++ b/recipes/bioconductor-gsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "GSCA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d13fe52313daf563f250c0f7f02f06a19ed7a6be70f28f686321b920f36e33e5 + sha256: b90399fd68600c9f6ec632316e74b55f12a6e97f91e5a264fa4292d923e84390 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-rhdf5 + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - r-base - r-ggplot2 - r-gplots @@ -27,7 +27,7 @@ requirements: - r-shiny - r-sp run: - - bioconductor-rhdf5 + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - r-base - r-ggplot2 - r-gplots @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.' - extra: identifiers: - biotools:gsca diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index d83520e7f367e..40283d7fc77c2 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "GSEABase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d8836f07130346dac66aebd141cba26951dc55691b527e6e3459655a98a1f34e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ead00709a662c67665f4c176df3b32789118ce3269cb730c4e69ccb8b5487b85 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotate >=1.45.3' - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.13.8' - - 'bioconductor-graph >=1.37.2' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.45.3' - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.13.8' - - 'bioconductor-graph >=1.37.2' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-xml test: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).' - extra: identifiers: - biotools:gseabase diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml index 8c14acf730db9..ebcea4bb2027e 100644 --- a/recipes/bioconductor-gsealm/meta.yaml +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "GSEAlm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bf7f96d77e3f519823d03145e450ac622f3c239a9af210c327233ec6d63ae2cf + sha256: aa23f37fcd8673044ba263c2daea9e4b775801be0c1d7800b196d9e749af762e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.' - extra: identifiers: - biotools:gsealm diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml index 5d3f01a93cb76..f4e0586c4e318 100644 --- a/recipes/bioconductor-gsreg/meta.yaml +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "GSReg" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,29 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c6034b862751f5fce5669f121dcddbd7e427b5bee3e7dd9a839a0437cd9ebfe5 + sha256: 3a3bcbe759a31640819d1d914d425aa1e76202a29713a32ebbffbd6ca42e96f6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-annotationdbi - - bioconductor-genomicfeatures - - bioconductor-homo.sapiens - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-genomicfeatures - - bioconductor-homo.sapiens - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).' - extra: identifiers: - biotools:gsreg diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml index ad31aef880993..2b3df63deaeb0 100644 --- a/recipes/bioconductor-gsri/meta.yaml +++ b/recipes/bioconductor-gsri/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "GSRI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5a12d448b6a939c9ba90772911f8f13fab12763c4ceff3008976e4631ca3518b + sha256: 783e8a8d24ebe663da7e0a062ef4d6f6d01d1d7ef500223ea1a9d554dafe618b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-genefilter - - bioconductor-gseabase - - 'bioconductor-les >=1.1.6' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-les >=1.30.0,<1.32.0' - r-base - r-fdrtool run: - - bioconductor-biobase - - bioconductor-genefilter - - bioconductor-gseabase - - 'bioconductor-les >=1.1.6' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-les >=1.30.0,<1.32.0' - r-base - r-fdrtool test: @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).' - extra: identifiers: - biotools:gsri diff --git a/recipes/bioconductor-gsva/meta.yaml b/recipes/bioconductor-gsva/meta.yaml index f0a4dab2c8d7e..dc3ae9129af4a 100644 --- a/recipes/bioconductor-gsva/meta.yaml +++ b/recipes/bioconductor-gsva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GSVA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 09f0ca21a1a0c5ac3b9c4d7ef71fe37a12d419e1782ab39d79b854ca0e0771ff + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 70bb8cab331f3257bf18ba3c3315fccdc7e711d2646e632636af9a19b445bd46 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-geneplotter - - 'bioconductor-gseabase >=1.17.4' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base - r-shiny - r-shinythemes run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-geneplotter - - 'bioconductor-gseabase >=1.17.4' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base - r-shiny - r-shinythemes + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.' - extra: identifiers: - biotools:gsva diff --git a/recipes/bioconductor-gtrellis/build.sh b/recipes/bioconductor-gtrellis/build.sh index b58dbca4d229f..da43ce2168312 100644 --- a/recipes/bioconductor-gtrellis/build.sh +++ b/recipes/bioconductor-gtrellis/build.sh @@ -1,4 +1,4 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml index 9789283c7796d..26a1abffb7bf4 100644 --- a/recipes/bioconductor-gtrellis/meta.yaml +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -1,43 +1,41 @@ -{% set version = "1.11.1" %} +{% set version = "1.12.1" %} {% set name = "gtrellis" %} -{% set bioc = "3.6" %} - +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: - url: 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - sha256: 1b913487cee2bbb0a151b41406e37d98c27b085b8f66622d6d1eb41bd5eea457 + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 46f271ed43225e5c264c4bcc4c52bc65f7f5ba40c8e0e121273f426ff770abbd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - r-base >=3.3.2 - - 'bioconductor-iranges' - - 'bioconductor-genomicranges' - - r-gridbase - - r-circlize >=0.4.1 - - r-getoptlong >=0.1.6 + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - r-base + - 'r-circlize >=0.3.3' + - r-getoptlong run: - - r-base >=3.3.2 - - 'bioconductor-iranges' - - 'bioconductor-genomicranges' - - r-gridbase - - r-circlize >=0.4.1 - - r-getoptlong >=0.1.6 + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - r-base + - 'r-circlize >=0.3.3' + - r-getoptlong test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL (>= 2) + license: 'MIT + file LICENSE' summary: 'Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.' - extra: identifiers: - biotools:gtrellis diff --git a/recipes/bioconductor-guideseq/conda_build_config.yaml b/recipes/bioconductor-guideseq/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-guideseq/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml index 058a66e8f7e94..d6f014722aed7 100644 --- a/recipes/bioconductor-guideseq/meta.yaml +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GUIDEseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,45 +10,45 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f8336a97486f5bcde8a743caeca617090a89961b2ee6f0dbd55c4583ebf852f7 + sha256: 02b1c2a033ee3baf3caf97fc9db1457d7ae883e855a793781d8df2e6d9e4ec2d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-chippeakanno - - bioconductor-crisprseek - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=1.7.3' - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.5.5' - - bioconductor-limma - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' + - 'bioconductor-crisprseek >=1.20.0,<1.22.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-hash - r-matrixstats run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-chippeakanno - - bioconductor-crisprseek - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=1.7.3' - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.5.5' - - bioconductor-limma - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' + - 'bioconductor-crisprseek >=1.20.0,<1.22.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-hash @@ -60,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.' - extra: identifiers: - biotools:guideseq diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index f96e766ce0607..075aa976b853d 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.3" %} +{% set version = "1.24.0" %} {% set name = "Gviz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,58 +8,59 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2a45bd2c3722b72ea6b5a749cb005d9e3f379d6d5bdfbdae3885cf7f65fe32bf + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a45f8ea3d11f7d66078866bcecb1914db91ac88a093108e420b9d009d58914ba build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.27.5' - - 'bioconductor-biobase >=2.15.3' - - 'bioconductor-biocgenerics >=0.11.3' - - 'bioconductor-biomart >=2.11.0' - - 'bioconductor-biostrings >=2.33.11' - - 'bioconductor-biovizbase >=1.13.8' - - 'bioconductor-bsgenome >=1.33.1' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicalignments >=1.1.16' - - 'bioconductor-genomicfeatures >=1.17.22' - - 'bioconductor-genomicranges >=1.17.20' - - 'bioconductor-iranges >=1.99.18' - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-rtracklayer >=1.25.13' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-xvector >=0.5.7' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-digest >=0.6.8' - r-lattice - - 'r-latticeextra >=0.6_28' + - 'r-latticeextra >=0.6-26' - 'r-matrixstats >=0.8.14' - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.27.5' - - 'bioconductor-biobase >=2.15.3' - - 'bioconductor-biocgenerics >=0.11.3' - - 'bioconductor-biomart >=2.11.0' - - 'bioconductor-biostrings >=2.33.11' - - 'bioconductor-biovizbase >=1.13.8' - - 'bioconductor-bsgenome >=1.33.1' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicalignments >=1.1.16' - - 'bioconductor-genomicfeatures >=1.17.22' - - 'bioconductor-genomicranges >=1.17.20' - - 'bioconductor-iranges >=1.99.18' - - 'bioconductor-rsamtools >=1.17.28' - - 'bioconductor-rtracklayer >=1.25.13' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-xvector >=0.5.7' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-digest >=0.6.8' - r-lattice - - 'r-latticeextra >=0.6_28' + - 'r-latticeextra >=0.6-26' - 'r-matrixstats >=0.8.14' - r-rcolorbrewer test: @@ -69,7 +70,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.' - extra: identifiers: - biotools:gviz diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml index 9deadd223ec5e..11dc930e04a21 100644 --- a/recipes/bioconductor-hapfabia/meta.yaml +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -1,45 +1,40 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hapFabia" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b01e0ce9645f2cb5891106f362ecc9e1be53d6461907cde1df4f613d6015cc56 - + sha256: cd048ee9d404032bfc7a7d926589e7973a064ee07500423581674dbbbb457606 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - 'bioconductor-fabia >=2.3.1' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-fabia >=2.26.0,<2.28.0' - r-base run: - - bioconductor-biobase - - 'bioconductor-fabia >=2.3.1' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-fabia >=2.26.0,<2.28.0' - r-base - + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.1)' summary: 'A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.' - extra: identifiers: - biotools:hapfabia diff --git a/recipes/bioconductor-harman/conda_build_config.yaml b/recipes/bioconductor-harman/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-harman/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml index cc1053e0d305a..5603d87020996 100644 --- a/recipes/bioconductor-harman/meta.yaml +++ b/recipes/bioconductor-harman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Harman" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d8bcc35b9aed9b05213f9e835ed6b544f563525f9a010b842cd3badd689f439f + sha256: dc1afe939d228f239690e1482caf807927dfccf7497fff4e5c44640a623023bc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - 'r-rcpp >=0.11.2' run: - r-base - 'r-rcpp >=0.11.2' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENCE' summary: 'Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.' - extra: identifiers: - biotools:harman diff --git a/recipes/bioconductor-harshlight/conda_build_config.yaml b/recipes/bioconductor-harshlight/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-harshlight/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml index ac0b9ecb1aa13..55aced634b1a6 100644 --- a/recipes/bioconductor-harshlight/meta.yaml +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "Harshlight" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c0a85d943b7ea1108db93fda3dfd708279a7abd3a77a003dd0039af55a229449 + sha256: c5286c8ed1071d19b5b2ee6275c3a18749a989809b76c592fa959b1aee7d1278 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy - - bioconductor-altcdfenvs - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-altcdfenvs >=2.42.0,<2.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-affy - - bioconductor-altcdfenvs - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-altcdfenvs >=2.42.0,<2.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.' - extra: identifiers: - biotools:harshlight diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index b0ad5adc83224..10719b3660979 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "HDF5Array" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 500275365ecf557798e9f40248097a93c7c55520a8e17de9361b2b1d88fa8d4d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c5effb43e2b657130ad2f98dea2864bed7c3fb816d4cb4c85c023d99eafb84e8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - 'bioconductor-delayedarray >=0.3.18' - - bioconductor-iranges - - bioconductor-rhdf5 - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biocgenerics - - 'bioconductor-delayedarray >=0.3.18' - - bioconductor-iranges - - bioconductor-rhdf5 - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'An array-like container for convenient access and manipulation of HDF5 datasets. Supports delayed operations and block processing.' - extra: identifiers: - biotools:hdf5array diff --git a/recipes/bioconductor-heatmaps/meta.yaml b/recipes/bioconductor-heatmaps/meta.yaml index 02f252cd1e65d..3c120a8bab863 100644 --- a/recipes/bioconductor-heatmaps/meta.yaml +++ b/recipes/bioconductor-heatmaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "heatmaps" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,33 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e817cbd91e775bcba69a48c94c1050ec8cc04309d2a6ed1ff14c31167aff6e4e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9cec782a3346ffe0ac7f7c2d53262735e2ddcc408cf27aa4da07b9fe88eccb01 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-ebimage - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-ebimage - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-kernsmooth - r-matrix @@ -47,3 +48,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.' + + diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index 1ade632a5c5fa..f3610e42c30fb 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "Heatplus" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d6d88fe64da2b3fb6300d393587f4984f8acf6b355c797b1a1493d8c9d0f3452 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d3af59cbfcff1f48b5f49eee84c33ea76cde2145d92caca50fe4fb568fceb54c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.' - extra: identifiers: - biotools:heatplus diff --git a/recipes/bioconductor-helloranges/meta.yaml b/recipes/bioconductor-helloranges/meta.yaml index 9f6cdb1e60614..cb0cefd686536 100644 --- a/recipes/bioconductor-helloranges/meta.yaml +++ b/recipes/bioconductor-helloranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "HelloRanges" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,43 +10,43 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c20f9d41bd94c1e8a7016841a26c7d112f110d77c66b42808cd1409a4e9e715d + sha256: e4fca3d307adf5e91c8f7b34ee7f1c4830136bb86c90e078f2bf302314bf5372 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - 'bioconductor-biostrings >=2.41.3' - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.29.6' - - 'bioconductor-iranges >=2.11.8' - - bioconductor-rsamtools - - 'bioconductor-rtracklayer >=1.33.8' - - 'bioconductor-s4vectors >=0.11.6' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.19.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-docopt run: - - bioconductor-biocgenerics - - 'bioconductor-biostrings >=2.41.3' - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.29.6' - - 'bioconductor-iranges >=2.11.8' - - bioconductor-rsamtools - - 'bioconductor-rtracklayer >=1.33.8' - - 'bioconductor-s4vectors >=0.11.6' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.19.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-docopt test: @@ -56,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.' - extra: identifiers: - biotools:helloranges diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml index 96d0ce099b3f8..0d4fff59aa706 100644 --- a/recipes/bioconductor-help/meta.yaml +++ b/recipes/bioconductor-help/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HELP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0c5a6ec4edc05ee0db003c435f7a6353f518ed130ffd0713794698e82ebf2608 + sha256: 44d9ed27cf2e684659b52a6a3889dca8476f014256853e730b31b6ff663104f4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.' - extra: identifiers: - biotools:help diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml index 1f8588e6f49dc..2a1b81196a9d1 100644 --- a/recipes/bioconductor-hem/meta.yaml +++ b/recipes/bioconductor-hem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "HEM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 87c676b2fa9bd2d3fdc7debcb56ffef4aaea79c60df5468d6ca7e26f4835e682 + sha256: c5acc5cbb29bdb1cd13e9be960d569f542941205ad177391db2b714e7124181c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package fits heterogeneous error models for analysis of microarray data' - extra: identifiers: - biotools:hem diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 8bf98f6934b07..8306bc4d6dc3b 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133a.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: 75eaffa2bd09a694958b816fd575bb4cbdd35d3bbe60139ff0808516c931149a build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U133 Set annotation data (chip hgu133a) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-hgu133a.db/post-link.sh b/recipes/bioconductor-hgu133a.db/post-link.sh index d61d8ae014118..eb12635cc0ae1 100644 --- a/recipes/bioconductor-hgu133a.db/post-link.sh +++ b/recipes/bioconductor-hgu133a.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="hgu133a.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.2.3_src_all.tar.gz" ) MD5="ce0397160fe78a92671e492a22542a79" diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml index 705306713941e..1b4b7ca97b219 100644 --- a/recipes/bioconductor-hgu133a2.db/meta.yaml +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133a2.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,18 +12,18 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: 687e3bcc499440778a7482599d1f0dad48ff8222737b0a22dcb32757921490eb build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -33,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U133A 2.0 Array annotation data (chip hgu133a2) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-hgu133a2.db/post-link.sh b/recipes/bioconductor-hgu133a2.db/post-link.sh index eca43ab44d4a2..d7e23461451ca 100644 --- a/recipes/bioconductor-hgu133a2.db/post-link.sh +++ b/recipes/bioconductor-hgu133a2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu133a2.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" ) MD5="15cad9bc3f5ef6fca5300638a9c8bb86" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index 6b62238916cdf..a0a04505b0a0d 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu133plus2.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-hgu133plus2.db/post-link.sh b/recipes/bioconductor-hgu133plus2.db/post-link.sh index 6cb8a91edf26a..d3494be33bab3 100644 --- a/recipes/bioconductor-hgu133plus2.db/post-link.sh +++ b/recipes/bioconductor-hgu133plus2.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="hgu133plus2.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.2.3_src_all.tar.gz" ) MD5="45a376b6092da75907b9e73bbd90e5bf" diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml index 616b2751e7dc7..d3a84a02442ef 100644 --- a/recipes/bioconductor-hgu95av2.db/meta.yaml +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu95av2.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,18 +12,18 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: c56a023573de68a82fba79952dd10774ea096a1eb3083b15ad3cb21bc2f35189 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -33,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-hgu95av2.db/post-link.sh b/recipes/bioconductor-hgu95av2.db/post-link.sh index d10c50fa90126..682fa8336e6e6 100644 --- a/recipes/bioconductor-hgu95av2.db/post-link.sh +++ b/recipes/bioconductor-hgu95av2.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="hgu95av2.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95av2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" ) MD5="a0ee1ba7f115a1504ca89619a0bc56dd" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-hiannotator/meta.yaml b/recipes/bioconductor-hiannotator/meta.yaml index 7997beea0b9bf..11c56c44a050a 100644 --- a/recipes/bioconductor-hiannotator/meta.yaml +++ b/recipes/bioconductor-hiannotator/meta.yaml @@ -1,28 +1,26 @@ -{% set version = "1.11.1" %} +{% set version = "1.14.0" %} {% set name = "hiAnnotator" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fd3f91cea9300b0debd0fdc70b0a25a41e9d4500c706354d8f4c951ea33a5656 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3ff1bf88402f050625733d2edc135247693f61419084d8b1db90e0567c8bf9a9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-rtracklayer + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-dplyr - r-foreach @@ -30,33 +28,22 @@ requirements: - r-iterators - r-scales run: - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-rtracklayer + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-dplyr - r-foreach - r-ggplot2 - r-iterators - r-scales - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/hiAnnotator.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'hiAnnotator contains set of functions which allow users to annotate a GRanges object - with custom set of annotations. The basic philosophy of this package is to take two GRanges - objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated - annotation per seqnames and rows from the query matching seqnames and rows from the subject - (i.e. genes or cpg islands). The package comes with three types of annotation functions which - calculates if a position from query is: within a feature, near a feature, or count features in - defined window sizes. Moreover, each function is equipped with parallel backend to utilize the - foreach package. In addition, the package is equipped with wrapper functions, which finds - appropriate columns needed to make a GRanges object from a common data frame.' - + summary: 'hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.' extra: identifiers: - biotools:hiannotator diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml index a81356b7e755c..54f4ed53f2318 100644 --- a/recipes/bioconductor-hibag/meta.yaml +++ b/recipes/bioconductor-hibag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "HIBAG" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b4f74bde8943961a88200c84b197e30a8d520eb8a6f88d42dd684e838d5b644e + sha256: 8dae626b80ac14b9b420b3e8c7099809113d8f4f0ac5bf074e65faee9dd036e9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.' - extra: identifiers: - biotools:hibag diff --git a/recipes/bioconductor-hiccompare/conda_build_config.yaml b/recipes/bioconductor-hiccompare/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-hiccompare/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-hiccompare/meta.yaml b/recipes/bioconductor-hiccompare/meta.yaml index 6a190359fb4f0..3626bdb8852a6 100644 --- a/recipes/bioconductor-hiccompare/meta.yaml +++ b/recipes/bioconductor-hiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HiCcompare" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,7 +8,9 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - sha256: 60e77bfb50f3f5732f41d3fe3044cb7ca8872e51e8682fc087f2df7c30a145e4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c244a2fc060a7c858a42456e9b964aa6a6faf6a10d87b40c0c9aaeae603758ca build: number: 0 rpaths: @@ -16,12 +18,12 @@ build: - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-genomicranges - - bioconductor-interactionset - - bioconductor-iranges - - bioconductor-qdnaseq - - bioconductor-s4vectors + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-interactionset >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-dplyr @@ -32,12 +34,12 @@ requirements: - r-mgcv - r-pheatmap run: - - bioconductor-biocparallel - - bioconductor-genomicranges - - bioconductor-interactionset - - bioconductor-iranges - - bioconductor-qdnaseq - - bioconductor-s4vectors + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-interactionset >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-dplyr @@ -52,16 +54,9 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - license_file: LICENSE - summary: 'HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states. HiCcompare differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, HiCcompare provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. HiCcompare also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.' - + license: 'MIT + file LICENSE' + summary: 'HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.' extra: identifiers: - biotools:HiCcompare - doi:10.1186/s12859-018-2288-x - authors: - - John Stansfield - - Mikhail Dozmorov - maintainers: - - John Stansfield diff --git a/recipes/bioconductor-hicrep/meta.yaml b/recipes/bioconductor-hicrep/meta.yaml index 34f05b9eba9bd..8772b43dfd03f 100644 --- a/recipes/bioconductor-hicrep/meta.yaml +++ b/recipes/bioconductor-hicrep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "hicrep" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a2ac992960f769c6845495ccbe175d76c8a51dd3d8e1e22147960df6ec47ea3b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9493bab6af88b05cbd02532a8a406f87c35613e471c5207cafb6f235cebd4fb5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,3 +28,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.0)' summary: 'Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance-dependence. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwise differences between Hi-C matrices under a wide range of settings, and can be used to determine optimal sequencing depth. Compared to existing approaches, it consistently shows higher accuracy in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages than existing approaches. This R package `hicrep` implements our approach.' + + diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index fa19b24195b86..fee62f2e700e8 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HilbertVis" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: af8c8b5cbfc89ec22bfd6c6b633721941d26b383c75560012c1f64764bdc34fa + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d54a7859f5addcfaedb252ba91be6b6f7d1a0c938a847adc36a230baaa71ff9f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,9 @@ requirements: run: - r-base - r-lattice + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Functions to visualize long vectors of integer data by means of Hilbert curves' - extra: identifiers: - biotools:hilbertvis diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml index 81f0387279cf3..9b92d4e98070f 100644 --- a/recipes/bioconductor-hitc/meta.yaml +++ b/recipes/bioconductor-hitc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HiTC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 77562f40fe7e692e70327ea77b72e132c7666ed5ec0005c5dfdf1a2f83ea0809 + sha256: 5f54f9737ad49251158f16d61cf34da61548dd5cf6401f3ce734149746287362 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-matrix - r-rcolorbrewer run: - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-matrix - r-rcolorbrewer @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The HiTC package was developed to explore high-throughput ''C'' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.' - extra: identifiers: - biotools:hitc diff --git a/recipes/bioconductor-hmmcopy/meta.yaml b/recipes/bioconductor-hmmcopy/meta.yaml index b801d76342d99..52775d556f2ef 100644 --- a/recipes/bioconductor-hmmcopy/meta.yaml +++ b/recipes/bioconductor-hmmcopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HMMcopy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2fc5b3a90012c55de4370acbb20be0292885c59931464dc43a2115a9a07e0e4a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 722eadf9a270ed3ad47a514f94dcca7101f777eb61c795014934c807b516a2f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - readline 6.2* - - 'bioconductor-geneplotter >=1.24.0' - - 'bioconductor-iranges >=1.4.16' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base run: - - readline 6.2* - - 'bioconductor-geneplotter >=1.24.0' - - 'bioconductor-iranges >=1.4.16' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.' - extra: identifiers: - biotools:hmmcopy diff --git a/recipes/bioconductor-hom.hs.inp.db/meta.yaml b/recipes/bioconductor-hom.hs.inp.db/meta.yaml index 23640c45b7fa5..4175f07801259 100644 --- a/recipes/bioconductor-hom.hs.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.hs.inp.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.2" %} {% set name = "hom.Hs.inp.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 8dfe718726c80dcd990ddedde2e6f3027056d4fe4ee15bc6597b2880186b3d3a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.29.20' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.29.20' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Homology information for Homo Sapiens from Inparanoid assembled using data from public repositories' + + diff --git a/recipes/bioconductor-hom.hs.inp.db/post-link.sh b/recipes/bioconductor-hom.hs.inp.db/post-link.sh index f73a066b8ddd0..eb334fce0dafa 100644 --- a/recipes/bioconductor-hom.hs.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.hs.inp.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="hom.Hs.inp.db_3.1.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Hs.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.hs.inp.db/bioconductor-hom.hs.inp.db_3.1.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.hs.inp.db/bioconductor-hom.hs.inp.db_3.1.2_src_all.tar.gz" ) MD5="b0708148e9c6656527e004fbaf80c05c" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-homo.sapiens/conda_build_config.yaml b/recipes/bioconductor-homo.sapiens/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-homo.sapiens/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index 112c7413c3e2c..c818fa177a26b 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Homo.sapiens" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.17.11' - - bioconductor-genomicfeatures - - bioconductor-go.db - - bioconductor-org.hs.eg.db - - 'bioconductor-organismdbi >=1.11.39' - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base run: - - 'bioconductor-annotationdbi >=1.17.11' - - bioconductor-genomicfeatures - - bioconductor-go.db - - bioconductor-org.hs.eg.db - - 'bioconductor-organismdbi >=1.11.39' - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-organismdbi >=1.22.0,<1.24.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - r-base - wget test: diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml index 9a8beacec7fc8..b450e789184d8 100644 --- a/recipes/bioconductor-hopach/meta.yaml +++ b/recipes/bioconductor-hopach/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "hopach" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dde929c9838c9857849b02ce25ace59150687f77bd0ad06e2eeadc35fe5a48ec + sha256: c4562460a3dd571329f58b082f42a603f8490689af2618aabc350fe3e5188f49 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-cluster run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-cluster - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).' - extra: identifiers: - biotools:hopach diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index 1920aab10c551..c5971981fab79 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.2" %} {% set name = "hpar" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 481a3759a327513d348ab6882e77f936a0abda2dae6519b630a8b7fe6a3abb68 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 088d47923e7b6c18a75b6be6cc0e1502fbff175dd2f4fad238d838adfe86e2ac build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -26,8 +27,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'A simple interface to and data from the Human Protein Atlas project.' - + summary: 'The hpar package provides a simple R interface to and data from the Human Protein Atlas project.' extra: identifiers: - biotools:hpar diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index 181030cbc4bff..b8c5f82d337b0 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.112.0" %} +{% set version = "0.114.0" %} {% set name = "HSMMSingleCell" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 11b6dcb7a3ee86323740aa4c3627abb4c546a890ad0d3e0a262fcf2aa49be773 + sha256: 672e8202ea70c7098ce15b4383227310394da6faebbca4b353c90e0aa657e0a8 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.' + + diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index a1b6ca2ab5f51..92778374059b3 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="HSMMSingleCell_0.112.0.tar.gz" +FN="HSMMSingleCell_0.114.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/HSMMSingleCell_0.112.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_0.112.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/HSMMSingleCell_0.114.0.tar.gz" + "https://bioarchive.galaxyproject.org/HSMMSingleCell_0.114.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_0.114.0_src_all.tar.gz" ) -MD5="07190931796761fc34c6c1391a6d4cfc" +MD5="2b928efcb786a4486c79673d4ff457e3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-htqpcr/conda_build_config.yaml b/recipes/bioconductor-htqpcr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-htqpcr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-htqpcr/meta.yaml b/recipes/bioconductor-htqpcr/meta.yaml index 627ee7f663afe..2aa3be0bd6c60 100644 --- a/recipes/bioconductor-htqpcr/meta.yaml +++ b/recipes/bioconductor-htqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "HTqPCR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 51518a4b0ff5d945645b27a908cf9192373826d91deb1ef937be8c59017dfe2f + sha256: 18e3ac081022dc455f4f2f66f8a4f735fce90858d85fa3dc97e44137c1f5991c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-gplots - r-rcolorbrewer run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-gplots - r-rcolorbrewer @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).' - extra: identifiers: - biotools:htqpcr diff --git a/recipes/bioconductor-htseqtools/meta.yaml b/recipes/bioconductor-htseqtools/meta.yaml index d9937bd5f85a6..29941bc0362d5 100644 --- a/recipes/bioconductor-htseqtools/meta.yaml +++ b/recipes/bioconductor-htseqtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.3" %} {% set name = "htSeqTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9fe152ae580734ff31909e5f45fadc3ea76fb10434ec388cba4b4008065c2fd6 + sha256: e7ee1b65265dc44256ec0618a907ae095a19c9aa3723a15229aa3f22011530a1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-bsgenome - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicranges >=1.17.11' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-mass run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.0' - - bioconductor-bsgenome - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicranges >=1.17.11' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-mass test: @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.' - extra: identifiers: - biotools:htseqtools diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml index 7e9580b15b7e8..bee9c945a5de7 100644 --- a/recipes/bioconductor-htsfilter/meta.yaml +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "HTSFilter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b10f6bd6734f603840718911ae53fd5ca600102ab064c70501701e3f994027e0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c4597ad7589c74ace67fd5c7c0540bafc796c7f0dd081a450d2e2bb64f4deb44 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocparallel >=1.4.3' - - 'bioconductor-deseq >=1.22.1' - - 'bioconductor-deseq2 >=1.10.1' - - 'bioconductor-edger >=3.9.14' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base run: - - bioconductor-biobase - - 'bioconductor-biocparallel >=1.4.3' - - 'bioconductor-deseq >=1.22.1' - - 'bioconductor-deseq2 >=1.10.1' - - 'bioconductor-edger >=3.9.14' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base test: commands: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.' - extra: identifiers: - biotools:htsfilter diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml index 2c7941d1e5308..5ef1474b28b12 100644 --- a/recipes/bioconductor-hybridmtest/meta.yaml +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HybridMTest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 72e0867f646a15cc4689bcf6115ff7c6b6717bcd2f605436f7ecebafa8c22e53 + sha256: ed79e3d2df7e52193e251efbe5ed5b62380fcf5b0340776c0036ca084bef9251 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-fdrtool - r-mass - r-survival run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-fdrtool - r-mass @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL Version 2 or later' summary: 'Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.' - extra: identifiers: - biotools:hybridmtest diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml index 1623dc6b535c3..36dc7ecb8ab78 100644 --- a/recipes/bioconductor-hyperdraw/meta.yaml +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "hyperdraw" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 199eb413797c62e8215c593f1689fdac9d8aaf88287943fa97add9759019d101 + sha256: ecc1fc2a682b262eb72d80d8ace1159c1a1a8c99a7fa93c63c3dae2bb75e8ece build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-hypergraph - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-hypergraph >=1.52.0,<1.54.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base run: - - bioconductor-graph - - bioconductor-hypergraph - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-hypergraph >=1.52.0,<1.54.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base test: commands: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Functions for visualizing hypergraphs.' - extra: identifiers: - biotools:hyperdraw diff --git a/recipes/bioconductor-hypergraph/meta.yaml b/recipes/bioconductor-hypergraph/meta.yaml index 5efaae3836404..9629da00621c8 100644 --- a/recipes/bioconductor-hypergraph/meta.yaml +++ b/recipes/bioconductor-hypergraph/meta.yaml @@ -1,40 +1,35 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "hypergraph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 654505b2f783a8e06d770beef3e2745fba662da60e01328347c82e6fae2b0eb0 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 35d530dd00739ac6a5d39aaec79b88c3088535cb94850091a2404dc278cac0fe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package that implements some simple capabilities for representing and manipulating hypergraphs.' - extra: identifiers: - biotools:hypergraph diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml index 0cdde3ba3b097..ff2503f36762a 100644 --- a/recipes/bioconductor-iaseq/meta.yaml +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "iASeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2f524cf5e53c8a4c2582db11e5edba2861ff85d1f7c65c7659c40b3ff41e7ce + sha256: 5bc4b06bc9a00541500f59b47ea69ca649a06f6893f5c6d70e29e2a537ba93fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.' - extra: identifiers: - biotools:iaseq diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml index 29fc3f0a80505..049a252ec16f3 100644 --- a/recipes/bioconductor-ibh/meta.yaml +++ b/recipes/bioconductor-ibh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ibh" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d5f281ecf80e390feac5910e862f5fa500c379da07e797870720a10adc50c121 + sha256: dfa0ff19dcc58c02413ebbb59e861f732bea30cd02baf4391f44569c549490ce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-simpintlists + - 'bioconductor-simpintlists >=1.16.0,<1.18.0' - r-base run: - - bioconductor-simpintlists + - 'bioconductor-simpintlists >=1.16.0,<1.18.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.' - extra: identifiers: - biotools:ibh diff --git a/recipes/bioconductor-icens/meta.yaml b/recipes/bioconductor-icens/meta.yaml index 022cbeac952b9..05d6f4e2f5da0 100644 --- a/recipes/bioconductor-icens/meta.yaml +++ b/recipes/bioconductor-icens/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "Icens" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1512f06313f02781109fff207fc27a70b5e09127be3334d50f321e275e6d51a5 + sha256: 74bc104fb871de276531fabef56643d2e2a05bcb3feec3077865a558b92a78f7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Many functions for computing the NPMLE for censored and truncated data.' - extra: identifiers: - biotools:icens diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml index 59663e05abb9b..6bbce08657571 100644 --- a/recipes/bioconductor-ichip/meta.yaml +++ b/recipes/bioconductor-ichip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "iChip" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 801f1b2d172aec0ac67d89688ded007272672af2bd6db5589756fa356dd99709 + sha256: 9230c90087696bb4d35f0e9221b2f288a30da0b398f01614270d2e41c9189342 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.' - extra: identifiers: - biotools:ichip diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml index e6af4469ef037..4064a76a4fc30 100644 --- a/recipes/bioconductor-icobra/meta.yaml +++ b/recipes/bioconductor-icobra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "iCOBRA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4dc3c2b7c90b7f16d21fd94b162338d19b1cc41730b279f7d5dbf2844c3b50f8 + sha256: 47bae461e90a3dbf971c96bc2a545fa4957d1c8149005e1c55b8cf191eb83339 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dplyr - r-dt @@ -31,7 +31,7 @@ requirements: - r-shinydashboard - r-upsetr run: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dplyr - r-dt @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results.' - extra: identifiers: - biotools:icobra diff --git a/recipes/bioconductor-ideal/build.sh b/recipes/bioconductor-ideal/build.sh index 76fd99f6c993a..da43ce2168312 100644 --- a/recipes/bioconductor-ideal/build.sh +++ b/recipes/bioconductor-ideal/build.sh @@ -1,5 +1,4 @@ #!/bin/bash - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ideal/meta.yaml b/recipes/bioconductor-ideal/meta.yaml index 426ea3d28c021..5318385622a52 100644 --- a/recipes/bioconductor-ideal/meta.yaml +++ b/recipes/bioconductor-ideal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ideal" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e9eb699cb91074d63ee67c3818b5bb40d1a79e96fb691f854fc1d3329137d03b + sha256: c5f3d116a78fc815cd99dd4b7b7640b0b7db3ad046cc26b92de3d75319aabc77 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocparallel - - bioconductor-deseq2 - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-goseq - - bioconductor-gostats - - bioconductor-ihw - - bioconductor-iranges - - bioconductor-limma - - bioconductor-pcaexplorer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-goseq >=1.32.0,<1.34.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-ihw >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-pcaexplorer >=2.6.0,<2.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-d3heatmap - r-dplyr @@ -51,20 +51,20 @@ requirements: - r-stringr - r-upsetr run: - - bioconductor-annotationdbi - - bioconductor-biocparallel - - bioconductor-deseq2 - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-goseq - - bioconductor-gostats - - bioconductor-ihw - - bioconductor-iranges - - bioconductor-limma - - bioconductor-pcaexplorer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-goseq >=1.32.0,<1.34.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-ihw >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-pcaexplorer >=2.6.0,<2.8.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-d3heatmap - r-dplyr @@ -90,3 +90,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.' + + diff --git a/recipes/bioconductor-ideoviz/meta.yaml b/recipes/bioconductor-ideoviz/meta.yaml index d4e1058199923..633af7f0f97c2 100644 --- a/recipes/bioconductor-ideoviz/meta.yaml +++ b/recipes/bioconductor-ideoviz/meta.yaml @@ -1,51 +1,45 @@ -{% set version = "1.10.0" %} +{% set version = "1.16.0" %} {% set name = "IdeoViz" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d353161b4b487481ba4a3bd0cfb74af0af7258f4b9ea0a8b6d303ef1117b1aac - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9fb75f79df3b3f9ae2603fcceb12a9657842124e22c4f035f26246e86710a17e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-rcolorbrewer - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/IdeoViz.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Plots data associated with arbitrary genomic intervals along chromosomal ideogram.' - extra: identifiers: - biotools:ideoviz diff --git a/recipes/bioconductor-idiogram/meta.yaml b/recipes/bioconductor-idiogram/meta.yaml index eec34e0bfc0aa..5c6e7f7c1cb7d 100644 --- a/recipes/bioconductor-idiogram/meta.yaml +++ b/recipes/bioconductor-idiogram/meta.yaml @@ -1,45 +1,39 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "idiogram" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 024836393eda7473cbed2bf282a50ccfd602c84169693aba60d547875b44630c - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d7ae785f13ac7270f927561a16703209e26c822f2682dca2783b789702911e0d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotate - - bioconductor-biobase + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-plotrix run: - - bioconductor-annotate - - bioconductor-biobase + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-plotrix - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/idiogram.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A package for plotting genomic data by chromosomal location' - extra: identifiers: - biotools:idiogram diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 4ca5209fefa57..23de3cae91305 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "IHW" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2d2252a467296d23252e3c3064889a25b1b29fd3935bb901c309c4356e8a6b93 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5127685a6aba22ff330415c45feb4c80de3021c75c2665406c063d8a27f3da4e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-lpsymphony + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-lpsymphony >=1.8.0,<1.10.0' - r-base - r-fdrtool - r-slam run: - - bioconductor-biocgenerics - - bioconductor-lpsymphony + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-lpsymphony >=1.8.0,<1.10.0' - r-base - r-fdrtool - r-slam @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.' - extra: identifiers: - biotools:IHW diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index e9ce7076db4f6..d45cb451c9f6f 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation450kanno.ilmn12.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Manifests and annotation for Illumina''s 450k array data.' + + diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh index 1797cec76df10..a6ce3c30c4b34 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" ) MD5="2f569646ca8adc49863224b1cd076a79" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml index bb3a04ade7721..6d1a038af1b39 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation450kmanifest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-minfi + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - bioconductor-minfi + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Manifest for Illumina''s 450k array data' + + diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh index 2fffc9b030c3d..93ab2a247224d 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz" ) MD5="664d1f5a3892974334faa26757269509" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml index ba3d115439497..3f7c6f290ecfa 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'An annotation package for Illumina''s EPIC methylation arrays.' + + diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh index a5c6748d47c0e..1dd8c36173496 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" ) MD5="6a8e2398a0f930aa7828a1412fb21e88" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml index ed2eee1e3165c..d5a59d8760983 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 062aa3c78e3fc518849adc73b8540aa50f85ecab8ef91b535b48a1bfeedab3e5 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'An annotation package for Illumina''s EPIC methylation arrays.' + + diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh index 7af53e9ce9437..62576b4fca412 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" ) MD5="2dac8e889486386eaea1bb7ce1beea2e" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml index 09676a9f0da88..c93082f153b61 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - 'bioconductor-minfi >=1.19.15' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'An annotation package for Illumina''s EPIC methylation arrays.' + + diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh index 642158fa1154c..104cb7c559697 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" ) MD5="2d0c05917bcbf9ba1e354380d4e17a77" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml index 655ee23d00e15..12d23577c5465 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.3.0" %} {% set name = "IlluminaHumanMethylationEPICmanifest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-minfi + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base run: - - bioconductor-minfi + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A manifest package for Illumina''s EPIC methylation arrays.' + + diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh index a950c7331a095..1c63aaeebc559 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" ) MD5="c6b0268de177badfe0b8184002da7e16" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 325fc53cfdf38..4b18cf9fc2b1b 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "illuminaio" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b0fd2a0916992a66361826819900bcfc7a4cee3a03c3c5b169c08f96d5f6b10a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d0d9fca7d238e6045d4f613db26443bf87d44a9a4c367e73bfe9ff19ae047211 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,9 @@ requirements: run: - r-base - r-base64 + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Tools for parsing Illumina''s microarray output files, including IDAT.' - extra: identifiers: - biotools:illuminaio diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 717827be83d6e..4f3420a7f9797 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev2.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 03864df588d7261db6923d0d7cccdd9bbb753ce60e4cdf92ba2bc3ea1318916f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.29.20' - - 'bioconductor-org.mm.eg.db >=3.1.2' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.29.20' - - 'bioconductor-org.mm.eg.db >=3.1.2' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Illumina MouseWG6v2 annotation data (chip illuminaMousev2) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-illuminamousev2.db/post-link.sh b/recipes/bioconductor-illuminamousev2.db/post-link.sh index 843d8859926d6..86dc41728ebce 100644 --- a/recipes/bioconductor-illuminamousev2.db/post-link.sh +++ b/recipes/bioconductor-illuminamousev2.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="illuminaMousev2.db_1.26.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaMousev2.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz" ) MD5="fba228a71f264f976d8cdb035861974d" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-imagehts/conda_build_config.yaml b/recipes/bioconductor-imagehts/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-imagehts/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-imagehts/meta.yaml b/recipes/bioconductor-imagehts/meta.yaml index 535d9b66b6e71..6376dfcb80559 100644 --- a/recipes/bioconductor-imagehts/meta.yaml +++ b/recipes/bioconductor-imagehts/meta.yaml @@ -1,55 +1,45 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "imageHTS" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 76c66b4d3057dd3252db971518d6875155548ee7271da289ecb999a34f7d7c7e - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 39a5dc9d30b9c0d22cc63bd9ec3976c66daa362168a3ec484f55df895fe8ef0e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biobase - - bioconductor-cellhts2 >=2.10.0 - - bioconductor-ebimage >=4.3.12 - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-e1071 - r-hwriter run: - - bioconductor-biobase - - bioconductor-cellhts2 >=2.10.0 - - bioconductor-ebimage >=4.3.12 - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-e1071 - r-hwriter - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/imageHTS.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2.1 - summary: 'imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. - The package provides a modular and extensible framework to segment cells, extract quantitative cell - features, predict cell types and browse screen data through web interfaces. Designed to operate in - distributed environments, imageHTS provides a standardized access to remote data and facilitates the - dissemination of high-throughput microscopy-based datasets.' - + summary: 'imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.' extra: identifiers: - biotools:imagehts diff --git a/recipes/bioconductor-imas/meta.yaml b/recipes/bioconductor-imas/meta.yaml index ba7ed20bebf62..08217ede7197e 100644 --- a/recipes/bioconductor-imas/meta.yaml +++ b/recipes/bioconductor-imas/meta.yaml @@ -1,37 +1,34 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "IMAS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d3287da7eece1210d74714fb1e798bf0c4c58392c343aba6772134e41ca5c814 - + sha256: cef75e8992be51b77d0053e960560d2865bcf9d44fd6f2a6415b1eaebbb7c752 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-ivas - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-ivas >=2.0.0,<2.2.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-doparallel - r-foreach @@ -43,17 +40,17 @@ requirements: - r-matrix - r-survival run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-ivas - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-ivas >=2.0.0,<2.2.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-doparallel - r-foreach @@ -64,12 +61,12 @@ requirements: - r-lme4 - r-matrix - r-survival - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Integrative analysis of Multi-omics data for Alternative splicing.' + + diff --git a/recipes/bioconductor-impulsede/meta.yaml b/recipes/bioconductor-impulsede/meta.yaml index 81dc09baa4873..c00418258aef8 100644 --- a/recipes/bioconductor-impulsede/meta.yaml +++ b/recipes/bioconductor-impulsede/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ImpulseDE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 013b366155309ae595bae6dce37e9d081dfc2c929027ee8b53029959efcc8112 + sha256: 9246bcaaba1c6ea8cf52ca4b85dbdcb6a632ff56761dc7e54bacaee5450cc68c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. To optimize the running time, the code makes use of clustering steps and multi-threading.' - extra: identifiers: - biotools:impulsede diff --git a/recipes/bioconductor-impute/meta.yaml b/recipes/bioconductor-impute/meta.yaml index 2ac7e6f448ebe..49c95c6bde504 100644 --- a/recipes/bioconductor-impute/meta.yaml +++ b/recipes/bioconductor-impute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "impute" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5654e732d607c22ad7e5c36af76e888bfecb2cb01ef92918936c74bfb926192d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 19129a57c912280fae17c345174d3d6dd93c79875e300dc7b24f608a95bb6cb4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Imputation for microarray data (currently KNN only)' - extra: identifiers: - biotools:impute diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml index 5fafc2b3f7802..dae8e59314d5f 100644 --- a/recipes/bioconductor-inpower/meta.yaml +++ b/recipes/bioconductor-inpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "INPower" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b1dc0eec9f4ff676161575d6bd4da6d7400fccecd57b8613f105f93941ba59d + sha256: 3f1e0515b673117e6cdc4d3437e30a795ee17ecb4300ed55f1f5797e160b271a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 + file LICENSE' summary: 'An R package for computing the number of susceptibility SNPs and power of future studies' - extra: identifiers: - biotools:inpower diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml index 47762804014b6..bc8aa02aebbc9 100644 --- a/recipes/bioconductor-inspect/meta.yaml +++ b/recipes/bioconductor-inspect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "INSPEcT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,39 +10,39 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a16dbf2bd2d0a1c893ce4f6f82ae534f22548f12f9f0d3e782b92cc070f47fec + sha256: 1751702fbb09e762ae2a196aa11021d157e2bf602377b1dece5ccf1a3dbf60be build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-desolve - r-proc - r-rootsolve run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-desolve - r-proc @@ -54,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.' - extra: identifiers: - biotools:inspect diff --git a/recipes/bioconductor-interactionset/conda_build_config.yaml b/recipes/bioconductor-interactionset/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-interactionset/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-interactionset/meta.yaml b/recipes/bioconductor-interactionset/meta.yaml index d568cc1524bcc..cca74b999fef1 100644 --- a/recipes/bioconductor-interactionset/meta.yaml +++ b/recipes/bioconductor-interactionset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "InteractionSet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a9726644f75438b46267d7df756482db0019d0feee9b7c525b2d05d97123b7f2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 164dd6d8ed315881a6e3a202e3afc12dbed617ba988788529600b178b0cacf76 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.6' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.1.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-matrix - r-rcpp run: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.29.6' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.1.6' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-matrix - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.' - extra: identifiers: - biotools:interactionset diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml index 3b21a3414ed7e..b024944a3ef0a 100644 --- a/recipes/bioconductor-interactivedisplay/meta.yaml +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "interactiveDisplay" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2febc7f7e1be31ba594e08ba8f9712d0587285893c6c32f8db39dad1ddbafd07 + sha256: d22f03cabf6e9cff77b9389b9f3458d6099384d65d0049f6554466a2bc0a12b6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-category - - 'bioconductor-interactivedisplaybase >=1.7.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' - r-base - r-ggplot2 - r-gridsvg @@ -31,10 +31,10 @@ requirements: - r-shiny - r-xml run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-category - - 'bioconductor-interactivedisplaybase >=1.7.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' - r-base - r-ggplot2 - r-gridsvg @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.' - extra: identifiers: - biotools:interactivedisplay diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 2a0dda2df13fd..648b45e47ba83 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "interactiveDisplayBase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e5966f2b6d2e5f2f21a130f71c1b1b605cdb88f746fd989fe435622c0b49cb07 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e59499d2ed37e4dc136eecdd9bf924387aa269571266d3245175ee14c7478517 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-shiny run: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-shiny test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.' - extra: identifiers: - biotools:interactivedisplaybase diff --git a/recipes/bioconductor-interest/build.sh b/recipes/bioconductor-interest/build.sh index b58dbca4d229f..da43ce2168312 100644 --- a/recipes/bioconductor-interest/build.sh +++ b/recipes/bioconductor-interest/build.sh @@ -1,4 +1,4 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interest/meta.yaml b/recipes/bioconductor-interest/meta.yaml index 600186484b1e4..8e27b34f9861f 100644 --- a/recipes/bioconductor-interest/meta.yaml +++ b/recipes/bioconductor-interest/meta.yaml @@ -1,74 +1,67 @@ -{% set version = '1.2.2' %} +{% set version = "1.4.1" %} {% set name = "IntEREst" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' - version: {{ version }} - + version: '{{ version }}' source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - sha256: b8560d301118db28c409fb422a7457bc16f052a2e8a97a12cfc6f122569d62b2 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cb2ebcacbd951c029c9ceb32360baa9dda9109d95eeed94b5d38ac4b52e56754 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - r-base >=3.4 - - r-seqinr + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-dexseq >=1.26.0,<1.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - r-base - r-dbi - r-rmysql - - bioconductor-dexseq - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-rsamtools - - bioconductor-summarizedexperiment - - bioconductor-edger - - bioconductor-s4vectors - - bioconductor-deseq2 - - bioconductor-genomicalignments - - bioconductor-iranges - - bioconductor-genomicfeatures - - bioconductor-biostrings - - bioconductor-seqlogo - - run: - - r-base >=3.4 - r-seqinr + run: + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-dexseq >=1.26.0,<1.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - r-base - r-dbi - r-rmysql - - bioconductor-dexseq - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-rsamtools - - bioconductor-summarizedexperiment - - bioconductor-edger - - bioconductor-s4vectors - - bioconductor-deseq2 - - bioconductor-genomicalignments - - bioconductor-iranges - - bioconductor-genomicfeatures - - bioconductor-biostrings - - bioconductor-seqlogo - + - r-seqinr test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: 'https://bioconductor.org/packages/release/bioc/html/{{ name }}.html' - license: 'GPL-2' - summary: 'IntEREst (Intron-Exon Retention Estimator) - This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).' - + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).' extra: identifiers: - doi:10.18129/B9.bioc.IntEREst diff --git a/recipes/bioconductor-interminer/meta.yaml b/recipes/bioconductor-interminer/meta.yaml index 5e3a0c535bead..4e769511d9564 100644 --- a/recipes/bioconductor-interminer/meta.yaml +++ b/recipes/bioconductor-interminer/meta.yaml @@ -1,31 +1,28 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "InterMineR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cb0d3419beadafc131be34036c1b66df8cc0d14bcf261d3e262ca175f548643d - + sha256: 4261d607ec70ed1375b2f95c6af746db23dd59ce847999fc12be4b5052e3ce69 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-httr - r-igraph @@ -35,11 +32,11 @@ requirements: - r-xml - r-xml2 run: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-httr - r-igraph @@ -48,12 +45,12 @@ requirements: - r-sqldf - r-xml - r-xml2 - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. This R package provides interfaces with these databases through webservices. It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.' + + diff --git a/recipes/bioconductor-inversion/meta.yaml b/recipes/bioconductor-inversion/meta.yaml index 3d13c5c9c1a2d..bf46b9a1638d7 100644 --- a/recipes/bioconductor-inversion/meta.yaml +++ b/recipes/bioconductor-inversion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "inveRsion" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b151f3ff6207edf8da6aadf8d77497045272db06a3d3e03658f016de27b1ee89 + sha256: 4d6ac9f478fe77da8aa220c0d8dac0949ff99f5e3eeddfbc273f82ebb2d3ef9b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-haplo.stats run: - r-base - r-haplo.stats - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package to find genetic inversions in genotype (SNP array) data.' - extra: identifiers: - biotools:inversion diff --git a/recipes/bioconductor-ioniser/meta.yaml b/recipes/bioconductor-ioniser/meta.yaml index d5dd6615e6df4..7786a3139bae6 100644 --- a/recipes/bioconductor-ioniser/meta.yaml +++ b/recipes/bioconductor-ioniser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "IONiseR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9db18c62271287a01fd8b49026a474cbf17b2a9d3fed476d39a0de4e527d2de3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3e0711320179a7a2f3971cb33842bbfc5f98a1ddb3d0b0891780e281fa76322d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-rhdf5 - - bioconductor-shortread - - bioconductor-xvector + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-bit64 - r-dplyr @@ -32,12 +33,12 @@ requirements: - r-tibble - r-tidyr run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-rhdf5 - - bioconductor-shortread - - bioconductor-xvector + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-bit64 - r-dplyr @@ -53,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.' - extra: identifiers: - biotools:ioniser diff --git a/recipes/bioconductor-ipac/meta.yaml b/recipes/bioconductor-ipac/meta.yaml index 151654c4d04af..656362e67f268 100644 --- a/recipes/bioconductor-ipac/meta.yaml +++ b/recipes/bioconductor-ipac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.2" %} {% set name = "iPAC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f9053904d89b7a54da678a83c971e72f94186338e882beba9055a239debeb6f4 + sha256: f5a446e34d6139f6f05be29a9cb8a448fc2ad65e642a923a998a409d92cee21c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-multtest + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-gdata - r-scatterplot3d run: - - bioconductor-biostrings - - bioconductor-multtest + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-gdata - r-scatterplot3d @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'iPAC is a novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.' - extra: identifiers: - biotools:ipac diff --git a/recipes/bioconductor-ipo/meta.yaml b/recipes/bioconductor-ipo/meta.yaml index 889a98884c89b..d8c3e0108e47e 100644 --- a/recipes/bioconductor-ipo/meta.yaml +++ b/recipes/bioconductor-ipo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "IPO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c2c05fb377651d127a1f1fc8e4dc6f2b3d6466dde888a9b19df39061c9feb870 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f13e09841eb4c83d7fe3e2dd5b98d11bb29ea386c068215177087ee9e7d06c39 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-camera - - 'bioconductor-xcms >=1.50.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-rsm run: - - bioconductor-biocparallel - - bioconductor-camera - - 'bioconductor-xcms >=1.50.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-rsm test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.' - extra: identifiers: - biotools:ipo diff --git a/recipes/bioconductor-ippd/meta.yaml b/recipes/bioconductor-ippd/meta.yaml index ed6c64cbd1429..af896e0fe6fac 100644 --- a/recipes/bioconductor-ippd/meta.yaml +++ b/recipes/bioconductor-ippd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "IPPD" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2e505fcf1e5025c3057ae7616d1d3ab5135bf19a202e982cc613659d66a15d68 + sha256: 47c671a0beea2cb498d6d3e07d043805837afbc3dd4e8f38cd0f74a3a6f65dfe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-bitops @@ -33,7 +31,9 @@ requirements: - r-mass - r-matrix - r-xml - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (version 2 or later)' summary: 'The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.' - extra: identifiers: - biotools:ippd diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml index 9141ade489f47..5d851e588b922 100644 --- a/recipes/bioconductor-iranges/meta.yaml +++ b/recipes/bioconductor-iranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.12" %} {% set name = "IRanges" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a51e7219a9adedcc3ec708db570dbe8ed1156b0bd2bc882fbf5577cad3fa0cef + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 768285a716728bd8e506ce9bd3552f39f2673c66caf6fc5603c037f930d628ab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.23.3' - - 'bioconductor-s4vectors >=0.15.5' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - 'bioconductor-biocgenerics >=0.23.3' - - 'bioconductor-s4vectors >=0.15.5' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.' - extra: identifiers: - biotools:iranges diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml index 4e4a9204a5c82..d8edcfb64aab7 100644 --- a/recipes/bioconductor-iseq/meta.yaml +++ b/recipes/bioconductor-iseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "iSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3b84c53f24767267423624ea81c88b0c9b65aca8ecaebf8f0cedcd091ba9d767 + sha256: c60fc7cc08676ba1d93e82a80973ad6ff93953eb44d235d4d27ee28fe5a8d510 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze ChIP-seq data with and without controls and replicates.' - extra: identifiers: - biotools:iseq diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml index 0185026904b0c..178e2ee8d9510 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -1,38 +1,36 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "IsoformSwitchAnalyzeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2ee026380092487f7be3236765219752c434b377a2644809ea8f4f23f2f0632d - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 21d5419ad3361793d6b39903f732bfbaffcf5bca7edae1ee2b969e75709d67fc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-cummerbund - - bioconductor-drimseq - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-splicer - - bioconductor-tximport + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-cummerbund >=2.22.0,<2.24.0' + - 'bioconductor-drimseq >=1.8.0,<1.10.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-tximport >=1.8.0,<1.10.0' - r-base - r-dbi + - r-futile.logger - r-ggplot2 - r-gridextra - r-plyr @@ -40,35 +38,35 @@ requirements: - r-reshape2 - r-venndiagram run: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-cummerbund - - bioconductor-drimseq - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-splicer - - bioconductor-tximport + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-cummerbund >=2.22.0,<2.24.0' + - 'bioconductor-drimseq >=1.8.0,<1.10.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-tximport >=1.8.0,<1.10.0' - r-base - r-dbi + - r-futile.logger - r-ggplot2 - r-gridextra - r-plyr - r-rcolorbrewer - r-reshape2 - r-venndiagram - + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'IsoformSwitchAnalyzeR enabels identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' - + summary: 'IsoformSwitchAnalyzeR enables identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' extra: identifiers: - biotools:IsoformSwitchAnalyzeR diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml index 9d820e8ed9ab3..3ef00057a78db 100644 --- a/recipes/bioconductor-isolde/meta.yaml +++ b/recipes/bioconductor-isolde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ISoLDE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 797f3d70e1078e47365f138c3fc2ef77ef65c41a447d1f4195bef176931ab40b + sha256: f8818e5f486f93027a1c25901db3750423508a52a375a1e236d572a79662000e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.0)' summary: 'This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.' - extra: identifiers: - biotools:isolde diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index f5ed58077906b..b8cb59b24e338 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "isomiRs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,66 +8,67 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4229dfe18af5ab0fab11eb5e7b0ee7f08b9f816989efe9d0c08cb2d01d5fec2d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a3144607ec7b762f47ffca04c00208ddca725eb5e4bb741ae98cc48da4e6f649 build: - # problems loading nlopter library? - skip: True # [osx] - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-deseq2 - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-targetscan.hs.eg.db >=0.6.1,<0.8.0' + - r-assertive.sets - r-base - r-discriminer - r-dplyr - - r-gamlss - - r-gamlss.dist - r-ggally - r-ggplot2 - r-gplots - r-gridextra - r-gtools - - r-lme4 - r-rcolorbrewer - - r-rcppeigen - r-readr - r-reshape + - r-rlang + - r-tibble - r-tidyr - - 'r-tmb >=1.7.6' run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-deseq2 - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-targetscan.hs.eg.db >=0.6.1,<0.8.0' + - r-assertive.sets - r-base - r-discriminer - r-dplyr - - r-gamlss - - r-gamlss.dist - r-ggally - r-ggplot2 - r-gplots - r-gridextra - r-gtools - - r-lme4 - r-rcolorbrewer - - r-rcppeigen - r-readr - r-reshape + - r-rlang + - r-tibble - r-tidyr - - 'r-tmb >=1.7.6' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -75,7 +76,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Characterization of miRNAs and isomiRs, clustering and differential expression.' - extra: identifiers: - biotools:isomirs diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml index 3757e1409375c..4600ed96e385b 100644 --- a/recipes/bioconductor-iterativebma/meta.yaml +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "iterativeBMA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c49d0fe3f33a8003b688bd5300e6dde3cca6c7e045cdeb2322185c822766832 + sha256: 42abbb1fbde3e556c7cf10f1544fe18093e9b0f6aac88e204eaeb7dff734fd94 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-bma - r-leaps run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-bma - r-leaps @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).' - extra: identifiers: - biotools:iterativebma diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml index 800b7ce59898a..c957b55260e4a 100644 --- a/recipes/bioconductor-iterativebmasurv/meta.yaml +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "iterativeBMAsurv" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b1f2d77d70931771a78319e6c4f00cc085d50324ea0cffae8584e9c8d3b5d824 + sha256: 5fca0142b00cb06024829f018c50822c7014489a15d19ccb6b2b2e6ee3a20cfb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.' - extra: identifiers: - biotools:iterativebmasurv diff --git a/recipes/bioconductor-ivas/meta.yaml b/recipes/bioconductor-ivas/meta.yaml index 236b0b7a8e8f5..a654827dc6353 100644 --- a/recipes/bioconductor-ivas/meta.yaml +++ b/recipes/bioconductor-ivas/meta.yaml @@ -1,34 +1,32 @@ -{% set version = "1.98.0" %} +{% set version = "2.0.0" %} {% set name = "IVAS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4adc643b0094bb56b8f2e5682659b140d7380d33bf89232f88271ed02d97f1d9 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c4e24044672745db223dad17fcac1ddbb749d11bcc8cb51995fcfcdea05b5a26 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-doparallel - r-foreach @@ -37,15 +35,15 @@ requirements: - r-lme4 - r-matrix run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-doparallel - r-foreach @@ -53,16 +51,13 @@ requirements: - r-ggplot2 - r-lme4 - r-matrix - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identification of genetic variants affecting alternative splicing.' - extra: identifiers: - biotools:ivas diff --git a/recipes/bioconductor-iwtomics/meta.yaml b/recipes/bioconductor-iwtomics/meta.yaml index 03c4a84ac5d28..755f69893b89c 100644 --- a/recipes/bioconductor-iwtomics/meta.yaml +++ b/recipes/bioconductor-iwtomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "IWTomics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e18b580c3088e452e2df3c7ea09b6ceca65d0f246ddd5afbb9e413d767f4b7d9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 52eaa007db7ad9564f5bc777c623bdfa02139d9e7e0a3388652365d1d94b9342 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fda - r-gtable - r-kernsmooth run: - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fda - r-gtable @@ -39,3 +40,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.' + + diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index 8c772539e84d0..493d5959f789c 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "JASPAR2014" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3423d5f824e238a7d863f1b901fcac0b2b40dc5404487f1563c4c9d1fd5bb90e + sha256: 1a216837d63548d9f07526bfdaee36c9f534c4e2268c5fa1672cfcf8a9835e1d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.29.19' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base run: - - 'bioconductor-biostrings >=2.29.19' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'Data package for JASPAR 2014. To search this databases, please use the package TFBSTools.' + + diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index 884d02201da8d..dc6c0e6c89a77 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="JASPAR2014_1.14.0.tar.gz" +FN="JASPAR2014_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/JASPAR2014_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/JASPAR2014_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2014_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.16.0_src_all.tar.gz" ) -MD5="21e7ecfc41e509059808970620eefb13" +MD5="62bc9538b7fb9dc6d8a926aa61bbc42e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index 412886873f9b8..7b05c2bc2aa62 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "JASPAR2016" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a6e24ac8588a5bef2bc314e6e2bd1e562186f8703d1d00a6b6469d295d15264e + sha256: 0c419dd94d66bb02289b5827ab1dfbe7ba739acc82af5bc929f93de85532e9d8 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1).' + + diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index 4f50c7d46208b..f25e74d11874a 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="JASPAR2016_1.6.0.tar.gz" +FN="JASPAR2016_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/JASPAR2016_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.6.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/JASPAR2016_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2016_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.8.0_src_all.tar.gz" ) -MD5="f2a5fcd3b7e2aa1a8775441cdb400e5a" +MD5="19d1e3810b4cda2b16d382b2d646c27d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-jaspar2018/build.sh b/recipes/bioconductor-jaspar2018/build.sh new file mode 100644 index 0000000000000..b58dbca4d229f --- /dev/null +++ b/recipes/bioconductor-jaspar2018/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-jaspar2018/meta.yaml b/recipes/bioconductor-jaspar2018/meta.yaml index 4fdee53f85f25..0cd614c48dcf6 100644 --- a/recipes/bioconductor-jaspar2018/meta.yaml +++ b/recipes/bioconductor-jaspar2018/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} {% set name = "JASPAR2018" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 84d1ebe90e03045a1efeefe66f1aab311dae343df4be0bd4cc40a55b995ba64f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4439bc1b556eaf66c2b7e30bab28dc9da323b9cba8c53043f587822228473b2b build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,7 +21,6 @@ requirements: - r-base run: - r-base - - wget test: commands: - '$R -e "library(''{{ name }}'')"' @@ -28,3 +28,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).' + + diff --git a/recipes/bioconductor-jaspar2018/post-link.sh b/recipes/bioconductor-jaspar2018/post-link.sh old mode 100644 new mode 100755 index 9d5166923f4d5..63cbb3b91da35 --- a/recipes/bioconductor-jaspar2018/post-link.sh +++ b/recipes/bioconductor-jaspar2018/post-link.sh @@ -1,10 +1,10 @@ #!/bin/bash -FN="JASPAR2018_1.0.0.tar.gz" +FN="JASPAR2018_1.1.0.tar.gz" URLS=( - "https://bioconductor.org/packages/3.6/bioc/src/contrib/JASPAR2018_1.0.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.0.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.7/bioc/src/contrib/JASPAR2018_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.0_src_all.tar.gz" ) -MD5="dbc27f8cd378d3ab40c1cc679de28f48" +MD5="7f6d748701d83294d6138b265657712a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-jmosaics/meta.yaml b/recipes/bioconductor-jmosaics/meta.yaml index 40bc2231e9ae1..edb91ab47f03e 100644 --- a/recipes/bioconductor-jmosaics/meta.yaml +++ b/recipes/bioconductor-jmosaics/meta.yaml @@ -28,3 +28,4 @@ about: home: http://bioconductor.org/packages/release/bioc/html/jmosaics.html license: 'GPL (>= 2)' summary: 'jmosaics detects enriched regions of ChIP-seq data sets jointly.' + diff --git a/recipes/bioconductor-junctionseq/meta.yaml b/recipes/bioconductor-junctionseq/meta.yaml index 332f0f0a354b4..632cc15cc95ff 100644 --- a/recipes/bioconductor-junctionseq/meta.yaml +++ b/recipes/bioconductor-junctionseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "JunctionSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 33f75e2d1ba0b5004c6957a3cfe0e33e92b874751d751179a31344566f37ab05 + sha256: 1a2ef1242f0f2c93559c97c57595f49a18b733c9f1df04add82908d683736aa8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-biobase >=2.30.0' - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-biocparallel - - 'bioconductor-deseq2 >=1.10.0' - - bioconductor-genefilter - - bioconductor-geneplotter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-hmisc - r-locfit @@ -39,16 +37,16 @@ requirements: - r-statmod - r-stringr run: - - 'bioconductor-biobase >=2.30.0' - - 'bioconductor-biocgenerics >=0.7.5' - - bioconductor-biocparallel - - 'bioconductor-deseq2 >=1.10.0' - - bioconductor-genefilter - - bioconductor-geneplotter - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-hmisc - r-locfit @@ -57,7 +55,10 @@ requirements: - 'r-rcpparmadillo >=0.3.4.4' - r-statmod - r-stringr - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -65,7 +66,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.' - extra: identifiers: - biotools:junctionseq diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index facb89989cff4..d134f39436107 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "KCsmart" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b81c4b6626f6e83ba2f76f024be54fbe35c04e8d0e3939bccb8093ba12a32e28 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f59ff9b95fad22a288befde7d70432ac5f1c6ec6fb48393486a23c8437dcf6eb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-multtest - - bioconductor-siggenes + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' - r-base - r-kernsmooth run: - - bioconductor-biocgenerics - - bioconductor-multtest - - bioconductor-siggenes + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' - r-base - r-kernsmooth test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Multi sample aCGH analysis package using kernel convolution' - extra: identifiers: - biotools:kcsmart diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index 18ccb56087027..6034ac82e2fe2 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "kebabs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 82b8f95cc46a84245d1a314ffdaa6aa09ffd6242d321f77c69ee7fbef2af7ed5 + sha256: 060e19e97316757ec24008fa9e4d4a370e81dcfceb0e886f15cf78ad2d0104e8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'bioconductor-biostrings >=2.35.5' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.5.11' - - 'bioconductor-xvector >=0.7.3' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-apcluster - r-base - r-e1071 @@ -32,10 +30,10 @@ requirements: - r-matrix - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biostrings >=2.35.5' - - bioconductor-iranges - - 'bioconductor-s4vectors >=0.5.11' - - 'bioconductor-xvector >=0.7.3' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-apcluster - r-base - r-e1071 @@ -43,7 +41,10 @@ requirements: - r-liblinear - r-matrix - 'r-rcpp >=0.11.2' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,3 +52,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.1)' summary: 'The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.' + + diff --git a/recipes/bioconductor-kegg.db/meta.yaml b/recipes/bioconductor-kegg.db/meta.yaml index 5f52521bf3598..9301a3edf51dc 100644 --- a/recipes/bioconductor-kegg.db/meta.yaml +++ b/recipes/bioconductor-kegg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "KEGG.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.34.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.34.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'file LICENSE' summary: 'A set of annotation maps for KEGG assembled using data from KEGG' + + diff --git a/recipes/bioconductor-kegg.db/post-link.sh b/recipes/bioconductor-kegg.db/post-link.sh index 759fe3f64ca8f..709d08d83b1f5 100644 --- a/recipes/bioconductor-kegg.db/post-link.sh +++ b/recipes/bioconductor-kegg.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="KEGG.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/KEGG.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kegg.db/bioconductor-kegg.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-kegg.db/bioconductor-kegg.db_3.2.3_src_all.tar.gz" ) MD5="023ac22f57063627c2e62d1ae5e011b0" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index 52d13c1a5a3fc..04b5db93e41a4 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "KEGGdzPathwaysGEO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0579a620447f70977fec8d02d6aec16b43ee4d9952ba038f57d305d4181a920c + sha256: 19696755848b79a7fb9b9e0f225b63d8ea2909cff32198fe22f5e601340283eb build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package.' + + diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index 5397b03f5fb7a..bd723f1826f0f 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="KEGGdzPathwaysGEO_1.16.0.tar.gz" +FN="KEGGdzPathwaysGEO_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.18.0_src_all.tar.gz" ) -MD5="814209c8cae15c1ecdc7efddb8a1b090" +MD5="d701ac5a9236c01ea5354080d0142eed" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index 221ce82b358d3..e16b787354866 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "KEGGgraph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fc2b2128e2b096c2cb1797796f748a1d1f5471bb1bf6b200dae441ddab671109 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 326afc5c49c29fd6722641b48e68c89cc01bf892a06499951b61ea43e817ad96 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - 'r-xml >=2.3-0' run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - 'r-xml >=2.3-0' test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.' - extra: identifiers: - biotools:kegggraph diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml index be03eec9dd775..6dc12e5ebfb97 100644 --- a/recipes/bioconductor-kegglincs/meta.yaml +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.2" %} {% set name = "KEGGlincs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d8920cecc27219f510cda690b9446fafe1528801b25bc75183a200714083889e + sha256: fa61e9faa467beb8500f68dcce170d8a093bf073798d13e9a58f9d6eea6b0d45 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-hgu133a.db - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-kodata - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-kodata >=1.6.0,<1.8.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-gtools - r-httr @@ -32,12 +32,12 @@ requirements: - r-rjsonio - r-xml run: - - bioconductor-annotationdbi - - bioconductor-hgu133a.db - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-kodata - - 'bioconductor-org.hs.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-kodata >=1.6.0,<1.8.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-gtools - r-httr @@ -52,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'See what is going on ''under the hood'' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.' - extra: identifiers: - biotools:kegglincs diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml index 579be37081e97..0b9653018785f 100644 --- a/recipes/bioconductor-keggorthology/meta.yaml +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "keggorthology" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 96212cea18230facf342e2a99096835b83940f5a2149019b2a694f2bc63afa84 + sha256: 9d57ff72633e6d05b6201f8aaec51de8f0764d00acce8e6724055cbfceb1bc7c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-hgu95av2.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-hgu95av2.db >=3.2.3,<3.4.0' - r-base - r-dbi run: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-hgu95av2.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-hgu95av2.db >=3.2.3,<3.4.0' - r-base - r-dbi test: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.' - extra: identifiers: - biotools:keggorthology diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 9af21ceb558d4..84160896b11c5 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.2" %} {% set name = "KEGGREST" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 124ebab423d71ca19e72419225f2455b6af7741d4295e3e4bb9b9f22294271c4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4a3be78265f680f725bd4a9ea4f35cffc90ea1d98c5020281dac2e84e7aa1572 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-httr - r-png run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-httr - r-png @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.' - extra: identifiers: - biotools:keggrest diff --git a/recipes/bioconductor-kimod/meta.yaml b/recipes/bioconductor-kimod/meta.yaml index 644868a6fa071..3e06e522220c8 100644 --- a/recipes/bioconductor-kimod/meta.yaml +++ b/recipes/bioconductor-kimod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "kimod" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ac2fed88431f934bc321ec41fcdfbcbba2fa059c46d08cf43e629ebfcc5e6955 + sha256: c91a16dbce166039ff2c3c2848df2a8096ae1c51c77134c3408487c5c445280d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster test: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package allows to work with mixed omics data (transcriptomics, proteomics, microarray-chips, rna-seq data), introducing the following improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques on the residuals matrices for all methods, that enable perform confidence ellipses for the projection of individuals, variables and biplot methodology to project variables (gene expression) on the compromise. Since the main purpose of the package is to use these techniques to omic data analysis, it includes an example data from four different microarray platforms (i.e.,Agilent, Affymetrix HGU 95, Affymetrix HGU 133 and Affymetrix HGU 133plus 2.0) on the NCI-60 cell lines.NCI60_4arrays is a list containing the NCI-60 microarray data with only few hundreds of genes randomly selected in each platform to keep the size of the package small. The data are the same that the package omicade4 used to implement the co-inertia analysis. The references in packages follow the style of the APA-6th norm.' - extra: identifiers: - biotools:kimod diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml index 57867a6d72fa5..e2106ffdf8e75 100644 --- a/recipes/bioconductor-kodata/meta.yaml +++ b/recipes/bioconductor-kodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "KOdata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 397b5a16e14fa9d62ac0987856a9d483ead2527a40aab512cd8551a5ed582eb6 + sha256: 9aa4e4082fadfae9f2b4c97082f47f00b3aeb5b465e3666547261924a2ccf717 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs.' + + diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh index 24172062c8693..74bcf8dea98a7 100644 --- a/recipes/bioconductor-kodata/post-link.sh +++ b/recipes/bioconductor-kodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="KOdata_1.4.0.tar.gz" +FN="KOdata_1.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/KOdata_1.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/KOdata_1.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.4.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/KOdata_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/KOdata_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.6.0_src_all.tar.gz" ) -MD5="205ff9b0327541c7fae4a83f6092b892" +MD5="dc3b30e0ba2762efc3f80d0b9718e709" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-lapmix/meta.yaml b/recipes/bioconductor-lapmix/meta.yaml index 942a0438235b3..95aeb71df3d8f 100644 --- a/recipes/bioconductor-lapmix/meta.yaml +++ b/recipes/bioconductor-lapmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "lapmix" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 65f54b8662f1641d4310ddaec3d424f5123ad1bc2939b878587b0dacb152edac + sha256: 49c79ea0e469b65e65013a1160efa2e94f55f645c45cefe13d2918427f4c30ab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes.' - extra: identifiers: - biotools:lapmix diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml index 9b95c375ba805..0502b670e6eed 100644 --- a/recipes/bioconductor-lbe/meta.yaml +++ b/recipes/bioconductor-lbe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "LBE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 209bfcc9a21c4a2559f73b3a4aa75077f432ddad9d4cb62df3c150f99bb7061c + sha256: d0dcc9afb41446a8678ef0462f0338c3ae8c3ae560d014401c591250922fcaba build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.' - extra: identifiers: - biotools:lbe diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml index 74315e947af2d..2bb2ed3d1f005 100644 --- a/recipes/bioconductor-les/meta.yaml +++ b/recipes/bioconductor-les/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "les" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e9e493b1dc2725beec76cb0260bb8d0b4ac0762788f38a0e0b118825d87bc777 + sha256: 4e7b1092231c92a8a999c9305d0b42cdf2ba15ad7e1931c5fdf85afd39847788 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The ''les'' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.' - extra: identifiers: - biotools:les diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml index 3104c0ec17e8f..1d06b4c260a42 100644 --- a/recipes/bioconductor-lfa/meta.yaml +++ b/recipes/bioconductor-lfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "lfa" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 70e7638bb4d4acb8a4e71c01357a6118ce6570342bafd36267a262cec500801b + sha256: 811f74e732d71c8587289fa21542859343a5f2acedbe4e49deca34d13fed3db4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-corpcor run: - r-base - r-corpcor - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.' - extra: identifiers: - biotools:lfa diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 147a994a24c83..cd63ac25ce235 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.9" %} +{% set version = "3.36.5" %} {% set name = "limma" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ac4d09c4532c6c0f5a589f5bc2e65d89f39f20df3d0c3a24b00ec4f282a94ef8 + sha256: dd387189502b1ab1496abb1ab51d84e3144a3628d3b8a61d76869ea84be22334 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -30,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Data analysis, linear models and differential expression for microarray data.' - extra: identifiers: - biotools:limma diff --git a/recipes/bioconductor-linc/meta.yaml b/recipes/bioconductor-linc/meta.yaml index 5a09b92bf018c..cfc99e0181c48 100644 --- a/recipes/bioconductor-linc/meta.yaml +++ b/recipes/bioconductor-linc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "LINC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cde9f0069dd8a1db8483a969dddd7107d16fd89a76ba867305664c5d2fcb8b4a + sha256: fa99f4972967990f8a5517a948573fcd50df811c86affbbf1349e8144f37c855 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-clusterprofiler - - bioconductor-dose - - bioconductor-ggtree - - bioconductor-org.hs.eg.db - - bioconductor-reactomepa - - bioconductor-sva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-clusterprofiler >=3.8.1,<3.10.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-ggtree >=1.12.7,<1.14.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-reactomepa >=1.24.0,<1.26.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-ape - r-base - r-ggplot2 @@ -35,13 +33,13 @@ requirements: - 'r-rcpp >=0.11.0' - r-reshape2 run: - - bioconductor-biobase - - bioconductor-clusterprofiler - - bioconductor-dose - - bioconductor-ggtree - - bioconductor-org.hs.eg.db - - bioconductor-reactomepa - - bioconductor-sva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-clusterprofiler >=3.8.1,<3.10.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-ggtree >=1.12.7,<1.14.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-reactomepa >=1.24.0,<1.26.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-ape - r-base - r-ggplot2 @@ -49,7 +47,10 @@ requirements: - r-png - 'r-rcpp >=0.11.0' - r-reshape2 - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -57,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with the sets of protein-coding genes predict the biological contexts of lincRNAs according to the ''Guilty by Association'' approach.' - extra: identifiers: - biotools:linc diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml index 479c18f67df75..19a46e1079e14 100644 --- a/recipes/bioconductor-liquidassociation/meta.yaml +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "LiquidAssociation" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8ed8895daf684d68196ea3e2464300c3968bb0535da84dc19a949b33822e2750 + sha256: 4ced300a886d072525ba67663e38b61546cd4dda9d650df0c1109b29977fe26e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-org.sc.sgd.db - - bioconductor-yeastcc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' + - 'bioconductor-yeastcc >=1.20.0,<1.22.0' - r-base - r-geepack run: - - bioconductor-biobase - - bioconductor-org.sc.sgd.db - - bioconductor-yeastcc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' + - 'bioconductor-yeastcc >=1.20.0,<1.22.0' - r-base - r-geepack test: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.' - extra: identifiers: - biotools:liquidassociation diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml index f0bf3486ba1ae..c2d8b9063b5bb 100644 --- a/recipes/bioconductor-lmdme/meta.yaml +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "lmdme" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c32a048d9c26b6b1faab9f9694ba52110918ca240f8dd617b8978954b873829c + sha256: 2f9ffe3b00ec3647ce97a97a2d1295cc1aafd8cf8cfd8733a428af7db210ec32 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma - - bioconductor-stemhypoxia + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-stemhypoxia >=1.16.0,<1.18.0' - r-base - r-pls run: - - bioconductor-limma - - bioconductor-stemhypoxia + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-stemhypoxia >=1.16.0,<1.18.0' - r-base - r-pls test: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.' - extra: identifiers: - biotools:lmdme diff --git a/recipes/bioconductor-lmgene/conda_build_config.yaml b/recipes/bioconductor-lmgene/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-lmgene/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-lmgene/meta.yaml b/recipes/bioconductor-lmgene/meta.yaml index b400de9a8788c..d96dfdcd880d5 100644 --- a/recipes/bioconductor-lmgene/meta.yaml +++ b/recipes/bioconductor-lmgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "LMGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c0724e49af72c94475c8b521036a2fb5ae615002feb7a1657a7cbe7e6b3b7bdb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9a602a29c969ca5ba6f93c3e6014f40242e5e841cf19a3fa2d1a6617efb2a49e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - 'bioconductor-biobase >=2.5.5' - - bioconductor-multtest + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-survival run: - - bioconductor-affy - - 'bioconductor-biobase >=2.5.5' - - bioconductor-multtest + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-survival test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'LMGene package for analysis of microarray data using a linear model and glog data transformation' - extra: identifiers: - biotools:lmgene diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml index ab9c0e4288da9..728828b5a2b71 100644 --- a/recipes/bioconductor-lobstahs/meta.yaml +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "LOBSTAHS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a4175dc76a2ce2b6a1653350ed0590cbcdb46c8c79aac11730380bb4553d7eeb + sha256: 4bcf09ab10499f0c40ef9bcdcfb447a5ae0224a6b60f8f1e33b31c389081f9f8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-camera - - bioconductor-xcms + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base run: - - bioconductor-camera - - bioconductor-xcms + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3) + file LICENSE' summary: 'LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.' - extra: identifiers: - biotools:lobstahs diff --git a/recipes/bioconductor-logitt/conda_build_config.yaml b/recipes/bioconductor-logitt/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-logitt/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-logitt/meta.yaml b/recipes/bioconductor-logitt/meta.yaml index 4bb2b398b1b22..ec69b83e50f09 100644 --- a/recipes/bioconductor-logitt/meta.yaml +++ b/recipes/bioconductor-logitt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "logitT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 96bf3b3e9e8cbb4343204c064173ca27c93a396c8f9e445af6acadce58294b22 + sha256: e788db17ee40993ffb464460e63d2a790d203135cfbcf176d60ddea9b2092e7a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base run: - - bioconductor-affy + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -32,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R.' - extra: identifiers: - biotools:logitt diff --git a/recipes/bioconductor-lol/meta.yaml b/recipes/bioconductor-lol/meta.yaml index 0ce24cd5bbc59..c387b9ac2441d 100644 --- a/recipes/bioconductor-lol/meta.yaml +++ b/recipes/bioconductor-lol/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "lol" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e3356066abce1843daf46078b28e36b927055e7e6c31e09958366e0cf8279403 + sha256: 147983f5f1a7dd599d0c363e26c7336d185324a204f6fa807ba24b6490cfc0cf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Various optimization methods for Lasso inference with matrix warpper' - extra: identifiers: - biotools:lol diff --git a/recipes/bioconductor-lola/meta.yaml b/recipes/bioconductor-lola/meta.yaml index de32b38f4fe12..d4a67400e5784 100644 --- a/recipes/bioconductor-lola/meta.yaml +++ b/recipes/bioconductor-lola/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "LOLA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cd888afea7cfa96ed0fb5db67b83b3804512b1472d1e5d17c6ad2198f78a6f72 + sha256: fe640761901f36c325ca8a577ed80b9eb72e71151fee9d01b40abfee37b3075e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-reshape2 run: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-reshape2 @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.' - extra: identifiers: - biotools:lola diff --git a/recipes/bioconductor-lpe/meta.yaml b/recipes/bioconductor-lpe/meta.yaml index d182cae1350d0..346677eb88ace 100644 --- a/recipes/bioconductor-lpe/meta.yaml +++ b/recipes/bioconductor-lpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "LPE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8cd8855d2ff9deecef869bed34f4e6151dd697e1e97e62e17bd73b38c305d581 + sha256: aca45e60269876d9490d4eb66b66a9fcf6f2c9b0f144b404f7ae03159cd04716 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional ''BH'' or ''BY'' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.' - extra: identifiers: - biotools:lpe diff --git a/recipes/bioconductor-lpeadj/meta.yaml b/recipes/bioconductor-lpeadj/meta.yaml index 75032c69dfa52..2f36df11d812d 100644 --- a/recipes/bioconductor-lpeadj/meta.yaml +++ b/recipes/bioconductor-lpeadj/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "LPEadj" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2e5de18246415264d0490ff688c5ee80488cad5fb00a590f6acfc8f94ac0082 + sha256: fc320f61faefa13016d0b2a0a447f167f60951b747d8463f75af51364c64eadf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-lpe + - 'bioconductor-lpe >=1.54.0,<1.56.0' - r-base run: - - bioconductor-lpe + - 'bioconductor-lpe >=1.54.0,<1.56.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.' - extra: identifiers: - biotools:lpeadj diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml index 355462b89c329..22162263f6216 100644 --- a/recipes/bioconductor-lpnet/meta.yaml +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "lpNet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 41ef36c643c3b5380c0d9bb139496c05bc8579d969f72c3c41d881a039f47d64 + sha256: a93576d46ff8d549c86f2fc4a03fa66dfe2320f57928693121446990454d4ab2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-nem + - 'bioconductor-nem >=2.54.0,<2.56.0' - r-base - r-lpsolve run: - - bioconductor-nem + - 'bioconductor-nem >=2.54.0,<2.56.0' - r-base - r-lpsolve test: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic License 2.0' summary: 'lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.' - extra: identifiers: - biotools:lpnet diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index a9e15233ea84e..0e9cdfc30a501 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "lpsymphony" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 542788a46197349824865aa423c7884f1fd77d7c9713015c4b5c2bd4019ea6e9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d94a93d4365f2e5e2cbd8e078c4deec2592e96122105a577cc8122db0ec518c0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: EPL summary: 'This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users'' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.' - extra: identifiers: - biotools:lpsymphony diff --git a/recipes/bioconductor-lumi/conda_build_config.yaml b/recipes/bioconductor-lumi/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-lumi/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-lumi/meta.yaml b/recipes/bioconductor-lumi/meta.yaml index 0363ed3f37711..f1a59c3d96245 100644 --- a/recipes/bioconductor-lumi/meta.yaml +++ b/recipes/bioconductor-lumi/meta.yaml @@ -1,33 +1,31 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "lumi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 52a98db2580c6404ad7b0b674c26c3eb7df629784f63a806ae5dd002cf08c0bf - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d272815d5c876f5254f5388da3fd6fcff47d3467be2e0d881f41ad8a4769b419 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - 'bioconductor-affy >=1.23.4' - - bioconductor-annotate - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.5.5' - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-methylumi >=2.3.2' - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - r-kernsmooth @@ -37,14 +35,14 @@ requirements: - r-nleqslv - r-rsqlite run: - - 'bioconductor-affy >=1.23.4' - - bioconductor-annotate - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.5.5' - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-methylumi >=2.3.2' - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-dbi - r-kernsmooth @@ -53,20 +51,13 @@ requirements: - 'r-mgcv >=1.4-0' - r-nleqslv - r-rsqlite - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' - summary: 'The lumi package provides an integrated solution for the Illumina microarray data - analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality - control, BeadArray-specific variance stabilization, normalization and gene annotation at - the probe level. It also includes the functions of processing Illumina methylation microarrays, - especially Illumina Infinium methylation microarrays.' - + summary: 'The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.' extra: identifiers: - biotools:lumi diff --git a/recipes/bioconductor-lumihumanall.db/conda_build_config.yaml b/recipes/bioconductor-lumihumanall.db/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-lumihumanall.db/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml index 13cf9085dc685..6423c2f1e8d64 100644 --- a/recipes/bioconductor-lumihumanall.db/meta.yaml +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiHumanAll.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,18 +12,18 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: a2c1bd766e756eb7e01cf196c1809c8a282a4c4caaf1482a0d1961b2c2a8c24e build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.23.25' - - 'bioconductor-org.hs.eg.db >=2.10.1' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.23.25' - - 'bioconductor-org.hs.eg.db >=2.10.1' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -33,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Illumina Human Illumina expression annotation data (chip lumiHumanAll) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-lumihumanall.db/post-link.sh b/recipes/bioconductor-lumihumanall.db/post-link.sh index 52e08acd78dca..362182f027941 100644 --- a/recipes/bioconductor-lumihumanall.db/post-link.sh +++ b/recipes/bioconductor-lumihumanall.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="lumiHumanAll.db_1.22.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiHumanAll.db_1.22.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" ) MD5="ce7e219b50833ceab203f0bbfb11d917" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml index e3e7972bdcc1a..9f9350ea444ec 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "LungCancerACvsSCCGEO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 05e85af977bd740452edec788a24301aba9adc3a7bad29104ff4ea15a3a11974 + sha256: c3b9d6199eb489716b62e1109a056248d6a94f97078782bd738b9ba3c5af8d1f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).' + + diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh index f5e4e1389cdf9..10fdf4fef21c0 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="LungCancerACvsSCCGEO_1.14.0.tar.gz" +FN="LungCancerACvsSCCGEO_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.16.0_src_all.tar.gz" ) -MD5="275e2efe74fcf1823f8547902537e175" +MD5="bad0119977d894701fb20976d5ed8482" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-lvsmirna/conda_build_config.yaml b/recipes/bioconductor-lvsmirna/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-lvsmirna/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-lvsmirna/meta.yaml b/recipes/bioconductor-lvsmirna/meta.yaml index 10aa8d38ebaea..a5d9e847037f6 100644 --- a/recipes/bioconductor-lvsmirna/meta.yaml +++ b/recipes/bioconductor-lvsmirna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "LVSmiRNA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,38 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bcd16c6920f0d0552696068e07625381a7e5daf8b678c321c001759df46c7624 + sha256: 605280d9b3dd048e41f7bf3d5c225b642b199b1b3ab35c361122ce239f5018f9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-limma - - bioconductor-vsn - - bioconductor-zlibbioc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-mass - r-quantreg - r-sparsem run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-limma - - bioconductor-vsn - - bioconductor-zlibbioc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-mass - r-quantreg - r-sparsem - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -49,7 +49,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Normalization of Agilent miRNA arrays.' - extra: identifiers: - biotools:lvsmirna diff --git a/recipes/bioconductor-m3d/meta.yaml b/recipes/bioconductor-m3d/meta.yaml index 74f01dfe73656..352fe0a8f2251 100644 --- a/recipes/bioconductor-m3d/meta.yaml +++ b/recipes/bioconductor-m3d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "M3D" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,35 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f49f19f08e965ec869f4fe5913c471e6fbb2874d0afff5a21a3af71428ef6bf0 + sha256: 306c0dc66599465d9799e2c3dbdf5cd94af4dda040ffeb14df29ac0edd432942 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-biseq - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biseq >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-rcpp run: - - bioconductor-biocgenerics - - bioconductor-biseq - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biseq >=1.20.0,<1.22.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-rcpp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic License 2.0' summary: 'This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.' - extra: identifiers: - biotools:m3d diff --git a/recipes/bioconductor-m3drop/meta.yaml b/recipes/bioconductor-m3drop/meta.yaml index f7f9be8464250..dc34c1ff3d440 100644 --- a/recipes/bioconductor-m3drop/meta.yaml +++ b/recipes/bioconductor-m3drop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "M3Drop" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 244deb9e0dc8f093e8c24e7fe5202098b1676cb5e08b514ec9fa0902e3b7408b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cfe0157b46306c5de17b0f651eb2b4c6a30819b3200fc70093ab2e0f61a89c31 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.' - extra: identifiers: - biotools:m3drop diff --git a/recipes/bioconductor-maanova/meta.yaml b/recipes/bioconductor-maanova/meta.yaml index b5d4fa3f9220a..59ec8335899df 100644 --- a/recipes/bioconductor-maanova/meta.yaml +++ b/recipes/bioconductor-maanova/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "maanova" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1818c4d535605cb5f4aba28ba0137569962e11f1c191e9113db0dc8abc9972ef + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ab170030f4581a7377913e8c27881854dfe69e5c2310b20d7b81be06fb84209d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree.' - extra: identifiers: - biotools:maanova diff --git a/recipes/bioconductor-macat/meta.yaml b/recipes/bioconductor-macat/meta.yaml index 938e502353012..60d4811ba918d 100644 --- a/recipes/bioconductor-macat/meta.yaml +++ b/recipes/bioconductor-macat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "macat" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 453e555fdc2e90368eb7aaedbc0d8f752bc08f92dbde085d1372d91057e11299 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5def6e15d502df965e996b04ea5afaa1651fb5d9524afce3608a9018483c7d6c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-biobase + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-annotate - - bioconductor-biobase + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library ''stjudem''.' - extra: identifiers: - biotools:macat diff --git a/recipes/bioconductor-macorrplot/meta.yaml b/recipes/bioconductor-macorrplot/meta.yaml index 554519ce033ae..cc4e717f88865 100644 --- a/recipes/bioconductor-macorrplot/meta.yaml +++ b/recipes/bioconductor-macorrplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "maCorrPlot" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 39ecc1b42a08a4066844d980fdb3c247b4bb335650c31e76490795784f59c64b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3b2720f6235214af8dbed9ca8b08ba33f1c65e9d2aba01216976303bbbcdde1e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Graphically displays correlation in microarray data that is due to insufficient normalization' - extra: identifiers: - biotools:macorrplot diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index 8e46268f36835..4815b0ab23272 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "made4" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4c27b973c9e8498e6f287da37029ca6bae57aabff7185a5275e2c5430f7147db + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b2748031828a253b0b3f77516933af95ee00e80af7720298a4e19cc49ec34a62 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.' - extra: identifiers: - biotools:made4 diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml index 4460edae637b7..5ecc3e5885bcf 100644 --- a/recipes/bioconductor-madseq/meta.yaml +++ b/recipes/bioconductor-madseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "MADSEQ" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,50 +10,52 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0d52a0eec1af9bac3447d41cf4a86c2e65c770a68227c4192380ac164f538079 + sha256: 00b90dd7263a14723a0405319c7a2598b27938f9271d722f51afb468f1857ec6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-variantannotation - - bioconductor-zlibbioc + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-coda - 'r-rjags >=4-6' + - r-vcfr - r-vgam run: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-variantannotation - - bioconductor-zlibbioc + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-coda - 'r-rjags >=4-6' + - r-vcfr - r-vgam test: commands: @@ -62,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.' - extra: identifiers: - biotools:madseq diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index ba6573804992d..9b627b9df2a62 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -1,30 +1,27 @@ -{% set version = "1.4.27" %} +{% set version = "1.6.15" %} {% set name = "maftools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 20e37e98b23ec3629abe7183f60ee2f7450dc33a1e292c7be7f02bcdeb3608d4 - + sha256: 8d10a210677136232c2a6fb7c1d76fef3ac4387b78ba0aee4edac7c2947d54a3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biostrings - - bioconductor-complexheatmap - - bioconductor-rsamtools - - bioconductor-variantannotation + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-changepoint - r-cometexacttest @@ -39,12 +36,11 @@ requirements: - r-rjson - r-survival - r-wordcloud - run: - - bioconductor-biostrings - - bioconductor-complexheatmap - - bioconductor-rsamtools - - bioconductor-variantannotation + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-changepoint - r-cometexacttest @@ -59,12 +55,12 @@ requirements: - r-rjson - r-survival - r-wordcloud - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.' + + diff --git a/recipes/bioconductor-maigespack/meta.yaml b/recipes/bioconductor-maigespack/meta.yaml index 5e95f43ca1d73..f4a0de968aec2 100644 --- a/recipes/bioconductor-maigespack/meta.yaml +++ b/recipes/bioconductor-maigespack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "maigesPack" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b2241940bd8edacc6f58f5fe913a1c3bfc4fc14331ef55276bded52cf29c22b1 + sha256: 98cf2ae3afe8c07e454ad1cc566e5d45b6dfe509d557a2f868d5d95c1ab12207 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-convert - - bioconductor-graph - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-convert >=1.56.0,<1.58.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base run: - - bioconductor-convert - - bioconductor-graph - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-convert >=1.56.0,<1.58.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data' - extra: identifiers: - biotools:maigespack diff --git a/recipes/bioconductor-makecdfenv/conda_build_config.yaml b/recipes/bioconductor-makecdfenv/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-makecdfenv/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-makecdfenv/meta.yaml b/recipes/bioconductor-makecdfenv/meta.yaml index 758efa133b206..b721590f5bd54 100644 --- a/recipes/bioconductor-makecdfenv/meta.yaml +++ b/recipes/bioconductor-makecdfenv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "makecdfenv" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0a2482b880ea8bc4afc4b90ee4e66b95c9f26a752a63ebf6c0b7312542fbd59d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2bd03184374ccde9683d2b614183918217f9364fa5b51035a67b34dac11d04b5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-affyio - - bioconductor-biobase - - bioconductor-zlibbioc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - bioconductor-affy - - bioconductor-affyio - - bioconductor-biobase - - bioconductor-zlibbioc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.' - extra: identifiers: - biotools:makecdfenv diff --git a/recipes/bioconductor-manta/meta.yaml b/recipes/bioconductor-manta/meta.yaml index 5af80044658e2..9267df19495c9 100644 --- a/recipes/bioconductor-manta/meta.yaml +++ b/recipes/bioconductor-manta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "manta" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 06f42b534ea7e0f7d8a2cb97c14d569401f9f49087a78ed41508f5f95b2e1d18 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b0790ed4d465257a1bd7edf9318ee8691e668648ddb747fb98768f3f8d221c18 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-edger >=2.5.13' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - 'r-caroline >=0.6.6' - r-hmisc run: - - 'bioconductor-edger >=2.5.13' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - 'r-caroline >=0.6.6' - r-hmisc @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for robust comparative metatranscriptomics.' - extra: identifiers: - biotools:manta diff --git a/recipes/bioconductor-mantelcorr/meta.yaml b/recipes/bioconductor-mantelcorr/meta.yaml index e6a01caf7084c..383fc9fdc27ce 100644 --- a/recipes/bioconductor-mantelcorr/meta.yaml +++ b/recipes/bioconductor-mantelcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "MantelCorr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 163551f347fb0da414b6eb1dd523eb43db6c257e3c08e052bc81ccbb3d33d24a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d46af1b33116d753766509325dd3df961a77bbdff2cbf50b168a059d61860c31 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).' - extra: identifiers: - biotools:mantelcorr diff --git a/recipes/bioconductor-mapredictdsc/conda_build_config.yaml b/recipes/bioconductor-mapredictdsc/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-mapredictdsc/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml index d9848302ef16c..c5346a79ff404 100644 --- a/recipes/bioconductor-mapredictdsc/meta.yaml +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "maPredictDSC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 782eb25ac55afba8545bb91d11a7aa8e7fb8267f67d4be5fa40b6466f4f99f0b + sha256: d632461eae6b5153f6962c09fece614f26bd1f93c3dabdc6432d5be4d457a363 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-annotationdbi - - bioconductor-gcrma - - bioconductor-hgu133plus2.db - - bioconductor-limma - - bioconductor-lungcanceracvssccgeo - - bioconductor-roc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-lungcanceracvssccgeo >=1.16.0,<1.18.0' + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - r-caret - r-class @@ -32,13 +32,13 @@ requirements: - r-mass - r-rocr run: - - bioconductor-affy - - bioconductor-annotationdbi - - bioconductor-gcrma - - bioconductor-hgu133plus2.db - - bioconductor-limma - - bioconductor-lungcanceracvssccgeo - - bioconductor-roc + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-lungcanceracvssccgeo >=1.16.0,<1.18.0' + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - r-caret - r-class @@ -52,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.' - extra: identifiers: - biotools:mapredictdsc diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index dd1544fd4ab37..fda8d59a595e3 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "marray" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2caad6eab11df6f58022ebbfb357e03af6b4cd07945cd415b1f2306f501c8991 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0d019856af63d85064f2618fa10b2be6e838f5e26e56b5c22a1e073f20756914 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - bioconductor-limma + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.' - extra: identifiers: - biotools:marray diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index 4f5b890f79032..6ea20e864dfc8 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "maSigPro" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a06d8b226f47c66dcc4cca92dad943d2899d93617969bd345eee6a41aae3d9b4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c83be0c892cf6ae6852096d794e9a3d65ed96bdadeb7026581598063c6745411 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass - r-mclust - r-venn run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass - r-mclust @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.' - extra: identifiers: - biotools:masigpro diff --git a/recipes/bioconductor-maskbad/conda_build_config.yaml b/recipes/bioconductor-maskbad/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-maskbad/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml index b8e5e379fbd6b..802dde7bfbe4e 100644 --- a/recipes/bioconductor-maskbad/meta.yaml +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "maskBAD" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e8520c0db92e73eb06e1a641b088f28c2cbc7ea5ea965f34f871f3f17ccae265 + sha256: d72601b240e9f5c044c777bff2082ac7dc346fe3c86ed3676e7341b86f4f22de build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - 'bioconductor-gcrma >=2.27.1' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' - r-base run: - - bioconductor-affy - - 'bioconductor-gcrma >=2.27.1' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL version 2 or newer' + license: 'GPL (>= 2)' summary: 'Package includes functions to analyze and mask microarray expression data.' - extra: identifiers: - biotools:maskbad diff --git a/recipes/bioconductor-massarray/meta.yaml b/recipes/bioconductor-massarray/meta.yaml index ec30b94bdb767..464e5b81f646d 100644 --- a/recipes/bioconductor-massarray/meta.yaml +++ b/recipes/bioconductor-massarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MassArray" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 36c68047822ea78d9d5d1e66828fd2fb4bff1d57a64a8a8a15f691fe27346d84 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a1f6e69106e3ce3d2f356703008c580fd63bbe664fc226bd82368b31a6f025da build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom''s MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.' - extra: identifiers: - biotools:massarray diff --git a/recipes/bioconductor-massir/meta.yaml b/recipes/bioconductor-massir/meta.yaml index e55fbf9b2a532..a416a99340202 100644 --- a/recipes/bioconductor-massir/meta.yaml +++ b/recipes/bioconductor-massir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "massiR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d4e26951b1cd7cf838be9dcf38041091aadf9f8af29d71777f9e476e2a3b6b9d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cbe2608b58442c535b78513537ab0e1dea58279fa5af975b5100e4c9ea0600b0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster - r-diptest - r-gplots run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-cluster - r-diptest @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Predicts the sex of samples in gene expression microarray datasets' - extra: identifiers: - biotools:massir diff --git a/recipes/bioconductor-massspecwavelet/meta.yaml b/recipes/bioconductor-massspecwavelet/meta.yaml index 43c95ac339040..24303bda7fc11 100644 --- a/recipes/bioconductor-massspecwavelet/meta.yaml +++ b/recipes/bioconductor-massspecwavelet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "MassSpecWavelet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e0c3af15cb76931212ca9ad2851207e561d2d8d44a4695129b52dde3882615e0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1f028a643031034a21d1c11a3a93bdc994e6f770e9c0bb097dd3c01d3880195e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,9 @@ requirements: run: - r-base - r-waveslim + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Processing Mass Spectrometry spectrum by using wavelet based algorithm' - extra: identifiers: - biotools:massspecwavelet diff --git a/recipes/bioconductor-mast/conda_build_config.yaml b/recipes/bioconductor-mast/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-mast/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-mast/meta.yaml b/recipes/bioconductor-mast/meta.yaml index b44bfec8942e1..7f5e432a95f82 100644 --- a/recipes/bioconductor-mast/meta.yaml +++ b/recipes/bioconductor-mast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "MAST" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 524b5dfa4131581649410852ff999d007ed57c4b1f6ae2244b60fbff0afa5871 + sha256: ebaeaf51c011113e3c2871773c3b10e0cd61fc9e4d9f7bb4afe83f40ebf02bff build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.5.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-abind - r-base - r-data.table @@ -30,10 +31,11 @@ requirements: - r-reshape2 - r-stringr run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.5.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-abind - r-base - r-data.table @@ -48,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL(>= 2)' summary: 'Methods and models for handling zero-inflated single cell assay data.' - extra: identifiers: - biotools:mast diff --git a/recipes/bioconductor-matter/meta.yaml b/recipes/bioconductor-matter/meta.yaml index 5d0c680b91997..2ca0418b609c9 100644 --- a/recipes/bioconductor-matter/meta.yaml +++ b/recipes/bioconductor-matter/meta.yaml @@ -8,39 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: 713c5f73024d38c60d7e457b02dc7a28dba4dcb3b5474d771679bc5960c23d0e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('fortran') }} host: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-biglm - - r-irlba - r-digest + - r-irlba run: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-biglm - - r-irlba - r-digest + - r-irlba + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, and arrays.' - + summary: 'Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, arrays, lists, and data frames.' extra: identifiers: - biotools:matter - doi:10.1038/nmeth.3252 - skip-lints: - - bioconductor_37 diff --git a/recipes/bioconductor-mbamethyl/meta.yaml b/recipes/bioconductor-mbamethyl/meta.yaml index a8f7e9575a282..bcf7f107b713b 100644 --- a/recipes/bioconductor-mbamethyl/meta.yaml +++ b/recipes/bioconductor-mbamethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MBAmethyl" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0940e1d2469a6c209b53e2ce97714c2b42adcabdbd4cd37e00e106bd285950c0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ba443711fabff88ce89bd4e723760c6fccefd7b3f8d36d08c21c25716bee4b1d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.' - extra: identifiers: - biotools:mbamethyl diff --git a/recipes/bioconductor-mbased/meta.yaml b/recipes/bioconductor-mbased/meta.yaml index db9f1b78fcc61..c2ba19b017cc4 100644 --- a/recipes/bioconductor-mbased/meta.yaml +++ b/recipes/bioconductor-mbased/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MBASED" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ae2286c1d997e8b514fc24b0d71926ee28f61bdbc016c9cc647c2426dea849fb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c5770fa061f34e461613f9946d4d18d0a1d9b276ab60883060f31f8c199b1ed3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomicranges - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-runit run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-genomicranges - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-runit test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.' - extra: identifiers: - biotools:mbased diff --git a/recipes/bioconductor-mbttest/meta.yaml b/recipes/bioconductor-mbttest/meta.yaml index cc89ca76c9f7b..135fa3168f50a 100644 --- a/recipes/bioconductor-mbttest/meta.yaml +++ b/recipes/bioconductor-mbttest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.5.0" %} +{% set version = "1.8.1" %} {% set name = "MBttest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -9,10 +9,10 @@ source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9f9638711176a13fd416f31a69fd40a3778a808e9b6fd3083c16d71a0c6c5c3f + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f971d2ebf2c5e81a1e29a0d05c84392adbe414c4ba3ceba967281c4158008386 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.' - extra: identifiers: - biotools:mbttest diff --git a/recipes/bioconductor-mcrestimate/meta.yaml b/recipes/bioconductor-mcrestimate/meta.yaml index 3fc65beb55cec..5b9fc46483c72 100644 --- a/recipes/bioconductor-mcrestimate/meta.yaml +++ b/recipes/bioconductor-mcrestimate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "MCRestimate" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 234beb71a27eb29c92a96e3c09c9928d7915b2ab63e7770fba8a346aea5d8ad8 + sha256: f9bd512483fa6b8fd4e1b1d55ae50a722fec4528f20e846b621e396c951b36fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - 'bioconductor-golubesets >=1.4.6' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-golubesets >=1.22.0,<1.24.0' - r-base - 'r-e1071 >=1.5-12' - 'r-pamr >=1.22' - 'r-randomforest >=3.9-6' - 'r-rcolorbrewer >=0.1-3' run: - - 'bioconductor-biobase >=2.5.5' - - 'bioconductor-golubesets >=1.4.6' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-golubesets >=1.22.0,<1.24.0' - r-base - 'r-e1071 >=1.5-12' - 'r-pamr >=1.22' @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package includes a function for combining preprocessing and classification methods to calculate misclassification errors' - extra: identifiers: - biotools:mcrestimate diff --git a/recipes/bioconductor-mdgsa/meta.yaml b/recipes/bioconductor-mdgsa/meta.yaml index 0a0bcdc6b0311..6e59c0a694701 100644 --- a/recipes/bioconductor-mdgsa/meta.yaml +++ b/recipes/bioconductor-mdgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "mdgsa" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 63fb4e58efbae048dc16f24435d9ba00af5cf706cc4b48b4dbff06c243be3b76 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 26a2dfe9c83daf777cf76c0f452fe19baffc9080c4e7043edccd3ee3091a8fe7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-go.db - - bioconductor-kegg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - r-base - r-cluster - r-dbi - r-matrix run: - - bioconductor-annotationdbi - - bioconductor-go.db - - bioconductor-kegg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - r-base - r-cluster - r-dbi @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Functions to preform a Gene Set Analysis in several genomic dimensions. Including methods for miRNAs.' - extra: identifiers: - biotools:mdgsa diff --git a/recipes/bioconductor-mdqc/meta.yaml b/recipes/bioconductor-mdqc/meta.yaml index 05debce9f4474..cb74c51677b73 100644 --- a/recipes/bioconductor-mdqc/meta.yaml +++ b/recipes/bioconductor-mdqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "mdqc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 20a78f2ad54d2cb1b6f1346c328469bf25b692fde308b030d174eb49289c194e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 651ef51f80b42aee74ae6fcedd34c0bc44261b8c6dd828e7a38a01f5cde68d98 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array''s quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.' - extra: identifiers: - biotools:mdqc diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml index d087ea7a22257..ba4a286abb21e 100644 --- a/recipes/bioconductor-measurementerror.cor/meta.yaml +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "MeasurementError.cor" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 485255ba0804cdc0560a6a15e4cb2c4f728e6a105e4aabfd401cccd3a04f7e3e + sha256: e1f6fd5283877bffd2dadf347b4c8e2d18a4053c6dc13b4ebcfba90447143496 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -28,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation' - extra: identifiers: - biotools:measurementerror.cor diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index e999464e4d496..d0e2837c93207 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MEDIPS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6d3487517aee8411efd236a408bf8bdc805001e1667bc7899188e5f18820b51a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 455c89e4898263be0ee3d937cec61a1d6e2e75b4f6e373d97bc8020ef751acce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-dnacopy - - bioconductor-edger - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-gtools run: - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-dnacopy - - bioconductor-edger - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-gtools test: @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.' - extra: identifiers: - biotools:medips diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml index d236689c60eda..d921758ea592f 100644 --- a/recipes/bioconductor-medme/meta.yaml +++ b/recipes/bioconductor-medme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MEDME" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 37154c7d207b4f5f03bc26e19c57b6a798ba9eb8fa666d073e99fcf1c24ff78c + sha256: 6720cc486f736e58f350f0b7a7f8b685cacfbc12660575b3b7865db3eb1f5973 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-drc - r-mass run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-drc - r-mass - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Description: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments' - extra: identifiers: - biotools:medme diff --git a/recipes/bioconductor-meigor/meta.yaml b/recipes/bioconductor-meigor/meta.yaml index 0f4430c44a210..43eef27b964c1 100644 --- a/recipes/bioconductor-meigor/meta.yaml +++ b/recipes/bioconductor-meigor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MEIGOR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: db8717398347cf12e790303fd55287def0310056e985e198ccc7cc7dac3a9c17 + sha256: 3498f08b7d834c7b8f879d0a074261325870490d2df69e07672a83ade172a912 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cnorode + - 'bioconductor-cnorode >=1.22.0,<1.24.0' - r-base - r-desolve - r-rsolnp - r-snowfall run: - - bioconductor-cnorode + - 'bioconductor-cnorode >=1.22.0,<1.24.0' - r-base - r-desolve - r-rsolnp @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Global Optimization' - extra: identifiers: - biotools:meigor diff --git a/recipes/bioconductor-mergemaid/meta.yaml b/recipes/bioconductor-mergemaid/meta.yaml index a25383d86b0b3..01588439c286d 100644 --- a/recipes/bioconductor-mergemaid/meta.yaml +++ b/recipes/bioconductor-mergemaid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "MergeMaid" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4a65bedc6a224db2a5d49f9c4e5699fd35bd6a255ed003b8d2629cca4dcd522f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c27c0907ec96bd2fab59c072e58a0a45d0b74b736858935fd9e8f0dda23a7b14 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass - r-survival run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass - r-survival @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be ''list'',''matrix'', or ''ExpressionSet''. The main function is ''mergeExprs'' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function ''intcor'' calculate the correlation coefficients. Other functions use the output from ''modelOutcome'' to graphically display the results and cross-validate associations of gene expression data with survival.' - extra: identifiers: - biotools:mergemaid diff --git a/recipes/bioconductor-mergeomics/meta.yaml b/recipes/bioconductor-mergeomics/meta.yaml index e2850a51feca1..74bfa1edca90d 100644 --- a/recipes/bioconductor-mergeomics/meta.yaml +++ b/recipes/bioconductor-mergeomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Mergeomics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e6cfea99508166af890eb9b364ea402ac7806cc33bb25fcca848d6f128134dd4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 19e07d1023d86f5d2debae383e4ef5e5ac51044ce90698b6c248771a76887f86 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).' - extra: identifiers: - biotools:mergeomics diff --git a/recipes/bioconductor-mesh.db/meta.yaml b/recipes/bioconductor-mesh.db/meta.yaml index ab7f3e1ad7520..5aeb6bfef0983 100644 --- a/recipes/bioconductor-mesh.db/meta.yaml +++ b/recipes/bioconductor-mesh.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.9.0" %} +{% set version = "1.10.0" %} {% set name = "MeSH.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b4a3007127c0d6b912d4eb7ce21aedd68dc78951504a8953e819c6ef6eb92ee + sha256: bf8fc760ff396641bea95f73a8688adc43efa18d827cb2c537e4181b9bc807ee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-meshdbi + - 'bioconductor-meshdbi >=1.16.0,<1.18.0' - r-base run: - - bioconductor-meshdbi + - 'bioconductor-meshdbi >=1.16.0,<1.18.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire MeSH assembled using data from MeSH.' + + diff --git a/recipes/bioconductor-mesh.db/post-link.sh b/recipes/bioconductor-mesh.db/post-link.sh index 603377e4b8c97..702d0ead2a246 100644 --- a/recipes/bioconductor-mesh.db/post-link.sh +++ b/recipes/bioconductor-mesh.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.db_1.9.0.tar.gz" +FN="MeSH.db_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/MeSH.db_1.9.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.db_1.9.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.9.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/MeSH.db_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.db_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.10.0_src_all.tar.gz" ) -MD5="8e29b2c99bc3aa3ee25bc8c581d3dac8" +MD5="f47e271183018989338e75970620ce41" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-meshdbi/meta.yaml b/recipes/bioconductor-meshdbi/meta.yaml index f9648730c63ec..fdeb406290a93 100644 --- a/recipes/bioconductor-meshdbi/meta.yaml +++ b/recipes/bioconductor-meshdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MeSHDbi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ddb114ad405bdf9002526d144c81b9054a8a3dd95681d0d614963302544d3982 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: aa4b5dea29fe4853eaf22b592ebf27b6fc47551614aa9f095e666ca47b9523d0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.31.19' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.31.19' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-rsqlite test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.' - extra: identifiers: - biotools:meshdbi diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml index b9352729bed6d..b36be7b608a67 100644 --- a/recipes/bioconductor-meshes/meta.yaml +++ b/recipes/bioconductor-meshes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "meshes" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 020206f48961464fb1e38b35ed53b71d88f4a41dc629b747f85c036c8284e2eb + sha256: 89c8ec6bb5917e010e0db16eaad2129931df482b3b2472dd4ffd52a55b2959c0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-dose >=2.11.7' - - 'bioconductor-gosemsim >=1.99.3' - - bioconductor-mesh.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-mesh.db >=1.10.0,<1.12.0' - r-base - r-rvcheck run: - - bioconductor-annotationdbi - - 'bioconductor-dose >=2.11.7' - - 'bioconductor-gosemsim >=1.99.3' - - bioconductor-mesh.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-mesh.db >=1.10.0,<1.12.0' - r-base - r-rvcheck test: @@ -38,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.' - extra: identifiers: - biotools:meshes diff --git a/recipes/bioconductor-meshsim/meta.yaml b/recipes/bioconductor-meshsim/meta.yaml index c2fdebbe101fa..1e33c427e3f14 100644 --- a/recipes/bioconductor-meshsim/meta.yaml +++ b/recipes/bioconductor-meshsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version="1.7.0" %} -{% set name="MeSHSim" %} -{% set bioc="3.5" %} +{% set version = "1.7.0" %} +{% set name = "MeSHSim" %} +{% set bioc = "3.5" %} package: name: 'bioconductor-{{ name|lower}}' @@ -33,6 +33,9 @@ about: license: GPL-2 summary: 'Provide for measuring semantic similarity over MeSH headings and MEDLINE documents' + identifiers: + - biotools:meshsim + - doi:10.1142/S0219720015420020 extra: identifiers: - biotools:meshsim diff --git a/recipes/bioconductor-messina/meta.yaml b/recipes/bioconductor-messina/meta.yaml index b64eae65bbcd5..7ba2acc0311e5 100644 --- a/recipes/bioconductor-messina/meta.yaml +++ b/recipes/bioconductor-messina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "messina" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,16 +8,15 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 156ba193500eb312fdbd6a18905688680d2bda7a987585b0bb445b83ed6e0311 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 10c4fc3c43d7efe7d4338ea2a86ac2a537466449927f875c7df4ac5585bba2d6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - 'r-foreach >=1.4.1' @@ -32,6 +31,10 @@ requirements: - 'r-plyr >=1.8' - 'r-rcpp >=0.11.1' - 'r-survival >=2.37-4' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'EPL (>= 1.0)' summary: 'Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.' - extra: identifiers: - biotools:messina diff --git a/recipes/bioconductor-metaarray/meta.yaml b/recipes/bioconductor-metaarray/meta.yaml index 0d27ee374b9c5..3e5f9b33ce70f 100644 --- a/recipes/bioconductor-metaarray/meta.yaml +++ b/recipes/bioconductor-metaarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "metaArray" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fbb49fb1d98ecf691f63dbdd3540e5258d4ed6b5bd3d595f79d749f580ab70d8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6d17b3fe4860060594b99b873e476217e7c9f2f4e30501c9f16ca252accaaaea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-mergemaid + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-mergemaid >=2.52.0,<2.54.0' - r-base run: - - bioconductor-biobase - - bioconductor-mergemaid + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-mergemaid >=2.52.0,<2.54.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: '1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform' - extra: identifiers: - biotools:metaarray diff --git a/recipes/bioconductor-metab/meta.yaml b/recipes/bioconductor-metab/meta.yaml index 22b4f62220792..b20639b56a207 100644 --- a/recipes/bioconductor-metab/meta.yaml +++ b/recipes/bioconductor-metab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Metab" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c7de781da1c3fc0e13a77999f570e9df8f3532173d0d229b544363f8376cd73e + sha256: a18734efc0f37beebe0a7f64fe896630d62e8919dda375c0c92257f6297dd62a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-xcms + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-pander - r-svdialogs run: - - bioconductor-xcms + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-pander - r-svdialogs @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Metab is an R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) (http://chemdata.nist.gov/mass-spc/amdis/downloads/). In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, Metab considerably speed up the data mining process in metabolomics and produces better quality results. Metab was developed using interactive features, allowing users with lack of R knowledge to appreciate its functionalities.' - extra: identifiers: - biotools:metab diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml index d1ae8a5514ddf..95a21acd4d4ea 100644 --- a/recipes/bioconductor-metabosignal/meta.yaml +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MetaboSignal" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,36 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 29240127a63d40fa7ad31c5e5cb48a024b1a21e84db14f957b487bbf1c63cd63 + sha256: 36a9dc2ccebcc22046a6f57f4708ad3a3e6572df8aa01c1eb0eb89e0281543fe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biomart - - bioconductor-ensdb.hsapiens.v75 - - bioconductor-hpar - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-mwastools - - bioconductor-mygene - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.101.0' + - 'bioconductor-hpar >=1.22.2,<1.24.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-mwastools >=1.4.0,<1.6.0' + - 'bioconductor-mygene >=1.16.2,<1.18.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-igraph - r-rcurl run: - - bioconductor-annotationdbi - - bioconductor-biomart - - bioconductor-ensdb.hsapiens.v75 - - bioconductor-hpar - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-mwastools - - bioconductor-mygene - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.101.0' + - 'bioconductor-hpar >=1.22.2,<1.24.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-mwastools >=1.4.0,<1.6.0' + - 'bioconductor-mygene >=1.16.2,<1.18.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-igraph - r-rcurl @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.' - extra: identifiers: - biotools:metabosignal diff --git a/recipes/bioconductor-metacca/meta.yaml b/recipes/bioconductor-metacca/meta.yaml index a8572f54415db..b4cff6184c4b5 100644 --- a/recipes/bioconductor-metacca/meta.yaml +++ b/recipes/bioconductor-metacca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "metaCCA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 011750c3b1448bf403439eb7d995195a747dfc6a3ad31fc1b4ad3d1185294609 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b68b951ccb5e5e4f0091545315c566649ac82ec4bc818a7ebe23b65de7ad64b6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.' - extra: identifiers: - biotools:metacca diff --git a/recipes/bioconductor-metagenomeseq/meta.yaml b/recipes/bioconductor-metagenomeseq/meta.yaml index 3aaadf037a890..4b04416b81d7c 100644 --- a/recipes/bioconductor-metagenomeseq/meta.yaml +++ b/recipes/bioconductor-metagenomeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "metagenomeSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 81b6286e84f98681b9ab4218851c159413b106b57a964297ff9b19dae09ff245 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1e1e3933f47c7867b3654cd918870c86f7d411b96525bf3cb8ffb4cb7eb47ce1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-foreach - r-glmnet @@ -27,8 +28,8 @@ requirements: - r-matrixstats - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-foreach - r-glmnet @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.' - extra: identifiers: - biotools:metagenomeseq diff --git a/recipes/bioconductor-metahdep/meta.yaml b/recipes/bioconductor-metahdep/meta.yaml index 860da19204dda..0ad1d65a1b9ac 100644 --- a/recipes/bioconductor-metahdep/meta.yaml +++ b/recipes/bioconductor-metahdep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "metahdep" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d27d54f0f52a41c78e5ebb1304d05064fe6e4c191e8ac5310ab927db47ff6583 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: fbe74ec3a8b05e7fb6e27a329f401740e9517d860cb819dc9d551172170ab224 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,9 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies' - extra: identifiers: - biotools:metahdep diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index 7da4f77dff5c7..8dbd387804c81 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "metaMS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 15d79ce9834f4402687b4efb52f1d6802e0894c507e66032cc80f5e02e88e0d2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d5a22f272df23f75c69da2d4cd1505772e4cfdf1a209be4f07b1e489f4cae3f0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-camera - - 'bioconductor-xcms >=1.35' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-matrix - r-robustbase run: - - bioconductor-biocgenerics - - bioconductor-camera - - 'bioconductor-xcms >=1.35' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-camera >=1.36.0,<1.38.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-matrix - r-robustbase @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'MS-based metabolomics data processing and compound annotation pipeline.' - extra: identifiers: - biotools:metams diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index c8a78c35af48b..775b1dc8eda78 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "metaSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3997ca1dbf9703e628ffeb61203839103adface0f066d7aa3aabe3c52dc919b5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d493c972e22285478ad115544e85eeb52ae06b2955d55ca1eec014a0f2dfeb1e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-noiseq + - 'bioconductor-noiseq >=2.24.0,<2.26.0' - r-base - r-rcpp - r-snow run: - - bioconductor-noiseq + - 'bioconductor-noiseq >=2.24.0,<2.26.0' - r-base - r-rcpp - r-snow + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The probabilities by one-sided NOISeq are combined by Fisher''s method or Stouffer''s method' - extra: identifiers: - biotools:metaseq diff --git a/recipes/bioconductor-metcirc/meta.yaml b/recipes/bioconductor-metcirc/meta.yaml index f4c2d1260621a..752abe81b3e5a 100644 --- a/recipes/bioconductor-metcirc/meta.yaml +++ b/recipes/bioconductor-metcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "MetCirc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4382943a58d4c5dd3c8db3be44cde4411c9ee03882d508817d668830c8b7ca80 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 06a75184e2424e261730d58ad8f4b7ee511f1a9075a41af997c6693a55b9817a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data: create an MSP object, a format for MS/MS library data, bin m/z values of precursors, calculate similarity between precursors based on the normalised dot product and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.' - extra: identifiers: - biotools:metcirc diff --git a/recipes/bioconductor-methped/meta.yaml b/recipes/bioconductor-methped/meta.yaml index 2a7905de4d2d8..4e11dae6f5057 100644 --- a/recipes/bioconductor-methped/meta.yaml +++ b/recipes/bioconductor-methped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MethPed" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 024a5599ee593b1ce7aa44e5781252903ccde636d9940ec911b9eca9ce168454 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6f8a451a4402d9b9ca298e596932a978f13679cbaf0c906647dc354a119270e6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-randomforest run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-randomforest test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).' - extra: identifiers: - biotools:methped diff --git a/recipes/bioconductor-methtargetedngs/meta.yaml b/recipes/bioconductor-methtargetedngs/meta.yaml index 3674cf62ce708..1544dc7b545e6 100644 --- a/recipes/bioconductor-methtargetedngs/meta.yaml +++ b/recipes/bioconductor-methtargetedngs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MethTargetedNGS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f006a78b2fc06117fd042264fcd5f52851d59ae8c7e640039c42d1770d2cad93 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 35a8ee457c74f7d65edf9f626f3469493b9fe42aab9577d1b8631d208b933f73 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-gplots - r-seqinr - r-stringr run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-gplots - r-seqinr @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Perform step by step methylation analysis of Next Generation Sequencing data.' - extra: identifiers: - biotools:methtargetedngs diff --git a/recipes/bioconductor-methyanalysis/conda_build_config.yaml b/recipes/bioconductor-methyanalysis/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-methyanalysis/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-methyanalysis/meta.yaml b/recipes/bioconductor-methyanalysis/meta.yaml index cdbf9cf465e08..62f04996595da 100644 --- a/recipes/bioconductor-methyanalysis/meta.yaml +++ b/recipes/bioconductor-methyanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "methyAnalysis" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,52 +10,52 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 83e201c2f3c37f0e29be1f20c6e0384eeb5d48874789a9330ef21176c9d9af32 + sha256: 71a4c455b3588f58cf259bdc4227f8a86549be36017de5df36515b3a9d9dba87 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.34.0' - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-genoset - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-lumi - - bioconductor-methylumi - - bioconductor-org.hs.eg.db - - bioconductor-rtracklayer - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genoset >=1.36.0,<1.38.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base run: - - bioconductor-annotate - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.34.0' - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-genoset - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-lumi - - bioconductor-methylumi - - bioconductor-org.hs.eg.db - - bioconductor-rtracklayer - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genoset >=1.36.0,<1.38.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base test: commands: @@ -64,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The methyAnalysis package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.' - extra: identifiers: - biotools:methyanalysis diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index 67cccba955079..de4aacf2e0e23 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.3" %} {% set name = "methylKit" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b60bc07554e124e9edf9b6087f1fe38f32ce8c4c5384d82cb0e26599abe0a340 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 33590c69b9a36d913730f2cb7daf4a1cd601141ac0f5bdbd0f454b2d1a398ada build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-fastseg - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.18.1' - - bioconductor-iranges - - bioconductor-limma - - bioconductor-qvalue - - bioconductor-rhtslib # not in DESCRIPTION - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.13.13' + - 'bioconductor-fastseg >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook @@ -38,16 +38,17 @@ requirements: - r-r.utils - r-rcpp run: - - bioconductor-fastseg - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.18.1' - - bioconductor-iranges - - bioconductor-limma - - bioconductor-qvalue - - bioconductor-rhtslib # not in DESCRIPTION - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.13.13' + - 'bioconductor-fastseg >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook @@ -56,6 +57,10 @@ requirements: - r-mclust - r-r.utils - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -63,7 +68,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.' - extra: identifiers: - biotools:methylkit diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index 99bcdf8833bc5..3974004b3836d 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "methylMnM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b028097051c7a446303fa85e8aef2c6a277f55be2bb1a7192238781fe99b0153 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 22584a7d451e4a7c7114c0372f3fc420e3c81f6511362f21e65cf57c77011cbe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-edger + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - r-statmod run: - - bioconductor-edger + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - r-statmod + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.' - extra: identifiers: - biotools:methylmnm diff --git a/recipes/bioconductor-methylpipe/meta.yaml b/recipes/bioconductor-methylpipe/meta.yaml index aa34c9bfcce73..d918e99a3351b 100644 --- a/recipes/bioconductor-methylpipe/meta.yaml +++ b/recipes/bioconductor-methylpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "methylPipe" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,44 +8,48 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 69939878022e1e20081a7a3309e0acb5cd895cac4a64da3a91e9ce5f1d48df1c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1e05797af340863c335d3537282025e0c7092cae9aaa85b6dc8b030cc673622c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-marray - - bioconductor-rsamtools - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-gplots run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-marray - - bioconductor-rsamtools - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-gplots + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -53,7 +57,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.' - extra: identifiers: - biotools:methylpipe diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 8359953c3a257..4b5fa59c34a7c 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MethylSeekR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 546ad60c07f0b25a1b79b0aef23af305954449bd51e94b19d169e2b7a4503e34 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a77c81e78e8bdfe9fef27d56af407467395fcfad4d8e42a64e891acf65cfeda5 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bsgenome >=1.26.1' - - 'bioconductor-geneplotter >=1.34.0' - - 'bioconductor-genomicranges >=1.10.5' - - 'bioconductor-iranges >=1.16.3' - - 'bioconductor-rtracklayer >=1.16.3' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - 'r-mhsmm >=0.4.4' run: - - 'bioconductor-bsgenome >=1.26.1' - - 'bioconductor-geneplotter >=1.34.0' - - 'bioconductor-genomicranges >=1.10.5' - - 'bioconductor-iranges >=1.16.3' - - 'bioconductor-rtracklayer >=1.16.3' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - 'r-mhsmm >=0.4.4' - - r-kernsmooth test: commands: - '$R -e "library(''{{ name }}'')"' @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This is a package for the discovery of regulatory regions from Bis-seq data' - extra: identifiers: - biotools:methylseekr diff --git a/recipes/bioconductor-methylumi/meta.yaml b/recipes/bioconductor-methylumi/meta.yaml index 785b6896f1e50..90edd5fb2aa44 100644 --- a/recipes/bioconductor-methylumi/meta.yaml +++ b/recipes/bioconductor-methylumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.1" %} +{% set version = "2.26.0" %} {% set name = "methylumi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2c81232bb11f2494a57b70d3664a70f21b31799e96a477ba5c301dc6748f1c16 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 57c7dd21135f97eb787d09ed8807eb5c5971b0c43dd55627208d9b0256ab662d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0' - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-minfi - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.4.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-lattice @@ -37,19 +38,19 @@ requirements: - r-reshape2 - r-scales run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0' - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-minfi - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.4.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-lattice @@ -63,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.' - extra: identifiers: - biotools:methylumi diff --git a/recipes/bioconductor-mgfm/meta.yaml b/recipes/bioconductor-mgfm/meta.yaml index 716c73329840c..2bec5be092414 100644 --- a/recipes/bioconductor-mgfm/meta.yaml +++ b/recipes/bioconductor-mgfm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MGFM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3afe951ac1e19e7150e477930165008bb40212cf1681129ef136976c1509597a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a2a7559087deeb218da2bf445cef955435d497fe0b66df8e1b14c963a7169ccf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - bioconductor-annotate - - bioconductor-annotationdbi + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package is designed to detect marker genes from Microarray gene expression data sets' - extra: identifiers: - biotools:mgfm diff --git a/recipes/bioconductor-mgfr/meta.yaml b/recipes/bioconductor-mgfr/meta.yaml index 64a5f1f0e67f0..3c110f8cbacec 100644 --- a/recipes/bioconductor-mgfr/meta.yaml +++ b/recipes/bioconductor-mgfr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MGFR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 213cd85703ee20bd07e047fca52adb200752da1807e9a511f618e9508b79dd12 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c93e06fdf48156fc542ae73cc67305ab625eab81008b01c87cfe4a779196d4d9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-biomart + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' - r-base run: - - bioconductor-annotate - - bioconductor-biomart + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package is designed to detect marker genes from RNA-seq data.' - extra: identifiers: - biotools:mgfr diff --git a/recipes/bioconductor-mgsa/meta.yaml b/recipes/bioconductor-mgsa/meta.yaml index 751b2c1b15aef..7524f7bdb49a7 100644 --- a/recipes/bioconductor-mgsa/meta.yaml +++ b/recipes/bioconductor-mgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "mgsa" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6baa2fdf3f7962d40d25b4a5f1b8ff66b49bb945383d9482d1a19796f3aef020 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: fa5422aff3b0539b354139b8f3895127160a37a7c83b4940ed2a0001140fd86b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,10 @@ requirements: run: - r-base - r-gplots + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.' - extra: identifiers: - biotools:mgsa diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 4d308fc1f35dc..9f8ad8f6be1e7 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4122a.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' sha256: bd57e228a20744ed325b970ddd5ca731ca45e957c39d72eebcd7f2d4b0cc9574 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.mm.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.34.3' - - 'bioconductor-org.mm.eg.db >=3.3.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories' + + diff --git a/recipes/bioconductor-mgug4122a.db/post-link.sh b/recipes/bioconductor-mgug4122a.db/post-link.sh index 49f937afbc3d2..3d8878f2bb00e 100644 --- a/recipes/bioconductor-mgug4122a.db/post-link.sh +++ b/recipes/bioconductor-mgug4122a.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="mgug4122a.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgug4122a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz" ) MD5="5fcdce909ac1c0ccbf06bf6411f6fe52" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-michip/meta.yaml b/recipes/bioconductor-michip/meta.yaml index 0172e85143449..f45f2768bc45b 100644 --- a/recipes/bioconductor-michip/meta.yaml +++ b/recipes/bioconductor-michip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MiChip" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4ad127ef1b1316c47a24b2f9889545e44358d924bf35426b57f24b8244cc7cc9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 69eb53f00ca96f769a54ba865d8b984179e7cb365a19b21b5adcf1dc73ca6594 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.' - extra: identifiers: - biotools:michip diff --git a/recipes/bioconductor-microbiome/meta.yaml b/recipes/bioconductor-microbiome/meta.yaml index e39677cbebfc0..c7552d3f1e6e5 100644 --- a/recipes/bioconductor-microbiome/meta.yaml +++ b/recipes/bioconductor-microbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.1" %} {% set name = "microbiome" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f07592421944a233f657d8fe3feaa3643ed0559fd4c90717613996dc507db1a0 + sha256: 59d98634f9b71ec447995e8f2bcb77d654dae598843e9c467e5f087135e7b8e0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-phyloseq + - 'bioconductor-phyloseq >=1.24.2,<1.26.0' - r-base - r-dplyr - r-ggplot2 @@ -26,7 +26,7 @@ requirements: - r-tidyr - r-vegan run: - - bioconductor-phyloseq + - 'bioconductor-phyloseq >=1.24.2,<1.26.0' - r-base - r-dplyr - r-ggplot2 @@ -40,3 +40,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Utilities for microbiome analysis.' + + diff --git a/recipes/bioconductor-microrna/meta.yaml b/recipes/bioconductor-microrna/meta.yaml index ddf11fdf6b843..402534456689d 100644 --- a/recipes/bioconductor-microrna/meta.yaml +++ b/recipes/bioconductor-microrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "microRNA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d276e6a849990865879d56297f93b81e357178d5931c40e9604f0e9fbc0b8855 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3a9b7411555aa850b571a082425ac3717485621e0b2fa0d83ced75cfe054c5a8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.11.32' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base run: - - 'bioconductor-biostrings >=2.11.32' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Different data resources for microRNAs and some functions for manipulating them.' - extra: identifiers: - biotools:microrna diff --git a/recipes/bioconductor-mineica/conda_build_config.yaml b/recipes/bioconductor-mineica/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-mineica/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml index 8ee85684b2f9c..a11a9243ae579 100644 --- a/recipes/bioconductor-mineica/meta.yaml +++ b/recipes/bioconductor-mineica/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MineICA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: beddc6b0f594a43aa5ebf9bbed8b872b6453600bd2f8bc72cca8ea49422cb8fd + sha256: e009aafcc3e787349413f1405e4d7efd00e0e9357910fdca01ea7b035753c9b3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-biomart - - bioconductor-gostats - - bioconductor-graph - - bioconductor-lumi - - bioconductor-lumihumanall.db - - bioconductor-marray - - bioconductor-rgraphviz + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-lumihumanall.db >=1.22.0,<1.24.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-cluster - r-colorspace @@ -46,17 +46,17 @@ requirements: - r-scales - r-xtable run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-biomart - - bioconductor-gostats - - bioconductor-graph - - bioconductor-lumi - - bioconductor-lumihumanall.db - - bioconductor-marray - - bioconductor-rgraphviz + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-lumihumanall.db >=1.22.0,<1.24.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-cluster - r-colorspace @@ -80,7 +80,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.' - extra: identifiers: - biotools:mineica diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml index 961da6f7f33a6..ff49d3c766fb4 100644 --- a/recipes/bioconductor-minet/meta.yaml +++ b/recipes/bioconductor-minet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.36.0" %} +{% set version = "3.38.0" %} {% set name = "minet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c8dabac10814a69fab810600b60c85358fafa62d34a9363b7d176e77209fe9c5 + sha256: f96653b88e780c232e1fa2baa67efe62e7a2642e0ffbe3cf77aef9239ca07e93 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-infotheo run: - r-base - r-infotheo - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'This package implements various algorithms for inferring mutual information networks from data.' - extra: identifiers: - biotools:minet diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index 5756d088cee6a..ec36df4909fba 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.2" %} {% set name = "minfi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,40 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 27b66608e7aceed1b701b5f85fb35d0356b9c964164b1545cf2afef4b7d265de + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e0567ac79a10eff553198943eed842a1000cefc18df03d30201a9bbdbf50d9ff build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.33.2' - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-biostrings - - 'bioconductor-bumphunter >=1.1.9' - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-geoquery - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-limma - - bioconductor-preprocesscore - - bioconductor-s4vectors - - bioconductor-siggenes - - 'bioconductor-summarizedexperiment >=1.1.6' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bumphunter >=1.22.0,<1.24.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-hdf5array >=1.8.1,<1.10.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-beanplot - r-data.table - r-lattice - r-mass - - 'r-matrixstats >=0.50.0' - r-mclust - r-nlme - r-nor1mix @@ -45,27 +49,30 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biobase >=2.33.2' - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-biostrings - - 'bioconductor-bumphunter >=1.1.9' - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-geoquery - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-limma - - bioconductor-preprocesscore - - bioconductor-s4vectors - - bioconductor-siggenes - - 'bioconductor-summarizedexperiment >=1.1.6' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bumphunter >=1.22.0,<1.24.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-hdf5array >=1.8.1,<1.10.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-beanplot - r-data.table - r-lattice - r-mass - - 'r-matrixstats >=0.50.0' - r-mclust - r-nlme - r-nor1mix @@ -79,7 +86,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools to analyze & visualize Illumina Infinium methylation arrays.' - extra: identifiers: - biotools:minfi diff --git a/recipes/bioconductor-minimumdistance/conda_build_config.yaml b/recipes/bioconductor-minimumdistance/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-minimumdistance/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml index 613055bfce6f0..2d199601fdeb9 100644 --- a/recipes/bioconductor-minimumdistance/meta.yaml +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "MinimumDistance" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ea74a8add036e054380cf5e8f73dc8b51b8f64e3917931602263115a2044fc8 + sha256: c14a2d2ccbc66010d589b8ee0b276917cd5e1ed653eb22a85acbac5c8835adb8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-dnacopy - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.17.16' - - bioconductor-iranges - - bioconductor-oligoclasses - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-summarizedexperiment >=0.2.0' - - 'bioconductor-vanillaice >=1.31.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-vanillaice >=1.42.4,<1.44.0' - r-base - r-data.table - r-ff @@ -35,16 +35,16 @@ requirements: - r-lattice - r-matrixstats run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-dnacopy - - bioconductor-genomeinfodb - - 'bioconductor-genomicranges >=1.17.16' - - bioconductor-iranges - - bioconductor-oligoclasses - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-summarizedexperiment >=0.2.0' - - 'bioconductor-vanillaice >=1.31.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-vanillaice >=1.42.4,<1.44.0' - r-base - r-data.table - r-ff @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.' - extra: identifiers: - biotools:minimumdistance diff --git a/recipes/bioconductor-mipp/meta.yaml b/recipes/bioconductor-mipp/meta.yaml index 83de7e92bdc24..b16fd404c7d04 100644 --- a/recipes/bioconductor-mipp/meta.yaml +++ b/recipes/bioconductor-mipp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "MiPP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 35ed9a26100431c2cb7b6d20ed814952d9e5cbe8a8908e0d55ba99824805b1cd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 450c675a8ef7acc06876ae79e56b87e67f8dbdbfc22f7e3d44f3cb40e1de8f7c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-e1071 - r-mass run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-e1071 - r-mass @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package finds optimal sets of genes that seperate samples into two or more classes.' - extra: identifiers: - biotools:mipp diff --git a/recipes/bioconductor-mirage/meta.yaml b/recipes/bioconductor-mirage/meta.yaml index 83ef3897650df..79478da4951e0 100644 --- a/recipes/bioconductor-mirage/meta.yaml +++ b/recipes/bioconductor-mirage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MiRaGE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 11a6e99bc916081bc97e28d29837a6f465c4647cb6153d1045a1d1bb8f207ac9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 661e3447c487e305d9f645aebfa69b166082c3c87ed38b17995c4f8473c45900 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.23.3' - - bioconductor-biocgenerics - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.23.3' - - bioconductor-biocgenerics - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.' - extra: identifiers: - biotools:mirage diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml index b434bd8d61a4d..d5c28935320ac 100644 --- a/recipes/bioconductor-mirbaseversions.db/meta.yaml +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.5" %} +{% set version = "1.1.0" %} {% set name = "miRBaseVersions.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 70835ad0b5653bfe2e770da5f75c121df01849dd9a549386d1d42e2f88efb333 + sha256: 1cc65f746c705d061aa6f5172563389d5abe412dd446c5cd1b456afa1218c026 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi - r-gtools - r-rsqlite run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi - r-gtools @@ -36,4 +36,6 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Annotation package containing all available miRNA names from all versions (data from http://www.mirbase.org/).' + summary: 'Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).' + + diff --git a/recipes/bioconductor-mirbaseversions.db/post-link.sh b/recipes/bioconductor-mirbaseversions.db/post-link.sh index 2b23170567b22..df3d08cff07d2 100644 --- a/recipes/bioconductor-mirbaseversions.db/post-link.sh +++ b/recipes/bioconductor-mirbaseversions.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="miRBaseVersions.db_0.99.5.tar.gz" +FN="miRBaseVersions.db_1.1.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/miRBaseVersions.db_0.99.5.tar.gz" - "https://bioarchive.galaxyproject.org/miRBaseVersions.db_0.99.5.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_0.99.5_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz" + "https://bioarchive.galaxyproject.org/miRBaseVersions.db_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz" ) -MD5="b67d191fa4c71f49ab5d24f3d785c82a" +MD5="9944ab7a474f84a40100c56298f9cb77" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml index 73650288b3739..9578399f6a617 100644 --- a/recipes/bioconductor-mirintegrator/meta.yaml +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mirIntegrator" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 05d58bdd586e6b80fb310e68575f320fea0c4d58e79a95ee88430f2a0ff6e817 + sha256: 69f2b51176831ce0ce2640c98c26d17520eb0c9d11838fef666218d35e8bf11b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-org.hs.eg.db - - bioconductor-rgraphviz - - bioconductor-rontotools + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rontotools >=2.8.0,<2.10.0' - r-base - r-ggplot2 run: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-org.hs.eg.db - - bioconductor-rgraphviz - - bioconductor-rontotools + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rontotools >=2.8.0,<2.10.0' - r-base - r-ggplot2 test: @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.' - extra: identifiers: - biotools:mirintegrator diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml index 0cb6dc1ea19c3..3a0529f45cf85 100644 --- a/recipes/bioconductor-mirnameconverter/meta.yaml +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "miRNAmeConverter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9cc7988e323fc6f9896ec4b6c6c04cf7e9bc183b380b4a1f6a527557f18b1ab2 + sha256: 30ad6cc9cc62c47ddfc87f0888b9c0de72f0a1ca48442a61da957967c276fa82 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-mirbaseversions.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-mirbaseversions.db >=1.1.0,<1.3.0' - r-base - r-dbi + - r-reshape2 run: - - bioconductor-annotationdbi - - bioconductor-mirbaseversions.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-mirbaseversions.db >=1.1.0,<1.3.0' - r-base - r-dbi + - r-reshape2 test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Package containing an S4 class for translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).' - + summary: 'Translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).' extra: identifiers: - biotools:mirnameconverter diff --git a/recipes/bioconductor-mirnapath/meta.yaml b/recipes/bioconductor-mirnapath/meta.yaml index 77b0a90706f58..f73457de51ea0 100644 --- a/recipes/bioconductor-mirnapath/meta.yaml +++ b/recipes/bioconductor-mirnapath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "miRNApath" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a85b2ecf0809ce055e439f640effbb3908fcc2d3119b1f95f8880605de3c2384 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 67b80c37e539794715f2d5a2052555a5aa61f1bdc214286f122ff6bf01135b73 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2.1 summary: 'This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.' - extra: identifiers: - biotools:mirnapath diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml index cc4757b70ef88..92b1ff74a75a3 100644 --- a/recipes/bioconductor-mirnatap.db/meta.yaml +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -1,43 +1,41 @@ {% set version = "0.99.10" %} {% set name = "miRNAtap.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 43e735987bae9aa68b6e7544c5d1d87ebf7edcc075427114508eb8b47c7d91c8 - build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-mirnatap + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-mirnatap >=1.14.0,<1.16.0' - r-base - r-dbi - r-rsqlite run: - - bioconductor-annotationdbi - - bioconductor-mirnatap + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-mirnatap >=1.14.0,<1.16.0' - r-base - r-dbi - r-rsqlite - wget - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: GPL-2 summary: 'This package holds the database for miRNAtap.' + + diff --git a/recipes/bioconductor-mirnatap.db/post-link.sh b/recipes/bioconductor-mirnatap.db/post-link.sh index f72cd811042db..645cf3dbbd1af 100644 --- a/recipes/bioconductor-mirnatap.db/post-link.sh +++ b/recipes/bioconductor-mirnatap.db/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="miRNAtap.db_0.99.10.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" + "https://bioarchive.galaxyproject.org/miRNAtap.db_0.99.10.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" ) MD5="48010280b68d6f1ddbff3b374132ce0a" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-mirnatap/meta.yaml b/recipes/bioconductor-mirnatap/meta.yaml index 7827cebf78058..f21e0a79d998d 100644 --- a/recipes/bioconductor-mirnatap/meta.yaml +++ b/recipes/bioconductor-mirnatap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "miRNAtap" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,16 +8,17 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8247ce22e8ae1d6c6078ae1efeb61aa35b567ddb1e0acabb6c37c56cf49e0353 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cf5dbfa8557d27d2ccd51953f14457a394d0af6e92dd577097e10ccbb70a648d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi - r-plyr @@ -25,7 +26,7 @@ requirements: - r-sqldf - r-stringr run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi - r-plyr @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).' - extra: identifiers: - biotools:mirnatap diff --git a/recipes/bioconductor-mirsynergy/meta.yaml b/recipes/bioconductor-mirsynergy/meta.yaml index 25b6b32a6966b..3ef6b70625724 100644 --- a/recipes/bioconductor-mirsynergy/meta.yaml +++ b/recipes/bioconductor-mirsynergy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Mirsynergy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 930a36ea599d31d56c6a52b4ad7b7bab9887c5e259f25d6924aaedb15cd88cd7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f33a4dda5b24aeb2b6c3d391df0722c5a4faee12f342848d94b2207626d13df9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion.' - extra: identifiers: - biotools:mirsynergy diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml index 6c3f014ea6063..3da59f67e8313 100644 --- a/recipes/bioconductor-missmethyl/meta.yaml +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "missMethyl" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,40 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c35b7e3b64c7ea1cff0aa09deb4e8f1058110555a62ef5e02f859ad28fb777bb + sha256: 3ac149ded3ef2eb2b1cbdec20706e11dfb2d45ef2eb3201dcd8f6570b0659afc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-go.db - - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 - - bioconductor-illuminahumanmethylation450kmanifest - - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 - - bioconductor-illuminahumanmethylationepicmanifest - - bioconductor-limma - - bioconductor-methylumi - - bioconductor-minfi - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.8.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.5.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr run: - - bioconductor-annotationdbi - - bioconductor-go.db - - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 - - bioconductor-illuminahumanmethylation450kmanifest - - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 - - bioconductor-illuminahumanmethylationepicmanifest - - bioconductor-limma - - bioconductor-methylumi - - bioconductor-minfi - - bioconductor-org.hs.eg.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.8.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.5.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - r-base - r-biasedurn - r-ruv @@ -56,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Normalisation and testing for differential variability and differential methylation for data from Illumina''s Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene''s test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.' - extra: identifiers: - biotools:missmethyl diff --git a/recipes/bioconductor-mlinterfaces/conda_build_config.yaml b/recipes/bioconductor-mlinterfaces/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-mlinterfaces/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml index 1c8f2608dd630..506ad63596abc 100644 --- a/recipes/bioconductor-mlinterfaces/meta.yaml +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.1" %} {% set name = "MLInterfaces" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: da4e4ba5af1ad8c6e322ddc05f2064860e4f6dc01bb35c02f6dfeee9d700c6df + sha256: 2ac720b4aaf59b61becb23423b108863a85e404b9d42c33e47275fd0eddf22dd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.11' - - bioconductor-genefilter + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base - r-cluster - r-fpc @@ -39,10 +39,10 @@ requirements: - r-shiny - 'r-threejs >=0.2.2' run: - - bioconductor-annotate - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.11' - - bioconductor-genefilter + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base - r-cluster - r-fpc @@ -66,7 +66,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.' - extra: identifiers: - biotools:mlinterfaces diff --git a/recipes/bioconductor-mlp/conda_build_config.yaml b/recipes/bioconductor-mlp/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-mlp/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-mlp/meta.yaml b/recipes/bioconductor-mlp/meta.yaml index f14c49d0b1244..4afc56e334fcc 100644 --- a/recipes/bioconductor-mlp/meta.yaml +++ b/recipes/bioconductor-mlp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MLP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 072ebd445d88ff80b5a5713cfc45fdc3d5dcf23638ea6d63cd36ff95d3e00a56 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a288ebcf30964f9a87e593a6b7240284d8d4924eebec4bf1f9899709eb9965e8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-annotationdbi + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-gdata - r-gmodels @@ -26,8 +27,8 @@ requirements: - r-gtools - r-plotrix run: - - bioconductor-affy - - bioconductor-annotationdbi + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-gdata - r-gmodels @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Mean Log P Analysis' - extra: identifiers: - biotools:mlp diff --git a/recipes/bioconductor-mlseq/meta.yaml b/recipes/bioconductor-mlseq/meta.yaml index ea66ff75e093f..f4969f9760259 100644 --- a/recipes/bioconductor-mlseq/meta.yaml +++ b/recipes/bioconductor-mlseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.3" %} {% set name = "MLSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,46 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 649bac4857fa7ff2e37db58cec4dfa2b7a970948f9e88fc51ed252c1e218cbe4 + sha256: 09663f7b24051519e3f587c95a35122a4f571907ec1a93db0b40d9b7e119f26d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-sseq >=1.18.0,<1.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-caret - - r-randomforest + - r-foreach + - r-ggplot2 + - r-plyr + - r-xtable run: - - bioconductor-biobase - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-sseq >=1.18.0,<1.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-caret - - r-randomforest + - r-foreach + - r-ggplot2 + - r-plyr + - r-xtable test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) - summary: 'This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART, to RNA-Seq data.' - + summary: 'This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.' extra: identifiers: - biotools:mlseq diff --git a/recipes/bioconductor-mmdiff/conda_build_config.yaml b/recipes/bioconductor-mmdiff/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-mmdiff/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-mmdiff/meta.yaml b/recipes/bioconductor-mmdiff/meta.yaml index 0a9245a258946..168b12743e341 100644 --- a/recipes/bioconductor-mmdiff/meta.yaml +++ b/recipes/bioconductor-mmdiff/meta.yaml @@ -39,3 +39,4 @@ about: home: http://bioconductor.org/packages/release/bioc/html/MMDiff.html license: Artistic-2.0 summary: 'This package detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).' + diff --git a/recipes/bioconductor-mmdiff2/meta.yaml b/recipes/bioconductor-mmdiff2/meta.yaml index 9af8fcb37b831..e5c6257b40cbf 100644 --- a/recipes/bioconductor-mmdiff2/meta.yaml +++ b/recipes/bioconductor-mmdiff2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MMDiff2" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 50681858e01b1697fb47b28b40ff79489c68dbd571a00f146e0a82617833c98d + sha256: 0f5051f1460df312c86a4841c4b49723659e891f68bafce67a4cbbfeaef87379 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny run: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-locfit @@ -48,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).' - extra: identifiers: - biotools:mmdiff2 diff --git a/recipes/bioconductor-mmnet/meta.yaml b/recipes/bioconductor-mmnet/meta.yaml index cc1357e27c718..e4c924604569c 100644 --- a/recipes/bioconductor-mmnet/meta.yaml +++ b/recipes/bioconductor-mmnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version="1.13.0" %} -{% set name="mmnet" %} -{% set bioc="3.5" %} +{% set version = "1.13.0" %} +{% set name = "mmnet" %} +{% set bioc = "3.5" %} package: name: 'bioconductor-{{ name|lower}}' @@ -55,6 +55,9 @@ about: license: 'GPL (>= 2)' summary: 'This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.' + identifiers: + - biotools:mmnet + - doi:10.1155/2015/167249 extra: identifiers: - biotools:mmnet diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index ec18d4afa3408..92186068fe13d 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "monocle" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6344d6cd9d3a43ca81c5351f9283e3877d6f1cb4c3b31815362072f9a508505c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 55c6863b78832d61487e63981c4afbe49c523f7d5799043dfb2349637e69be32 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocviews - - 'bioconductor-hsmmsinglecell >=0.101.5' - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocviews >=1.48.3,<1.50.0' + - 'bioconductor-hsmmsinglecell >=0.114.0,<0.116.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-cluster - r-combinat @@ -39,6 +40,8 @@ requirements: - r-plyr - r-proxy - r-qlcmatrix + - 'r-rann >=2.5' + - 'r-rcpp >=0.12.0' - r-reshape2 - r-rtsne - r-slam @@ -47,11 +50,11 @@ requirements: - 'r-vgam >=1.0-1' - r-viridis run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocviews - - 'bioconductor-hsmmsinglecell >=0.101.5' - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocviews >=1.48.3,<1.50.0' + - 'bioconductor-hsmmsinglecell >=0.114.0,<0.116.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-cluster - r-combinat @@ -69,6 +72,8 @@ requirements: - r-plyr - r-proxy - r-qlcmatrix + - 'r-rann >=2.5' + - 'r-rcpp >=0.12.0' - r-reshape2 - r-rtsne - r-slam @@ -76,6 +81,10 @@ requirements: - r-tibble - 'r-vgam >=1.0-1' - r-viridis + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -83,7 +92,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.' - extra: identifiers: - biotools:monocle diff --git a/recipes/bioconductor-mops/meta.yaml b/recipes/bioconductor-mops/meta.yaml index 701c27e43a9b6..36df584fcdcad 100644 --- a/recipes/bioconductor-mops/meta.yaml +++ b/recipes/bioconductor-mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MoPS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 01e18291534115e6ba3609ab3956bb9f73be8b153e24b18c99564e906ae68a3c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c6755294077ca4882ff1888801a67d964f73f2de263d038db2fdd7631445b26f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identification and characterization of periodic fluctuations in time-series data.' - extra: identifiers: - biotools:mops diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index a77fc32f1fe54..606425c54e40e 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "mosaics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,41 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 720a0358bbaf14f9ba049b317c6180a54722012f6af4b891cccd3b3fd5470423 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 92790b8e556304e5292db09054e392754b28692eb01daf923515848feeb1ae61 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-lattice - r-mass - r-rcpp run: - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-lattice - r-mass - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.' - extra: identifiers: - biotools:mosaics diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index b8281da53c874..9632b3fdec70b 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "motifbreakR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,47 +8,48 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b2745617aa46cbf3b610fb7a78dc46b88f01950bf817e6af85d4e7fda471cec9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9bee8e72857e467d0f39b1baff54bad69e8e53615156b25b489dbcf0f1695c99 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-motifdb - - bioconductor-motifstack - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-motifdb >=1.22.0,<1.24.0' + - 'bioconductor-motifstack >=1.24.1,<1.26.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-grimport - r-matrixstats - r-stringr - r-tfmpvalue run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-motifdb - - bioconductor-motifstack - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-motifdb >=1.22.0,<1.24.0' + - 'bioconductor-motifstack >=1.24.1,<1.26.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-grimport - r-matrixstats @@ -61,7 +62,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 22).' - extra: identifiers: - biotools:motifbreakr diff --git a/recipes/bioconductor-motifcounter/meta.yaml b/recipes/bioconductor-motifcounter/meta.yaml index 9012a06175eec..851ddd0a8de38 100644 --- a/recipes/bioconductor-motifcounter/meta.yaml +++ b/recipes/bioconductor-motifcounter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "motifcounter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 80ad9a1c25eb7acb0fcdf55fea365a5e8a4c3084aa33c2cf043c151e14f387cc + sha256: 789db94396699281cf357a9d3f09ac3ab9ba02ba8a100a95cc996aa489de532c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: '''motifcounter'' provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. As an input, ''motifcounter'' requires a motif in terms of a position frequency matrix (PFM). Furthermore, a set of DNA sequences is required to estimated a higher-order background model (BGM). The package provides functions to investigate the the per-position and per strand log-likelihood scores between the PFM and the BGM across a given sequence of set of sequences. Furthermore, the package facilitates motif matching based on an automatically derived score threshold. To this end the distribution of scores is efficiently determined and the score threshold is chosen for a user-prescribed significance level. This allows to control for the false positive rate. Moreover, ''motifcounter'' implements a motif match enrichment test based on two the number of motif matches that are expected in random DNA sequences. Motif enrichment is facilitated by either a compound Poisson approximation or a combinatorial approximation of the motif match counts. Both models take higher-order background models, the motif''s self-similarity, and hits on both DNA strands into account. The package is in particular useful for long motifs and/or relaxed choices of score thresholds, because the implemented algorithms efficiently bypass the need for enumerating a (potentially huge) set of DNA words that can give rise to a motif match.' + + diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index f53e3a60290a4..24ff4da86f3f9 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MotifDb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 69020a6c071d98f231dbbc567e6af74db4fd9d65dbea56c79e088599973ef399 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 79db31ce111250bb16bb78434632833cc369b6e0c65b7d37fc1f2b8e63b2ac60 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-splitstackshape run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-splitstackshape test: @@ -38,8 +39,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | file LICENSE' - summary: 'More than 8000 annotated position frequency matrices from 13 public sources, for multiple organisms.' - + summary: 'More than 9000 annotated position frequency matrices from 14 public sources, for multiple organisms.' extra: identifiers: - biotools:motifdb diff --git a/recipes/bioconductor-motifrg/meta.yaml b/recipes/bioconductor-motifrg/meta.yaml index f0ba3055665df..0e0487a5afce8 100644 --- a/recipes/bioconductor-motifrg/meta.yaml +++ b/recipes/bioconductor-motifrg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "motifRG" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8438486c644597fbd4be6da5eb1d6eb6003e248df9c482d34dbbf34fb3a07fa4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3760c720798edbeae5ba2387bc293a1f949281f0c9bcd5a0c25f343f5bf4b057 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.26' - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-iranges - - bioconductor-seqlogo - - bioconductor-xvector + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-biostrings >=2.26' - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-iranges - - bioconductor-seqlogo - - bioconductor-xvector + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base test: commands: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for discriminative motif discovery using regression methods' - extra: identifiers: - biotools:motifrg diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index f90047f5fc98d..fd75642a2f759 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "motifStack" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: eea682a86b79fcdeb3f5cc9ad0d48cfbbfa0e683a7351b2ca7d5ad3bbce5a24b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 24e32273232a69e8ac054d45022907aabfb84b7168f9beb49b3d732567cf72a5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-motiv + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-motiv >=1.36.0,<1.38.0' - r-ade4 - r-base - r-grimport @@ -26,8 +27,8 @@ requirements: - r-scales - r-xml run: - - bioconductor-biostrings - - bioconductor-motiv + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-motiv >=1.36.0,<1.38.0' - r-ade4 - r-base - r-grimport @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.' - extra: identifiers: - biotools:motifstack diff --git a/recipes/bioconductor-motiv/build.sh b/recipes/bioconductor-motiv/build.sh index b1760a2ba6b9f..da43ce2168312 100644 --- a/recipes/bioconductor-motiv/build.sh +++ b/recipes/bioconductor-motiv/build.sh @@ -1,13 +1,4 @@ #!/bin/bash - -export CFLAGS="$(gsl-config --cflags)" -export LDFLAGS="$(gsl-config --libs)" - -if [ `uname` == Darwin ] ; then - export LDFLAGS="-Wl,-rpath ${PREFIX}/lib $LDFLAGS" -fi -export LD_LIBRARY_PATH=$PREFIX/lib - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index d4fd12b95a422..3abde93d6a4bf 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MotIV" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,39 +8,38 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 06be19672eea04d778970040805097e8cc6543acbea476c5f5bd2231f8fa7353 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: da12f8071ef2e9bb2dd5dea46073e22b4981dbc2f1913a41774f2325580eb68f build: - ## Library not loaded: @rpath/libc++.1.dylib - skip: True # [osx] - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-biostrings >=1.24.0' - - 'bioconductor-iranges >=1.13.5' - - bioconductor-rgadem - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgadem >=2.28.0,<2.30.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-lattice - - gsl - openblas run: - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-biostrings >=1.24.0' - - 'bioconductor-iranges >=1.13.5' - - bioconductor-rgadem - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgadem >=2.28.0,<2.30.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-lattice - - gsl - openblas - + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -48,7 +47,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.' - extra: identifiers: - biotools:motiv diff --git a/recipes/bioconductor-mpfe/meta.yaml b/recipes/bioconductor-mpfe/meta.yaml index edc8547f03188..7360be8d20d64 100644 --- a/recipes/bioconductor-mpfe/meta.yaml +++ b/recipes/bioconductor-mpfe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MPFE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1c7c609ee20bc7cf3fd491b406cf37130aebacd4112612486a26703535d0014a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d9c09c28caa072cd8c879f24f642bf05a5987a193fa2efa869ed6cbe78e782d0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.' - extra: identifiers: - biotools:mpfe diff --git a/recipes/bioconductor-mqtl.nmr/meta.yaml b/recipes/bioconductor-mqtl.nmr/meta.yaml index 8d263eebec7a7..028c81232b82c 100644 --- a/recipes/bioconductor-mqtl.nmr/meta.yaml +++ b/recipes/bioconductor-mqtl.nmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "mQTL.NMR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 27ee15251211ec2c1155e3ed49bfdc1a381656913deca4ae80d07aeb54a23246 + sha256: 5f27ce08968976380dc3cbeca5381c0043cd53be281292a5517d6e6c6bd1d062 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base - r-genabel @@ -31,7 +29,6 @@ requirements: - r-mass - r-outliers - r-qtl - - libcxx # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data. Distinctive features include normalisation using most-used approaches, peak alignment using RSPA approach, dimensionality reduction using SRV and binning approaches, and mQTL analysis for animal and human cohorts.' - extra: identifiers: - biotools:mqtl.nmr diff --git a/recipes/bioconductor-msmseda/meta.yaml b/recipes/bioconductor-msmseda/meta.yaml index e2a24473ba820..c7a190c92f246 100644 --- a/recipes/bioconductor-msmseda/meta.yaml +++ b/recipes/bioconductor-msmseda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "msmsEDA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8cbf8947c568f1744258fb0944b99c6e6497a184d551edf4b966c7d51026f0b4 + sha256: 025ba8acc9cc34ce841340b66f4171742423bc86d72acc8117c9816a0918344a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-msnbase + - 'bioconductor-msnbase >=2.6.4,<2.8.0' - r-base - r-gplots - r-mass - r-rcolorbrewer run: - - bioconductor-msnbase + - 'bioconductor-msnbase >=2.6.4,<2.8.0' - r-base - r-gplots - r-mass @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.' - extra: identifiers: - biotools:msmseda diff --git a/recipes/bioconductor-msnbase/conda_build_config.yaml b/recipes/bioconductor-msnbase/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-msnbase/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index 27ce94b96d4e6..97d2e3c6c63a8 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -1,77 +1,81 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.4" %} {% set name = "MSnbase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: - url: https://depot.galaxyproject.org/software/bioconductor-msnbase/bioconductor-msnbase_2.4.0_src_all.tar.gz - sha256: 79b47e78dccb1260c81661f9c93cfaf4887eef13678686987aa36728698d0e37 - + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 35872e6a5057deb33ff46bb544c0c15c781f6ae15f3551b437b6b41c166a3bb2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy - - 'bioconductor-biobase >=2.15.2' - - 'bioconductor-biocgenerics >=0.7.1' - - bioconductor-biocparallel - - bioconductor-impute - - bioconductor-iranges - - 'bioconductor-mzid >=1.5.2' - - 'bioconductor-mzr >=2.11.11' - - bioconductor-pcamethods - - bioconductor-preprocesscore - - 'bioconductor-protgenerics >=1.9.1' - - bioconductor-s4vectors - - bioconductor-vsn + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-mzid >=1.18.0,<1.20.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-pcamethods >=1.72.0,<1.74.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-digest - r-ggplot2 - r-lattice - 'r-maldiquant >=1.16' + - r-mass - r-plyr - r-rcpp + - r-scales - r-xml run: - - bioconductor-affy - - 'bioconductor-biobase >=2.15.2' - - 'bioconductor-biocgenerics >=0.7.1' - - bioconductor-biocparallel - - bioconductor-impute - - bioconductor-iranges - - 'bioconductor-mzid >=1.5.2' - - 'bioconductor-mzr >=2.11.11' - - bioconductor-pcamethods - - bioconductor-preprocesscore - - 'bioconductor-protgenerics >=1.9.1' - - bioconductor-s4vectors - - bioconductor-vsn + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-mzid >=1.18.0,<1.20.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-pcamethods >=1.72.0,<1.74.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-digest - r-ggplot2 - r-lattice - 'r-maldiquant >=1.16' + - r-mass - r-plyr - r-rcpp + - r-scales - r-xml - + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'MSnbase provides infrastructure to manipulation, processing and visualisation mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.' - + summary: 'MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.' extra: identifiers: - biotools:msnbase diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml index 15b770b8a967f..5a361b3fa9be4 100644 --- a/recipes/bioconductor-msnid/meta.yaml +++ b/recipes/bioconductor-msnid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "MSnID" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bddf02c93ecfe24159eac615e5ef14fd4efc50b89c1c93cccb0b3932270285ff + sha256: 27503867660c54d397ff1b29972185e7ba1a3317e4014f7e24201012212b589c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - 'bioconductor-msnbase >=1.12.1' - - 'bioconductor-mzid >=1.3.5' - - bioconductor-mzr - - bioconductor-protgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-mzid >=1.18.0,<1.20.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - r-base - r-data.table - r-doparallel @@ -35,11 +33,11 @@ requirements: - r-rcpp - r-reshape2 run: - - bioconductor-biobase - - 'bioconductor-msnbase >=1.12.1' - - 'bioconductor-mzid >=1.3.5' - - bioconductor-mzr - - bioconductor-protgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-mzid >=1.18.0,<1.20.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - r-base - r-data.table - r-doparallel @@ -49,7 +47,9 @@ requirements: - r-r.cache - r-rcpp - r-reshape2 - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -57,7 +57,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.' - extra: identifiers: - biotools:msnid diff --git a/recipes/bioconductor-mspurity/build.sh b/recipes/bioconductor-mspurity/build.sh index d56f700cf16c5..da43ce2168312 100755 --- a/recipes/bioconductor-mspurity/build.sh +++ b/recipes/bioconductor-mspurity/build.sh @@ -1,4 +1,4 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mspurity/meta.yaml b/recipes/bioconductor-mspurity/meta.yaml index a48729abfced0..0904084cbc4d3 100644 --- a/recipes/bioconductor-mspurity/meta.yaml +++ b/recipes/bioconductor-mspurity/meta.yaml @@ -1,29 +1,25 @@ -{% set version="1.5.4" %} -{% set name="msPurity" %} -{% set bioc="3.6" %} - +{% set version = "1.6.2" %} +{% set name = "msPurity" %} +{% set bioc = "3.7" %} package: - name: 'bioconductor-{{ name|lower}}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: - url: https://github.com/computational-metabolomics/msPurity/archive/8ca81e16abad872865802dd66e3035267cdaf52c.zip - sha256: 23dc3ad6abab52734d611292190f5df1d40d4840ff5f1655c46b63837564884d - + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ebea0db0b8717636f27bd00504abe0432c64106dc6ecbdbeeab6f79d6c36fee9 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - 'libnetcdf 4.4.*' - - 'r-base >=3.4.1' - - 'bioconductor-xcms >=3.0.0' - - 'bioconductor-camera >=1.34.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - r-base - r-dbi - r-dosnow - r-fastcluster @@ -35,10 +31,8 @@ requirements: - r-rsqlite - r-stringr run: - - 'libnetcdf 4.4.*' - - 'r-base >=3.4.1' - - 'bioconductor-xcms >=3.0.0' - - 'bioconductor-camera >=1.34.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - r-base - r-dbi - r-dosnow - r-fastcluster @@ -49,6 +43,9 @@ requirements: - r-reshape2 - r-rsqlite - r-stringr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -56,7 +53,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data. Spectral matching of fragmentation spectra can also be run against a SQLite database of library spectra.' - extra: identifiers: - biotools:mspurity diff --git a/recipes/bioconductor-mspuritydata/meta.yaml b/recipes/bioconductor-mspuritydata/meta.yaml index 6ba2b18f6bc33..76e46174a4827 100644 --- a/recipes/bioconductor-mspuritydata/meta.yaml +++ b/recipes/bioconductor-mspuritydata/meta.yaml @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Fragmentation spectral libraries and data to test the msPurity package' + + diff --git a/recipes/bioconductor-mulcom/meta.yaml b/recipes/bioconductor-mulcom/meta.yaml index 961a96508e44a..5988cda4d03c6 100644 --- a/recipes/bioconductor-mulcom/meta.yaml +++ b/recipes/bioconductor-mulcom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Mulcom" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0c5d74308b1ae2ffe1a5a9899443d65ab93a13591595be2814ab054b8cd504b6 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 740638739fdd6ca10836a440bb7049fe119aa97baacbdf58c592bf992f3c0d4a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-fields run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-fields + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test' - extra: identifiers: - biotools:mulcom diff --git a/recipes/bioconductor-multiassayexperiment/conda_build_config.yaml b/recipes/bioconductor-multiassayexperiment/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-multiassayexperiment/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml index d076557dc71a3..ee43d23a286cf 100644 --- a/recipes/bioconductor-multiassayexperiment/meta.yaml +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.9" %} +{% set version = "1.6.0" %} {% set name = "MultiAssayExperiment" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 983a2d790601cef7b33f03daf3c09611e8cffeed22cbf8a0f1c9dbd99d15794d + sha256: ab6ff66caa4cbc429f8d160a932c6428e086b65b9e6c1269940467419acab0f4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-genomicranges >=1.25.93' - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.3.81' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - - r-reshape2 - - r-shiny - - r-shinydashboard - r-tidyr run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-genomicranges >=1.25.93' - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.3.81' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - - r-reshape2 - - r-shiny - - r-shinydashboard - r-tidyr test: commands: @@ -47,8 +41,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Multi-assay ''omics experiments on a set of samples are increasingly commonplace in biomedical research. MultiAssayExperiment implements data structures and methods for representing, manipulating, and integrating multi-assay experiments via efficient construction, subsetting, and extraction operations. These methods are implemented matching Bioconductor user experience by straightforward extending concept and design of single-assay classes such as SummarizedExperiment or ExpressionSet.' - + summary: 'Multi-assay ''omics experiments on a set of samples are increasingly commonplace in biomedical research. MultiAssayExperiment implements data structures and methods for representing, manipulating, and integrating multi-assay experiments via efficient construction, subsetting, and extraction operations. These methods are implemented matching Bioconductor user experience by straightforward extending concept and design of single-assay classes such as SummarizedExperiment.' extra: identifiers: - biotools:multiassayexperiment diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml index 5b2bab0b90b28..48637214d0deb 100644 --- a/recipes/bioconductor-multiclust/meta.yaml +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "multiClust" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 54d89a94cc076584b235d29446167c3718a529713b04b2024a46ecf7886c7106 + sha256: c4032c4c0de98a50b3027a8edae51d7c26c4833d0ec09d246d93c1ffa1087461 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-ctc + - 'bioconductor-ctc >=1.54.0,<1.56.0' - r-amap - r-base - r-cluster @@ -26,7 +26,7 @@ requirements: - r-mclust - r-survival run: - - bioconductor-ctc + - 'bioconductor-ctc >=1.54.0,<1.56.0' - r-amap - r-base - r-cluster @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.' - extra: identifiers: - biotools:multiclust diff --git a/recipes/bioconductor-multidataset/meta.yaml b/recipes/bioconductor-multidataset/meta.yaml index 3d53436dc85e5..9f0aa79bd91ef 100644 --- a/recipes/bioconductor-multidataset/meta.yaml +++ b/recipes/bioconductor-multidataset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MultiDataSet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,35 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8f88ec7eb2e7abdcd3dd7d8217c98e9008b5c3e8604435b53275188b673b2840 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8da10a20a8088ed48b71e0e96759340a82cb508557571321be2ed0671f817877 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-ggrepel - r-qqman run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-ggrepel @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'Implementation of the BRGE''s (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.' - extra: identifiers: - biotools:multidataset diff --git a/recipes/bioconductor-multimed/meta.yaml b/recipes/bioconductor-multimed/meta.yaml index 882ffbd634f7e..ab3047b773825 100644 --- a/recipes/bioconductor-multimed/meta.yaml +++ b/recipes/bioconductor-multimed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "2.2.0" %} {% set name = "MultiMed" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4bb91c0e762d117112d35d55c7688781cde8238a7c8223cff34bdb45c68e88ac + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0b394a6bafa856306414b1f2e6caa64cd08cfc9ff14154865a24876273848794 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -26,8 +27,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' - summary: 'Implements permutation method with joint correction for testing multiple mediators' - + summary: 'Implements methods for testing multiple mediators' extra: identifiers: - biotools:multimed diff --git a/recipes/bioconductor-multiomicsviz/meta.yaml b/recipes/bioconductor-multiomicsviz/meta.yaml index 2895afa65c086..3118b449593fb 100644 --- a/recipes/bioconductor-multiomicsviz/meta.yaml +++ b/recipes/bioconductor-multiomicsviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "multiOmicsViz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a134a57169ba6b7b64c6ebad4f2cae60f16d9fb7be6b9856b498e71bc57f14ff + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f130b07ba454588aab44c38dd1f9755c10b3c47db1751e6386f2767eb43e5f87 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-doparallel - r-foreach run: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-doparallel - r-foreach @@ -33,3 +34,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Calculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.' + + diff --git a/recipes/bioconductor-multiscan/meta.yaml b/recipes/bioconductor-multiscan/meta.yaml index 654a31edc8eb6..5f973ae8242e5 100644 --- a/recipes/bioconductor-multiscan/meta.yaml +++ b/recipes/bioconductor-multiscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "multiscan" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c6fc3ade1e5ca1325f0dc3967ff9060389e4b26cbb91ce12de72213b8f02cb1d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: cda31408f2caff745b30c5c8f9716d0cbc86f652933336908e142fe44c8c8262 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Estimates gene expressions from several laser scans of the same microarray' - extra: identifiers: - biotools:multiscan diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 3066311a0df81..42669b64c87ab 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "multtest" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 32edf91f94d7a7ccb5ef1a33792da2e02c3fdad137badae8b05bd09e48cb2158 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e0d2f003b0afd674fb4f16255b20afa146491e65442a05511f81d337054c2485 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-mass - r-survival run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-mass - r-survival + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.' - extra: identifiers: - biotools:multtest diff --git a/recipes/bioconductor-mutationalpatterns/build.sh b/recipes/bioconductor-mutationalpatterns/build.sh index 4bc8e1853b492..da43ce2168312 100644 --- a/recipes/bioconductor-mutationalpatterns/build.sh +++ b/recipes/bioconductor-mutationalpatterns/build.sh @@ -1,3 +1,4 @@ #!/bin/bash - -$R CMD INSTALL --build . +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml index f08d8fd7df641..7a5ead38e7f90 100644 --- a/recipes/bioconductor-mutationalpatterns/meta.yaml +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -1,12 +1,16 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.1" %} {% set name = "MutationalPatterns" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: 'http://bioconductor.org/packages/3.6/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - sha256: 8124877e921031cf192d4184d583a7b0188c7011b0db99711f62bb56ae7e8456 + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 49726301308e489ec9de4d42bc29d1858af57b5b858de690edb20a22431907fb build: number: 0 rpaths: @@ -14,42 +18,45 @@ build: - lib/ requirements: host: - - r-base >=3.4.0 - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-genomeinfodb >=1.12.0 - - bioconductor-iranges - - bioconductor-summarizedexperiment - - bioconductor-variantannotation - - r-ggplot2 - - r-plyr - - r-pracma - - r-nmf - - r-reshape2 - - r-ggdendro - - r-cowplot + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - r-base + - 'r-cowplot >=0.9.2' + - 'r-ggdendro >=0.1-20' + - 'r-ggplot2 >=2.1.0' + - 'r-nmf >=0.20.6' + - 'r-plyr >=1.8.3' + - 'r-pracma >=1.8.8' + - 'r-reshape2 >=1.4.1' run: - - r-base >=3.4.0 - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomicranges - - bioconductor-genomeinfodb >=1.12.0 - - bioconductor-iranges - - bioconductor-summarizedexperiment - - bioconductor-variantannotation - - r-ggplot2 - - r-plyr - - r-pracma - - r-nmf - - r-reshape2 - - r-ggdendro - - r-cowplot - + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - r-base + - 'r-cowplot >=0.9.2' + - 'r-ggdendro >=0.1-20' + - 'r-ggplot2 >=2.1.0' + - 'r-nmf >=0.20.6' + - 'r-plyr >=1.8.3' + - 'r-pracma >=1.8.8' + - 'r-reshape2 >=1.4.1' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: http://bioconductor.org/packages/release/bioc/html/{{ name }}.html - license: MIT - summary: R package for extracting and visualizing mutational patterns in base substitution catalogues + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution catalogs.' + + diff --git a/recipes/bioconductor-mvcclass/meta.yaml b/recipes/bioconductor-mvcclass/meta.yaml index b2c4880deee78..e83d9c70a5041 100644 --- a/recipes/bioconductor-mvcclass/meta.yaml +++ b/recipes/bioconductor-mvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MVCClass" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1e2a7ab7f5b7f9e8d6c387e2483f0dbd5e3c45ad35c1244c8e29e9e5293ed50f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 734c2f1b85cf8975ba7dd4c0083ca72df406e5904fd76921b53576a6f4d6ed98 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Creates classes used in model-view-controller (MVC) design' - extra: identifiers: - biotools:mvcclass diff --git a/recipes/bioconductor-mvgst/meta.yaml b/recipes/bioconductor-mvgst/meta.yaml index d89f350d7e1dd..37f28bcaa867d 100644 --- a/recipes/bioconductor-mvgst/meta.yaml +++ b/recipes/bioconductor-mvgst/meta.yaml @@ -46,6 +46,9 @@ about: license: GPL-3 summary: 'mvGST provides platform-independent tools to identify GO terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. Given a matrix of one-sided p-values (rows for genes, columns for contrasts), mvGST uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify each gene set as being significantly more active (1), less active (-1), or not significantly differentially active (0) in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile.' + identifiers: + - biotools:mvgst + - doi:10.1038/nmeth.3252 extra: identifiers: - biotools:mvgst diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml index 98f084baa2778..549b280a9194c 100644 --- a/recipes/bioconductor-mwastools/meta.yaml +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MWASTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 096058b6ec448c9f9b566ab029a2395365b009e83bf6c584f0e67f8c2d36eb5d + sha256: fab7dc5e332606b16f1332e3a623458e251b712086b012c23e4e10c3a4a73ad1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-complexheatmap - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-qvalue - - bioconductor-summarizedexperiment + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-boot - r-car @@ -33,11 +33,11 @@ requirements: - r-ppcor - r-rcurl run: - - bioconductor-complexheatmap - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-qvalue - - bioconductor-summarizedexperiment + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-boot - r-car @@ -54,3 +54,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'CC BY-NC-ND 4.0' summary: 'MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.' + + diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml index 5e2e23b3c4b06..5cd6f483178c5 100644 --- a/recipes/bioconductor-mygene/meta.yaml +++ b/recipes/bioconductor-mygene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.2" %} {% set name = "mygene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,16 +10,16 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a446efd2261103702a2df190599f494b0a417dd147ce44582ea7a434b1be1363 + sha256: 7cfa9b71549c5148d7f126525ba9aea82ba1492a8c8350bb0d687724ffe2b23f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicfeatures - - bioconductor-s4vectors + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -27,8 +27,8 @@ requirements: - r-plyr - r-sqldf run: - - bioconductor-genomicfeatures - - bioconductor-s4vectors + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It''s designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.' - extra: identifiers: - biotools:mygene diff --git a/recipes/bioconductor-myvariant/meta.yaml b/recipes/bioconductor-myvariant/meta.yaml index 5c96c0e348ad2..822f74daaccaf 100644 --- a/recipes/bioconductor-myvariant/meta.yaml +++ b/recipes/bioconductor-myvariant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "myvariant" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,18 +8,19 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 383c9402214832ebe8714890bef464555e2599adfdbb3b24d7b8932f8bc790e4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b2f7cf18c94d9462a74877a9ec8a65465d54bcc13ce72e9c5e35ee5e91e038a8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomeinfodb - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-hmisc - r-httr @@ -27,9 +28,9 @@ requirements: - r-magrittr - r-plyr run: - - bioconductor-genomeinfodb - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-hmisc - r-httr @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services' - extra: identifiers: - biotools:myvariant diff --git a/recipes/bioconductor-mzid/meta.yaml b/recipes/bioconductor-mzid/meta.yaml index 31fcd71e10832..4c2fa342b3043 100644 --- a/recipes/bioconductor-mzid/meta.yaml +++ b/recipes/bioconductor-mzid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "mzID" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,16 +8,17 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 696157651d4d03295582c71ce55e48b25955477f6f00270c47ed9ba26603677a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 80cc2da24167f589b7b60f7ce5974f8d31a02f5a64e96f980008a30769071318 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-protgenerics + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - r-base - r-doparallel - r-foreach @@ -25,7 +26,7 @@ requirements: - r-plyr - r-xml run: - - bioconductor-protgenerics + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - r-base - r-doparallel - r-foreach @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less ''pretty'' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.' - extra: identifiers: - biotools:mzid diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index a39232182c8f3..91163ff7c6457 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -1,47 +1,45 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "mzR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0c61b01e17d652eecd9dd4c20fcfdc59ace4dc4c30723de6d8e277a7c1b86ff4 + sha256: 2fabfa09eb86627bab92e57ed4ba52b4c02279fafb382295a4b0e355f01215a4 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics >=0.13.6 - - bioconductor-protgenerics >=1.9.1 - - bioconductor-zlibbioc # not in DESCRIPTION - - r-ncdf4 # not in DESCRIPTION + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - libnetcdf - r-base - 'r-rcpp >=0.10.1' - - boost - - libnetcdf 4.4.* run: - - bioconductor-biobase - - bioconductor-biocgenerics >=0.13.6 - - bioconductor-protgenerics >=1.9.1 - - bioconductor-zlibbioc # not in DESCRIPTION - - r-ncdf4 # not in DESCRIPTION - - boost - - libnetcdf 4.4.* + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - libnetcdf - r-base - - r-rcpp >=0.10.1 - + - 'r-rcpp >=0.10.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nadfinder/conda_build_config.yaml b/recipes/bioconductor-nadfinder/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-nadfinder/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-nadfinder/meta.yaml b/recipes/bioconductor-nadfinder/meta.yaml index 070a32560025c..a6e9cf809d3c1 100644 --- a/recipes/bioconductor-nadfinder/meta.yaml +++ b/recipes/bioconductor-nadfinder/meta.yaml @@ -1,60 +1,68 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "NADfinder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f82acce340f5e0951aae71953277ccc3cb8d78ca2a3e02d19624477ed75bff5a - + sha256: 01928a0c1fb3bf283a7a9fdd1a31ddaa3276cfdd5d155856fa701288425a6c2a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-trackviewer + - 'bioconductor-atacseqqc >=1.4.3,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-csaw >=1.14.1,<1.16.0' + - 'bioconductor-empiricalbrownsmethod >=1.8.0,<1.10.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-trackviewer >=1.16.1,<1.18.0' - r-base - r-baseline + - r-corrplot + - r-metap - r-signal - run: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-trackviewer + - 'bioconductor-atacseqqc >=1.4.3,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-csaw >=1.14.1,<1.16.0' + - 'bioconductor-empiricalbrownsmethod >=1.8.0,<1.10.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-trackviewer >=1.16.1,<1.18.0' - r-base - r-baseline + - r-corrplot + - r-metap - r-signal - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolar- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including normalization, smoothing, peak calling, peak trimming and annotation.' + summary: 'Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including normalization, smoothing, peak calling, peak trimming and annotation.' + + diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index 135676064934d..070a05a9b0166 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "ncdfFlow" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,41 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 68017eb7a8f9f7b0eb88ce28eaf70d874615bfcba009560650e7e3d5bea378e7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4207f655bebb5b0186616730967db07b9e413f5448b2e3a943e79c2a0ce63f7d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-flowcore >=1.37.15' - - bioconductor-flowviz - - bioconductor-zlibbioc - - bioconductor-rhdf5lib + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-bh + - r-rcpp - r-rcpparmadillo - - hdf5 run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-flowcore >=1.37.15' - - bioconductor-flowviz - - bioconductor-zlibbioc - - bioconductor-rhdf5lib + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-bh + - r-rcpp - r-rcpparmadillo - - hdf5 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.' - extra: identifiers: - biotools:ncdfflow diff --git a/recipes/bioconductor-ncigraph/meta.yaml b/recipes/bioconductor-ncigraph/meta.yaml index 64b348b6eb7d7..5df9fb7c25a06 100644 --- a/recipes/bioconductor-ncigraph/meta.yaml +++ b/recipes/bioconductor-ncigraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "NCIgraph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 201e4e2e7d2634b6959c241cef8f1de38185d24c1e310d116c44eb1724b68d24 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7ac8d694bb1f475c72417160e51f3f059aca04f5c99dd97b84564580d0339bcf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-rbgl - - bioconductor-rcy3 + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rcy3 >=2.0.88,<2.2.0' - r-base - r-r.methodss3 run: - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-rbgl - - bioconductor-rcy3 + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rcy3 >=2.0.88,<2.2.0' - r-base - r-r.methodss3 test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.' - extra: identifiers: - biotools:ncigraph diff --git a/recipes/bioconductor-ndexr/meta.yaml b/recipes/bioconductor-ndexr/meta.yaml index da6e671f31b53..9e194468c3ea8 100644 --- a/recipes/bioconductor-ndexr/meta.yaml +++ b/recipes/bioconductor-ndexr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "ndexr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b7a637c92314d654f9faa35980f5abf4bcf78064cc32676d14ef023fb6acf746 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 738a9d8ef249857b38ba863cf2958b069c3ebc0b5a7c42681f0ff8aa41580b62 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -37,3 +38,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: BSD summary: 'This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.' + + diff --git a/recipes/bioconductor-nem/meta.yaml b/recipes/bioconductor-nem/meta.yaml index d829ad48fc5d0..04b66ab22969d 100644 --- a/recipes/bioconductor-nem/meta.yaml +++ b/recipes/bioconductor-nem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "nem" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 684e172ac25d4652bae9a6435edc00c2ca638d8a9bb57c508cef80fd2d5a2404 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5a4fbc3eec8738bbfad002bb17a8a1e9d0263fe73441cc88fbbd7a70923c3910 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-limma - - 'bioconductor-rbgl >=1.8.1' - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-boot - r-e1071 @@ -28,16 +29,19 @@ requirements: - r-rcolorbrewer - r-statmod run: - - bioconductor-graph - - bioconductor-limma - - 'bioconductor-rbgl >=1.8.1' - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-boot - r-e1071 - r-plotrix - r-rcolorbrewer - r-statmod + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +49,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package ''nem'' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.' - extra: identifiers: - biotools:nem diff --git a/recipes/bioconductor-netbiov/meta.yaml b/recipes/bioconductor-netbiov/meta.yaml index 74f7e250b19ee..08992288d2ec7 100644 --- a/recipes/bioconductor-netbiov/meta.yaml +++ b/recipes/bioconductor-netbiov/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "netbiov" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 74f0922918d3b145fe2f55ff2efb258000645f422330d24e02ec1aabe5cdb8f7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 198051eefeef33e89b625387d421150a4fb5fb2e6f4004fb99934f30bf89ab80 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package that provides an effective visualization of large biological networks' - extra: identifiers: - biotools:netbiov diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index f786cdfdb5c7e..810846c1aa6ef 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "NetPathMiner" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7ca816073dcbf155aa6cfd76fe3176e29738cd8c09e6d1f2422eabed945797b5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f6882eedbd2240810596239a08d9e8847e8bbdc042c9791cfb0a35b2a9f73923 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,11 @@ requirements: run: - r-base - 'r-igraph >=1.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.' - extra: identifiers: - biotools:netpathminer diff --git a/recipes/bioconductor-netreg/meta.yaml b/recipes/bioconductor-netreg/meta.yaml index ae4dd12102088..98700d1989d27 100644 --- a/recipes/bioconductor-netreg/meta.yaml +++ b/recipes/bioconductor-netreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "netReg" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f0a22d86640b6f9bbbabe6cf2d3d44186a4456020db9745ee62adc5faa31b0b2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 696418c4f8f2b938316eb12e9349d4d588c44428310ec97fd8e7327c174bfc4a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} + - automake + - make host: - r-base - r-rcpp - r-rcpparmadillo + - openblas run: - r-base - r-rcpp + - r-rcpparmadillo + - openblas test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the likelihood of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.' + license: 'GPL-3 | BSL-1.0 + file LICENSE' + summary: 'netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the loss function of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.' + + diff --git a/recipes/bioconductor-networkbma/meta.yaml b/recipes/bioconductor-networkbma/meta.yaml index db8318a8e7fd8..fb67520985b21 100644 --- a/recipes/bioconductor-networkbma/meta.yaml +++ b/recipes/bioconductor-networkbma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "networkBMA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aaa479ba072f440e1458d8449a5bbd9b9dc794689a2f573f8dcff31843843313 + sha256: 996b0c7e10f738ff01f8aeecd1f42ebfe9da2e1206c7c49918dcfa8ab403dbc0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-bh @@ -35,7 +33,10 @@ requirements: - 'r-rcpp >=0.10.3' - 'r-rcpparmadillo >=0.3.810.2' - 'r-rcppeigen >=0.3.1.2.1' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.' - extra: identifiers: - biotools:networkbma diff --git a/recipes/bioconductor-nnnorm/meta.yaml b/recipes/bioconductor-nnnorm/meta.yaml index 0f8e6ac3a44bd..b2453f9152d1a 100644 --- a/recipes/bioconductor-nnnorm/meta.yaml +++ b/recipes/bioconductor-nnnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "nnNorm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 19526e1bb55147e6544a55a0ea1f4302ab88696012d3178a6335ce9d5082a136 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e213fc1f4d6089520b2a547d20fcd96af40c9ff68388b24c39d7f904c193207a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-marray + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-nnet run: - - bioconductor-marray + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-nnet test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.' - extra: identifiers: - biotools:nnnorm diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index 5544f499136be..c1af239df1613 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "NOISeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9903c0f0ebc2485623ac03334d6ad043aa4b4b3447242ed3f5d1839a9c105e6a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cb151bea959fbafa2a96a24ba507f158f740d66c2da5e306efd78fbf268a522a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.13.11' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - 'r-matrix >=1.2' run: - - 'bioconductor-biobase >=2.13.11' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - 'r-matrix >=1.2' test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.' - extra: identifiers: - biotools:noiseq diff --git a/recipes/bioconductor-nondetects/conda_build_config.yaml b/recipes/bioconductor-nondetects/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-nondetects/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-nondetects/meta.yaml b/recipes/bioconductor-nondetects/meta.yaml index 6fe9f2aaff238..517202de67f1f 100644 --- a/recipes/bioconductor-nondetects/meta.yaml +++ b/recipes/bioconductor-nondetects/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "nondetects" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4011aca813ccb68b302233b37e9f6b58868b2a7ef31e4f909ef624fed0970674 + sha256: 46044bcb1f09f71b7f0d17a1ca215ba1ee97fe4c0b14869ef0b688f0f78a9567 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.22.0' - - 'bioconductor-htqpcr >=1.16.0' - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-htqpcr >=1.34.0,<1.36.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - r-arm - r-base - r-mvtnorm run: - - 'bioconductor-biobase >=2.22.0' - - 'bioconductor-htqpcr >=1.16.0' - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-htqpcr >=1.34.0,<1.36.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - r-arm - r-base - r-mvtnorm test: @@ -36,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Methods to model and impute non-detects in the results of qPCR experiments.' - extra: identifiers: - biotools:nondetects diff --git a/recipes/bioconductor-npgsea/meta.yaml b/recipes/bioconductor-npgsea/meta.yaml index f969561b35527..8be80611ba54c 100644 --- a/recipes/bioconductor-npgsea/meta.yaml +++ b/recipes/bioconductor-npgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "npGSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2b47297c1f215623c6a0c02da35a9ff0781e8f841ec6b0b4bb8dc8d473b4296d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 40ca8fdafbda0b288f8c3465a91d23f7db6feaf3dc9ea63a63ef691f67f13cf6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-gseabase >=1.24.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-gseabase >=1.24.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.' - extra: identifiers: - biotools:npgsea diff --git a/recipes/bioconductor-ntw/meta.yaml b/recipes/bioconductor-ntw/meta.yaml index 94e06ca5d307b..f26e7582047ce 100644 --- a/recipes/bioconductor-ntw/meta.yaml +++ b/recipes/bioconductor-ntw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "NTW" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 189e5aa0a113648d81e977831afbe02cf5da31386c8e453d4ca1e4eacc30723e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 311829ee41e2ac40ca82331958451a16a148235611b5a6ae34030315c61a089a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.' - extra: identifiers: - biotools:ntw diff --git a/recipes/bioconductor-nucleosim/meta.yaml b/recipes/bioconductor-nucleosim/meta.yaml index 9c25ff5bd8400..f5071218fc135 100644 --- a/recipes/bioconductor-nucleosim/meta.yaml +++ b/recipes/bioconductor-nucleosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "nucleoSim" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b3185e2b265b9ae40f86ca373469d8eba0931e4e5092db5a7f7174d83c59dd3f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2f8448759d313c54f61cfe069dba508ae62529c09f9a69e6c85bb26c8e3e65a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform.' - extra: identifiers: - biotools:nucleosim diff --git a/recipes/bioconductor-nucler/meta.yaml b/recipes/bioconductor-nucler/meta.yaml index e23714f087411..d2b7c046bdbe8 100644 --- a/recipes/bioconductor-nucler/meta.yaml +++ b/recipes/bioconductor-nucler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.1" %} {% set name = "nucleR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,43 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 715d690fa2f00a16e08388f6caf7663e8f68705e91dbff94868574531bf1f610 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b20deb9686ab3a6d55ed0818d7d71fdf3763a3b0495c08912691d5eaf9291d99 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.39' - - bioconductor-shortread + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.39' - - bioconductor-shortread + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'Nucleosome positioning for Tiling Arrays and NGS experiments.' - extra: identifiers: - biotools:nucler diff --git a/recipes/bioconductor-nudge/meta.yaml b/recipes/bioconductor-nudge/meta.yaml index 0b46ebb87aea5..83ef42971bbac 100644 --- a/recipes/bioconductor-nudge/meta.yaml +++ b/recipes/bioconductor-nudge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "nudge" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ae582bb26aa87108ca8bb15f0a33d4c50aee3f398d382192df701bdba0e9e2fa + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: feaddf8bd5bc0d715d69d9f1d755a923c503bf523c9303bc0085ad169c31ce64 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)' - extra: identifiers: - biotools:nudge diff --git a/recipes/bioconductor-occugene/meta.yaml b/recipes/bioconductor-occugene/meta.yaml index 5dc555c6639f6..c9a8beeb907c6 100644 --- a/recipes/bioconductor-occugene/meta.yaml +++ b/recipes/bioconductor-occugene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "occugene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 371a540a7f8c6e6256b06d35c2072665c96c521a63a349c9bc8a8613f61c8ed3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 73eb1db8d96deaa1e2ba5137f1e02fafd15c6d8366ff59256337520c1ab2df2f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.' - extra: identifiers: - biotools:occugene diff --git a/recipes/bioconductor-ogsa/meta.yaml b/recipes/bioconductor-ogsa/meta.yaml index f04b9c8dafef5..6d1e5f2caaf3f 100644 --- a/recipes/bioconductor-ogsa/meta.yaml +++ b/recipes/bioconductor-ogsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "OGSA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fabec47527ca0a479424a971637e7dd8c727cff24aa3cabd6cb9579f3c80ddc4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4e6fbb9d12b9283d26d4543c5d513c829c0c8a1061ab0d3591f7877095849434 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-limma >=3.18.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - 'r-gplots >=2.8.0' run: - - bioconductor-biobase - - 'bioconductor-limma >=3.18.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - 'r-gplots >=2.8.0' test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (== 2)' summary: 'OGSA provides a global estimate of pathway deregulation in cancer subtypes by integrating the estimates of significance for individual pathway members that have been identified by outlier analysis.' - extra: identifiers: - biotools:ogsa diff --git a/recipes/bioconductor-oligo/conda_build_config.yaml b/recipes/bioconductor-oligo/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-oligo/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-oligo/meta.yaml b/recipes/bioconductor-oligo/meta.yaml index a3eb2f23bcc19..b48d25885cfd0 100644 --- a/recipes/bioconductor-oligo/meta.yaml +++ b/recipes/bioconductor-oligo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "oligo" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,40 +8,44 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: be0018a90754f43ce6ec3d551a3d1606b0a45d163b0254b65c232e0247d656e6 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 4c7d85628fec0db359e58bd42b16f084cdcbe7ab07044310b9162e95ede4b073 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affxparser >=1.39.4' - - 'bioconductor-affyio >=1.35.0' - - 'bioconductor-biobase >=2.27.3' - - 'bioconductor-biocgenerics >=0.13.11' - - 'bioconductor-biostrings >=2.35.12' - - 'bioconductor-oligoclasses >=1.29.6' - - 'bioconductor-preprocesscore >=1.29.0' - - bioconductor-zlibbioc + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - 'r-dbi >=0.3.1' - r-ff - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-affxparser >=1.39.4' - - 'bioconductor-affyio >=1.35.0' - - 'bioconductor-biobase >=2.27.3' - - 'bioconductor-biocgenerics >=0.13.11' - - 'bioconductor-biostrings >=2.35.12' - - 'bioconductor-oligoclasses >=1.29.6' - - 'bioconductor-preprocesscore >=1.29.0' - - bioconductor-zlibbioc + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - 'r-dbi >=0.3.1' - r-ff - 'r-rsqlite >=1.0.0' + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -49,7 +53,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).' - extra: identifiers: - biotools:oligo diff --git a/recipes/bioconductor-oligoclasses/conda_build_config.yaml b/recipes/bioconductor-oligoclasses/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-oligoclasses/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-oligoclasses/meta.yaml b/recipes/bioconductor-oligoclasses/meta.yaml index 854ab0698a8bc..4cf4709a72528 100644 --- a/recipes/bioconductor-oligoclasses/meta.yaml +++ b/recipes/bioconductor-oligoclasses/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "oligoClasses" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,39 +8,40 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 296b2df1023e910f43b1a6668a51131c17e7a11df0872574a4e097f22b209e76 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 62c218d5484e9e55d352b351c8cee23a89f5301f3ff66a9a65a330f79a7ee11b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affyio >=1.23.2' - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-biocinstaller - - 'bioconductor-biostrings >=2.23.6' - - 'bioconductor-genomicranges >=1.23.7' - - 'bioconductor-iranges >=2.5.17' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dbi - r-ff - r-foreach - r-rsqlite run: - - 'bioconductor-affyio >=1.23.2' - - 'bioconductor-biobase >=2.17.8' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-biocinstaller - - 'bioconductor-biostrings >=2.23.6' - - 'bioconductor-genomicranges >=1.23.7' - - 'bioconductor-iranges >=2.5.17' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dbi - r-ff @@ -53,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.' - extra: identifiers: - biotools:oligoclasses diff --git a/recipes/bioconductor-olin/meta.yaml b/recipes/bioconductor-olin/meta.yaml index b7111bec9370b..b84694aa7bf00 100644 --- a/recipes/bioconductor-olin/meta.yaml +++ b/recipes/bioconductor-olin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "OLIN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ecfa1b1ed16b35237f7d464734b9a1499942d24fcd8667633af7873f9b8264a1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a84c520b2ef0976afb0cb4aa5bb8b8c3e1bda0f2ddf241d42554626af692dcf9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-locfit run: - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-locfit test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data' - extra: identifiers: - biotools:olin diff --git a/recipes/bioconductor-omicade4/meta.yaml b/recipes/bioconductor-omicade4/meta.yaml index 04bed38eba7b9..bf8257fb7233b 100644 --- a/recipes/bioconductor-omicade4/meta.yaml +++ b/recipes/bioconductor-omicade4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "omicade4" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 86f0d08b3255b0375df5281d22b38d2f65b2e05185f6fc5b041c2f7a40620339 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 522895abae63a4b3c1bdb2b237875543793139fe2a5363d90d1d7d38583549ee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-made4 + - 'bioconductor-made4 >=1.54.0,<1.56.0' - r-ade4 - r-base run: - - bioconductor-made4 + - 'bioconductor-made4 >=1.54.0,<1.56.0' - r-ade4 - r-base test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Multiple co-inertia analysis of omics datasets' - extra: identifiers: - biotools:omicade4 diff --git a/recipes/bioconductor-omiccircos/meta.yaml b/recipes/bioconductor-omiccircos/meta.yaml index 8c43942e51502..ecec856992876 100644 --- a/recipes/bioconductor-omiccircos/meta.yaml +++ b/recipes/bioconductor-omiccircos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "OmicCircos" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a30a101128b700dbe2e7c179ca848cf278435531f9cd97b553ac3c0aac19bc8d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 250785e0b674c03fbad7c822ea281edc1c3d8f540dc27e6b432d3e7ed9b0b775 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'OmicCircos is an R application and package for generating high-quality circular plots for omics data.' - extra: identifiers: - biotools:omiccircos diff --git a/recipes/bioconductor-oncosimulr/meta.yaml b/recipes/bioconductor-oncosimulr/meta.yaml index 0c3c3a1a0553a..5b622b64daa84 100644 --- a/recipes/bioconductor-oncosimulr/meta.yaml +++ b/recipes/bioconductor-oncosimulr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "OncoSimulR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,17 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b354f94334a13ecf1610cc2b8e9e493c6d2475e5f7224fda7246a271abf715ac + sha256: d7d3e904dbfc41ff07295646fae09ebab391c8ee279c1a1552bbf8fe0e773190 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-graph - - bioconductor-nem - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-nem >=2.54.0,<2.56.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-car - r-data.table @@ -35,9 +33,9 @@ requirements: - 'r-rcpp >=0.12.4' - r-smatr run: - - bioconductor-graph - - bioconductor-nem - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-nem >=2.54.0,<2.56.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-car - r-data.table @@ -49,7 +47,10 @@ requirements: - r-rcolorbrewer - 'r-rcpp >=0.12.4' - r-smatr - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -57,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.' - extra: identifiers: - biotools:oncosimulr diff --git a/recipes/bioconductor-oppar/meta.yaml b/recipes/bioconductor-oppar/meta.yaml index da9ab7d36a1d7..afbfbc8bd9b24 100644 --- a/recipes/bioconductor-oppar/meta.yaml +++ b/recipes/bioconductor-oppar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "oppar" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e5881b10759779af46e23fbd38b220b97a838cefbb48c59671a57684e5739c40 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c88064bde4d6d43720023b0a69c91802fdf6b80adae10b65c6ae7f1fe170b7b0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-gseabase - - bioconductor-gsva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' - r-base run: - - bioconductor-biobase - - bioconductor-gseabase - - bioconductor-gsva + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.' - extra: identifiers: - biotools:oppar diff --git a/recipes/bioconductor-orderedlist/meta.yaml b/recipes/bioconductor-orderedlist/meta.yaml index 6cc8f6131e695..8dadd5feb335b 100644 --- a/recipes/bioconductor-orderedlist/meta.yaml +++ b/recipes/bioconductor-orderedlist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "OrderedList" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f92d6d72ba5a5e92ba0bb54ac46c3ef63447c9097f1b64f91eab47bf47b469ea + sha256: 267ddf93548d5aa25f7b639e5787ceb9c02fbdf534156a0abc9be0cb5fa7c3f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.5.12' - - 'bioconductor-twilight >=1.9.2' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-twilight >=1.56.0,<1.58.0' - r-base run: - - 'bioconductor-biobase >=1.5.12' - - 'bioconductor-twilight >=1.9.2' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-twilight >=1.56.0,<1.58.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.' - extra: identifiers: - biotools:orderedlist diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index 4e3be141c40fb..e537cb4fed12e 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Bt.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0e29e4929696938205ad173c9057a3c8afeda50a92c8666da911e282fa2594e1 + sha256: 246a3b073ea158b65924959efda8ee93dc46d37f7c67ef12ebcaaec283763dd2 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Bovine, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index 75f362b045271..5c14f8bad2fe7 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Bt.eg.db_3.5.0.tar.gz" +FN="org.Bt.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Bt.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Bt.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.6.0_src_all.tar.gz" ) -MD5="ac5441ee014eeac07e97dccd79bcfcdc" +MD5="1d8a03220647ee7256efa1008ea0a5af" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index 2c6d95de17239..d232d799961d6 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Ce.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 692ecae53641e32e19ee9211934a3d7babdc88ae0282bc34e4fe57da2364ef09 + sha256: a2f51c3d9f4bbea08ce6bda32dc2facfc947683358e2df24339992e945bd754b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index 28858e2621386..6c428a911297b 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Ce.eg.db_3.5.0.tar.gz" +FN="org.Ce.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Ce.eg.db_3.5.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Ce.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.6.0_src_all.tar.gz" ) -MD5="c33ea27e95df69fd1dd64d3ba1672d20" +MD5="0e9ad2243b191e62f1c3979313aa71f5" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index 567b7b058dc33..555741a7c663a 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Cf.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 733ddce63a2ef0a7be3a62df73124dbaf9be80bc5a0ed13267e6999d9a73b165 + sha256: a3dc6907618777570e16974ca3c2a3ed5be32a1eb4bb9f03384545414988fcf7 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Canine, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index a5e79846c0ab0..b7b665d0903f4 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Cf.eg.db_3.5.0.tar.gz" +FN="org.Cf.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Cf.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Cf.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.6.0_src_all.tar.gz" ) -MD5="940e0ec6aff006739fcaf77c18fdcb7d" +MD5="7cc3516927a6458cbfb8b9e7176823ea" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index f4fd3bfab2c84..3a1fe2a664a7a 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,26 +1,27 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Dm.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: edb4d45892b36dcd1d0ef519b50557a067852efa082ea0f6099ff3d1c254780c + sha256: fd83e931a4921b5171b9ad4445eac1c3c8166eaa63dd0c16ed8185751ce2927e build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Fly, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index 175d1941c6718..c8aee75217a76 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Dm.eg.db_3.5.0.tar.gz" +FN="org.Dm.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Dm.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Dm.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.6.0_src_all.tar.gz" ) -MD5="6d77f8cb76054dc5db521efcdcb3db9e" +MD5="a7cada385422fb2098293db5756cb7d4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index dd65bb481b00c..e61b8b071eaf5 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Dr.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 201ee036671fecfd973adc5212398e1c7ac73addcbc87c30dd4c7f6915cea420 + sha256: 8e3a7e70140bf960125a1578b42596af2c1fad7096d6ab0295f4d8de5fff4142 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Zebrafish, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index 23be5917e53b8..49fb4f1e681f1 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Dr.eg.db_3.5.0.tar.gz" +FN="org.Dr.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Dr.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Dr.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.6.0_src_all.tar.gz" ) -MD5="4692a5271060b44f8f684ac2d244fed0" +MD5="c4b2a8e03bec92727ac090bf8e7400cf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index b7b4d3fd34940..1702d8cce1f9c 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Gg.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 78600092d295756495c221e90d5316bea4448844ddbc0aae2c587647d44cafe0 + sha256: a6f0f0b30b09b035d8cb543dc1ccfcba0a6112056cad60219c2bf7852899a74a build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Chicken, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index ecbd48bc346ac..f5a674b53ceb1 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Gg.eg.db_3.5.0.tar.gz" +FN="org.Gg.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Gg.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Gg.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.6.0_src_all.tar.gz" ) -MD5="5e893d822ca6e7af68a2f62445bbe400" +MD5="72d349d2b23ce102db13cd8266458994" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index bb9a94379f718..137b7d8ec8e5c 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Hs.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4724452fcd36c3192263822e95ea5262d99429fa38f4d37a2a58b2114c51dcec + sha256: 27c838a6d343e9cb869d20dacf489fc0e3eac7a881a8bc2840a3a0ad10235b49 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index 3f885319b7167..ebc72584bd388 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Hs.eg.db_3.5.0.tar.gz" +FN="org.Hs.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Hs.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Hs.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.6.0_src_all.tar.gz" ) -MD5="9f0d948c0d1b0be3188d51d8ca57fde4" +MD5="3fa8de2859f317b59636f0e41b132e85" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index cc3b11270c4e3..1a9571b92ad87 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Mm.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cf34b2a1bc1663e82c49d56855a531b4105ace79a047351624769138c70d0287 + sha256: f93956413ce7a76e24bb6b9243de357f49d6a03cfe6584a694451a8f4c84a450 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index 04b8ec6e18830..39a487db71fa5 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Mm.eg.db_3.5.0.tar.gz" +FN="org.Mm.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Mm.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Mm.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.6.0_src_all.tar.gz" ) -MD5="84b6d4a45dbd80a4ac00edc0a2b51001" +MD5="1cb7de12010250de0b6fbbe799d653ea" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 7befbcf100ae4..15ff0a33244c7 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Rn.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a4971a0c56cfcb48f603b24ffd0538c6864b12d7865e2fc91e90ae89808a7687 + sha256: 0e0927f75b4005c782fa06c39c09a52730ab87e3a6ab4f897b9a53f860e8586c build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index d28127e1aeb25..62b0e6712ca4f 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Rn.eg.db_3.5.0.tar.gz" +FN="org.Rn.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Rn.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Rn.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.6.0_src_all.tar.gz" ) -MD5="fb3218e500ecc6a4e8a4857ab310a23e" +MD5="e6b4e03ec625bdfc7515ffacc4681659" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.sc.sgd.db/meta.yaml b/recipes/bioconductor-org.sc.sgd.db/meta.yaml index d1c37127bba8c..c114242d699ed 100644 --- a/recipes/bioconductor-org.sc.sgd.db/meta.yaml +++ b/recipes/bioconductor-org.sc.sgd.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Sc.sgd.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bc3cee6d5b49be33daeb5b98c7d8fb2630b31e10850b715e73e9c1625e517cc0 + sha256: a2e0efb7d0d273a79fb082fea8561c7651a7800dca340b4f66be2419d2bcf95e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Yeast, primarily based on mapping using ORF identifiers from SGD.' + + diff --git a/recipes/bioconductor-org.sc.sgd.db/post-link.sh b/recipes/bioconductor-org.sc.sgd.db/post-link.sh index d5f1087373d48..6c7bd2a3a6a48 100644 --- a/recipes/bioconductor-org.sc.sgd.db/post-link.sh +++ b/recipes/bioconductor-org.sc.sgd.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Sc.sgd.db_3.5.0.tar.gz" +FN="org.Sc.sgd.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Sc.sgd.db_3.5.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Sc.sgd.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.6.0_src_all.tar.gz" ) -MD5="8cf82678baac5bb3342f965c7e8b3d47" +MD5="ba42c9278bf146817519a97723c018d6" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index f09e74d8ededf..f0cda8db6e227 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "org.Ss.eg.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cc08bee98f13c47605755e7ab41f9cdaa840749c5e0931a2bbc22ad31ba93ff2 + sha256: 32096d204442da58ecbc2ef3f758caef1b74364ed1302a1d7194bb8a7b6eb40a build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Pig, primarily based on mapping using Entrez Gene identifiers.' + + diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index d8df8281eba65..ed0c4765083ba 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Ss.eg.db_3.5.0.tar.gz" +FN="org.Ss.eg.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Ss.eg.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Ss.eg.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.6.0_src_all.tar.gz" ) -MD5="da8874c9958f6a40c84afbc7718b701c" +MD5="77a060d5d281ec94dbcd2a7a623c3c24" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-organismdbi/conda_build_config.yaml b/recipes/bioconductor-organismdbi/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-organismdbi/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index fc1f86a3efd4e..13b11f80a2efc 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "OrganismDbi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 88366999db5785a29560d55f1a1c3baebdac4cea01c50f2e777c940a2c87bb7b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9b99d5edbdc7ee1b1ea2e0057e883c71742d34ae58709f8b2edec91548b46941 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.33.15' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biocinstaller - - 'bioconductor-genomicfeatures >=1.23.31' - - bioconductor-genomicranges - - bioconductor-graph - - bioconductor-iranges - - bioconductor-rbgl - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.33.15' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.10' - - bioconductor-biocinstaller - - 'bioconductor-genomicfeatures >=1.23.31' - - bioconductor-genomicranges - - bioconductor-graph - - bioconductor-iranges - - bioconductor-rbgl - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-dbi test: @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.' - extra: identifiers: - biotools:organismdbi diff --git a/recipes/bioconductor-osat/meta.yaml b/recipes/bioconductor-osat/meta.yaml index 5662cc42b6aa9..6f445e97cfcb2 100644 --- a/recipes/bioconductor-osat/meta.yaml +++ b/recipes/bioconductor-osat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "OSAT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: eda00064bf100a40796fe4ab7af072a13ff8d60d4cfdc4884110af2d204c8759 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7ea3bdf56713e324382d3890cac56be4c9a71c3098161e5ce235684b8af51b4c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .' - extra: identifiers: - biotools:osat diff --git a/recipes/bioconductor-oscope/meta.yaml b/recipes/bioconductor-oscope/meta.yaml index 148ee9abbb157..7f043cf795a74 100644 --- a/recipes/bioconductor-oscope/meta.yaml +++ b/recipes/bioconductor-oscope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Oscope" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 060c2769c9f0839b2e4382c2fca8713db92c821bc83e9e991a545b177d52470a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e742d116992e508e20cc54bcb7214eaf8d913c7f50a60dc27ac8fd1f62236e78 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-ebseq + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-ebseq >=1.20.0,<1.22.0' - r-base - r-cluster - r-testthat run: - - bioconductor-biocparallel - - bioconductor-ebseq + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-ebseq >=1.20.0,<1.22.0' - r-base - r-cluster - r-testthat @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.' - extra: identifiers: - biotools:oscope diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index 57e595b634785..f82c3cdd6d394 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "OTUbase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2607e31441e63a08897ecae2a53522d3573fd505f275807fc2c241d744432c05 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: bc52aa0248f25745a4c04ff5f2fee01e838f196b1c4ff2c8c567fd94a559c024 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-shortread >=1.23.15' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-vegan run: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-iranges - - bioconductor-s4vectors - - 'bioconductor-shortread >=1.23.15' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base - r-vegan test: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides a platform for Operational Taxonomic Unit based analysis' - extra: identifiers: - biotools:otubase diff --git a/recipes/bioconductor-outlierd/meta.yaml b/recipes/bioconductor-outlierd/meta.yaml index 1f55fd6b03a9e..d1aa4e8539c22 100644 --- a/recipes/bioconductor-outlierd/meta.yaml +++ b/recipes/bioconductor-outlierd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "OutlierD" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: de08c5605451f9c8c7fadb72a08a9a92f5b02068d3c1499173b0f9cf400864d8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3246b79211deb22ff471af1959ddccb1f619e8680968d2ca52f28bab26dd8ccb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-quantreg run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-quantreg test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.' - extra: identifiers: - biotools:outlierd diff --git a/recipes/bioconductor-padog/meta.yaml b/recipes/bioconductor-padog/meta.yaml index 0eb676a7bde36..a690844d7206d 100644 --- a/recipes/bioconductor-padog/meta.yaml +++ b/recipes/bioconductor-padog/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "PADOG" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e5d42c8afe97a2c830b1e5b9eac982982ab768e086b5c38ddec01d08af90e8d2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: abbd2c0350d9c80a35ee33c88296bc9cd1bc2a8f67301714cd88a6b91bb9560f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-hgu133a.db - - bioconductor-hgu133plus2.db - - bioconductor-kegg.db - - bioconductor-keggdzpathwaysgeo - - bioconductor-limma + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' + - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-keggdzpathwaysgeo >=1.18.0,<1.20.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dorng - r-foreach - r-gsa - r-nlme run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-hgu133a.db - - bioconductor-hgu133plus2.db - - bioconductor-kegg.db - - bioconductor-keggdzpathwaysgeo - - bioconductor-limma + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' + - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-keggdzpathwaysgeo >=1.18.0,<1.20.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-dorng - r-foreach @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.' - extra: identifiers: - biotools:padog diff --git a/recipes/bioconductor-paircompviz/meta.yaml b/recipes/bioconductor-paircompviz/meta.yaml index 28dba0307bca7..21d8a5ba10bc0 100644 --- a/recipes/bioconductor-paircompviz/meta.yaml +++ b/recipes/bioconductor-paircompviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "paircompviz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4c0627f1996732d7da3b3231318539e8321c9ee112a2289be88bfd13c83c82fb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d84090d6cb65229004d7ce5b23bdf13beefcde83f3079d7564cf0dae56426bce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-rgraphviz + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base run: - - bioconductor-rgraphviz + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3.0)' summary: 'This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.' - extra: identifiers: - biotools:paircompviz diff --git a/recipes/bioconductor-pandar/meta.yaml b/recipes/bioconductor-pandar/meta.yaml index b3d0843bd2fd5..cb6f68985d3d5 100644 --- a/recipes/bioconductor-pandar/meta.yaml +++ b/recipes/bioconductor-pandar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pandaR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,16 +10,16 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 22ad4f7e766d846b2f39382611c756f9eb0f351fe3207c8100b309269b55f574 + sha256: 5ddcf4916cedc12997fd0b6df5eafb377bbb972cb08829e47d30bee996e23022 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-ggplot2 - r-hexbin @@ -29,8 +29,8 @@ requirements: - r-reshape - r-runit run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-ggplot2 - r-hexbin @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.' - extra: identifiers: - biotools:pandar diff --git a/recipes/bioconductor-pannbuilder/meta.yaml b/recipes/bioconductor-pannbuilder/meta.yaml index ce41c70661e22..e973e175ab0cb 100644 --- a/recipes/bioconductor-pannbuilder/meta.yaml +++ b/recipes/bioconductor-pannbuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.43.0" %} {% set name = "PAnnBuilder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 58ac892291232ed1746dbc58e1f5035cc30e9814a8ec04d03b2b0fb43e0d9a90 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 187847384bb39b2c8d21152d6f9a9b9bbc853d018e7bfd2b82652d6ba6ad3161 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.3.12' - - 'bioconductor-biobase >=1.17.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.3.12' - - 'bioconductor-biobase >=1.17.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-dbi - r-rsqlite @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'Processing annotation data from public data repositories and building protein-centric annotation data packages.' - extra: identifiers: - biotools:pannbuilder diff --git a/recipes/bioconductor-panp/conda_build_config.yaml b/recipes/bioconductor-panp/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-panp/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-panp/meta.yaml b/recipes/bioconductor-panp/meta.yaml index 5a15a40052312..8189868b695b6 100644 --- a/recipes/bioconductor-panp/meta.yaml +++ b/recipes/bioconductor-panp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "panp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f43036eabf7768798477014d1b21584c7ecd335af3ca96b8e09c7f1ee095cadd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 1ec9fa839fa3f1141dbc9069c46f8da44e3e0c35601c8508e88c6a56e6cdada9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.23.4' - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-affy >=1.23.4' - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.' - extra: identifiers: - biotools:panp diff --git a/recipes/bioconductor-panr/meta.yaml b/recipes/bioconductor-panr/meta.yaml index b31611029239d..fd645844c6417 100644 --- a/recipes/bioconductor-panr/meta.yaml +++ b/recipes/bioconductor-panr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "PANR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 69c096374454c9edf3a8ff67e9d107673582c31dde835cd45e8ac8e6addb7163 + sha256: 0ee265d6e8fbc3363898396db4bcd8282b56092754c094f0fb71a2af1be99fdd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-reder + - 'bioconductor-reder >=1.28.0,<1.30.0' - r-base - r-igraph - r-mass - r-pvclust run: - - bioconductor-reder + - 'bioconductor-reder >=1.28.0,<1.30.0' - r-base - r-igraph - r-mass @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.' - extra: identifiers: - biotools:panr diff --git a/recipes/bioconductor-panther.db/meta.yaml b/recipes/bioconductor-panther.db/meta.yaml index 9f6d569ca592f..6680b7a40d557 100644 --- a/recipes/bioconductor-panther.db/meta.yaml +++ b/recipes/bioconductor-panther.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "PANTHER.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,17 +12,17 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3e583f25e168a2896d20ced50761f80b11ae7c3a647e4dbb4a8bc1d9a35588ee build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-rsqlite run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-rsqlite - wget @@ -33,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.' + + diff --git a/recipes/bioconductor-panther.db/post-link.sh b/recipes/bioconductor-panther.db/post-link.sh index 718e34a7dc122..c22f8ba242176 100644 --- a/recipes/bioconductor-panther.db/post-link.sh +++ b/recipes/bioconductor-panther.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="PANTHER.db_1.0.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/PANTHER.db_1.0.4.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/PANTHER.db_1.0.4.tar.gz" "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.4_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.4_src_all.tar.gz" ) MD5="bfd7362a4823bd3fda1bfab8e5b7908e" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-papi/meta.yaml b/recipes/bioconductor-papi/meta.yaml index 9cf3a73a24faf..45754f95e15b2 100644 --- a/recipes/bioconductor-papi/meta.yaml +++ b/recipes/bioconductor-papi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PAPi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 39551b04e6d104046a517bc0dde490665e2b0c23f8381d944ad4b98b4f729eba + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6c36b1bd9006a2c3439e1cf1a5b6c63c68edcae50026b3867d1576f10ca5f16c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-keggrest + - 'bioconductor-keggrest >=1.20.2,<1.22.0' - r-base - r-svdialogs run: - - bioconductor-keggrest + - 'bioconductor-keggrest >=1.20.2,<1.22.0' - r-base - r-svdialogs test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL(>= 2)' summary: 'The Pathway Activity Profiling - PAPi - is an R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. See Aggio, R.B.M; Ruggiero, K. and Villas-Boas, S.G. (2010) - Pathway Activity Profiling (PAPi): from metabolite profile to metabolic pathway activity. Bioinformatics.' - extra: identifiers: - biotools:papi diff --git a/recipes/bioconductor-parody/meta.yaml b/recipes/bioconductor-parody/meta.yaml index bd9dc933d2b3d..3f7d3f107e6c1 100644 --- a/recipes/bioconductor-parody/meta.yaml +++ b/recipes/bioconductor-parody/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "parody" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 110dd7c4c177eae93d70e7206e03e2cc52081891f23f6210f0c2c1b2e5cd771c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 998ee212bd2ac9fee1fe3f15937826020769afdcc6d6d1192ee92a3c7a86e5e3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics' - extra: identifiers: - biotools:parody diff --git a/recipes/bioconductor-path2ppi/meta.yaml b/recipes/bioconductor-path2ppi/meta.yaml index 93dc02eaf7a04..52926bf486b91 100644 --- a/recipes/bioconductor-path2ppi/meta.yaml +++ b/recipes/bioconductor-path2ppi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Path2PPI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 634141bbfeded8b625e75178eea92594e079105befacc9a8f95660c506b6f957 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f73f951b581849f76a43a98da5a6fe474533e17a630e78621e0e7f936e0970ba build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.' - extra: identifiers: - biotools:path2ppi diff --git a/recipes/bioconductor-pathifier/meta.yaml b/recipes/bioconductor-pathifier/meta.yaml index 26b674afd4705..095790291d319 100644 --- a/recipes/bioconductor-pathifier/meta.yaml +++ b/recipes/bioconductor-pathifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "pathifier" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a74abd4c5e803de1952c85569f4cb85fae08cc537428dd2d43c38958ae75286b + sha256: 279b782138587b372ed3a7c6d9a2194202f1e1f652d8e4523e3b415541239742 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - r-base - - r-princurve + - 'r-princurve >=2.0.4' - r-r.oo run: - r-base - - r-princurve + - 'r-princurve >=2.0.4' - r-r.oo test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-1.0 summary: 'Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.' - extra: identifiers: - biotools:pathifier diff --git a/recipes/bioconductor-pathnet/meta.yaml b/recipes/bioconductor-pathnet/meta.yaml index 042015ee9796f..e56237366a638 100644 --- a/recipes/bioconductor-pathnet/meta.yaml +++ b/recipes/bioconductor-pathnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PathNet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dbf9dec859ed71ec489d70d90f44537dac51fa2e0b0e963caec331773c2175e7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8a3ab66135f274c44fc6415f51f48140b376bcde385faa498712e051a5676e70 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' - extra: identifiers: - biotools:pathnet diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml index 086052f7efa8c..a45e4314e362d 100644 --- a/recipes/bioconductor-pathostat/meta.yaml +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "PathoStat" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,68 +10,74 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e8c498faa8ca42f645abe8fcc28a2754987ed345cd9c362cb155d3c22b8180aa + sha256: 2a097c072861423bcf6e498d6a10a2c847ace11a464f45ecbc702de9352410d3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-batchqc - - bioconductor-biocstyle - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-limma - - bioconductor-phyloseq - - bioconductor-preprocesscore - - r-alluvial + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-phyloseq >=1.24.2,<1.26.0' - r-ape - r-base - r-corpcor + - r-devtools - r-dplyr - r-dt - r-ggplot2 - - r-gtools + - r-glmnet + - r-gmodels - r-knitr - r-matrixstats - - r-mcmcpack - - r-pander + - r-plotly - r-plyr + - r-rcolorbrewer - r-rentrez - r-reshape2 - - r-rmarkdown + - r-rocr - r-scales - r-shiny + - r-shinyjs - r-tidyr + - r-vegan + - r-webshot - r-xml run: - - bioconductor-batchqc - - bioconductor-biocstyle - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-limma - - bioconductor-phyloseq - - bioconductor-preprocesscore - - r-alluvial + - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-phyloseq >=1.24.2,<1.26.0' - r-ape - r-base - r-corpcor + - r-devtools - r-dplyr - r-dt - r-ggplot2 - - r-gtools + - r-glmnet + - r-gmodels - r-knitr - r-matrixstats - - r-mcmcpack - - r-pander + - r-plotly - r-plyr + - r-rcolorbrewer - r-rentrez - r-reshape2 - - r-rmarkdown + - r-rocr - r-scales - r-shiny + - r-shinyjs - r-tidyr + - r-vegan + - r-webshot - r-xml test: commands: @@ -80,7 +86,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.' - extra: identifiers: - biotools:pathostat diff --git a/recipes/bioconductor-pathprint/meta.yaml b/recipes/bioconductor-pathprint/meta.yaml index 706575688d23d..ef2af2e84229d 100644 --- a/recipes/bioconductor-pathprint/meta.yaml +++ b/recipes/bioconductor-pathprint/meta.yaml @@ -1,35 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.4" %} {% set name = "pathprint" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 921f52ebfa095a2698309ecb1e04478834b56137038593e7fb0313deb1645138 - + sha256: 911d04eafc4c71721fa1a65d7c74389d05a2e54710902004e7c6caa05ab113e8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - r-base run: - r-base - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ''pathway fingerprint'', a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.' + + diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml index d46d1aa6e30c2..8c4c270af1968 100644 --- a/recipes/bioconductor-pathrender/meta.yaml +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "pathRender" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7799606f8be32f984e3eac7a3beaa80d207bfa16e1ee3308bfec07c7f4b20587 + sha256: 329a09681d89938ae629526b3e80766af254482844a0e9e1d92d6144199607ee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-cmap - - bioconductor-graph - - bioconductor-rgraphviz + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-cmap >=1.15.1,<1.17.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-rcolorbrewer run: - - bioconductor-annotationdbi - - bioconductor-cmap - - bioconductor-graph - - bioconductor-rgraphviz + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-cmap >=1.15.1,<1.17.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-rcolorbrewer test: @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'build graphs from pathway databases, render them by Rgraphviz.' - extra: identifiers: - biotools:pathrender diff --git a/recipes/bioconductor-pathvar/meta.yaml b/recipes/bioconductor-pathvar/meta.yaml index fa9f1aee168b4..2082e9ddc4886 100644 --- a/recipes/bioconductor-pathvar/meta.yaml +++ b/recipes/bioconductor-pathvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "pathVar" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06068a120838bcaa26f55a2d50ee93a8a25d85ec5cf6b0ef56d8e557352105d1 + sha256: 4eb965ee2da7dfd2407bf8dccfbee333c970c44d46ebf2020f522b9b75bd8f19 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.' - extra: identifiers: - biotools:pathvar diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index fcf9dacd585e2..109c89458ca90 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "pathview" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 10fc82bbaede59d601a8175f87549ac5878fa6ec8b5e29eeafa7837d72fa4a48 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5381d31827aac6b05bf084c06350fc2ecf29bb280243347f800498d891a56bf4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-org.hs.eg.db - - bioconductor-rgraphviz + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-png - r-xml run: - - bioconductor-annotationdbi - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-org.hs.eg.db - - bioconductor-rgraphviz + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-png - r-xml @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3.0)' summary: 'Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.' - extra: identifiers: - biotools:pathview diff --git a/recipes/bioconductor-pbase/meta.yaml b/recipes/bioconductor-pbase/meta.yaml index f4367d6da268b..16d7c020c6c5f 100644 --- a/recipes/bioconductor-pbase/meta.yaml +++ b/recipes/bioconductor-pbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.18.0" %} +{% set version = "0.20.0" %} {% set name = "Pbase" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,56 +10,56 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3d846d81f7ec04b52aabe2c8d98d787c8144f8f3c33bb603ca1937f46b0dca9f + sha256: 8c458b8265aa425b8edf715eaab650e31eea4ce90c56b1b18490052d0d24b9b2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-annotationfilter - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biomart - - bioconductor-biostrings - - 'bioconductor-cleaver >=1.3.6' - - 'bioconductor-ensembldb >=1.99.13' - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - 'bioconductor-msnbase >=1.15.5' - - bioconductor-mzid - - 'bioconductor-mzr >=1.99.1' - - bioconductor-pviz - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-cleaver >=1.18.0,<1.20.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-mzid >=1.18.0,<1.20.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-pviz >=1.14.0,<1.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-rcpp run: - - bioconductor-annotationfilter - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biomart - - bioconductor-biostrings - - 'bioconductor-cleaver >=1.3.6' - - 'bioconductor-ensembldb >=1.99.13' - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - 'bioconductor-msnbase >=1.15.5' - - bioconductor-mzid - - 'bioconductor-mzr >=1.99.1' - - bioconductor-pviz - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-cleaver >=1.18.0,<1.20.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-mzid >=1.18.0,<1.20.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-pviz >=1.14.0,<1.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-rcpp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -67,7 +67,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.' - extra: identifiers: - biotools:pbase diff --git a/recipes/bioconductor-pbcmc/meta.yaml b/recipes/bioconductor-pbcmc/meta.yaml index dcc9734430dcb..59e3efb01f8d8 100644 --- a/recipes/bioconductor-pbcmc/meta.yaml +++ b/recipes/bioconductor-pbcmc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "pbcmc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2f2bb7a7c527ed5c2f317b1961d71002cdc60f422a292e984e2b096cb78c6b88 + sha256: 8a8cab9b7217dcaca40bbf039aa808f74e3e66d992fcb69060fbfaf4bb287073 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-biocparallel >=1.3.13' - - bioconductor-genefu - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genefu >=2.12.0,<2.14.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-cowplot - r-ggplot2 - r-gridextra - r-reshape2 run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-biocparallel >=1.3.13' - - bioconductor-genefu - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genefu >=2.12.0,<2.14.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-cowplot - r-ggplot2 @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'The pbcmc package characterizes uncertainty assessment on gene expression classifiers, a. k. a. molecular signatures, based on a permutation test. In order to achieve this goal, synthetic simulated subjects are obtained by permutations of gene labels. Then, each synthetic subject is tested against the corresponding subtype classifier to build the null distribution. Thus, classification confidence measurement can be provided for each subject, to assist physician therapy choice. At present, it is only available for PAM50 implementation in genefu package but it can easily be extend to other molecular signatures.' - extra: identifiers: - biotools:pbcmc diff --git a/recipes/bioconductor-pcaexplorer/meta.yaml b/recipes/bioconductor-pcaexplorer/meta.yaml index 8a47bc07e70eb..23fdc7a21634d 100644 --- a/recipes/bioconductor-pcaexplorer/meta.yaml +++ b/recipes/bioconductor-pcaexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "pcaExplorer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ccf6de150be601a1ed5f369e4c56d08d2bde65bfde26c4c234688ff0275416fd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f2231a38edffb178860aeac9af51f026e57914ff688ea68b9d5fe2455a9a7e6b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biomart - - bioconductor-deseq2 - - bioconductor-genefilter - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-gostats - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-d3heatmap - r-dt @@ -47,18 +48,18 @@ requirements: - r-threejs - r-tidyr run: - - bioconductor-annotationdbi - - bioconductor-biomart - - bioconductor-deseq2 - - bioconductor-genefilter - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-gostats - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-d3heatmap - r-dt @@ -83,7 +84,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.' - extra: identifiers: - biotools:pcaexplorer diff --git a/recipes/bioconductor-pcagopromoter/meta.yaml b/recipes/bioconductor-pcagopromoter/meta.yaml index cc09056f516e5..fb49ac4b94e23 100644 --- a/recipes/bioconductor-pcagopromoter/meta.yaml +++ b/recipes/bioconductor-pcagopromoter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "pcaGoPromoter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5fcfb0cf2e97e063642675540ea426c2492d22013f1579872ed30a708cb6e10c + sha256: 54f59073eed0031d6b2d73f43394e25b76784b0b9618588153850626c76af622 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biostrings + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-ellipse run: - - bioconductor-annotationdbi - - bioconductor-biostrings + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-ellipse test: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains functions to ease the analyses of DNA micro arrays. It utilizes principal component analysis as the initial multivariate analysis, followed by functional interpretation of the principal component dimensions with overrepresentation analysis for GO terms and regulatory interpretations using overrepresentation analysis of predicted transcription factor binding sites with the primo algorithm.' - extra: identifiers: - biotools:pcagopromoter diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index 664b5764edf8f..811d94c09934e 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "pcaMethods" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 68aeb04c7b0fffcf2a9e3fce039d69db2c102d122e3b86e01489800e5e192246 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 07284d96b9049f95280b31e06057c18c3aebf07d0ffc91c137d0e75391f3296d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-mass - 'r-rcpp >=0.11.3' run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-mass - 'r-rcpp >=0.11.3' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.' - extra: identifiers: - biotools:pcamethods diff --git a/recipes/bioconductor-pcan/meta.yaml b/recipes/bioconductor-pcan/meta.yaml index 7c786c2d33b89..d1830658226be 100644 --- a/recipes/bioconductor-pcan/meta.yaml +++ b/recipes/bioconductor-pcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "PCAN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cdea4399888be63216d69fbbf30394516fc3fe26b0ef88a11c6df714dd0cd546 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4cdf96ce949fbb33f14ae1736efcf76dd780412a29c90e1d5e70b6f4dce48e43 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base run: - - bioconductor-biocparallel + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'CC BY-NC-ND 4.0' summary: 'Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).' - extra: identifiers: - biotools:pcan diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index 67a88fc649b46..da374f8f7ab4b 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "PCHiCdata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dd1307f6213e4106e67e998024e1d690010682b45442a155dcb63e2ccde710b7 + sha256: 1ffb05620d982bd57421d20e535fce5aa8fea5ee86dda375b8d3f23ae6957d2e build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-chicago + - 'bioconductor-chicago >=1.8.0,<1.10.0' - r-base run: - - bioconductor-chicago + - 'bioconductor-chicago >=1.8.0,<1.10.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.' + + diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index a015fc259200c..1ab160ae7bce8 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="PCHiCdata_1.6.0.tar.gz" +FN="PCHiCdata_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/PCHiCdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.6.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/PCHiCdata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/PCHiCdata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.8.0_src_all.tar.gz" ) -MD5="d8dcf967d070f86647b12580e51ed07a" +MD5="e2f47759614488314cbae936a38b7330" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-pcot2/meta.yaml b/recipes/bioconductor-pcot2/meta.yaml index 2694029c2d4da..5646b95e33abf 100644 --- a/recipes/bioconductor-pcot2/meta.yaml +++ b/recipes/bioconductor-pcot2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "pcot2" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 85e5d41226cc2c514d2a94b8458691e565a427f9d92bbbd611afdceb5386d5df + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: dfcf06e36e80cbb3ab85d2cc7786612512c3f1b84a78c7d0d2ef928046dfb4bb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-amap - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-amap - r-base test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons.' - extra: identifiers: - biotools:pcot2 diff --git a/recipes/bioconductor-pcpheno/meta.yaml b/recipes/bioconductor-pcpheno/meta.yaml index bb7c54116d212..b15da47f2a2fb 100644 --- a/recipes/bioconductor-pcpheno/meta.yaml +++ b/recipes/bioconductor-pcpheno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "PCpheno" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,40 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 51390c27f53cefb769b725bfbd3cacdb02a242b1e8e1a3b628fcb8884d08fce9 + sha256: c1a90074a87604403e642e7dface19f9b3edfb71e538a82b61f020c9f5f2dcb3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotate >=1.17.4' - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-category - - bioconductor-go.db - - bioconductor-graph - - bioconductor-gseabase - - bioconductor-kegg.db - - bioconductor-ppidata - - bioconductor-ppistats - - 'bioconductor-scisi >=1.3.0' - - bioconductor-slgi + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-ppidata >=0.18.0,<0.20.0' + - 'bioconductor-ppistats >=1.46.0,<1.48.0' + - 'bioconductor-scisi >=1.52.0,<1.54.0' + - 'bioconductor-slgi >=1.40.0,<1.42.0' - r-base run: - - 'bioconductor-annotate >=1.17.4' - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-category - - bioconductor-go.db - - bioconductor-graph - - bioconductor-gseabase - - bioconductor-kegg.db - - bioconductor-ppidata - - bioconductor-ppistats - - 'bioconductor-scisi >=1.3.0' - - bioconductor-slgi + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-ppidata >=0.18.0,<0.20.0' + - 'bioconductor-ppistats >=1.46.0,<1.48.0' + - 'bioconductor-scisi >=1.52.0,<1.54.0' + - 'bioconductor-slgi >=1.40.0,<1.42.0' - r-base test: commands: @@ -52,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.' - extra: identifiers: - biotools:pcpheno diff --git a/recipes/bioconductor-pdinfobuilder/conda_build_config.yaml b/recipes/bioconductor-pdinfobuilder/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-pdinfobuilder/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-pdinfobuilder/meta.yaml b/recipes/bioconductor-pdinfobuilder/meta.yaml index 3c6c116561e41..70fbafad106fe 100644 --- a/recipes/bioconductor-pdinfobuilder/meta.yaml +++ b/recipes/bioconductor-pdinfobuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "pdInfoBuilder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,40 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c100dc18d204ce086f5a14f9503cd256e1c0b3bb89ba6139eb11de3b3f3e4433 + sha256: 96f94b99e7db9a2a38dfa19cc518c87fddc465aeb654b5033933959914bcb172 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-affxparser >=1.39.4' - - 'bioconductor-biobase >=2.27.3' - - 'bioconductor-biocgenerics >=0.13.11' - - 'bioconductor-biostrings >=2.35.12' - - 'bioconductor-iranges >=2.1.43' - - 'bioconductor-oligo >=1.31.5' - - 'bioconductor-oligoclasses >=1.29.6' - - 'bioconductor-s4vectors >=0.5.22' + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-affxparser >=1.39.4' - - 'bioconductor-biobase >=2.27.3' - - 'bioconductor-biocgenerics >=0.13.11' - - 'bioconductor-biostrings >=2.35.12' - - 'bioconductor-iranges >=2.1.43' - - 'bioconductor-oligo >=1.31.5' - - 'bioconductor-oligoclasses >=1.29.6' - - 'bioconductor-s4vectors >=0.5.22' + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +51,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.' - extra: identifiers: - biotools:pdinfobuilder diff --git a/recipes/bioconductor-peca/conda_build_config.yaml b/recipes/bioconductor-peca/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-peca/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-peca/meta.yaml b/recipes/bioconductor-peca/meta.yaml index 17456b3b3fb1a..094c365561e83 100644 --- a/recipes/bioconductor-peca/meta.yaml +++ b/recipes/bioconductor-peca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "PECA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7b2646b80522e8ed5f11a041dcf55b6ab812449c7ecc9d9e76a1a467b75e76b0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c5b2e956f358d0c71ba825d877f4fa8c9085bdb6dc6ab750230535c5996bc42f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-genefilter - - bioconductor-limma - - bioconductor-preprocesscore - - bioconductor-rots + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rots >=1.8.0,<1.10.0' - r-aroma.affymetrix - r-aroma.core - r-base run: - - bioconductor-affy - - bioconductor-genefilter - - bioconductor-limma - - bioconductor-preprocesscore - - bioconductor-rots + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rots >=1.8.0,<1.10.0' - r-aroma.affymetrix - r-aroma.core - r-base @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.' - extra: identifiers: - biotools:peca diff --git a/recipes/bioconductor-pepstat/meta.yaml b/recipes/bioconductor-pepstat/meta.yaml index eeacf8d627d9a..3606270eb4883 100644 --- a/recipes/bioconductor-pepstat/meta.yaml +++ b/recipes/bioconductor-pepstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pepStat" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9557008b00cc6cd6f5541f0ecb2fc8371848268794fc89932a8d79f7419aca2e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8e38350bee8eb0ebbaff0a1f3f7a1351a926593656b81dc64d6829d3523c3f4a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr run: - - bioconductor-biobase - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-data.table - r-fields @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Statistical analysis of peptide microarrays' - extra: identifiers: - biotools:pepstat diff --git a/recipes/bioconductor-pepxmltab/meta.yaml b/recipes/bioconductor-pepxmltab/meta.yaml index 494e160e2c1e1..efe4dfe2e16bc 100644 --- a/recipes/bioconductor-pepxmltab/meta.yaml +++ b/recipes/bioconductor-pepxmltab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pepXMLTab" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 80eacb29e93e02b9a333b8a9df936e77b61d301d7d64d556c430dc8adb7c4b18 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9e7613524c4d765c98dde2ba858e0727217f34427c76f6ee7213ac52bf157b24 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.' - extra: identifiers: - biotools:pepxmltab diff --git a/recipes/bioconductor-pfam.db/meta.yaml b/recipes/bioconductor-pfam.db/meta.yaml index 566b6712f1418..8d8fb59ddf021 100644 --- a/recipes/bioconductor-pfam.db/meta.yaml +++ b/recipes/bioconductor-pfam.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} {% set name = "PFAM.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bd7af3d85b94e146f6d404a425f83b612c33a53216467d5d7498195d8d2c8891 + sha256: 3d020c7c6e0001bfc5b787d499bd6955d8916cc518c05d198082f219f4e599fe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.39.3' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of protein ID mappings for PFAM assembled using data from public repositories' + + diff --git a/recipes/bioconductor-pfam.db/post-link.sh b/recipes/bioconductor-pfam.db/post-link.sh index 85b683613d6ec..7122705ed29e1 100644 --- a/recipes/bioconductor-pfam.db/post-link.sh +++ b/recipes/bioconductor-pfam.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PFAM.db_3.5.0.tar.gz" +FN="PFAM.db_3.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/PFAM.db_3.5.0.tar.gz" - "https://bioarchive.galaxyproject.org/PFAM.db_3.5.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.5.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/PFAM.db_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/PFAM.db_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.6.0_src_all.tar.gz" ) -MD5="1f3bc8e59cabb4e481073aa7326781d2" +MD5="84bf0f03fdf923d0be6d1c9eb18d54fb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-pgsea/meta.yaml b/recipes/bioconductor-pgsea/meta.yaml index c241eea01dbe9..6583101d6bbc9 100644 --- a/recipes/bioconductor-pgsea/meta.yaml +++ b/recipes/bioconductor-pgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "PGSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6434ee209072599ea508237137ab7475893a9db9e30ecc2f251b22bc337413bc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a6ede559ce880fbf526dc09fa92252d00e5628eff1cae9605b1277ede196335b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annaffy - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.5.5' - - bioconductor-go.db - - bioconductor-kegg.db + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - r-base run: - - bioconductor-annaffy - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.5.5' - - bioconductor-go.db - - bioconductor-kegg.db + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - r-base test: commands: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Parametric Analysis of Gene Set Enrichment' - extra: identifiers: - biotools:pgsea diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/conda_build_config.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml index 5cf5b6fb415f0..2fd9f058d2491 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.2" %} {% set name = "phastCons100way.UCSC.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d562071ea6a9a9f65e43241f3721f95f6d3543d44c6e94ba5ff7df3376d6f625 + sha256: ca052a0f6e874bcc8079b29e3cc1a29cb6b852b32d5a7a45dea5cff7c924acca build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bsgenome - - bioconductor-genomicranges - - 'bioconductor-genomicscores >=1.0.0' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-bsgenome - - bioconductor-genomicranges - - 'bioconductor-genomicscores >=1.0.0' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - wget test: diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh index 64086feb1b61c..e75d327f1937a 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="phastCons100way.UCSC.hg19_3.6.0.tar.gz" +FN="phastCons100way.UCSC.hg19_3.7.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.6.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz" + "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.7.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz" ) -MD5="62955c9b6b2d13c0e7b7870b213dbff1" +MD5="65aa706a567f7e328dbba0095f995cf1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-phenodist/conda_build_config.yaml b/recipes/bioconductor-phenodist/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-phenodist/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-phenodist/meta.yaml b/recipes/bioconductor-phenodist/meta.yaml index 544b8a8a50952..9c25417ed1eed 100644 --- a/recipes/bioconductor-phenodist/meta.yaml +++ b/recipes/bioconductor-phenodist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.27.0" %} {% set name = "phenoDist" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ea07b71c85eafabdbfaba53305647b494e27fcdddf1dcd9479dfccc550481356 + sha256: 338291a89db5663cb4b96dde94f93d542c6a7331a4041557545d86e5e5158f9a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-imagehts + - 'bioconductor-imagehts >=1.30.0,<1.32.0' - r-base - r-e1071 run: - - bioconductor-imagehts + - 'bioconductor-imagehts >=1.30.0,<1.32.0' - r-base - r-e1071 test: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2.1 summary: 'PhenoDist is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters.' - extra: identifiers: - biotools:phenodist diff --git a/recipes/bioconductor-philr/meta.yaml b/recipes/bioconductor-philr/meta.yaml index e1fdbff1c90a8..0b7c58127b535 100644 --- a/recipes/bioconductor-philr/meta.yaml +++ b/recipes/bioconductor-philr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "philr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f95426adf361d97d2d042ea52b75ddbdedec7b1d4a9cd534108d87db2edcceac + sha256: 09f25c62ac4c8332a2066b932c141716ed7d0d0d2e00fecfb63a564e78c71d1e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-ggtree + - 'bioconductor-ggtree >=1.12.7,<1.14.0' - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr run: - - bioconductor-ggtree + - 'bioconductor-ggtree >=1.12.7,<1.14.0' - r-ape - r-base - r-ggplot2 @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.' - extra: identifiers: - biotools:philr diff --git a/recipes/bioconductor-phosphonormalizer/meta.yaml b/recipes/bioconductor-phosphonormalizer/meta.yaml index 9b01be7baea88..c9103885ae6fc 100644 --- a/recipes/bioconductor-phosphonormalizer/meta.yaml +++ b/recipes/bioconductor-phosphonormalizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "phosphonormalizer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fecf78aebe6dfc4398d16e7f4ea711119b6d5782af7819cc13c0dc0155ce1fd0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9cde4fffab81f5523e754d8cb5f4e7a3e9d370863311f586bf78f42834ccb882 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.' + + diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index b998b34015718..c65b83ab85d3e 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.3" %} +{% set version = "1.24.2" %} {% set name = "phyloseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c0de813c5eeb68c02d20455552a6feda97a59d2391777dc35a727fcb40115e36 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 1415d5b3ad475b46dc1e6d4ca962c45b544469e4adf403e783fa714fb4d6b11c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.36.2' - - 'bioconductor-biocgenerics >=0.22.0' - - 'bioconductor-biomformat >=1.0.0' - - 'bioconductor-biostrings >=2.40.0' - - 'bioconductor-multtest >=2.28.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomformat >=1.8.0,<1.10.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - 'r-ade4 >=1.7.4' - 'r-ape >=5.0' - r-base @@ -33,13 +34,13 @@ requirements: - 'r-plyr >=1.8.3' - 'r-reshape2 >=1.4.1' - 'r-scales >=0.4.0' - - 'r-vegan >=2.4' + - 'r-vegan >=2.5' run: - - 'bioconductor-biobase >=2.36.2' - - 'bioconductor-biocgenerics >=0.22.0' - - 'bioconductor-biomformat >=1.0.0' - - 'bioconductor-biostrings >=2.40.0' - - 'bioconductor-multtest >=2.28.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomformat >=1.8.0,<1.10.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - 'r-ade4 >=1.7.4' - 'r-ape >=5.0' - r-base @@ -51,7 +52,7 @@ requirements: - 'r-plyr >=1.8.3' - 'r-reshape2 >=1.4.1' - 'r-scales >=0.4.0' - - 'r-vegan >=2.4' + - 'r-vegan >=2.5' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -59,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.' - extra: identifiers: - biotools:phyloseq diff --git a/recipes/bioconductor-piano/meta.yaml b/recipes/bioconductor-piano/meta.yaml index 0e081a6e01097..3d074fcc5456e 100644 --- a/recipes/bioconductor-piano/meta.yaml +++ b/recipes/bioconductor-piano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "piano" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3c827ea666831863feee0ced05e2b44bf409abc800e8fcbddf230cc69e30be78 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 11e0122d1189add38471fb1525f43b66a118512c687cb84acbfb55f4c797acdf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-fgsea - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-fgsea >=1.6.0,<1.8.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-gplots - r-igraph - r-relations run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-fgsea - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-fgsea >=1.6.0,<1.8.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-gplots - r-igraph @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.' - extra: identifiers: - biotools:piano diff --git a/recipes/bioconductor-pickgene/meta.yaml b/recipes/bioconductor-pickgene/meta.yaml index f050677eab4b1..2ceca0dd3bd93 100644 --- a/recipes/bioconductor-pickgene/meta.yaml +++ b/recipes/bioconductor-pickgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "pickgene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89be1ef9162466cdf9d1db8fe61d8bbaf5684aa1d1e50cdcb6d60575ad748f93 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 30c46613430711840bd7453bd3c597e077258c1e2cc5e6d3169c4a138b232ddb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Functions to Analyze Microarray (Gene Expression) Data.' - extra: identifiers: - biotools:pickgene diff --git a/recipes/bioconductor-pics/meta.yaml b/recipes/bioconductor-pics/meta.yaml index a24418b189236..820e7953e90fe 100644 --- a/recipes/bioconductor-pics/meta.yaml +++ b/recipes/bioconductor-pics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "PICS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 152337736219ec4e35c9de1df551d895b61742e3a65df795bd38fbc8f5876449 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 32c6d019d362f6baaad3a097cb437e6cc0d9e46204c4bfcf78211958c9ec892b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.1.3' - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + - openblas run: - - 'bioconductor-biocgenerics >=0.1.3' - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base + - openblas + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.' - extra: identifiers: - biotools:pics diff --git a/recipes/bioconductor-ping/meta.yaml b/recipes/bioconductor-ping/meta.yaml index fffc01f297047..615f8038e91af 100644 --- a/recipes/bioconductor-ping/meta.yaml +++ b/recipes/bioconductor-ping/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "PING" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,41 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1a4c8d39fe34d0e34f4c6f9e42263ef493edae84d559c0aeb783982adea06bd3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b1a058aee9b313bbaf9855eaad021354d061f4097aa327c5ec5ba4c19344f827 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-bsgenome - - bioconductor-chipseq - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-pics - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-pics >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fda run: - - bioconductor-biocgenerics - - bioconductor-bsgenome - - bioconductor-chipseq - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-pics - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-pics >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-fda + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.' - extra: identifiers: - biotools:ping diff --git a/recipes/bioconductor-pint/meta.yaml b/recipes/bioconductor-pint/meta.yaml index 5520037b67f83..4bc1a9953e17a 100644 --- a/recipes/bioconductor-pint/meta.yaml +++ b/recipes/bioconductor-pint/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "pint" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7515b9e76b1c24531b2b4233fdf56a764d7e404bc8101625c31dbf52ebd6e553 + sha256: 4d8805cff5d576139e6a7efd68fa3c88b1ecdae4f1248a8a0bdc2a7c88524cce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Pairwise data integration for functional genomics, including tools for DNA/RNA/miRNA dependency screens.' - extra: identifiers: - biotools:pint diff --git a/recipes/bioconductor-pkgdeptools/meta.yaml b/recipes/bioconductor-pkgdeptools/meta.yaml index d035566faede3..b253ff6c69a00 100644 --- a/recipes/bioconductor-pkgdeptools/meta.yaml +++ b/recipes/bioconductor-pkgdeptools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "pkgDepTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1887d4627fa7707d01ab581daa2a0c3af53227426d8eb9554a9522da10e43f68 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f7e5e3199cf227ab2267bfc6affdf94b4e9afec17d966e502e24967a42e13681 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base run: - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained.' - extra: identifiers: - biotools:pkgdeptools diff --git a/recipes/bioconductor-plethy/meta.yaml b/recipes/bioconductor-plethy/meta.yaml index 3eb030aa7f572..c4d6875195a4c 100644 --- a/recipes/bioconductor-plethy/meta.yaml +++ b/recipes/bioconductor-plethy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "plethy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ac66dc688626dc0652303a8b3bd9e9ec0fad64d1e0bf57e5f7dbb3063431ff08 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e840e9572a14cc8cba3c8d6a4167175a64715c6d09456c893d51fe01c4085add build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-streamer + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-streamer >=1.26.0,<1.28.0' - r-base - 'r-dbi >=0.5-1' - r-ggplot2 @@ -30,11 +31,11 @@ requirements: - r-reshape2 - 'r-rsqlite >=1.1' run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-streamer + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-streamer >=1.26.0,<1.28.0' - r-base - 'r-dbi >=0.5-1' - r-ggplot2 @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.' - extra: identifiers: - biotools:plethy diff --git a/recipes/bioconductor-plgem/meta.yaml b/recipes/bioconductor-plgem/meta.yaml index 1d69b045b9fea..45ec52c62dddc 100644 --- a/recipes/bioconductor-plgem/meta.yaml +++ b/recipes/bioconductor-plgem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "plgem" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 56296df547e7ea940406a6f0305968da2c4e05e57d862692e02ae328f7bdfd69 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 295cf196d66bbaa9acfcbde37a9bf77191a815299834f1eb1ddbfad5f006d389 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.' - extra: identifiers: - biotools:plgem diff --git a/recipes/bioconductor-plier/conda_build_config.yaml b/recipes/bioconductor-plier/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-plier/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-plier/meta.yaml b/recipes/bioconductor-plier/meta.yaml index bc3bc23b13abf..b16f80743bed9 100644 --- a/recipes/bioconductor-plier/meta.yaml +++ b/recipes/bioconductor-plier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "plier" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7daf8556ea66cc0be722ba23078291a38eeb8d59dc45e82b6d0fdfc759911558 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c658643f7380b61dd09f213a9eef0bcb5d284c796dacd9520905d40723912e0e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-affy - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.' - extra: identifiers: - biotools:plier diff --git a/recipes/bioconductor-plpe/meta.yaml b/recipes/bioconductor-plpe/meta.yaml index 7d851be223b6f..3d00be9e38cb1 100644 --- a/recipes/bioconductor-plpe/meta.yaml +++ b/recipes/bioconductor-plpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "PLPE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fbef60b65c303a1ffd10ae51ddd0d22120014448c58f868e2cfe68b8679316f1 + sha256: 9b3f2099b79d052210e7fa2ebd1b42035ac4d7571fc345ae4cf37d1612b56053 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-lpe + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-lpe >=1.54.0,<1.56.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-lpe + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-lpe >=1.54.0,<1.56.0' - r-base - r-mass test: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package performs tests for paired high-throughput data.' - extra: identifiers: - biotools:plpe diff --git a/recipes/bioconductor-plw/conda_build_config.yaml b/recipes/bioconductor-plw/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-plw/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-plw/meta.yaml b/recipes/bioconductor-plw/meta.yaml index 28c30f3e06798..34369e21fccd8 100644 --- a/recipes/bioconductor-plw/meta.yaml +++ b/recipes/bioconductor-plw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "plw" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 45ac13d5dff00441e279aeaf9246158ab14628ef96eec58758793048754edad7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b2efadc2037b501a9fc91a8b8e3658e3e8a2e937c58c150b05221ce9a034998b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.23.4' + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base - r-mass run: - - 'bioconductor-affy >=1.23.4' + - 'bioconductor-affy >=1.58.0,<1.60.0' - r-base - r-mass + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW).' - extra: identifiers: - biotools:plw diff --git a/recipes/bioconductor-pmm/meta.yaml b/recipes/bioconductor-pmm/meta.yaml index 264b37ecb6354..c8c94f6fa2971 100644 --- a/recipes/bioconductor-pmm/meta.yaml +++ b/recipes/bioconductor-pmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pmm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d1b8b2e8e84b72052917f64d858e1deb4c0271fbe8431a2ed68918062e80f5af + sha256: bfb8b5126ab41da2b1947c39ca5d1f573e857283f93053b076c461a5bda103e1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.' - extra: identifiers: - biotools:pmm diff --git a/recipes/bioconductor-podkat/meta.yaml b/recipes/bioconductor-podkat/meta.yaml index 2e91bfe7ad16c..fbaa531f561ef 100644 --- a/recipes/bioconductor-podkat/meta.yaml +++ b/recipes/bioconductor-podkat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "podkat" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,40 +8,43 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 84315f7a5278a3c40b50aaa92b7be45951279bbe731e4772c23c23ceb27d2331 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 631a2427117cf742bfb7e95d39525c4ce4813f4c37a86f4d5f359b53a77648a4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - 'bioconductor-bsgenome >=1.32.0' - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biostrings - - 'bioconductor-bsgenome >=1.32.0' - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -49,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.' - extra: identifiers: - biotools:podkat diff --git a/recipes/bioconductor-polyfit/meta.yaml b/recipes/bioconductor-polyfit/meta.yaml index 10998ca110a5e..bf4d4342ae1dc 100644 --- a/recipes/bioconductor-polyfit/meta.yaml +++ b/recipes/bioconductor-polyfit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Polyfit" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 30ecefffbff416ffc00af08d09643bcd153f5355bd66654ad01a290ecb3376be + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e176aff4d0eeecce3c53fd16b74d66c6b531465498063853c6b42d5a9c5499bd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-deseq + - 'bioconductor-deseq >=1.32.0,<1.34.0' - r-base run: - - bioconductor-deseq + - 'bioconductor-deseq >=1.32.0,<1.34.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Polyfit is an add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values.' - extra: identifiers: - biotools:polyfit diff --git a/recipes/bioconductor-ppidata/meta.yaml b/recipes/bioconductor-ppidata/meta.yaml index fe76ed0362e98..8fd1c09ffa508 100644 --- a/recipes/bioconductor-ppidata/meta.yaml +++ b/recipes/bioconductor-ppidata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.16.0" %} +{% set version = "0.18.0" %} {% set name = "ppiData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 05de1ef19ffbd9668f6d7cf93deb3cf596b145543af4cc164ea96f05a37a9203 + sha256: b13b804f9307b7f05356876bac395ade26b367c8642222d14c0dd04bc87c89ed build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-graph + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-graph + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - wget test: @@ -33,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository.' + + diff --git a/recipes/bioconductor-ppidata/post-link.sh b/recipes/bioconductor-ppidata/post-link.sh index e4f36cb7f677a..c21452f7a4827 100644 --- a/recipes/bioconductor-ppidata/post-link.sh +++ b/recipes/bioconductor-ppidata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ppiData_0.16.0.tar.gz" +FN="ppiData_0.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ppiData_0.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/ppiData_0.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ppidata/bioconductor-ppidata_0.16.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ppiData_0.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ppiData_0.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ppidata/bioconductor-ppidata_0.18.0_src_all.tar.gz" ) -MD5="9f3e9e544de3c60739e33c77c110f4ea" +MD5="277d47ac92b8255e643f3b155d7a9d9d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-ppinfer/meta.yaml b/recipes/bioconductor-ppinfer/meta.yaml index b57bf1c841791..afcbb546a4d53 100644 --- a/recipes/bioconductor-ppinfer/meta.yaml +++ b/recipes/bioconductor-ppinfer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "PPInfer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a04477dff3160e04f119b5e9c42c18043b7f5164db91dc964235ba6d138f8188 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f0072e2f58d648aa5a1fe3a6cc24478109577e4c907fc462a72598d6d49acb96 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-fgsea - - bioconductor-stringdb - - bioconductor-yeastexpdata + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-fgsea >=1.6.0,<1.8.0' + - 'bioconductor-stringdb >=1.20.0,<1.22.0' + - 'bioconductor-yeastexpdata >=0.26.0,<0.28.0' - r-base - r-ggplot2 - r-igraph - r-kernlab run: - - bioconductor-biomart - - bioconductor-fgsea - - bioconductor-stringdb - - bioconductor-yeastexpdata + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-fgsea >=1.6.0,<1.8.0' + - 'bioconductor-stringdb >=1.20.0,<1.22.0' + - 'bioconductor-yeastexpdata >=0.26.0,<0.28.0' - r-base - r-ggplot2 - r-igraph @@ -41,3 +42,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.' + + diff --git a/recipes/bioconductor-ppistats/meta.yaml b/recipes/bioconductor-ppistats/meta.yaml index bd722cd5557cb..d5f0f2063d0e4 100644 --- a/recipes/bioconductor-ppistats/meta.yaml +++ b/recipes/bioconductor-ppistats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ppiStats" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 79bc6fe85189bf919d015cf790491c49a60d76ed53c44fdbade784bb1cdbb993 + sha256: ec0ee6d94961d3df686b8058d30d65fefd8606119fb8025766407c61c59ddc7f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-category - - bioconductor-graph - - 'bioconductor-ppidata >=0.1.19' - - 'bioconductor-scisi >=1.13.2' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-ppidata >=0.18.0,<0.20.0' + - 'bioconductor-scisi >=1.52.0,<1.54.0' - r-base - r-lattice - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-category - - bioconductor-graph - - 'bioconductor-ppidata >=0.1.19' - - 'bioconductor-scisi >=1.13.2' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-ppidata >=0.18.0,<0.20.0' + - 'bioconductor-scisi >=1.52.0,<1.54.0' - r-base - r-lattice - r-rcolorbrewer @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for the analysis of protein interaction data.' - extra: identifiers: - biotools:ppistats diff --git a/recipes/bioconductor-pqsfinder/meta.yaml b/recipes/bioconductor-pqsfinder/meta.yaml index 030e9e9420ab5..f008790489891 100644 --- a/recipes/bioconductor-pqsfinder/meta.yaml +++ b/recipes/bioconductor-pqsfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "pqsfinder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,33 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d0c0b150578a652759674f0498f4e3439eb5932f77321a71b0bbe9179ad4c065 + sha256: f6e003939f0fcc580f9e9479a42743a79f9edbddbf6e4a5686000268481e8f21 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-bh >=1.62.0' - 'r-rcpp >=0.12.3' run: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-bh >=1.62.0' - 'r-rcpp >=0.12.3' - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'The main functionality of this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, this package is able to detect sequences responsible for G4s folded from imperfect G-runs containing bulges or mismatches and as such is more sensitive than competing algorithms.' - extra: identifiers: - biotools:pqsfinder diff --git a/recipes/bioconductor-prada/meta.yaml b/recipes/bioconductor-prada/meta.yaml index 2c30280ca6cc8..aecd722717036 100644 --- a/recipes/bioconductor-prada/meta.yaml +++ b/recipes/bioconductor-prada/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "prada" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 36e2b25c172eb24b4c5feccfe47760184035143f99d9cd438d79fd1a0281c8a5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 601a09c83d87dcdef2ae5e6dde37812c7c66178b2cf4a38279321b5845bb8d43 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-mass - r-rcolorbrewer - r-rrcov run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-mass - r-rcolorbrewer - r-rrcov + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy).' - extra: identifiers: - biotools:prada diff --git a/recipes/bioconductor-prebs/conda_build_config.yaml b/recipes/bioconductor-prebs/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-prebs/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-prebs/meta.yaml b/recipes/bioconductor-prebs/meta.yaml index 0963b2bff4df3..68f061c9a6106 100644 --- a/recipes/bioconductor-prebs/meta.yaml +++ b/recipes/bioconductor-prebs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "prebs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aea367817b8b6dca27f5f77a982697b362e529ab9735a23669856c3a64cc426b + sha256: 00a0f2d25b0214d735e21ee53345c36ede45c2b747aae92f67bc635bf7c6ee5c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - 'bioconductor-genomicranges >=1.13.3' - - bioconductor-iranges - - bioconductor-rpa - - bioconductor-s4vectors + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rpa >=1.36.0,<1.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - 'bioconductor-genomicranges >=1.13.3' - - bioconductor-iranges - - bioconductor-rpa - - bioconductor-s4vectors + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rpa >=1.36.0,<1.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.' - extra: identifiers: - biotools:prebs diff --git a/recipes/bioconductor-preda/meta.yaml b/recipes/bioconductor-preda/meta.yaml index 74f5fcdc4f268..5a712a5c21bfc 100644 --- a/recipes/bioconductor-preda/meta.yaml +++ b/recipes/bioconductor-preda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.1" %} {% set name = "PREDA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: df7dfca8540d5353ec578161cb986ad33308c75756816d3797df8a4630699c27 + sha256: 1a1ac227170f62fee5a8de030f96b60a76ffb0a55c1fdc7b891b7c4a75bd28ff build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - 'r-lokern >=1.0.9' run: - - bioconductor-annotate - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - 'r-lokern >=1.0.9' test: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Package for the position related analysis of quantitative functional genomics data.' - extra: identifiers: - biotools:preda diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index 6deaf5ef65811..53bd4b5b7ca2c 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "preprocessCore" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f022f2b97b8202403d5a28d17b12aec0f46ea1beae7bac5fca8eb5b4e67a2d57 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7371a739d3481544c2e95e956d873fcc03e8f03e4761fd573d3b95747ec8caa9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A library of core preprocessing routines.' - extra: identifiers: - biotools:preprocesscore diff --git a/recipes/bioconductor-prize/meta.yaml b/recipes/bioconductor-prize/meta.yaml index 9107a9a302666..b638938b99eea 100644 --- a/recipes/bioconductor-prize/meta.yaml +++ b/recipes/bioconductor-prize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Prize" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 86f14593571d1e874b76bd4a66081b0d81cfe24528a5d39c515aac9b8c254eed + sha256: cc5f5a907f8ad8bc5b331db6c08e0ede4c259ff7d5b92f0e0f3ab316c737d706 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The high throughput studies often produce large amounts of numerous genes and proteins of interest. While it is difficult to study and validate all of them. Analytic Hierarchy Process (AHP) offers a novel approach to narrowing down long lists of candidates by prioritizing them based on how well they meet the research goal. AHP is a mathematical technique for organizing and analyzing complex decisions where multiple criteria are involved. The technique structures problems into a hierarchy of elements, and helps to specify numerical weights representing the relative importance of each element. Numerical weight or priority derived from each element allows users to find alternatives that best suit their goal and their understanding of the problem.' - extra: identifiers: - biotools:prize diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index ded5c537b94e9..35b46d4ad264f 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "proBAMr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 13aaaa9384e9d356f3511860637659cd6fbad15f1537a833d6f21b479ca038ab + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c88e11f33b601d1df49e994a72c08afe59aad6cc9a12d2ece659cb826f8aca8e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biostrings - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base run: - - bioconductor-annotationdbi - - bioconductor-biostrings - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base test: commands: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.' - extra: identifiers: - biotools:probamr diff --git a/recipes/bioconductor-process/meta.yaml b/recipes/bioconductor-process/meta.yaml index d8e12a5cf8093..7224eeba730bc 100644 --- a/recipes/bioconductor-process/meta.yaml +++ b/recipes/bioconductor-process/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "PROcess" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 38eca809722fd2b1017d3cc95360332de61178740498652e1ef7ae0cdb6af0f4 + sha256: 2ec635ccc30b4e347a7f85b60a02dba2bdc0ba2b5b11622d40a9671a71d18a24 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-icens + - 'bioconductor-icens >=1.52.0,<1.54.0' - r-base run: - - bioconductor-icens + - 'bioconductor-icens >=1.52.0,<1.54.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package for processing protein mass spectrometry data.' - extra: identifiers: - biotools:process diff --git a/recipes/bioconductor-procoil/meta.yaml b/recipes/bioconductor-procoil/meta.yaml index 210dfa13fb7cf..a2d6d0adcc37b 100644 --- a/recipes/bioconductor-procoil/meta.yaml +++ b/recipes/bioconductor-procoil/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "procoil" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 938543df5066f2c06ffcbd79f298e15d77869f675655ef83925fbf7c6e565846 + sha256: b92f0583661c74b66a741973e9bc019a509440d25eeb1d02e81e111ef104f004 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-kebabs - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-kebabs >=1.14.0,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biostrings - - bioconductor-kebabs - - bioconductor-s4vectors + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-kebabs >=1.14.0,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base test: commands: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.' - extra: identifiers: - biotools:procoil diff --git a/recipes/bioconductor-profia/meta.yaml b/recipes/bioconductor-profia/meta.yaml index 2da64c464f19f..dcd3ae3fa33bc 100644 --- a/recipes/bioconductor-profia/meta.yaml +++ b/recipes/bioconductor-profia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "proFIA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f74b59f95a81b7c0c3ab9780c859219ee1c85dc6df2d1d257ff4e2ac6510565f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6c1be762b9e1028d3f538f8e7a01e2e6f5a036f6de07be26bdf7ba1a75d6cddc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocparallel - - bioconductor-ropls - - bioconductor-xcms + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-ropls >=1.12.0,<1.14.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-minpack.lm - r-missforest - r-pracma run: - - bioconductor-biobase - - bioconductor-biocparallel - - bioconductor-ropls - - bioconductor-xcms + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-ropls >=1.12.0,<1.14.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - r-minpack.lm - r-missforest - r-pracma + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: CeCILL summary: 'Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and generate the peak table. The workflow includes noise modelling, band detection and filtering then signal matching and missing value imputation. The peak table can then be exported as a .tsv file for further analysis. Visualisations to assess the quality of the data and of the signal made are easely produced.' - extra: identifiers: - biotools:profia diff --git a/recipes/bioconductor-proloc/conda_build_config.yaml b/recipes/bioconductor-proloc/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-proloc/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml index ed7f5c1b959e4..cf69eb5ce1243 100644 --- a/recipes/bioconductor-proloc/meta.yaml +++ b/recipes/bioconductor-proloc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.2" %} {% set name = "pRoloc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8039b509b59ab4a9ba4182e5e4a322de9e1a52ff08a5fce5997d9dcadd65d86b + sha256: 8772783ee6bd4df8f733ab1874c73f3c3bfd6fe82e7b5cd7d0033536732eff4e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biomart - - 'bioconductor-mlinterfaces >=1.37.1' - - 'bioconductor-msnbase >=1.19.20' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-mlinterfaces >=1.60.1,<1.62.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' - r-base - r-caret - r-class @@ -48,16 +46,15 @@ requirements: - r-rcolorbrewer - 'r-rcpp >=0.10.3' - r-rcpparmadillo - - 'r-rtsne >=0.13' - r-sampling - r-scales run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biomart - - 'bioconductor-mlinterfaces >=1.37.1' - - 'bioconductor-msnbase >=1.19.20' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-mlinterfaces >=1.60.1,<1.62.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' - r-base - r-caret - r-class @@ -80,10 +77,12 @@ requirements: - r-rcolorbrewer - 'r-rcpp >=0.10.3' - r-rcpparmadillo - - 'r-rtsne >=0.13' - r-sampling - r-scales - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -91,7 +90,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.' - extra: identifiers: - biotools:proloc diff --git a/recipes/bioconductor-prolocgui/conda_build_config.yaml b/recipes/bioconductor-prolocgui/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-prolocgui/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml index 66aea74dd2f74..a1203549e527a 100644 --- a/recipes/bioconductor-prolocgui/meta.yaml +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pRolocGUI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,17 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fcc718947eed8d7e5be79c8580fec0049c241879fc9dd1db5b1c413eedd98f34 + sha256: b254d49ec1c977e0904e8336cdc8ceaf4e4fff180770ced2b44ba0cfb53de4b1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-msnbase >=2.1.11' - - 'bioconductor-proloc >=1.11.1' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-proloc >=1.20.2,<1.22.0' - r-base - r-dplyr - 'r-dt >=0.1.40' @@ -28,9 +28,9 @@ requirements: - r-scales - 'r-shiny >=0.9.1' run: - - bioconductor-biobase - - 'bioconductor-msnbase >=2.1.11' - - 'bioconductor-proloc >=1.11.1' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-proloc >=1.20.2,<1.22.0' - r-base - r-dplyr - 'r-dt >=0.1.40' @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny.' - extra: identifiers: - biotools:prolocgui diff --git a/recipes/bioconductor-promise/meta.yaml b/recipes/bioconductor-promise/meta.yaml index ec3f94fac8aa2..9847b164acf0c 100644 --- a/recipes/bioconductor-promise/meta.yaml +++ b/recipes/bioconductor-promise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "PROMISE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f0cc0c96f57369033c1ebad66afb4c18cf34a33e67097b9ca91d0dd3f421886d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 24127027591044e485d0cb293de277037cdf3a506f91f4dbe533462cde45afed build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-gseabase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base run: - - bioconductor-biobase - - bioconductor-gseabase + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019' - extra: identifiers: - biotools:promise diff --git a/recipes/bioconductor-proper/meta.yaml b/recipes/bioconductor-proper/meta.yaml index dea81b6fb5f6e..875b57ecbd18d 100644 --- a/recipes/bioconductor-proper/meta.yaml +++ b/recipes/bioconductor-proper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PROPER" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a7582cf4fe3bb8719f8ccdc9678efac251c8222b852965f4735151e731bff44c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4ea98b7824e7bec9f69ae1cf43d8be86ef7c7b0041928b46625bf697b6159ee8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-edger + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base run: - - bioconductor-edger + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.' - extra: identifiers: - biotools:proper diff --git a/recipes/bioconductor-prot2d/meta.yaml b/recipes/bioconductor-prot2d/meta.yaml index c33761f977dc7..35d6ce626d26e 100644 --- a/recipes/bioconductor-prot2d/meta.yaml +++ b/recipes/bioconductor-prot2d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "prot2D" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 52274182dafbdfe2965efed6f19c846cf833d197e2bcd25dec29d6aa1c18e5ba + sha256: 9b9fa1a7e5d6c16bbff19671330ef02eb9dc6e92daba1eb15ce3106a564d914b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-impute - - bioconductor-limma - - bioconductor-mulcom - - bioconductor-qvalue + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-mulcom >=1.30.0,<1.32.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-fdrtool - r-mass - r-samr - r-st run: - - bioconductor-biobase - - bioconductor-impute - - bioconductor-limma - - bioconductor-mulcom - - bioconductor-qvalue + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-mulcom >=1.30.0,<1.32.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-fdrtool - r-mass @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments' - extra: identifiers: - biotools:prot2d diff --git a/recipes/bioconductor-proteomicsannotationhubdata/conda_build_config.yaml b/recipes/bioconductor-proteomicsannotationhubdata/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-proteomicsannotationhubdata/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml b/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml index 914162093a0b1..3cf6ee386b48e 100644 --- a/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml +++ b/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ProteomicsAnnotationHubData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,33 +10,33 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 05f2500decf77ab9fa6e94d4ec0220f53926b1b9341e1b9cb9abda91f12bcdd7 + sha256: d9581b7a047cad2489ddc313dbeace66a42194ac454651271f3d03db3e96bda0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationhub >=2.1.45' - - bioconductor-annotationhubdata - - bioconductor-biobase - - bioconductor-biocinstaller - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-msnbase - - 'bioconductor-mzr >=2.3.2' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-annotationhubdata >=1.10.2,<1.12.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' - r-base - r-rcurl run: - - 'bioconductor-annotationhub >=2.1.45' - - bioconductor-annotationhubdata - - bioconductor-biobase - - bioconductor-biocinstaller - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-msnbase - - 'bioconductor-mzr >=2.3.2' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-annotationhubdata >=1.10.2,<1.12.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' - r-base - r-rcurl test: @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'These recipes convert a variety and a growing number of public proteomics data sets into easily-used standard Bioconductor data structures.' - extra: identifiers: - biotools:proteomicsannotationhubdata diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 87ceb005e6251..2043f25c87948 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ProtGenerics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d17a08fb648de880af65c76f58483f70379807499dce41ee5296234240b9329a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 96b1140b0baeb7799e0abe11cc84a7905766c0eb12a828e2469e472578534b16 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'S4 generic functions needed by Bioconductor proteomics packages.' - extra: identifiers: - biotools:protgenerics diff --git a/recipes/bioconductor-psea/meta.yaml b/recipes/bioconductor-psea/meta.yaml index b9174023d76ae..bf07e36e1c8de 100644 --- a/recipes/bioconductor-psea/meta.yaml +++ b/recipes/bioconductor-psea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "PSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e7a6fa2312ad6215ede856df7f1bb4e2a0568731de7e9af2334092b61379879a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0d0c0cd836d52f1464f1e3faced8703b52e969719ad30692849de680c85419af build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-mass test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Deconvolution of gene expression data by Population-Specific Expression Analysis (PSEA).' - extra: identifiers: - biotools:psea diff --git a/recipes/bioconductor-psicquic/meta.yaml b/recipes/bioconductor-psicquic/meta.yaml index 2466be8a2fd15..3c86c686ae559 100644 --- a/recipes/bioconductor-psicquic/meta.yaml +++ b/recipes/bioconductor-psicquic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.1" %} {% set name = "PSICQUIC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ec3ef36e6d60759dc9debe2d46a3b2c06d75a7cc8d61d5e8f83867ed8f904245 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d9b363a9a8057baffee92e7c3c9d270d7ed22976180030d566ae14049f0933e2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-iranges + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-httr - r-plyr - r-rcurl run: - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-iranges + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-httr - r-plyr @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Apache License 2.0' summary: 'PSICQUIC is a project within the HUPO Proteomics Standard Initiative (HUPO-PSI). It standardises programmatic access to molecular interaction databases.' - extra: identifiers: - biotools:psicquic diff --git a/recipes/bioconductor-psygenet2r/conda_build_config.yaml b/recipes/bioconductor-psygenet2r/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-psygenet2r/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-psygenet2r/meta.yaml b/recipes/bioconductor-psygenet2r/meta.yaml index 4391ff3e2d31e..f31151eb62bbb 100644 --- a/recipes/bioconductor-psygenet2r/meta.yaml +++ b/recipes/bioconductor-psygenet2r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "psygenet2r" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 676110fc16054093b6028ed513dce84c8b516a1b715bcc4602e447e9e51ec075 + sha256: c5edc497c9016d1ea4e61467c2ca3537f3d2b2d4304f5cfe24ebe9370ec75b66 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bgeedb - - bioconductor-biobase - - bioconductor-biocinstaller - - bioconductor-biomart - - bioconductor-go.db - - bioconductor-topgo + - 'bioconductor-bgeedb >=2.6.2,<2.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-ggplot2 - r-igraph @@ -32,12 +32,12 @@ requirements: - r-reshape2 - r-stringr run: - - bioconductor-bgeedb - - bioconductor-biobase - - bioconductor-biocinstaller - - bioconductor-biomart - - bioconductor-go.db - - bioconductor-topgo + - 'bioconductor-bgeedb >=2.6.2,<2.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-ggplot2 - r-igraph @@ -50,9 +50,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT + license: 'MIT + file LICENSE' summary: 'Package to retrieve data from PsyGeNET database (www.psygenet.org) and to perform comorbidity studies with PsyGeNET''s and user''s data.' - extra: identifiers: - biotools:psygenet2r diff --git a/recipes/bioconductor-puma/conda_build_config.yaml b/recipes/bioconductor-puma/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-puma/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-puma/meta.yaml b/recipes/bioconductor-puma/meta.yaml index 8b758bb93a496..8cd1f47d2c82c 100644 --- a/recipes/bioconductor-puma/meta.yaml +++ b/recipes/bioconductor-puma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.20.0" %} +{% set version = "3.22.0" %} {% set name = "puma" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 31302d1937e27e2852a0d34f38fef6f602c77a81843ae50a75f7d32fd4bd9c5d + sha256: dd39ad777211a794773dc196541631162ae999b8426ef8de5863b2f83e788032 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-affy >=1.46.0' - - bioconductor-affyio - - 'bioconductor-biobase >=2.5.5' - - 'bioconductor-oligo >=1.32.0' - - bioconductor-oligoclasses + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - r-base - r-mclust run: - - 'bioconductor-affy >=1.46.0' - - bioconductor-affyio - - 'bioconductor-biobase >=2.5.5' - - 'bioconductor-oligo >=1.32.0' - - bioconductor-oligoclasses + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - r-base - r-mclust - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Most analyses of Affymetrix GeneChip data (including tranditional 3'' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3'' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.' - extra: identifiers: - biotools:puma diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index fc32b566eeaee..6e01406e1ef97 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.11.20" %} {% set name = "PureCN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: #url: https://depot.galaxyproject.org/software/bioconductor-purecn/bioconductor-purecn_{{ version }}_src_all.tar.gz sha256: 711861830f36d74f3db8d43aad7dd6e9c3aaaceaec28677cf29ad72643730863 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-dnacopy - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.20.3' - - 'bioconductor-iranges >=2.2.1' - - bioconductor-limma - - bioconductor-rhdf5 - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.14.1' - - r-base 3.4.* + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-edger >=3.22.0,<3.24.0' + - 'bioconductor-limma >=3.36.0,<3.38.0' + - r-base - r-data.table - r-deconstructsigs - r-futile.logger @@ -41,22 +41,22 @@ requirements: - r-rcolorbrewer - r-vgam run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-dnacopy - - bioconductor-edger - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.20.3' - - 'bioconductor-iranges >=2.2.1' - - bioconductor-limma - - bioconductor-rhdf5 - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.14.1' - - r-base 3.4.* + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-edger >=3.22.0,<3.24.0' + - 'bioconductor-limma >=3.36.0,<3.38.0' + - r-base - r-data.table - r-deconstructsigs - r-futile.logger @@ -73,7 +73,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.' - extra: identifiers: - biotools:purecn diff --git a/recipes/bioconductor-pvac/conda_build_config.yaml b/recipes/bioconductor-pvac/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-pvac/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-pvac/meta.yaml b/recipes/bioconductor-pvac/meta.yaml index 8a8ad9e634b81..4c86922d0bf74 100644 --- a/recipes/bioconductor-pvac/meta.yaml +++ b/recipes/bioconductor-pvac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "pvac" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 86502f2a4f52d07cf6fe34408e45027760f3d44c86e36fa80678467254f1bc52 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: afc020ec92f2d744d3d54c042c0592410ce46ea0f7f5028693a16a64a7176233 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.20.0' - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-affy >=1.20.0' - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).' - extra: identifiers: - biotools:pvac diff --git a/recipes/bioconductor-pvca/conda_build_config.yaml b/recipes/bioconductor-pvca/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-pvca/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-pvca/meta.yaml b/recipes/bioconductor-pvca/meta.yaml index aefe4f79f7217..d9421a513d469 100644 --- a/recipes/bioconductor-pvca/meta.yaml +++ b/recipes/bioconductor-pvca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "pvca" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fbfa536b88dae30d0fc925fdc3852af96bdf6fbdf203198244ea3283dd495bae + sha256: 2ff90cebdd80f32c30a1af3c2c417af37ee89ec88581ced8d8f2504962ef9a37 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-lme4 - r-matrix run: - - bioconductor-biobase - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-lme4 - r-matrix @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.' - extra: identifiers: - biotools:pvca diff --git a/recipes/bioconductor-pviz/meta.yaml b/recipes/bioconductor-pviz/meta.yaml index a7543b9a91a0f..7cd0031cc53e2 100644 --- a/recipes/bioconductor-pviz/meta.yaml +++ b/recipes/bioconductor-pviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Pviz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 65c2ce85d32bd5dd33725348747308df92cf320f203238db9818109c3bd23cde + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 722b05d01d1e26c4feeaae73c9c053b606d1babab0b921720c5c0aa60a1fbcfb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-biovizbase - - bioconductor-genomicranges - - 'bioconductor-gviz >=1.7.10' - - bioconductor-iranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-data.table run: - - bioconductor-biostrings - - bioconductor-biovizbase - - bioconductor-genomicranges - - 'bioconductor-gviz >=1.7.10' - - bioconductor-iranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-data.table test: @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Pviz adapts the Gviz package for protein sequences and data.' - extra: identifiers: - biotools:pviz diff --git a/recipes/bioconductor-pwmenrich/meta.yaml b/recipes/bioconductor-pwmenrich/meta.yaml index b6732c2877fa3..1a80d3537efb0 100644 --- a/recipes/bioconductor-pwmenrich/meta.yaml +++ b/recipes/bioconductor-pwmenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.14.0" %} +{% set version = "4.16.0" %} {% set name = "PWMEnrich" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0fea381553c165f3fdd55f00496c506467fd3aaa9f000fbd966ff85e74da80ab + sha256: fd648dda7ed9f4d6e570a76b0ee4b4992469b2910d1c75e803c80df6d72fe838 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-seqlogo + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-base - r-evd - r-gdata run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-seqlogo + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-base - r-evd - r-gdata @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.' - extra: identifiers: - biotools:pwmenrich diff --git a/recipes/bioconductor-pwomics/conda_build_config.yaml b/recipes/bioconductor-pwomics/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-pwomics/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-pwomics/meta.yaml b/recipes/bioconductor-pwomics/meta.yaml index 1223484c065ee..3eb315f0d8892 100644 --- a/recipes/bioconductor-pwomics/meta.yaml +++ b/recipes/bioconductor-pwomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "pwOmics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,37 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f973ef19cb2d5ced615656007556c39d65e5265a7a475d2f11b79a0b8bfbce09 + sha256: 7288ed9d0e6102383e884ecedc23c64cd81ff881e29f30542ed2962747ecfe33 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-annotationhub - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-genomicranges - - bioconductor-graph - - bioconductor-rbiopaxparser - - bioconductor-stringdb + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' + - 'bioconductor-stringdb >=1.20.0,<1.22.0' - r-base - r-data.table - r-gplots - r-igraph run: - - bioconductor-annotationdbi - - bioconductor-annotationhub - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-genomicranges - - bioconductor-graph - - bioconductor-rbiopaxparser - - bioconductor-stringdb + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' + - 'bioconductor-stringdb >=1.20.0,<1.22.0' - r-base - r-data.table - r-gplots @@ -52,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and phosphoproteins. A separate downstream analysis of phosphoproteomic data including pathway identification, transcription factor identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream transcription factors and potential proteomic regulators. The cross-platform comparative analysis allows for comprehensive analysis of single time point experiments and time-series experiments by providing static and dynamic analysis tools for data integration. In addition, it provides functions to identify individual signaling axes based on data integration.' - extra: identifiers: - biotools:pwomics diff --git a/recipes/bioconductor-qcmetrics/meta.yaml b/recipes/bioconductor-qcmetrics/meta.yaml index 654093e95f363..d9c46c67b0da8 100644 --- a/recipes/bioconductor-qcmetrics/meta.yaml +++ b/recipes/bioconductor-qcmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "qcmetrics" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e848b31d7b7b0931b0b483b9fb8f61bb544957bd3a7e7f2432289a647ebbfea9 + sha256: e85a7a296adcda4ee012ab1a1621290c3261ce2b799fb3b4817467654e108042 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-knitr - r-nozzle.r1 - r-pander - r-xtable run: - - bioconductor-biobase - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-knitr - r-nozzle.r1 @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.' - extra: identifiers: - biotools:qcmetrics diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index 1d3175757be25..25a4029e65847 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "QDNAseq.mm10" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c3356ba2be7fdcbfe0837613a52dc3e1601b953e2b1dec90f384e976cce5f9d + sha256: a8fc7be0a41bf03d12d1184413aa9d0eea562156b62ca06f23f8a6beb801d048 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-qdnaseq + - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' - r-base run: - - bioconductor-qdnaseq + - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL summary: 'This package provides QDNAseq bin annotations for the mouse genome build mm10.' + + diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 91395c6d1f40a..62206bcda0485 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="QDNAseq.mm10_1.8.0.tar.gz" +FN="QDNAseq.mm10_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/QDNAseq.mm10_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.8.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/QDNAseq.mm10_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.10.0_src_all.tar.gz" ) -MD5="dbbf1cb5ab643feaa7e0c2e5b8902c90" +MD5="89069a71fa4182e83c6029345d3aefdf" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index d31252ab60a51..85b2c8d2708bb 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "QDNAseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1eea2f1478e507bc5546ccca506ef6f7383d8e6063596ff0d1f9e10e34d9eb51 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8d73b6224d1c82a2e8c540ec3c7c29ac6993704f9a4e024f03cdf1ee5d4d46de build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.18.0' - - 'bioconductor-biocparallel >=1.6.6' - - 'bioconductor-cghbase >=1.18.0' - - 'bioconductor-cghcall >=2.18.0' - - 'bioconductor-dnacopy >=1.32.0' - - 'bioconductor-genomicranges >=1.20' - - 'bioconductor-iranges >=2.2' - - 'bioconductor-rsamtools >=1.20' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' run: - - 'bioconductor-biobase >=2.18.0' - - 'bioconductor-biocparallel >=1.6.6' - - 'bioconductor-cghbase >=1.18.0' - - 'bioconductor-cghcall >=2.18.0' - - 'bioconductor-dnacopy >=1.32.0' - - 'bioconductor-genomicranges >=1.20' - - 'bioconductor-iranges >=2.2' - - 'bioconductor-rsamtools >=1.20' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.' - extra: identifiers: - biotools:qdnaseq diff --git a/recipes/bioconductor-qpcrnorm/conda_build_config.yaml b/recipes/bioconductor-qpcrnorm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-qpcrnorm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-qpcrnorm/meta.yaml b/recipes/bioconductor-qpcrnorm/meta.yaml index 1cde79528542e..ea4b24554d2b5 100644 --- a/recipes/bioconductor-qpcrnorm/meta.yaml +++ b/recipes/bioconductor-qpcrnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "qpcrNorm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e5e68fa9ae5e17a60f4b52b831080785d123ff41998f4d0f69293c72dfa3edd1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 707f345dc26c1930c5c1429e45990ba50a3cfe378f51ce7cfc7357eefbd317ce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.' - extra: identifiers: - biotools:qpcrnorm diff --git a/recipes/bioconductor-qpgraph/meta.yaml b/recipes/bioconductor-qpgraph/meta.yaml index 22001bd8b7418..79bee7542d58f 100644 --- a/recipes/bioconductor-qpgraph/meta.yaml +++ b/recipes/bioconductor-qpgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "qpgraph" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,48 +10,49 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e0dab2d4606f6721acbddfce446c6f78a3fda416fbb2b504cbf31828186db583 + sha256: 8ece88886836fcb2693e43cee82a18c277b53548e40a716b3abc49d78fb3827e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-graph >=1.45.1' - - bioconductor-iranges - - bioconductor-rgraphviz - - bioconductor-s4vectors + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-matrix >=1.0' - r-mvtnorm - r-qtl run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocparallel - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-graph >=1.45.1' - - bioconductor-iranges - - bioconductor-rgraphviz - - bioconductor-s4vectors + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-matrix >=1.0' - r-mvtnorm - r-qtl - - libcxx # [osx] + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -59,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Estimate gene and eQTL networks from high-throughput expression and genotyping assays.' - extra: identifiers: - biotools:qpgraph diff --git a/recipes/bioconductor-qrqc/meta.yaml b/recipes/bioconductor-qrqc/meta.yaml index f32a0ed24a102..06c312d43fdb1 100644 --- a/recipes/bioconductor-qrqc/meta.yaml +++ b/recipes/bioconductor-qrqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "qrqc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,18 +8,19 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9109afd765a9a45d6f8c6af0ca63c5c80f33da6f8b5f45f7da75e69c313a195d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5c0acfd1c4e980b045411cd1c1de94f8de89c272e0e82edbe753ca6e82ee36bd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-biovizbase - - 'bioconductor-rsamtools >=1.19.38' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-brew - r-ggplot2 @@ -28,9 +29,9 @@ requirements: - r-testthat - r-xtable run: - - bioconductor-biostrings - - bioconductor-biovizbase - - 'bioconductor-rsamtools >=1.19.38' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biovizbase >=1.28.2,<1.30.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-brew - r-ggplot2 @@ -38,6 +39,9 @@ requirements: - r-reshape - r-testthat - r-xtable + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +49,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Quickly scans reads and gathers statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.' - extra: identifiers: - biotools:qrqc diff --git a/recipes/bioconductor-qsea/conda_build_config.yaml b/recipes/bioconductor-qsea/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-qsea/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml index af9f682711812..2da57e9688fea 100644 --- a/recipes/bioconductor-qsea/meta.yaml +++ b/recipes/bioconductor-qsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "qsea" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,46 +10,46 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 999dc5eaaaccf34f5f338ca1f78b7af4a0ada168b056d36af3f3d34a4caade01 + sha256: 8c06249fd05d91fd116e21f8261a83a2687d8895fa922c4c903477d42d0489df build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-hmmcopy - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-hmmcopy >=1.22.0,<1.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-gtools - r-zoo run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-hmmcopy - - bioconductor-iranges - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-hmmcopy >=1.22.0,<1.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-gtools - r-zoo - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -57,7 +57,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.' - extra: identifiers: - biotools:qsea diff --git a/recipes/bioconductor-qualifier/meta.yaml b/recipes/bioconductor-qualifier/meta.yaml index 1e38048ef5f38..eebb168125928 100644 --- a/recipes/bioconductor-qualifier/meta.yaml +++ b/recipes/bioconductor-qualifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "QUALIFIER" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 171b3941f32484a545ca6bbbc6f0cd82391286d1d9671551dbcd511bde58e9d2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: aa7e37c1e5749e42dbccf9b3cac7eb6a63c160ca4621a0870a847a031366e1eb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-flowcore - - bioconductor-flowviz - - bioconductor-flowworkspace - - bioconductor-ncdfflow + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' + - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' - r-base - r-data.table - r-hwriter @@ -31,11 +32,11 @@ requirements: - r-reshape - r-xml run: - - bioconductor-biobase - - bioconductor-flowcore - - bioconductor-flowviz - - bioconductor-flowworkspace - - bioconductor-ncdfflow + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' + - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' - r-base - r-data.table - r-hwriter @@ -51,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides quality control and quality assessment tools for gated flow cytometry data.' - extra: identifiers: - biotools:qualifier diff --git a/recipes/bioconductor-quantro/meta.yaml b/recipes/bioconductor-quantro/meta.yaml index c3516cd6173c5..ffccab5112639 100644 --- a/recipes/bioconductor-quantro/meta.yaml +++ b/recipes/bioconductor-quantro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "quantro" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7821670588ed73fd6768cd999dfd0557c2d4102506c584582dbd86bc012384ef + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 27733c7023986edb3465639e1fa799bf20c29756d0229ec083deaac18e2e5255 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-minfi + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - r-doparallel - r-foreach @@ -26,8 +27,8 @@ requirements: - r-iterators - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-minfi + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - r-doparallel - r-foreach @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.' - extra: identifiers: - biotools:quantro diff --git a/recipes/bioconductor-quantsmooth/meta.yaml b/recipes/bioconductor-quantsmooth/meta.yaml index 172d3b00ca40c..bfb6143e85e21 100644 --- a/recipes/bioconductor-quantsmooth/meta.yaml +++ b/recipes/bioconductor-quantsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "quantsmooth" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0f3a9dbaf0f5d219b8d6551860163ca3afce204c955e1771e2bf455d693518d8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d9375e834dcfec05b0e139382c44326b3e2b7917ba22785f45af15d0e6b98d2b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.' - extra: identifiers: - biotools:quantsmooth diff --git a/recipes/bioconductor-quartpac/meta.yaml b/recipes/bioconductor-quartpac/meta.yaml index 46648d9afdc6f..2a08a3cd37d26 100644 --- a/recipes/bioconductor-quartpac/meta.yaml +++ b/recipes/bioconductor-quartpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "QuartPAC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f991280bd845f866f289bde3c138ac053a50ee665518ac6cb05c698e9fa4ebd0 + sha256: 9b8b85da86c4c8778060744baf5dd7e342e85a62376d5ef8f7b7bda81881c210 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graphpac - - bioconductor-ipac - - bioconductor-spacepac + - 'bioconductor-graphpac >=1.22.1,<1.24.0' + - 'bioconductor-ipac >=1.24.2,<1.26.0' + - 'bioconductor-spacepac >=1.18.3,<1.20.0' - r-base - r-data.table run: - - bioconductor-graphpac - - bioconductor-ipac - - bioconductor-spacepac + - 'bioconductor-graphpac >=1.22.1,<1.24.0' + - 'bioconductor-ipac >=1.24.2,<1.26.0' + - 'bioconductor-spacepac >=1.18.3,<1.20.0' - r-base - r-data.table test: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identifies clustering of somatic mutations in proteins over the entire quaternary structure.' - extra: identifiers: - biotools:quartpac diff --git a/recipes/bioconductor-quasr/conda_build_config.yaml b/recipes/bioconductor-quasr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-quasr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-quasr/meta.yaml b/recipes/bioconductor-quasr/meta.yaml index 7aab03521fb01..8dd862752ddbd 100644 --- a/recipes/bioconductor-quasr/meta.yaml +++ b/recipes/bioconductor-quasr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "QuasR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,56 +10,57 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2af6cdccc266c96b88b1d52d095789660a47195c841f0139d63a7c97db89077d + sha256: 837ba80f1ca3408aa6511e2c7bf0d24683f2ae5cc854b2ab66f318a55369969e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocinstaller - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - 'bioconductor-genomicfeatures >=1.17.13' - - bioconductor-genomicfiles - - 'bioconductor-genomicranges >=1.13.3' - - bioconductor-iranges - - bioconductor-rbowtie - - 'bioconductor-rsamtools >=1.19.38' - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-shortread >=1.19.1' - - bioconductor-zlibbioc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbowtie >=1.20.0,<1.22.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocinstaller - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - 'bioconductor-genomicfeatures >=1.17.13' - - bioconductor-genomicfiles - - 'bioconductor-genomicranges >=1.13.3' - - bioconductor-iranges - - bioconductor-rbowtie - - 'bioconductor-rsamtools >=1.19.38' - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-shortread >=1.19.1' - - bioconductor-zlibbioc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbowtie >=1.20.0,<1.22.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -67,7 +68,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.' - extra: identifiers: - biotools:quasr diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml index 5a32c3c69672f..cb81ab31166a4 100644 --- a/recipes/bioconductor-quaternaryprod/meta.yaml +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.14.0" %} {% set name = "QuaternaryProd" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,34 +10,34 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 54eef0c74b8a77e29e9f747bb069223776ec20c1b8f5333763278c0998a52196 + sha256: 80062acdc4ac821389fe86388bb7d3a3ee5ec2f6154dd261a9cf43154a56598f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-dplyr - 'r-rcpp >=0.11.3' - - r-rlist + - 'r-yaml >=2.1.18' run: - r-base - r-dplyr - 'r-rcpp >=0.11.3' - - r-rlist - - libcxx # [osx] + - 'r-yaml >=2.1.18' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' - summary: 'QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-sorce alternative to commercial products such as Quiagen and Inginuity pathway analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher''s exact test. The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.' - + summary: 'QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher''s exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.' extra: identifiers: - biotools:quaternaryprod diff --git a/recipes/bioconductor-qusage/meta.yaml b/recipes/bioconductor-qusage/meta.yaml index 1856f4884100f..68330e57b18f0 100644 --- a/recipes/bioconductor-qusage/meta.yaml +++ b/recipes/bioconductor-qusage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "qusage" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9c6d6982b4106866993ac0786f7e6814f1fab92d3f6a069cfbb63d2780d9a923 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 649cbeefa4e3b56d6a9728035007febfc36c5b361312cfb920e19a6fc6204500 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-limma >=3.14' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-lsmeans - r-nlme run: - - bioconductor-biobase - - 'bioconductor-limma >=3.14' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-lsmeans - r-nlme @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)' - extra: identifiers: - biotools:qusage diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index a2d5738d6e75d..ddd4746a076c1 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "qvalue" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 311400705cd9c80b6e9573fcfa97e62ea7a5616a504d7300e3084e139ccda9e5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 485bf1c3086e4f1ee46dab4f24d9aaae1e8dfb7460074c3da7641f08819cbcd9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test''s p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.' + + diff --git a/recipes/bioconductor-r3cseq/meta.yaml b/recipes/bioconductor-r3cseq/meta.yaml index 452357ad95c4f..728785e88eee4 100644 --- a/recipes/bioconductor-r3cseq/meta.yaml +++ b/recipes/bioconductor-r3cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "r3Cseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e33fc52fcff0084d7663b9cecb7c95b01163b05c8084360c43e870943e8f50d9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4f098382523baaec799ca476a4a4b9b37d074e2287d54bddd8698cb722344b0b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-qvalue - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam run: - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-qvalue - - bioconductor-rsamtools - - bioconductor-rtracklayer + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-data.table - r-rcolorbrewer @@ -49,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.' - extra: identifiers: - biotools:r3cseq diff --git a/recipes/bioconductor-r4rna/meta.yaml b/recipes/bioconductor-r4rna/meta.yaml index fee10913a82d4..eab2552fe3740 100644 --- a/recipes/bioconductor-r4rna/meta.yaml +++ b/recipes/bioconductor-r4rna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "R4RNA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1bb37fdf35c597587bc2485d83e39d2f955c1d2905a94c7b827455f990c3bf63 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f142ff234c09f125799cb71ccd50cf7db6ac4a32856069b1015b07caa9ef02b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base run: - - 'bioconductor-biostrings >=2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.' - extra: identifiers: - biotools:r4rna diff --git a/recipes/bioconductor-raggedexperiment/meta.yaml b/recipes/bioconductor-raggedexperiment/meta.yaml index b109d379f7dc3..b9e781c65eeb7 100644 --- a/recipes/bioconductor-raggedexperiment/meta.yaml +++ b/recipes/bioconductor-raggedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RaggedExperiment" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d57f278151e20bca58c84b3f581a9a7a7cad9daa642c03f5e45f6eb3cc280d6f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 98d8ac3444bf3a507e751a7d6c43d649cc490281f4a6a7e6d8e7f56e5f4379dc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base test: commands: @@ -37,3 +38,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.' + + diff --git a/recipes/bioconductor-rain/meta.yaml b/recipes/bioconductor-rain/meta.yaml index 77d5df93cde6a..60d09328fec25 100644 --- a/recipes/bioconductor-rain/meta.yaml +++ b/recipes/bioconductor-rain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rain" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 050c9e62f9ba764d4077176ee200a23c6ea49ae6087e781a99982e12f3269fda + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d379e73af167fb35d1046e9a0c0af8248de837ed62105bdd6e463a11e584fa05 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-multtest + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-gmp run: - - bioconductor-multtest + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-gmp test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.' - extra: identifiers: - biotools:rain diff --git a/recipes/bioconductor-rama/meta.yaml b/recipes/bioconductor-rama/meta.yaml index 84c68a513acbb..36a51e769f1c9 100644 --- a/recipes/bioconductor-rama/meta.yaml +++ b/recipes/bioconductor-rama/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "rama" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 179e00ec1b7dd249cce8de3cdfda858b36d8ed153efdf4100395980acfd6c7bc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e76746a1a360ab02ce12bd63fde642e294f75982ce8940621b8a9f0e9dd5d7c8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,9 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.' - extra: identifiers: - biotools:rama diff --git a/recipes/bioconductor-ramigo/meta.yaml b/recipes/bioconductor-ramigo/meta.yaml index 2d49391d92275..6d6472b51db62 100644 --- a/recipes/bioconductor-ramigo/meta.yaml +++ b/recipes/bioconductor-ramigo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.23.0" %} +{% set version = "1.28.0" %} {% set name = "RamiGO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -9,25 +9,23 @@ source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bbd2b93b94cb9bb9e6f17ca1ef5d4489bc10dd14908a403e1a8a61ad2a2ab936 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9bb34c9a868822f328bafaa05cebf5c4bf1df45148999d9f67259243c866c42a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-rcytoscape + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-gsubfn - r-igraph - r-png - r-rcurl run: - - bioconductor-graph - - bioconductor-rcytoscape + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-gsubfn - r-igraph @@ -39,8 +37,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.' - + summary: 'R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Deprecated:Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.' extra: identifiers: - biotools:ramigo diff --git a/recipes/bioconductor-randpack/meta.yaml b/recipes/bioconductor-randpack/meta.yaml index 3d0ad3ab718db..f3fd6352897c8 100644 --- a/recipes/bioconductor-randpack/meta.yaml +++ b/recipes/bioconductor-randpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "randPack" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aaf60d98dd9e55bf96630d09b8b073fdff5e0ec6ab797c1b27b64a861cc967e1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d7d8e7875308441c68431f7654a354e64380cbcd3d3be94ad291cc16cb3d05f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic 2.0' summary: 'A suite of classes and functions for randomizing patients in clinical trials.' - extra: identifiers: - biotools:randpack diff --git a/recipes/bioconductor-rankprod/meta.yaml b/recipes/bioconductor-rankprod/meta.yaml index 2261f54d6ced9..209cd691ef05c 100644 --- a/recipes/bioconductor-rankprod/meta.yaml +++ b/recipes/bioconductor-rankprod/meta.yaml @@ -1,23 +1,21 @@ -{% set version = "3.4.0" %} +{% set version = "3.6.0" %} {% set name = "RankProd" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0618efa188bf81fe21e18eaaa2278b2d14164316f149668eb38edc137353caa0 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b05409063bef40dd0e321fb9b0ed9ec94b09968232a8585504938324bdc8f372 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - r-base @@ -27,16 +25,13 @@ requirements: - r-base - r-gmp - r-rmpfr - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'free for non-commercial users. Non-academic users MUST have requested from the author' + license: 'file LICENSE' summary: 'Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.' - extra: identifiers: - biotools:rankprod diff --git a/recipes/bioconductor-rarevariantvis/conda_build_config.yaml b/recipes/bioconductor-rarevariantvis/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rarevariantvis/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml index ab69896ca1ef3..200920625fac0 100644 --- a/recipes/bioconductor-rarevariantvis/meta.yaml +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "RareVariantVis" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,44 +10,44 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 573fb6f7091499f1e27e21fa0621f55d959470eb4a54f49e6f09b99d358e35b0 + sha256: ee65a6eda36b3f776e3e333c6080b8389f93929971a335d6922321e2a9c5e381 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-genomicscores - - bioconductor-iranges - - bioconductor-phastcons100way.ucsc.hg19 - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.2,<3.9.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-googlevis - r-gtools run: - - bioconductor-biocgenerics - - bioconductor-bsgenome - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-genomicscores - - bioconductor-iranges - - bioconductor-phastcons100way.ucsc.hg19 - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.2,<3.9.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-googlevis - r-gtools @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.' - extra: identifiers: - biotools:rarevariantvis diff --git a/recipes/bioconductor-rariant/conda_build_config.yaml b/recipes/bioconductor-rariant/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rariant/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rariant/meta.yaml b/recipes/bioconductor-rariant/meta.yaml index 25f3b815048af..ea1024f149efa 100644 --- a/recipes/bioconductor-rariant/meta.yaml +++ b/recipes/bioconductor-rariant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Rariant" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 648ae2d5e7ef8aa5698b99dd9895dba688f7f4b4bcd6ac1a2df1bfb6dd13dccd + sha256: da698f812d7a8bfac97043800a7f3f95eed9f7a8697b90cf3426ecc89f5517d9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-exomecopy - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-somaticsignatures - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-dplyr - r-ggplot2 @@ -34,15 +35,16 @@ requirements: - r-shiny - r-vgam run: - - bioconductor-exomecopy - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-somaticsignatures - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-exomecopy >=1.26.0,<1.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-dplyr - r-ggplot2 @@ -56,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The ''Rariant'' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.' - extra: identifiers: - biotools:rariant diff --git a/recipes/bioconductor-rbcbook1/meta.yaml b/recipes/bioconductor-rbcbook1/meta.yaml index beda8b9c6e1ab..8fae8eef80e3c 100644 --- a/recipes/bioconductor-rbcbook1/meta.yaml +++ b/recipes/bioconductor-rbcbook1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "RbcBook1" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e47918a50184a0d4f0b98ad8dc29609bcaf4f7befa7e43db5403b384e1fe4862 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c71579d58e40a18bb50f645e9af6355567e9b45d30155fa6df8202e5b58a5f77 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-rpart run: - - bioconductor-biobase - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-rpart test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'tools for building book' - extra: identifiers: - biotools:rbcbook1 diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 7d29dc7c2a6a0..75e4e633cd54f 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "RBGL" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 675b6e7cd9be8c007aba42477c83b478e8bdd92174bc45f6f529a11187684aa2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0e5a056a1a63e711bf73ec9978b525dfb7adb49f63e01cba2bd15f5cab384942 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.' - extra: identifiers: - biotools:rbgl diff --git a/recipes/bioconductor-rbioinf/meta.yaml b/recipes/bioconductor-rbioinf/meta.yaml index 57ebcc9ac6cb6..185ecf6af5aef 100644 --- a/recipes/bioconductor-rbioinf/meta.yaml +++ b/recipes/bioconductor-rbioinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RBioinf" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 90b7073ed0c2c40820842344983fb6ed78f167ae8fd30c0ed5a92e345b4b1307 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 78df3c853398434730b46bca69b43f1eff9947149bde054f889fe6d0b57ab52e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions and datasets and examples to accompany the monograph R For Bioinformatics.' - extra: identifiers: - biotools:rbioinf diff --git a/recipes/bioconductor-rbiopaxparser/meta.yaml b/recipes/bioconductor-rbiopaxparser/meta.yaml index cfc51c93690b1..7725448ccb2ff 100644 --- a/recipes/bioconductor-rbiopaxparser/meta.yaml +++ b/recipes/bioconductor-rbiopaxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "rBiopaxParser" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0487523dbddedf8af73c593e321c7f08812832fd1f687d7760c906abbba51bd9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5356f663cf55e8c1432d3c4b046aa74c1e7b5e2fc6f9b9e595061c66f7c76223 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.' - extra: identifiers: - biotools:rbiopaxparser diff --git a/recipes/bioconductor-rbm/meta.yaml b/recipes/bioconductor-rbm/meta.yaml index af63237e80368..3929ba4916aeb 100644 --- a/recipes/bioconductor-rbm/meta.yaml +++ b/recipes/bioconductor-rbm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RBM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4482853fa5baad0e749c16b2d3bfae3e836db87d8f4f2edc31a72a157d7215db + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 09e17448d6c2bb6cf86a0fc9a43f4059a57f6d4fe609b4dcae3330f1b1dc993b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base run: - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.' - extra: identifiers: - biotools:rbm diff --git a/recipes/bioconductor-rbowtie/meta.yaml b/recipes/bioconductor-rbowtie/meta.yaml index e696bf16a54b2..e0d66fe096f84 100644 --- a/recipes/bioconductor-rbowtie/meta.yaml +++ b/recipes/bioconductor-rbowtie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Rbowtie" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9bd442a72cd9901a67509791b9ac2182bcacb8fb35be7d3fe847dfca4d4c7d6c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 80b1b576de6afc0b4efe90e70bc56f246468d0a5cf94859069d21e8d70322a04 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-1.0 | file LICENSE' summary: 'This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.' - extra: identifiers: - biotools:rbowtie diff --git a/recipes/bioconductor-rbsurv/meta.yaml b/recipes/bioconductor-rbsurv/meta.yaml index 3f8e393637e32..b427c5b201445 100644 --- a/recipes/bioconductor-rbsurv/meta.yaml +++ b/recipes/bioconductor-rbsurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "rbsurv" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c5ad19dfa4113ee223fb808beb739c61d6c9703e57d16c38399c20441d6d8eec + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d463f2bc1d08b234530a4181e3812501bda3bcbebee55b81dd8cb1712554876d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-survival test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package selects genes associated with survival.' - extra: identifiers: - biotools:rbsurv diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index 1363e27558f1d..dcc2feb45c7c3 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.5.4" %} +{% set version = "1.6.0" %} {% set name = "RCAS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: - url: https://github.com/BIMSBbioinfo/{{ name }}/archive/{{ version }}.tar.gz - sha256: c1b62b863311a0974ac5287dc9031f448e12efbbc09f462bcd658bee3d14897e - + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a53507c0f0f831e9124205720b1d2459680dad6ac5e5ae26b06a899a813ab66e build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - 'bioconductor-genomation >=1.5.5' - - 'bioconductor-genomeinfodb >=1.12.0' - - 'bioconductor-genomicfeatures >=1.30.0' - - bioconductor-genomicranges - - bioconductor-motifrg - - bioconductor-org.hs.eg.db - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomation >=1.12.0,<1.14.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-motifrg >=1.24.0,<1.26.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-cowplot - r-data.table @@ -46,22 +46,22 @@ requirements: - r-plotrix - r-proxy - 'r-rmarkdown >=0.9.5' - - 'r-rsqlite >=2.0' + - r-rsqlite run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - 'bioconductor-genomation >=1.5.5' - - 'bioconductor-genomeinfodb >=1.12.0' - - 'bioconductor-genomicfeatures >=1.30.0' - - bioconductor-genomicranges - - bioconductor-motifrg - - bioconductor-org.hs.eg.db - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-topgo + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomation >=1.12.0,<1.14.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-motifrg >=1.24.0,<1.26.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-cowplot - r-data.table @@ -76,18 +76,14 @@ requirements: - r-plotrix - r-proxy - 'r-rmarkdown >=0.9.5' - - 'r-rsqlite >=2.0' - - r-mgcv - + - r-rsqlite test: commands: - - '$R -e "library(''{{ name }}''); runReport()" 2>&1 | grep testdata.RCAS.report.html > /dev/null' - + - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'RCAS is an automated system that provides dynamic genome annotations for custom input files that contain transcriptomic regions. Such transcriptomic regions could be, for instance, peak regions detected by CLIP-Seq analysis that detect protein-RNA interactions, RNA modifications (alias the epitranscriptome), CAGE-tag locations, or any other collection of target regions at the level of the transcriptome. RCAS is designed as a reporting tool for the functional analysis of RNA-binding sites detected by high-throughput experiments. It takes as input a BED format file containing the genomic coordinates of the RNA binding sites and a GTF file that contains the genomic annotation features usually provided by publicly available databases such as Ensembl and UCSC. RCAS performs overlap operations between the genomic coordinates of the RNA binding sites and the genomic annotation features and produces in-depth annotation summaries such as the distribution of binding sites with respect to gene features (exons, introns, 5''/3'' UTR regions, exon-intron boundaries, promoter regions, and whole transcripts). Moreover, by detecting the collection of targeted transcripts, RCAS can carry out functional annotation tables for enriched gene sets (annotated by the Molecular Signatures Database) and GO terms. As one of the most important questions that arise during protein-RNA interaction analysis; RCAS has a module for detecting sequence motifs enriched in the targeted regions of the transcriptome. A full interactive report in HTML format can be generated that contains interactive figures and tables that are ready for publication purposes.' - extra: identifiers: - biotools:rcas diff --git a/recipes/bioconductor-rcaspar/meta.yaml b/recipes/bioconductor-rcaspar/meta.yaml index 40453ee2e9b1d..83e34182188f7 100644 --- a/recipes/bioconductor-rcaspar/meta.yaml +++ b/recipes/bioconductor-rcaspar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RCASPAR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8f2ba7025d2264d2fb6b429ee6e6988dc16f3f5d0a213d6b31e9011cd0be29ec + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c64f4052b272075854b06c831d4ff054f5ea36b5552d1ee680d9cbed058eaa61 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.' - extra: identifiers: - biotools:rcaspar diff --git a/recipes/bioconductor-rcgh/conda_build_config.yaml b/recipes/bioconductor-rcgh/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rcgh/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rcgh/meta.yaml b/recipes/bioconductor-rcgh/meta.yaml index 7ae00e2607091..9e835b5de5e68 100644 --- a/recipes/bioconductor-rcgh/meta.yaml +++ b/recipes/bioconductor-rcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "rCGH" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4b4a7950ed4d96faad8499b799a57f285d23865604cc7011bb5ad6bd9a8cbdb6 + sha256: a1e5429e1be9fa134e3527bf760b3dca74819313fd72db8a7e563b56278c58d0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-acgh - - bioconductor-affy - - bioconductor-annotationdbi - - bioconductor-dnacopy - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-org.hs.eg.db - - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene + - 'bioconductor-acgh >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.6.0' - r-base - r-ggplot2 - r-lattice @@ -38,19 +38,19 @@ requirements: - r-plyr - 'r-shiny >=0.11.1' run: - - bioconductor-acgh - - bioconductor-affy - - bioconductor-annotationdbi - - bioconductor-dnacopy - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-org.hs.eg.db - - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene - - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene + - 'bioconductor-acgh >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.6.0' - r-base - r-ggplot2 - r-lattice @@ -64,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.' - extra: identifiers: - biotools:rcgh diff --git a/recipes/bioconductor-rchemcpp/meta.yaml b/recipes/bioconductor-rchemcpp/meta.yaml index ed935e4a6cde7..6d8981ed5b915 100644 --- a/recipes/bioconductor-rchemcpp/meta.yaml +++ b/recipes/bioconductor-rchemcpp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "Rchemcpp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: df8af3d20e06ec0d44a99cd7b7aedd06c7e55e50cb117a3cf01d7442d27cb9cc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f47733f4a375f15e60dfbd1f6bd04a835c66a80d6308a5dbcde7a4266e018139 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-chemminer + - 'bioconductor-chemminer >=3.32.1,<3.34.0' - r-base - 'r-rcpp >=0.11.1' run: - - bioconductor-chemminer + - 'bioconductor-chemminer >=3.32.1,<3.34.0' - r-base - 'r-rcpp >=0.11.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.1)' summary: 'The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.' - extra: identifiers: - biotools:rchemcpp diff --git a/recipes/bioconductor-rcy3/meta.yaml b/recipes/bioconductor-rcy3/meta.yaml index 2b6ef1796c180..c4c801d277827 100644 --- a/recipes/bioconductor-rcy3/meta.yaml +++ b/recipes/bioconductor-rcy3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "2.0.88" %} {% set name = "RCy3" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,37 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9baa983f28248667aa1948493eed0357df3cc863c3fef025bb450a04fb37e626 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 84e5eaa3077b08a54481c9c617118491343ab824c74a6826a1defde02b2ef74b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-graph >=1.48.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-httr - - r-rcurl + - r-igraph - r-rjsonio + - r-xml run: - - 'bioconductor-graph >=1.48.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-httr - - r-rcurl + - r-igraph - r-rjsonio + - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Vizualize, analyze and explore graphs, connecting R to Cytoscape (>= 3.3.0).' + license: 'MIT + file LICENSE' + summary: 'Vizualize, analyze and explore networks using Cytoscape via R.' + + diff --git a/recipes/bioconductor-rcytoscape/meta.yaml b/recipes/bioconductor-rcytoscape/meta.yaml index 979c967814cae..847862b22dc77 100644 --- a/recipes/bioconductor-rcytoscape/meta.yaml +++ b/recipes/bioconductor-rcytoscape/meta.yaml @@ -35,6 +35,8 @@ about: license: GPL-2 summary: 'Interactvive viewing and exploration of graphs, connecting R to Cytoscape.' + identifiers: + - biotools:rcytoscape extra: identifiers: - biotools:rcytoscape diff --git a/recipes/bioconductor-rdgidb/meta.yaml b/recipes/bioconductor-rdgidb/meta.yaml index c37c7b984f55c..e61e905dc34fa 100644 --- a/recipes/bioconductor-rdgidb/meta.yaml +++ b/recipes/bioconductor-rdgidb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "rDGIdb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aa3eca503d0a2961ab6e81b93a05f3697302b4c0c5eeebf035eda3fe227da59a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3c4930b2695455d29a8b9fc3cbff92197d75dd38fa4282b1e573bce40bf69d7a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,8 +31,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'The rDGIdb package provides a wrapper for the Drug Gene Interaction Database (DGIdb). For simplicity, the wrapper query function and output resembles the user interface and results format provided on the DGIdb website (http://dgidb.genome.wustl.edu/).' - + summary: 'The rDGIdb package provides a wrapper for the Drug Gene Interaction Database (DGIdb). For simplicity, the wrapper query function and output resembles the user interface and results format provided on the DGIdb website (http://www.dgidb.org/).' extra: identifiers: - biotools:rdgidb diff --git a/recipes/bioconductor-reactome.db/meta.yaml b/recipes/bioconductor-reactome.db/meta.yaml index e97c5865a953d..5eb5aaeb9dcae 100644 --- a/recipes/bioconductor-reactome.db/meta.yaml +++ b/recipes/bioconductor-reactome.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "reactome.db" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b02d51e09d156cb5b0142e1183e7955acea33bc5ea298509bb9d02a46b52f624 + sha256: 2da0eb17b5fce58cf4ee97d414f0c03b22f8b9487f7e31b4e5a02b9479898ff3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.33.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - 'bioconductor-annotationdbi >=1.33.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'CC BY 4.0' summary: 'A set of annotation maps for reactome assembled using data from reactome' + + diff --git a/recipes/bioconductor-reactome.db/post-link.sh b/recipes/bioconductor-reactome.db/post-link.sh index 40e94090b5634..a8955bee48571 100644 --- a/recipes/bioconductor-reactome.db/post-link.sh +++ b/recipes/bioconductor-reactome.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="reactome.db_1.62.0.tar.gz" +FN="reactome.db_1.64.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/reactome.db_1.62.0.tar.gz" - "https://bioarchive.galaxyproject.org/reactome.db_1.62.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.62.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/reactome.db_1.64.0.tar.gz" + "https://bioarchive.galaxyproject.org/reactome.db_1.64.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.64.0_src_all.tar.gz" ) -MD5="b05f11f22f01515aaa65c7be6a04a87d" +MD5="4dfc5160ef8673ff4a892cb4146d1eeb" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-reactomepa/meta.yaml b/recipes/bioconductor-reactomepa/meta.yaml index e1790dfac3987..afa5c10238c4f 100644 --- a/recipes/bioconductor-reactomepa/meta.yaml +++ b/recipes/bioconductor-reactomepa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ReactomePA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 824d7201a42378397661683075768e83b46b0de3aa382e1e31735fc08796937d + sha256: ef9896f14944f43514cc57cd3518e3e8060ed1f86274b84cef3939bfd8170a16 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-dose >=3.0.0' - - bioconductor-graphite - - bioconductor-reactome.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-graphite >=1.26.1,<1.28.0' + - 'bioconductor-reactome.db >=1.64.0,<1.66.0' - r-base + - r-ggplot2 + - r-ggraph - r-igraph run: - - bioconductor-annotationdbi - - 'bioconductor-dose >=3.0.0' - - bioconductor-graphite - - bioconductor-reactome.db + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-dose >=3.6.1,<3.8.0' + - 'bioconductor-enrichplot >=1.0.2,<1.2.0' + - 'bioconductor-graphite >=1.26.1,<1.28.0' + - 'bioconductor-reactome.db >=1.64.0,<1.66.0' - r-base + - r-ggplot2 + - r-ggraph - r-igraph test: commands: @@ -38,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.' - extra: identifiers: - biotools:reactomepa diff --git a/recipes/bioconductor-readqpcr/conda_build_config.yaml b/recipes/bioconductor-readqpcr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-readqpcr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-readqpcr/meta.yaml b/recipes/bioconductor-readqpcr/meta.yaml index 848d9cb1dd607..360ed34443308 100644 --- a/recipes/bioconductor-readqpcr/meta.yaml +++ b/recipes/bioconductor-readqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ReadqPCR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2211a848c2318b5646b2a3ea7d69b74dd868c19334e58d4d670b756cba8f57a9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 760a54616ab9113dbaea7ca981443f25793d5308c2cfd1c6ca2aea42cdf074ae build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-affy - - bioconductor-biobase + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The package provides functions to read raw RT-qPCR data of different platforms.' - extra: identifiers: - biotools:readqpcr diff --git a/recipes/bioconductor-recount/conda_build_config.yaml b/recipes/bioconductor-recount/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-recount/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml index da008f33fe8ff..e92599b61abc5 100644 --- a/recipes/bioconductor-recount/meta.yaml +++ b/recipes/bioconductor-recount/meta.yaml @@ -1,64 +1,56 @@ -{% set version = "1.4.5" %} +{% set version = "1.6.3" %} {% set name = "recount" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5f99095fd9c594f6d27c4af6baf5473fc1b80c452108fe0a1e0455748afa5c33 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 1ab27e802bfae64af83cd10d97c40bee50fa3eb97184e627b018778d81d1907c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biocparallel - - bioconductor-derfinder - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-geoquery - - bioconductor-iranges - - 'bioconductor-rtracklayer >=1.35.3' - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-derfinder >=1.14.0,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-downloader - r-rcurl - r-rentrez run: - - bioconductor-biocparallel - - bioconductor-derfinder - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-geoquery - - bioconductor-iranges - - 'bioconductor-rtracklayer >=1.35.3' - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-derfinder >=1.14.0,<1.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-downloader - r-rcurl - r-rentrez - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. - Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions - level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage - bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing - differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic - differential expression analyses with the data from the recount project as described - at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.' + summary: 'Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.' + + diff --git a/recipes/bioconductor-recoup/meta.yaml b/recipes/bioconductor-recoup/meta.yaml index fa723ced72591..5a1ff9ae97135 100644 --- a/recipes/bioconductor-recoup/meta.yaml +++ b/recipes/bioconductor-recoup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "recoup" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6bd41e1074b437530421321c24bbbb536355c1a5731a5c09c3d0b0b4b9602026 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0aec44ef2f910c4d1d77709d551b9605e7f715f8e9649391e224ceb2e564a541 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-complexheatmap - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-circlize - r-ggplot2 - r-plyr run: - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-complexheatmap - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-rtracklayer + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-circlize - r-ggplot2 @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.' - extra: identifiers: - biotools:recoup diff --git a/recipes/bioconductor-reder/meta.yaml b/recipes/bioconductor-reder/meta.yaml index 8376bb7d7584a..44c936d7b10d2 100644 --- a/recipes/bioconductor-reder/meta.yaml +++ b/recipes/bioconductor-reder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "RedeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ac5ba58faca018745ef83e5596d6330a42cc5f17708bd117d21731ae6a02ee0d + sha256: 78ddf06627aac2d18dd49022aeee9abda15853ad6ac8e3fd55042140d3d4a670 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.' - extra: identifiers: - biotools:reder diff --git a/recipes/bioconductor-refnet/conda_build_config.yaml b/recipes/bioconductor-refnet/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-refnet/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-refnet/meta.yaml b/recipes/bioconductor-refnet/meta.yaml index 11dbf3cf40861..20bd8634948b6 100644 --- a/recipes/bioconductor-refnet/meta.yaml +++ b/recipes/bioconductor-refnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RefNet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6d8c4b113b8e4d48b76e64e980752a5b07891d1a9ec03d2257f784ea259058eb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7b3ee3bcdb4ba12dcf66a8df6429c26626aaeaf676351a4dd1365e03fe2881a6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationhub - - bioconductor-biocgenerics - - bioconductor-iranges - - bioconductor-psicquic + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-psicquic >=1.18.1,<1.20.0' - r-base - r-rcurl - r-shiny run: - - bioconductor-annotationhub - - bioconductor-biocgenerics - - bioconductor-iranges - - bioconductor-psicquic + - 'bioconductor-annotationhub >=2.12.1,<2.14.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-psicquic >=1.18.1,<1.20.0' - r-base - r-rcurl - r-shiny @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Molecular interactions with metadata, some archived, some dynamically obtained' - extra: identifiers: - biotools:refnet diff --git a/recipes/bioconductor-refplus/conda_build_config.yaml b/recipes/bioconductor-refplus/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-refplus/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-refplus/meta.yaml b/recipes/bioconductor-refplus/meta.yaml index a113a5cc0b8bd..b56a45e6a7af6 100644 --- a/recipes/bioconductor-refplus/meta.yaml +++ b/recipes/bioconductor-refplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "RefPlus" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: be72103d4e7222293d60ce237c300fdf201fe99bee4ce137d33e687172d1a65f + sha256: 90233d707debd7503960345dddd5a8c245a18dd981bd09d34258aeeea323e5a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.20.0' - - 'bioconductor-affyplm >=1.18.0' - - 'bioconductor-biobase >=2.1.0' - - 'bioconductor-preprocesscore >=1.4.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyplm >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base run: - - 'bioconductor-affy >=1.20.0' - - 'bioconductor-affyplm >=1.18.0' - - 'bioconductor-biobase >=2.1.0' - - 'bioconductor-preprocesscore >=1.4.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyplm >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base test: commands: @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods.' - extra: identifiers: - biotools:refplus diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index 3a793045f4ded..6b57e0559e5cd 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "regioneR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d775697b0bdb3ef5b209ad676113e3d567fb1c57704dfd76fd1c2691e8b8f9ee + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4b7758319a8dc7db5b57d7d21e693da081a29af089fde1e9affcf8d7b0a27f25 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-memoise run: - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-memoise test: @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.' - extra: identifiers: - biotools:regioner diff --git a/recipes/bioconductor-regsplice/meta.yaml b/recipes/bioconductor-regsplice/meta.yaml index 2d27e306c5c3a..7b684590dc286 100644 --- a/recipes/bioconductor-regsplice/meta.yaml +++ b/recipes/bioconductor-regsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "regsplice" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a3ec0d3474c5244fe3719920f2e71a9dbe600f813d5315c7f893b6f85537f53f + sha256: 4031a2ddf1e35f3a9dee96596786d3b461c706aa4e0c419fc9520bd9506fcfbd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-edger - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-glmnet - r-pbapply run: - - bioconductor-edger - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-glmnet - r-pbapply @@ -38,9 +38,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT + license: 'MIT + file LICENSE' summary: 'Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.' - extra: identifiers: - biotools:regsplice diff --git a/recipes/bioconductor-repitools/conda_build_config.yaml b/recipes/bioconductor-repitools/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-repitools/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index f8761a8901443..490f7ba99eb25 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "Repitools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2af2e4bdcdd3fb93a9ead1b657ac3a7e6a8485f0a762ac20a85a3b60b982d6ab + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cc74a0f353877f2ddb9f013fd969dec74fa0f9605701c96c159248704e653932 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.8.0' - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-dnacopy - - 'bioconductor-edger >=3.4.0' - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - 'bioconductor-iranges >=1.20.0' - - bioconductor-ringo - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-ringo >=1.44.0,<1.46.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-aroma.affymetrix - r-base - r-cluster @@ -38,19 +39,19 @@ requirements: - r-mass - r-rsolnp run: - - 'bioconductor-biocgenerics >=0.8.0' - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-dnacopy - - 'bioconductor-edger >=3.4.0' - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - 'bioconductor-iranges >=1.20.0' - - bioconductor-ringo - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-ringo >=1.44.0,<1.46.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-aroma.affymetrix - r-base - r-cluster @@ -58,6 +59,9 @@ requirements: - r-gsmoothr - r-mass - r-rsolnp + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -65,7 +69,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.' - extra: identifiers: - biotools:repitools diff --git a/recipes/bioconductor-reportingtools/conda_build_config.yaml b/recipes/bioconductor-reportingtools/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-reportingtools/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-reportingtools/meta.yaml b/recipes/bioconductor-reportingtools/meta.yaml index bbbbfbf007017..6a9143751fd01 100644 --- a/recipes/bioconductor-reportingtools/meta.yaml +++ b/recipes/bioconductor-reportingtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.17.3" %} +{% set version = "2.20.0" %} {% set name = "ReportingTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cda3e0d59dfb93286af61eb93eddaad6265c1710414c86b30147e083f4b80d64 + sha256: 78fbf2d6b98f7683f303c551de46ec75077b35459febebcb827286b391c57e6d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.6' - - bioconductor-category - - 'bioconductor-deseq2 >=1.3.41' - - bioconductor-edger - - bioconductor-ggbio - - bioconductor-gostats - - bioconductor-gseabase - - bioconductor-iranges - - 'bioconductor-limma >=3.17.5' - - bioconductor-pfam.db + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-pfam.db >=3.6.0,<3.8.0' - r-base - r-ggplot2 - r-hwriter @@ -39,19 +39,19 @@ requirements: - r-r.utils - r-xml run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.6' - - bioconductor-category - - 'bioconductor-deseq2 >=1.3.41' - - bioconductor-edger - - bioconductor-ggbio - - bioconductor-gostats - - bioconductor-gseabase - - bioconductor-iranges - - 'bioconductor-limma >=3.17.5' - - bioconductor-pfam.db + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-category >=2.46.0,<2.48.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-pfam.db >=3.6.0,<3.8.0' - r-base - r-ggplot2 - r-hwriter @@ -66,7 +66,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.' - extra: identifiers: - biotools:reportingtools diff --git a/recipes/bioconductor-rfpred/meta.yaml b/recipes/bioconductor-rfpred/meta.yaml index 8f23612ab7491..7fd4bc6e649a8 100644 --- a/recipes/bioconductor-rfpred/meta.yaml +++ b/recipes/bioconductor-rfpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rfPred" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 83ddf6fd9da2fe431f6da70e5226de609bee1b90c2701b88d6918c02a7cfe9d4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9515489fd5b14bd5e694569e9c25abd978c9f16f91a2125ee834441fda42efde build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-data.table run: - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-data.table + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2 )' summary: 'Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).' - extra: identifiers: - biotools:rfpred diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 4cb66d57e8099..fe93954dddeae 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "rGADEM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dc4525963bcd5ff6cb58b0b4fe162a3fe873a5ff72be9a2c86d2c40cc4447ce5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4110213eb8d289cb19976c6a7242ec5b456675b8694e25c721f1566c33616dd6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-iranges - - bioconductor-seqlogo + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-base run: - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-iranges - - bioconductor-seqlogo + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.' - extra: identifiers: - biotools:rgadem diff --git a/recipes/bioconductor-rgalaxy/meta.yaml b/recipes/bioconductor-rgalaxy/meta.yaml index f5c8d01667bb7..22133654f98ed 100644 --- a/recipes/bioconductor-rgalaxy/meta.yaml +++ b/recipes/bioconductor-rgalaxy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "RGalaxy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3ba5e74ec2c01c28b5afcd8788008bb26cfd0efb0556d2a09691c22f83afa5b1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d6af5d039da3df327100f7400be4697ec0341d4a361222856a15b0dcf5719a91 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-optparse - r-roxygen2 - r-xml run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-optparse - r-roxygen2 @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Given an R function and its manual page, make the documented function available in Galaxy.' - extra: identifiers: - biotools:rgalaxy diff --git a/recipes/bioconductor-rgraph2js/meta.yaml b/recipes/bioconductor-rgraph2js/meta.yaml index 1681c87e489ab..effb2ac392ad1 100644 --- a/recipes/bioconductor-rgraph2js/meta.yaml +++ b/recipes/bioconductor-rgraph2js/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RGraph2js" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3c88f2668d406afde169176ff7942cc5675ea70ba39ad14fcb5e145275df196a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2dbf5f4f599396ccbe9ffffe1ed0576db16d94d0cf2ca62637a7a7c98ffbef88 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-digest - r-rjson - r-whisker run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-digest - r-rjson @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.' - extra: identifiers: - biotools:rgraph2js diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index ceea7269a88ca..37163f0428505 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "Rgraphviz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1bfb8ac90df797365cf883813505f3b63a01061f515c009924c424e59cf436f9 - patches: # [osx] - - rpath.patch # [osx] + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7ee16deb1c30f60bb5ad1382b99006b2472be61c9523e40d37c4b2dedd876780 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base run: - - bioconductor-graph + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: EPL summary: 'Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.' - extra: identifiers: - biotools:rgraphviz diff --git a/recipes/bioconductor-rgreat/meta.yaml b/recipes/bioconductor-rgreat/meta.yaml index 7090dc25615a5..413a2c1a58bb4 100644 --- a/recipes/bioconductor-rgreat/meta.yaml +++ b/recipes/bioconductor-rgreat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.1" %} +{% set version = "1.12.1" %} {% set name = "rGREAT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 060e17d46d961c7b2b1e69e9248e2bc969d788e97cc8fb7a22ae8cd4edda1710 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 21004917b590ea5a9b5146d90980f3c0ec37a752b74a2975f8e6f6a4dc0b899a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - 'r-getoptlong >=0.0.9' - r-rcurl - r-rjson run: - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - 'r-getoptlong >=0.0.9' - r-rcurl @@ -35,9 +36,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'MIT + LICENSE' summary: 'This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user''s input and automatically retrieving results from GREAT web server.' - extra: identifiers: - biotools:rgreat diff --git a/recipes/bioconductor-rgsea/meta.yaml b/recipes/bioconductor-rgsea/meta.yaml index 1ffbc551e6564..22fadc3f6fb9d 100644 --- a/recipes/bioconductor-rgsea/meta.yaml +++ b/recipes/bioconductor-rgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RGSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dc69828dbac664b5a4d10a12df61ea3549563b26ed1645acca823d7c017bc3f0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 39d3e7677fe0fcdf0afb8629463be11b917fcf9421d3875802a7e18d943945a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - bioconductor-biocgenerics + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=3) summary: 'Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.' - extra: identifiers: - biotools:rgsea diff --git a/recipes/bioconductor-rgsepd/conda_build_config.yaml b/recipes/bioconductor-rgsepd/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rgsepd/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rgsepd/meta.yaml b/recipes/bioconductor-rgsepd/meta.yaml index dfdc09329d179..649d805841464 100644 --- a/recipes/bioconductor-rgsepd/meta.yaml +++ b/recipes/bioconductor-rgsepd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rgsepd" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,33 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 720bf53d3229d2761432f140c640c8dbb9357e019c406b20aa96f776186d2a64 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ff51af7f5824f951b219c0b62ed0ca9d8c1fde7a47526885b55c498c14df72bd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biomart - - bioconductor-deseq2 - - bioconductor-go.db - - 'bioconductor-goseq >=1.17' - - bioconductor-org.hs.eg.db - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-goseq >=1.32.0,<1.34.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-gplots - r-hash run: - - bioconductor-annotationdbi - - bioconductor-biomart - - bioconductor-deseq2 - - bioconductor-go.db - - 'bioconductor-goseq >=1.17' - - bioconductor-org.hs.eg.db - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-goseq >=1.32.0,<1.34.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-gplots - r-hash @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.' - extra: identifiers: - biotools:rgsepd diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 597bebb09ae56..85a82ee88c089 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "rhdf5" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 81110d0f79b2ed1599c90d2a254671ad0eeb07fef92ed66b3456f5f0302aa890 - patches: # [osx] - - rpath.patch # [osx] + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a6bb589b3f785661965df73713f62c5db6ef719a1fbcfe48ba76a10921ab9595 build: - skip: True # [osx] - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-zlibbioc + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - r-base - run: - - bioconductor-zlibbioc + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides an interface between HDF5 and R. HDF5''s main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.' - extra: identifiers: - biotools:rhdf5 diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index 022893583eca4..cb88e9dafa167 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "Rhdf5lib" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3ce431b69998878c074184aece188c3b249ae64ca491be3617162f996f266c4e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6c74f2f3acd9119af339412aa67aef295aed62b2f03d8236cc106dc31453a9f8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides C and C++ hdf5 libraries.' + + diff --git a/recipes/bioconductor-rhtslib/build.sh b/recipes/bioconductor-rhtslib/build.sh index da43ce2168312..db15136537a5f 100644 --- a/recipes/bioconductor-rhtslib/build.sh +++ b/recipes/bioconductor-rhtslib/build.sh @@ -1,4 +1,6 @@ #!/bin/bash +export C_INCLUDE_PATH=${PREFIX}/include +export LIBRARY_PATH=${PREFIX}/lib mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 9a7ffac5af030..362a62785cf70 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -1,40 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "Rhtslib" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - patches: - - rpath.patch url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5260b08d54b284aa50ae22bcb4c0ffe132a9cf98824d96063f1564b708b983b7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3f0dc503b927187ea309db17b197eb87c7efb2482b8818da525de4cad0b2dc9b build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: build: - {{ compiler('c') }} + - automake + - make host: - - bioconductor-zlibbioc + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - - autoconf + - zlib run: - - bioconductor-zlibbioc + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + - zlib test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' - summary: 'This package provides version 1.1 of the ''HTSlib'' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").' - + summary: 'This package provides version 1.7 of the ''HTSlib'' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").' extra: identifiers: - biotools:rhtslib diff --git a/recipes/bioconductor-riboprofiling/conda_build_config.yaml b/recipes/bioconductor-riboprofiling/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-riboprofiling/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-riboprofiling/meta.yaml b/recipes/bioconductor-riboprofiling/meta.yaml index 37347fce29d30..df78b6291285b 100644 --- a/recipes/bioconductor-riboprofiling/meta.yaml +++ b/recipes/bioconductor-riboprofiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.1" %} +{% set version = "1.10.0" %} {% set name = "RiboProfiling" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -9,26 +9,26 @@ source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d67a7049a90b0b21d8cdc3e553c80fe0a263ba6b5e756d4df93fd2636b4c26f1 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 20529dc4f37161a5f8fbae56c1b7f3ddf35a81db9e8de9bb3f354ed9309dd213 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-ggplot2 @@ -36,17 +36,17 @@ requirements: - r-reshape2 - r-sqldf run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-data.table - r-ggplot2 @@ -60,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3''UTR, and 5''UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.' - extra: identifiers: - biotools:riboprofiling diff --git a/recipes/bioconductor-riboseqr/meta.yaml b/recipes/bioconductor-riboseqr/meta.yaml index 3c3c80ef8b6d9..bc4762ed02d14 100644 --- a/recipes/bioconductor-riboseqr/meta.yaml +++ b/recipes/bioconductor-riboseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "riboSeqR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: df557caa3d2a38fe6a13a05f5dbfcc59d251683622d2acad6cb285af8afde239 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 76db293ebfe2942f9f08df94bd9b0f589ae7a983120695ac741845d858685b75 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bayseq - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-seqlogo + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-abind - r-base run: - - bioconductor-bayseq - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-seqlogo + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-abind - r-base test: @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.' - extra: identifiers: - biotools:riboseqr diff --git a/recipes/bioconductor-rimmport/meta.yaml b/recipes/bioconductor-rimmport/meta.yaml index 4c6318ce7b6ba..44cde35a45cde 100644 --- a/recipes/bioconductor-rimmport/meta.yaml +++ b/recipes/bioconductor-rimmport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RImmPort" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 474ed609740cd3670c3219be41d8e643d908ee57434015b554eb8155c34c46ba + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f86e5fbf0353d1dba24d22cbf4b5d048793baf67d0534fc60e0937eb011de5a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.' - extra: identifiers: - biotools:rimmport diff --git a/recipes/bioconductor-ringo/conda_build_config.yaml b/recipes/bioconductor-ringo/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-ringo/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index ff895d6b8e3d8..dae378b386dd1 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "Ringo" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,39 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b8ff6e75db07b7fcb01f5a61359883ddbf5a156c9c07cad3cb7e906ed0679f9c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d19a7ee45bdd075c73d3c1b9edea43fb83d53386bb29f78062d7832bb27945f9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.14.1' - - 'bioconductor-biocgenerics >=0.1.11' - - bioconductor-genefilter - - bioconductor-limma - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-lattice - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biobase >=1.14.1' - - 'bioconductor-biocgenerics >=0.1.11' - - bioconductor-genefilter - - bioconductor-limma - - bioconductor-vsn + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base - r-lattice - r-matrix - r-rcolorbrewer + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.' - extra: identifiers: - biotools:ringo diff --git a/recipes/bioconductor-ripseeker/meta.yaml b/recipes/bioconductor-ripseeker/meta.yaml index 391901db99b14..f9afb44aae052 100644 --- a/recipes/bioconductor-ripseeker/meta.yaml +++ b/recipes/bioconductor-ripseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RIPSeeker" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: be8ccc6f0a44469ce264de98724f8cb5bb37da846c1c61068d87736633ff132f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d1f58470199d495f74f8a1a35e9ef0f302e7ecac875c5bd31fb23baaf1df2c79 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base test: commands: @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.' - extra: identifiers: - biotools:ripseeker diff --git a/recipes/bioconductor-risa/conda_build_config.yaml b/recipes/bioconductor-risa/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-risa/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-risa/meta.yaml b/recipes/bioconductor-risa/meta.yaml index b11a9f96db86f..b2097996a8790 100644 --- a/recipes/bioconductor-risa/meta.yaml +++ b/recipes/bioconductor-risa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Risa" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8b256b69e9a696794bc91ea7c3e94fbc00fa86531655ee8e9839408e535bd783 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 68e05f197833a1688c6afa66554cc7bb713ce3950eaf7964f20736bf8768ba9b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-affy - - 'bioconductor-biobase >=2.4.0' - - bioconductor-biocviews - - bioconductor-xcms + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocviews >=1.48.3,<1.50.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - 'r-rcpp >=0.9.13' run: - - bioconductor-affy - - 'bioconductor-biobase >=2.4.0' - - bioconductor-biocviews - - bioconductor-xcms + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocviews >=1.48.3,<1.50.0' + - 'bioconductor-xcms >=3.2.0,<3.4.0' - r-base - 'r-rcpp >=0.9.13' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.' - extra: identifiers: - biotools:risa diff --git a/recipes/bioconductor-rlmm/meta.yaml b/recipes/bioconductor-rlmm/meta.yaml index 428af71abb0f5..dc0c0e76eebcc 100644 --- a/recipes/bioconductor-rlmm/meta.yaml +++ b/recipes/bioconductor-rlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RLMM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 409102c03fbcff73871ecad3534c5b2dbbe78277b264da776cf4c3e50098ab06 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a4489271b863d660b8489cec6b6c947effe33bcdfe1ca52546cd29c9353ad0e7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.' - extra: identifiers: - biotools:rlmm diff --git a/recipes/bioconductor-rmat/meta.yaml b/recipes/bioconductor-rmat/meta.yaml index 4df1959a50a0b..5df528c344b2f 100644 --- a/recipes/bioconductor-rmat/meta.yaml +++ b/recipes/bioconductor-rmat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.28.0" %} +{% set version = "3.30.0" %} {% set name = "rMAT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 038853330a5f0a1b4805fff7dfeee1c0da223875809a1af75942ae77a373c732 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7c1af420fb92e41e920fda3d05558281986650012415b3ac733e5e35891cf6d3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affxparser - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.3' - - 'bioconductor-iranges >=1.13.10' + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base + - openblas run: - - bioconductor-affxparser - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.3' - - 'bioconductor-iranges >=1.13.10' + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base + - openblas + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +43,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: ''consult the README file available in the inst directory of the source distribution for necessary configuration instructions''. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!' - extra: identifiers: - biotools:rmat diff --git a/recipes/bioconductor-rmir.hs.mirna/meta.yaml b/recipes/bioconductor-rmir.hs.mirna/meta.yaml index 08a665142030d..1d4c2e8f26ac8 100644 --- a/recipes/bioconductor-rmir.hs.mirna/meta.yaml +++ b/recipes/bioconductor-rmir.hs.mirna/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "RmiR.Hs.miRNA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -12,16 +12,16 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 649da235d09f1c8d8cbb0a84bce7085f70ac945b80410bf9d4d9d18a40e2cb5f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'The Artistic License, Version 2.0' summary: 'Various databases of microRNA Targets' + + diff --git a/recipes/bioconductor-rmir.hs.mirna/post-link.sh b/recipes/bioconductor-rmir.hs.mirna/post-link.sh index 0eea80317d80d..7c304f5c1f086 100644 --- a/recipes/bioconductor-rmir.hs.mirna/post-link.sh +++ b/recipes/bioconductor-rmir.hs.mirna/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="RmiR.Hs.miRNA_1.0.7.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz" "https://bioarchive.galaxyproject.org/RmiR.Hs.miRNA_1.0.7.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz" ) MD5="4aedac188382447d9907d2617aa2e8e6" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-rmir/meta.yaml b/recipes/bioconductor-rmir/meta.yaml index 151595f514c64..52281ef39e737 100644 --- a/recipes/bioconductor-rmir/meta.yaml +++ b/recipes/bioconductor-rmir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RmiR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5d88fe5f233d49c11194dc0e23fad7212ec38ef49db17156eea8ad1cf189c882 + sha256: 3c49c47be5407575d7ea446651fac7da4d0f4420601bf0eb926252498cb9920f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-rmir.hs.mirna + - 'bioconductor-rmir.hs.mirna >=1.0.7,<1.2.0' - r-base - r-dbi - r-rsvgtipsdevice run: - - bioconductor-rmir.hs.mirna + - 'bioconductor-rmir.hs.mirna >=1.0.7,<1.2.0' - r-base - r-dbi - r-rsvgtipsdevice @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Useful functions to merge microRNA and respective targets using differents databases' - extra: identifiers: - biotools:rmir diff --git a/recipes/bioconductor-rnainteract/conda_build_config.yaml b/recipes/bioconductor-rnainteract/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rnainteract/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rnainteract/meta.yaml b/recipes/bioconductor-rnainteract/meta.yaml index ca11f22845bf4..d7db0668fa53a 100644 --- a/recipes/bioconductor-rnainteract/meta.yaml +++ b/recipes/bioconductor-rnainteract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "RNAinteract" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,19 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c5c74661cc1e77ab4661a7f14cc0cb622516a4d56c50da22222f5fba3704cb3 + sha256: a71c7861ce6aea6a8a825b787de415ca71d2ced8bfdc3ac65bf92462606935a3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-cellhts2 - - bioconductor-geneplotter - - bioconductor-limma - - 'bioconductor-splots >=1.13.12' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-splots >=1.46.0,<1.48.0' - r-abind - r-base - r-gplots @@ -34,11 +34,11 @@ requirements: - r-locfit - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-cellhts2 - - bioconductor-geneplotter - - bioconductor-limma - - 'bioconductor-splots >=1.13.12' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-splots >=1.46.0,<1.48.0' - r-abind - r-base - r-gplots @@ -56,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.' - extra: identifiers: - biotools:rnainteract diff --git a/recipes/bioconductor-rnaither/meta.yaml b/recipes/bioconductor-rnaither/meta.yaml index d3f7de527fa17..91a0b68befb7a 100644 --- a/recipes/bioconductor-rnaither/meta.yaml +++ b/recipes/bioconductor-rnaither/meta.yaml @@ -1,56 +1,49 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "RNAither" %} -{% set bioc = "3.5" %} +{% set bioc = "3.7" %} package: - name: 'bioconductor-{{ name|lower}}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a2caf44b8c1067e479c21e17702c3f90e60dae4e33415569e107000455b76681 - + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 82ff30db93fc94eecb8b3e1ee11112d9f37e9ac8e79ed17165be0ce630098053 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biomart - - bioconductor-geneplotter - - bioconductor-limma - - bioconductor-prada - - bioconductor-rankprod - - bioconductor-splots - - bioconductor-topgo + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-prada >=1.56.0,<1.58.0' + - 'bioconductor-rankprod >=3.6.0,<3.8.0' + - 'bioconductor-splots >=1.46.0,<1.48.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-car run: - - bioconductor-biomart - - bioconductor-geneplotter - - bioconductor-limma - - bioconductor-prada - - bioconductor-rankprod - - bioconductor-splots - - bioconductor-topgo + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-prada >=1.56.0,<1.58.0' + - 'bioconductor-rankprod >=3.6.0,<3.8.0' + - 'bioconductor-splots >=1.46.0,<1.48.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-car - test: commands: - '$R -e "library(''{{ name }}'')"' - about: - home: https://bioconductor.org/packages/release/bioc/html/RNAither.html + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable - normalization and statistical tests, leading to lists of significant genes and biological processes.' - + summary: 'RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.' extra: identifiers: - biotools:rnaither diff --git a/recipes/bioconductor-rnaprobr/meta.yaml b/recipes/bioconductor-rnaprobr/meta.yaml index f5593c28a426d..af327858fbcfb 100644 --- a/recipes/bioconductor-rnaprobr/meta.yaml +++ b/recipes/bioconductor-rnaprobr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.9.0" %} +{% set version = "1.12.0" %} {% set name = "RNAprobR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -9,32 +9,36 @@ source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 49429c52fe02fb129ee5cb6375a81d24602f853b2832cbe4970a74d04b68362f + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9e5e217ccb0af15db7a1994ff74ab2f4ed76233e8d6842178f03d383571a1934 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.10.0' - - 'bioconductor-biostrings >=2.32.1' - - 'bioconductor-genomicalignments >=1.5.12' - - 'bioconductor-genomicfeatures >=1.16.3' - - 'bioconductor-genomicranges >=1.16.4' - - 'bioconductor-rsamtools >=1.16.1' - - 'bioconductor-rtracklayer >=1.24.2' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-plyr >=1.8.1' run: - - 'bioconductor-biocgenerics >=0.10.0' - - 'bioconductor-biostrings >=2.32.1' - - 'bioconductor-genomicalignments >=1.5.12' - - 'bioconductor-genomicfeatures >=1.16.3' - - 'bioconductor-genomicranges >=1.16.4' - - 'bioconductor-rsamtools >=1.16.1' - - 'bioconductor-rtracklayer >=1.24.2' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - 'r-plyr >=1.8.1' test: @@ -44,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.' - extra: identifiers: - biotools:rnaprobr diff --git a/recipes/bioconductor-rnaseqcomp/meta.yaml b/recipes/bioconductor-rnaseqcomp/meta.yaml index 0532bcfbaed92..8d95466b6d210 100644 --- a/recipes/bioconductor-rnaseqcomp/meta.yaml +++ b/recipes/bioconductor-rnaseqcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "rnaseqcomp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 15d61e1d59bc704b43804d71a5a9a66a46bf63b977cf6ea6d508daa995610d14 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d7f106d539850825091ccc7bcbf51cb154fd743af5aed7c2ca1825c6118d50cc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.' - extra: identifiers: - biotools:rnaseqcomp diff --git a/recipes/bioconductor-rnaseqmap/meta.yaml b/recipes/bioconductor-rnaseqmap/meta.yaml index ec6f4043c21b7..e4ce9e37a42ad 100644 --- a/recipes/bioconductor-rnaseqmap/meta.yaml +++ b/recipes/bioconductor-rnaseqmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "rnaSeqMap" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,34 +8,38 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bb91fafd5b1425eb6adbbfa1363acdc13ad93f90d577b959b7e94b22f4ef1578 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 954e40aa612299bdbbbeead5a90b495216f9f65471a6af5e40a157d0c65b7f98 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-deseq - - bioconductor-edger - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-dbi run: - - bioconductor-biobase - - bioconductor-deseq - - bioconductor-edger - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-dbi + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,7 +47,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The rnaSeqMap library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time' - extra: identifiers: - biotools:rnaseqmap diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index cb50d562ffc41..274e4c9d63cc6 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RNASeqPower" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7536083a940ea9c8432591a4e496b5204cff2e9e3338d1e321b5176c9a46a523 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1ee658caaef9d9e4fd8a1085e459b318438d763f0e271a45fb941d5ea6e45630 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>=2)' summary: 'RNA-seq, sample size' - extra: identifiers: - biotools:rnaseqpower diff --git a/recipes/bioconductor-rnbeads.hg19/meta.yaml b/recipes/bioconductor-rnbeads.hg19/meta.yaml index 02d1fd89c517b..6031857b22cd2 100644 --- a/recipes/bioconductor-rnbeads.hg19/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RnBeads.hg19" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6251ef736a0718ef9cb2c5aee38cfc8aa986d2ae21331fcf0dc5a3eae016ac47 + sha256: 6546161385b2067afd17d4dd017a48810ec739743ece0d3e25a9ec273cc7db61 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly hg19.' + + diff --git a/recipes/bioconductor-rnbeads.hg19/post-link.sh b/recipes/bioconductor-rnbeads.hg19/post-link.sh index fb4a459bd74e6..e12ea3ef87d29 100644 --- a/recipes/bioconductor-rnbeads.hg19/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.hg19_1.10.0.tar.gz" +FN="RnBeads.hg19_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/RnBeads.hg19_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.10.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.hg19_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.12.0_src_all.tar.gz" ) -MD5="1e1328c5cac14fe65600dac4204e045a" +MD5="836e7eef20499109e4bece34a7dbc8b3" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-rnbeads.mm10/meta.yaml b/recipes/bioconductor-rnbeads.mm10/meta.yaml index 2518086f1f226..08971550d58a9 100644 --- a/recipes/bioconductor-rnbeads.mm10/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RnBeads.mm10" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3c20086be509f390d67fe7b26fdb30db3b0eb3b992b82f51da8c5c1868d0ad29 + sha256: 9b6d7862dfa9cf054096aece9de1b3abb709e201cda617eff3856997db3267b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly mm10.' + + diff --git a/recipes/bioconductor-rnbeads.mm10/post-link.sh b/recipes/bioconductor-rnbeads.mm10/post-link.sh index 04dc1c3e66a54..09713dbe84ac6 100644 --- a/recipes/bioconductor-rnbeads.mm10/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm10/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.mm10_1.10.0.tar.gz" +FN="RnBeads.mm10_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/RnBeads.mm10_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.mm10_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_1.10.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.mm10_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.mm10_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_1.12.0_src_all.tar.gz" ) -MD5="68e2e0ad075754e277fcba9ee9e333fa" +MD5="406fbbafb2bd367e01954fb63f9c07d7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-rnbeads.mm9/meta.yaml b/recipes/bioconductor-rnbeads.mm9/meta.yaml index 62a7e686fa860..4624b5d39db2c 100644 --- a/recipes/bioconductor-rnbeads.mm9/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm9/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RnBeads.mm9" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f477acc72f4193d86355a3f4e0f039e07464863bf9b8bc0246f84ea05b4283a8 + sha256: 620042666b30174331df8e829ebec5d0c5da28237a4430fe5e4a0d7168d5055e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly mm9.' + + diff --git a/recipes/bioconductor-rnbeads.mm9/post-link.sh b/recipes/bioconductor-rnbeads.mm9/post-link.sh index 581cff9ef9919..862b763953a33 100644 --- a/recipes/bioconductor-rnbeads.mm9/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm9/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.mm9_1.10.0.tar.gz" +FN="RnBeads.mm9_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/RnBeads.mm9_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.10.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.mm9_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.12.0_src_all.tar.gz" ) -MD5="79b0850962b66262f9bcd4701956fe02" +MD5="1d101b3ded7f6f2b8ac287ff06dca07d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-rnbeads.rn5/meta.yaml b/recipes/bioconductor-rnbeads.rn5/meta.yaml index 5b5f9efc68cb5..bdaa0a48b78c1 100644 --- a/recipes/bioconductor-rnbeads.rn5/meta.yaml +++ b/recipes/bioconductor-rnbeads.rn5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RnBeads.rn5" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c153bdbea13a5b0d470e4ab31426f8c7529aec9311d5b927566b36487c6efe0 + sha256: 800fc091bcecf71164140b5558f81f2b7d462096f03223159d9d6cb274200160 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly rn5.' + + diff --git a/recipes/bioconductor-rnbeads.rn5/post-link.sh b/recipes/bioconductor-rnbeads.rn5/post-link.sh index 2977cd39df0ab..65ffe2e09ac69 100644 --- a/recipes/bioconductor-rnbeads.rn5/post-link.sh +++ b/recipes/bioconductor-rnbeads.rn5/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.rn5_1.10.0.tar.gz" +FN="RnBeads.rn5_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/RnBeads.rn5_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.10.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.rn5_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.12.0_src_all.tar.gz" ) -MD5="948e180c1e327b1abb900cedc954de36" +MD5="01f48fb32494406174cd2721cc95af7f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-rnbeads/meta.yaml b/recipes/bioconductor-rnbeads/meta.yaml index a03e3ca53c271..db77dab6bae57 100644 --- a/recipes/bioconductor-rnbeads/meta.yaml +++ b/recipes/bioconductor-rnbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.8" %} +{% set version = "1.12.1" %} {% set name = "RnBeads" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bfa3f46656c023363c8b43528af4f81d2cfbc8fc37194aeb62fa1e1fd0595ccd + sha256: fb610fa5b63641311d1ce27789a8bdc220f864e84f02a34d11dfc0b4e3f4d80a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-limma - - bioconductor-methylumi - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-cluster - r-ff @@ -36,13 +36,13 @@ requirements: - r-matrixstats - r-plyr run: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-illuminaio - - bioconductor-iranges - - bioconductor-limma - - bioconductor-methylumi - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-cluster - r-ff @@ -60,3 +60,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.' + + diff --git a/recipes/bioconductor-rnits/conda_build_config.yaml b/recipes/bioconductor-rnits/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rnits/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rnits/meta.yaml b/recipes/bioconductor-rnits/meta.yaml index 25e40cfe9cb59..1d552efcec1cd 100644 --- a/recipes/bioconductor-rnits/meta.yaml +++ b/recipes/bioconductor-rnits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Rnits" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,31 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 778f39f28da8e513ab7ed6245aad53ed2f0eca223a08c06c8c97275de5faad01 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 25baebc9454e10cdefafa34ae48dbd9a14bfde6ebf7d280bbdd1ed6d2ea0b1ab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-impute - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-boot - r-ggplot2 - r-reshape2 run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-impute - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-boot - r-ggplot2 @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'R/Bioconductor package for normalization, curve registration and inference in time course gene expression data' - extra: identifiers: - biotools:rnits diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index e6ca4f962e132..950574b60fa3a 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "roar" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,33 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6e098e2f1e67a5728085a22ef4260acbdc7ea9a97f24ff9206f9d2cc074d0ae0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 514556917357a0dff936eb20ecd3894615d34b0b870d2f61f86c77a92e692d59 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=0.99.4' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=0.99.4' - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base test: commands: @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.' - extra: identifiers: - biotools:roar diff --git a/recipes/bioconductor-roc/meta.yaml b/recipes/bioconductor-roc/meta.yaml index 983bf7f64d758..219b9660b1772 100644 --- a/recipes/bioconductor-roc/meta.yaml +++ b/recipes/bioconductor-roc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ROC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bb693efdc8b5114d3e0a55982776eb89fad2ee7f3cf947b490557f80479ac028 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2814ca229c7dbb74479fbf7b76b20f816a70856beb9146a66346dc82061490a1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'utilities for ROC, with uarray focus' - extra: identifiers: - biotools:roc diff --git a/recipes/bioconductor-roleswitch/meta.yaml b/recipes/bioconductor-roleswitch/meta.yaml index e343b707ddddc..e3e71cdc8d856 100644 --- a/recipes/bioconductor-roleswitch/meta.yaml +++ b/recipes/bioconductor-roleswitch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Roleswitch" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 696a6918b1fcd17b3f0ab34596ff1dab581e3f11a3dcd95646a073ee262de5ca + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 06377ed38e766b7e7b4aa17dccbf664763d685b2aee272d710fbbea026cbd647 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-microrna + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-microrna >=1.38.0,<1.40.0' - r-base - r-dbi - r-plotrix - r-pracma - r-reshape run: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-microrna + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-microrna >=1.38.0,<1.40.0' - r-base - r-dbi - r-plotrix @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets ("targets") of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference. NB: in the paper, we used ProMISe as both the model name and inferred score name.' - extra: identifiers: - biotools:roleswitch diff --git a/recipes/bioconductor-rols/meta.yaml b/recipes/bioconductor-rols/meta.yaml index 253f5c8b1e4c2..62df0168365aa 100644 --- a/recipes/bioconductor-rols/meta.yaml +++ b/recipes/bioconductor-rols/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.2" %} {% set name = "rols" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c991eff8c619270c398436a1ddfb3974e62b8106222c1842fb24c535465840c9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2dd9cc4130ed5ff62f712969f556a05ce6e9cb4483a1ad181db59f61725e96bc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.23.1' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-httr - r-jsonlite - r-progress run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.23.1' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-httr - r-jsonlite @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.' - extra: identifiers: - biotools:rols diff --git a/recipes/bioconductor-rontotools/meta.yaml b/recipes/bioconductor-rontotools/meta.yaml index 8eb8548935a5e..cc0fe8abba7eb 100644 --- a/recipes/bioconductor-rontotools/meta.yaml +++ b/recipes/bioconductor-rontotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "ROntoTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0ddcb6d4ec551848b0e1afbf0989f3bf98c7695623b16fc94ecb2aaf91c2bd53 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 368956b887a88149dca733d933fef60d880990e015dca1126fdb9cf958d5dbcd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-boot run: - - bioconductor-graph - - bioconductor-kegggraph - - bioconductor-keggrest - - bioconductor-rgraphviz + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-boot test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'CC BY-NC-ND 4.0 + file LICENSE' summary: 'Suite of tools for functional analysis.' - extra: identifiers: - biotools:rontotools diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index b130c0a6cf10d..c3f1fdb81be5e 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ropls" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bc2e9062601bf1028c66d23ce7b716501daded22312d939906c2e2c89016d915 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a6fa8a4d7d2b1ebb69471b03f98f32e6c6dbd91f9b8aeed5182f8d150948c49f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: CeCILL summary: 'Latent variable modeling with Principal Component Analysis(PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).' - extra: identifiers: - biotools:ropls diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index da258681c6b3d..593c26aeb62df 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ROTS" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 509202ea048cf3e62f7d06dde89c03ceaa22aa0dc4e158488d41fc18315fb889 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e3620525682a1e0c80efbeeab9e6035e881b7f01e152cf2e8c064d6f156e5b8a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rcpp run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.' - extra: identifiers: - biotools:rots diff --git a/recipes/bioconductor-rpa/conda_build_config.yaml b/recipes/bioconductor-rpa/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-rpa/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-rpa/meta.yaml b/recipes/bioconductor-rpa/meta.yaml index 18f0d8ab257ff..6d53f98a80edf 100644 --- a/recipes/bioconductor-rpa/meta.yaml +++ b/recipes/bioconductor-rpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RPA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a3e308bab3c377cbf6d8cb5c8bf689fbff4515df0a456d6972c9d8e12f47ade8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b3b9d728cf632bbc752e6b44e3cd63096edf718024c0e00b504d592f51f93050 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biocgenerics - - bioconductor-phyloseq + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-phyloseq >=1.24.2,<1.26.0' - r-base run: - - bioconductor-affy - - bioconductor-biocgenerics - - bioconductor-phyloseq + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-phyloseq >=1.24.2,<1.26.0' - r-base test: commands: @@ -32,8 +33,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' - summary: 'Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. Lahti et al. "Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays", TCBB/IEEE, 2011. http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38' - + summary: 'Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.' extra: identifiers: - biotools:rpa diff --git a/recipes/bioconductor-rprotobuflib/build.sh b/recipes/bioconductor-rprotobuflib/build.sh index 76fd99f6c993a..da43ce2168312 100644 --- a/recipes/bioconductor-rprotobuflib/build.sh +++ b/recipes/bioconductor-rprotobuflib/build.sh @@ -1,5 +1,4 @@ #!/bin/bash - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rprotobuflib/meta.yaml b/recipes/bioconductor-rprotobuflib/meta.yaml index a154dc5bb465e..14d88603da90a 100644 --- a/recipes/bioconductor-rprotobuflib/meta.yaml +++ b/recipes/bioconductor-rprotobuflib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "RProtoBufLib" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0fb88eaabd190fa5e56cca3434876fbab3faa66eb423267941e5c360ed40f86e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 424e121ed7e573f8dbf7c9e2373f950f481967093ae20e1071c257d00fc7b04c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - r-base - - automake ==1.14 # needs alocal installed - - autoconf - - protobuf - - libtool run: - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: BSD_3_clause summary: 'This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.' + + diff --git a/recipes/bioconductor-rpsixml/meta.yaml b/recipes/bioconductor-rpsixml/meta.yaml index fdea0bb47faa6..f33e572138b4d 100644 --- a/recipes/bioconductor-rpsixml/meta.yaml +++ b/recipes/bioconductor-rpsixml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "RpsiXML" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9148d453886bcd7815fb230723a15545c3b7b5d7081786e521f894449b3b706b + sha256: fc74073cddd42122c78423d997aff5cd3d325792f5267b0f15b259f98851a324 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotate >=1.21.0' - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-graph >=1.21.0' - - 'bioconductor-hypergraph >=1.15.2' - - 'bioconductor-rbgl >=1.17.0' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-hypergraph >=1.52.0,<1.54.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - 'r-xml >=2.4.0' run: - - 'bioconductor-annotate >=1.21.0' - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-graph >=1.21.0' - - 'bioconductor-hypergraph >=1.15.2' - - 'bioconductor-rbgl >=1.17.0' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-hypergraph >=1.52.0,<1.54.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base - 'r-xml >=2.4.0' test: @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.' - extra: identifiers: - biotools:rpsixml diff --git a/recipes/bioconductor-rpx/meta.yaml b/recipes/bioconductor-rpx/meta.yaml index d2fca74dadac0..f902add0d78d9 100644 --- a/recipes/bioconductor-rpx/meta.yaml +++ b/recipes/bioconductor-rpx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "rpx" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b32232d16609fc1152311482e395e55bb6310561bde3c8b709eacc8fcbc09300 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a10a20d0e01568ae34a28352be193aa5e494378fadae3854fd0e77abb723f572 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.' - extra: identifiers: - biotools:rpx diff --git a/recipes/bioconductor-rrdp/meta.yaml b/recipes/bioconductor-rrdp/meta.yaml index 60dfeb369a5a5..e77374e5f46d0 100644 --- a/recipes/bioconductor-rrdp/meta.yaml +++ b/recipes/bioconductor-rrdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rRDP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f0152dbb2ef608995d4498137c3773480984b458406388177a560cb7a1848447 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 62f7bdf12d3322afb1756b7aa899244baa7b1d83763112bc7894700c6525b228 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.26.2' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base run: - - 'bioconductor-biostrings >=2.26.2' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 | file LICENSE' summary: 'Seamlessly interfaces RDP classifier (version 2.9).' - extra: identifiers: - biotools:rrdp diff --git a/recipes/bioconductor-rrho/meta.yaml b/recipes/bioconductor-rrho/meta.yaml index 750ab33b2910f..a89f77548ab0b 100644 --- a/recipes/bioconductor-rrho/meta.yaml +++ b/recipes/bioconductor-rrho/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RRHO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9326dea3bb0e4b347e8093e883e285a741b1ef946f15fee30a0faa65e620e6db + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6623394bcf317f9ae880fc19635b6d686b398a263841cda3cf61ff0135e8eb16 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.' - extra: identifiers: - biotools:rrho diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index e805a3e5cd3e8..4b648ecbdbab7 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.3" %} {% set name = "Rsamtools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,43 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ba2a6f2c13e7d001fb8e1a00bd73130a6a748c8d9daf41a16fceae2d5df1565e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 18da1af49cb11008d9c6b55e67f4a1859afd711e486ab09f23ee8e0185c8f2c2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.1.3' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.37.1' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicranges >=1.21.6' - - 'bioconductor-iranges >=2.3.7' - - 'bioconductor-s4vectors >=0.13.8' - - 'bioconductor-xvector >=0.15.1' - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-bitops run: - - 'bioconductor-biocgenerics >=0.1.3' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.37.1' - - 'bioconductor-genomeinfodb >=1.1.3' - - 'bioconductor-genomicranges >=1.21.6' - - 'bioconductor-iranges >=2.3.7' - - 'bioconductor-s4vectors >=0.13.8' - - 'bioconductor-xvector >=0.15.1' - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-bitops + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | file LICENSE' summary: 'This package provides an interface to the ''samtools'', ''bcftools'', and ''tabix'' utilities (see ''LICENCE'') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.' - extra: identifiers: - biotools:rsamtools diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index c1bcd7c137e37..16e1294e05aab 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.9" %} {% set name = "Rsubread" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - sha256: 205b2e24c1d6f8edf483f7eb5df13646d5cb77a6460ee9223c28f55d254273bb + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 57673882455021a2656e56798da722864b2b1e0aaa9ab5783952179e6af7b323 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - r-base run: - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Includes quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.' - + summary: 'Rsubread is a toolbox developed for the analyses of second and third generation sequencing data. It can be used for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and it is suitable for the analysis of both short and long reads.' extra: identifiers: - biotools:rsubread diff --git a/recipes/bioconductor-rsvsim/meta.yaml b/recipes/bioconductor-rsvsim/meta.yaml index 7e3f536702e4b..c75a9ae307c4d 100644 --- a/recipes/bioconductor-rsvsim/meta.yaml +++ b/recipes/bioconductor-rsvsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RSVSim" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ee7d7b71360e69e10c1d991a9f7de7ad7ae54a99efb6f1f7335443de99d84e38 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 354192b279452b0396eacea6e0b1df60326f2f4e165027b252e5dd81b87790dc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-shortread + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base run: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-shortread + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-base test: commands: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.' - extra: identifiers: - biotools:rsvsim diff --git a/recipes/bioconductor-rtca/meta.yaml b/recipes/bioconductor-rtca/meta.yaml index 5f6a4de635a01..42eafe36fdf63 100644 --- a/recipes/bioconductor-rtca/meta.yaml +++ b/recipes/bioconductor-rtca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RTCA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6864995caafd56b273a73d38fc4be465a00a9ded4509e410d64f62921dce5b78 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e187ce8ce9482b78ae2ba3ec90aee2e5d2c8829111e615c1b6799b50dada3c20 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-gtools - r-rcolorbrewer run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-gtools - r-rcolorbrewer @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.' - extra: identifiers: - biotools:rtca diff --git a/recipes/bioconductor-rtcga.mrna/meta.yaml b/recipes/bioconductor-rtcga.mrna/meta.yaml index f06bf2ce1aed2..703dc34713ecf 100644 --- a/recipes/bioconductor-rtcga.mrna/meta.yaml +++ b/recipes/bioconductor-rtcga.mrna/meta.yaml @@ -1,37 +1,35 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RTCGA.mRNA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fe4bbd73fd8ee12d3d26747731ea9f2a3f2dfe55fdc0fbc2a4dd219b224c9f6c - + sha256: 6d4d430ef650985036851f38f3171091c27b15433ec56742c6124a7ff6de56cb build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-rtcga + - 'bioconductor-rtcga >=1.10.0,<1.12.0' - r-base run: - - bioconductor-rtcga + - 'bioconductor-rtcga >=1.10.0,<1.12.0' - r-base - wget - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot.' + + diff --git a/recipes/bioconductor-rtcga.mrna/post-link.sh b/recipes/bioconductor-rtcga.mrna/post-link.sh index c52a9192d9596..07dc9fc5b27e4 100644 --- a/recipes/bioconductor-rtcga.mrna/post-link.sh +++ b/recipes/bioconductor-rtcga.mrna/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="RTCGA.mRNA_1.6.0.tar.gz" +FN="RTCGA.mRNA_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/RTCGA.mRNA_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.6.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RTCGA.mRNA_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.8.0_src_all.tar.gz" ) -MD5="c827c30a04a81ed7405a1e00d974da70" +MD5="1d681a78685d12c2210f80cbb1429314" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga/meta.yaml b/recipes/bioconductor-rtcga/meta.yaml index 018e4836cb674..a08438224c210 100644 --- a/recipes/bioconductor-rtcga/meta.yaml +++ b/recipes/bioconductor-rtcga/meta.yaml @@ -1,23 +1,21 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RTCGA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 668da8ca6c303e387590b5d829080fd177de14c229b63f35ee53ffe384ae93f4 - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9b58175428a99bc3b46ec5e5f50d809442c78c6bc9aa0d7bb32bbbc8b15d2a48 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - r-assertthat @@ -53,21 +51,13 @@ requirements: - r-viridis - r-xml - r-xml2 - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze - data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence - analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download - and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. - This may have an beneficial infuence on impact on development of science and improvement of patients'' treatment. - Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.' - + summary: 'The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients'' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.' extra: identifiers: - biotools:rtcga diff --git a/recipes/bioconductor-rtcgatoolbox/meta.yaml b/recipes/bioconductor-rtcgatoolbox/meta.yaml index 3b6464fcd27f7..51f4951894966 100644 --- a/recipes/bioconductor-rtcgatoolbox/meta.yaml +++ b/recipes/bioconductor-rtcgatoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "RTCGAToolbox" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 50f53871d3dfe53d1b10df9ac732000dce91e4108a96f471a8d73d42fc4c7264 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 34cc165a907c64898dd096234155b946d6ff87a097c1cc0b65eb68856ee573b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-limma >=3.18' - - bioconductor-raggedexperiment - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-raggedexperiment >=1.4.0,<1.6.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - 'r-data.table >=1.9.4' - r-httr @@ -33,18 +34,19 @@ requirements: - r-rcircos - r-rcurl - r-rjsonio + - r-stringr - r-survival - r-xml run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-limma >=3.18' - - bioconductor-raggedexperiment - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-raggedexperiment >=1.4.0,<1.6.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - 'r-data.table >=1.9.4' - r-httr @@ -52,6 +54,7 @@ requirements: - r-rcircos - r-rcurl - r-rjsonio + - r-stringr - r-survival - r-xml test: @@ -59,9 +62,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'file LICENSE' summary: 'Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.' - extra: identifiers: - biotools:rtcgatoolbox diff --git a/recipes/bioconductor-rtopper/meta.yaml b/recipes/bioconductor-rtopper/meta.yaml index f11185dc9ab86..9b187f0cdf969 100644 --- a/recipes/bioconductor-rtopper/meta.yaml +++ b/recipes/bioconductor-rtopper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RTopper" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c118a0d58b84421b6daab4eb9929441fd88c900abf58317ecf5de750b993cca2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b0bc090c0cdd2c717b069b6a86e8b4855929f2c8d1b1835670824d141dcf6869 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base run: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.' - extra: identifiers: - biotools:rtopper diff --git a/recipes/bioconductor-rtracklayer/meta.yaml b/recipes/bioconductor-rtracklayer/meta.yaml index d2b32429d0538..1422f107b808a 100644 --- a/recipes/bioconductor-rtracklayer/meta.yaml +++ b/recipes/bioconductor-rtracklayer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.3" %} +{% set version = "1.40.6" %} {% set name = "rtracklayer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,44 +8,47 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 93584e9d01405e9d908e4623e8e5bf5aa41000ce984a0013a66596513f731fce + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9470a3d892d7decd97a5fbe53298e6dada3847a595f00be2e02d057d3dedbdf3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-biocgenerics >=0.13.8' - - 'bioconductor-biostrings >=2.43.7' - - 'bioconductor-genomeinfodb >=1.3.14' - - 'bioconductor-genomicalignments >=1.5.4' - - 'bioconductor-genomicranges >=1.21.20' - - 'bioconductor-iranges >=2.11.12' - - 'bioconductor-rsamtools >=1.17.8' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-xvector >=0.9.4' - - bioconductor-zlibbioc - - 'r-rcurl >=1.4*' - - 'r-xml >=1.98*' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + - 'r-rcurl >=1.4-2' + - 'r-xml >=1.98-0' run: - - 'bioconductor-biocgenerics >=0.13.8' - - 'bioconductor-biostrings >=2.43.7' - - 'bioconductor-genomeinfodb >=1.3.14' - - 'bioconductor-genomicalignments >=1.5.4' - - 'bioconductor-genomicranges >=1.21.20' - - 'bioconductor-iranges >=2.11.12' - - 'bioconductor-rsamtools >=1.17.8' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-xvector >=0.9.4' - - bioconductor-zlibbioc - - 'r-rcurl >=1.4*' - - 'r-xml >=1.98*' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + - 'r-rcurl >=1.4-2' + - 'r-xml >=1.98-0' + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -53,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 + file LICENSE' summary: 'Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.' - extra: identifiers: - biotools:rtracklayer diff --git a/recipes/bioconductor-rtreemix/meta.yaml b/recipes/bioconductor-rtreemix/meta.yaml index c9f8b58e91201..caa072e1ce1f1 100644 --- a/recipes/bioconductor-rtreemix/meta.yaml +++ b/recipes/bioconductor-rtreemix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "Rtreemix" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 45487d9276358e2a02e8719fd87ebcc85cb87c17d4b0f6a5cbfbcff703cdeec0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 97a16f117b7ab351f3a151b03c4230b180058edf84ab0ec01f9e6bbf48d8c429 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-hmisc run: - - bioconductor-biobase - - bioconductor-graph + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-hmisc + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.' - extra: identifiers: - biotools:rtreemix diff --git a/recipes/bioconductor-rtrm/meta.yaml b/recipes/bioconductor-rtrm/meta.yaml index 7ae720866d4c7..b54406e3ac0eb 100644 --- a/recipes/bioconductor-rtrm/meta.yaml +++ b/recipes/bioconductor-rtrm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rTRM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b0e724c6b17c0d579b501a10a1d783099c9cf04af5af3a76dec2c700015e932d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cf70b7ce210d04f56a1e844e917d31696360dc55a3090a547b13ebf84025645a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi - 'r-igraph >=1.0' - r-rsqlite run: - - bioconductor-annotationdbi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - r-base - r-dbi - 'r-igraph >=1.0' @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.' - extra: identifiers: - biotools:rtrm diff --git a/recipes/bioconductor-rtrmui/meta.yaml b/recipes/bioconductor-rtrmui/meta.yaml index eb14d874ee31c..cbab80514bc2c 100644 --- a/recipes/bioconductor-rtrmui/meta.yaml +++ b/recipes/bioconductor-rtrmui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rTRMui" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f58628f803bcd0d64863e03d19c65dea8f28e5be5b0e4232633be61d5532a963 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3118083703ff70dea3e53e7cd004e8eb9a6560e48eab10c48597d79ef468794b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-motifdb - - bioconductor-org.hs.eg.db - - bioconductor-org.mm.eg.db - - bioconductor-rtrm + - 'bioconductor-motifdb >=1.22.0,<1.24.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtrm >=1.18.0,<1.20.0' - r-base - 'r-shiny >=0.9' run: - - bioconductor-motifdb - - bioconductor-org.hs.eg.db - - bioconductor-org.mm.eg.db - - bioconductor-rtrm + - 'bioconductor-motifdb >=1.22.0,<1.24.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rtrm >=1.18.0,<1.20.0' - r-base - 'r-shiny >=0.9' test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides a web interface to compute transcriptional regulatory modules with rTRM.' - extra: identifiers: - biotools:rtrmui diff --git a/recipes/bioconductor-ruvnormalize/meta.yaml b/recipes/bioconductor-ruvnormalize/meta.yaml index 38528d87b3db0..20c61635a6ac4 100644 --- a/recipes/bioconductor-ruvnormalize/meta.yaml +++ b/recipes/bioconductor-ruvnormalize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RUVnormalize" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fdba46a6c08b2fbadf7342fac15aaf7567114b34f9e3b57616120d0f1807371c + sha256: 0d2eb8ee36e315b797d0aa1dc5fb189ca344122105f645352ab118044f882ade build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-ruvnormalizedata + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ruvnormalizedata >=0.114.0,<0.116.0' - r-base run: - - bioconductor-biobase - - bioconductor-ruvnormalizedata + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-ruvnormalizedata >=0.114.0,<0.116.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.' - extra: identifiers: - biotools:ruvnormalize diff --git a/recipes/bioconductor-ruvnormalizedata/meta.yaml b/recipes/bioconductor-ruvnormalizedata/meta.yaml index 886f1698fa09f..bf6fed4bf7c2f 100644 --- a/recipes/bioconductor-ruvnormalizedata/meta.yaml +++ b/recipes/bioconductor-ruvnormalizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.112.0" %} +{% set version = "0.114.0" %} {% set name = "RUVnormalizeData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 647e0b08d9403da116431f5ca413e746ef5d17ed084ef286970457f6f272c4e9 + sha256: 6085d3cbf3770b481faee568fc2bf8ed68b869e837a322bee474aedd3736e4b1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Microarray gene expression data from the study of Vawter et al., 2004.' + + diff --git a/recipes/bioconductor-ruvnormalizedata/post-link.sh b/recipes/bioconductor-ruvnormalizedata/post-link.sh index 8c21d47ba6e28..996433b75aaa1 100644 --- a/recipes/bioconductor-ruvnormalizedata/post-link.sh +++ b/recipes/bioconductor-ruvnormalizedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RUVnormalizeData_0.112.0.tar.gz" +FN="RUVnormalizeData_0.114.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/RUVnormalizeData_0.112.0.tar.gz" - "https://bioarchive.galaxyproject.org/RUVnormalizeData_0.112.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_0.112.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RUVnormalizeData_0.114.0.tar.gz" + "https://bioarchive.galaxyproject.org/RUVnormalizeData_0.114.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_0.114.0_src_all.tar.gz" ) -MD5="78735fedff129098b3dce9844f5c3cdd" +MD5="116061e9ddf8357f83e5460ad86da991" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-ruvseq/meta.yaml b/recipes/bioconductor-ruvseq/meta.yaml index 6a26dd4b984ff..bf3a94ccce23e 100644 --- a/recipes/bioconductor-ruvseq/meta.yaml +++ b/recipes/bioconductor-ruvseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RUVSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9c539658c55b0bbe259e7c51a124641cd49b7af3aee185b9179185b05e907b42 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b2e3eee8e6072b5a31ee108d621722963e6da744d15dbd3f99c11ca74ad5259a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-edaseq >=1.99.1' - - bioconductor-edger + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-edaseq >=2.14.1,<2.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - r-mass run: - - bioconductor-biobase - - 'bioconductor-edaseq >=1.99.1' - - bioconductor-edger + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-edaseq >=2.14.1,<2.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' - r-base - r-mass test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.' - extra: identifiers: - biotools:ruvseq diff --git a/recipes/bioconductor-s4vectors/meta.yaml b/recipes/bioconductor-s4vectors/meta.yaml index 9beb1dc1103d4..c123a9068de32 100644 --- a/recipes/bioconductor-s4vectors/meta.yaml +++ b/recipes/bioconductor-s4vectors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.16.0" %} +{% set version = "0.18.3" %} {% set name = "S4Vectors" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8043a0a9f76e00ab96d4214a0ac888d7cf26c0917bb5b3e48ed5503bc6df480f + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c8b7f6045f48340a0d342572564cc8efa5c89915a60fdcf9b5a26379b3d07709 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.23.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base run: - - 'bioconductor-biocgenerics >=0.23.3' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).' - extra: identifiers: - biotools:s4vectors diff --git a/recipes/bioconductor-safe/meta.yaml b/recipes/bioconductor-safe/meta.yaml index 8d91b999fed76..ed2f33ef4f19a 100644 --- a/recipes/bioconductor-safe/meta.yaml +++ b/recipes/bioconductor-safe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "safe" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 02c272aeba2f6eef629827bcf2c5af0fd6467a2bd082917a57e1cfb775aceb72 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 06585dbf2589b828b28b0036149903255a8ed0524586f07f41003e8cfb564564 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-sparsem run: - - bioconductor-annotationdbi - - bioconductor-biobase + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-sparsem test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.' - extra: identifiers: - biotools:safe diff --git a/recipes/bioconductor-sagenhaft/meta.yaml b/recipes/bioconductor-sagenhaft/meta.yaml index 0e28e31577df3..82737af388317 100644 --- a/recipes/bioconductor-sagenhaft/meta.yaml +++ b/recipes/bioconductor-sagenhaft/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "sagenhaft" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9ec0314fde78fd3e9d3a4a7f48e3aacfd00c595a279826b16cf3a3fd0c6a723c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 633e1e20461413e77db52cd4f86f5588fae837c99696e64bb0942d6d63311d3a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.' - extra: identifiers: - biotools:sagenhaft diff --git a/recipes/bioconductor-sagx/meta.yaml b/recipes/bioconductor-sagx/meta.yaml index b659b25c7e571..18c813df89436 100644 --- a/recipes/bioconductor-sagx/meta.yaml +++ b/recipes/bioconductor-sagx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "SAGx" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: edd1acba32288f67e7fa742195775250188d5d27f30143a623f72f1d87865eba + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a59a6d8e5bc536be0ca046145abba776f0098072cc4c31cacfdabdc8cda61402 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base run: - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +35,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.' - extra: identifiers: - biotools:sagx diff --git a/recipes/bioconductor-sangerseqr/meta.yaml b/recipes/bioconductor-sangerseqr/meta.yaml index 625968c31cc47..5c43df3f5d2b9 100644 --- a/recipes/bioconductor-sangerseqr/meta.yaml +++ b/recipes/bioconductor-sangerseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "sangerseqR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5a8bcaf46162429b8f1ecfefe23b836e5c9ffdc186501789eb86c611f3aa5998 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 70cf453d88d8b4573fd0c948398a3a7127318c6470b4a5eb9a4787e2d5025d0c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-shiny run: - - bioconductor-biostrings + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - r-shiny test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.' - extra: identifiers: - biotools:sangerseqr diff --git a/recipes/bioconductor-santa/meta.yaml b/recipes/bioconductor-santa/meta.yaml index 3ed49ea84c71d..1fbf01b625bcb 100644 --- a/recipes/bioconductor-santa/meta.yaml +++ b/recipes/bioconductor-santa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "SANTA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9b3d45debf130c9a6866a78287b51f1276453d3683e4b61745961cb8851c808a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0bf040813afe4abf395a4231a539d47b02ebdc51b12a751aa975180477b796b3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -26,6 +27,9 @@ requirements: - r-igraph - r-matrix - r-snow + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).' - extra: identifiers: - biotools:santa diff --git a/recipes/bioconductor-savr/meta.yaml b/recipes/bioconductor-savr/meta.yaml index 66321586fce57..f3d3e4a229a4a 100644 --- a/recipes/bioconductor-savr/meta.yaml +++ b/recipes/bioconductor-savr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "savR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2b0a11dd32a4e512c94ef952b07c42f5fdf4f915bee6a519bca874e368f9a0fc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0bc9de78d8df417bbf01eb78e0a8337a135f52d6ac5fecbf23e3e0b9c1985c9f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'Parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.' - extra: identifiers: - biotools:savr diff --git a/recipes/bioconductor-sc3-scripts/meta.yaml b/recipes/bioconductor-sc3-scripts/meta.yaml index d654558735de7..fe27e9f2a5bc6 100644 --- a/recipes/bioconductor-sc3-scripts/meta.yaml +++ b/recipes/bioconductor-sc3-scripts/meta.yaml @@ -47,3 +47,4 @@ about: ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages. license_family: GPL + diff --git a/recipes/bioconductor-sc3/conda_build_config.yaml b/recipes/bioconductor-sc3/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-sc3/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-sc3/meta.yaml b/recipes/bioconductor-sc3/meta.yaml index 82d26f772d5b4..c675756455ffa 100644 --- a/recipes/bioconductor-sc3/meta.yaml +++ b/recipes/bioconductor-sc3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.6" %} +{% set version = "1.8.0" %} {% set name = "SC3" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9aa3703cf71fa5ad3fed2318788a3b33c90e6eadac5e63cab90495f883e3404e + sha256: 4865fd2e94a7a2fe26ac9fc9d6b7d0c0b4820eeab8e8b222420e4ae4836f8722 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-cluster - r-doparallel @@ -40,10 +38,10 @@ requirements: - r-shiny - r-writexls run: - - bioconductor-biocgenerics - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-cluster - r-doparallel @@ -59,6 +57,10 @@ requirements: - r-rrcov - r-shiny - r-writexls + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -66,7 +68,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A tool for unsupervised clustering and analysis of single cell RNA-Seq data.' - extra: identifiers: - biotools:sc3 diff --git a/recipes/bioconductor-scan.upc/conda_build_config.yaml b/recipes/bioconductor-scan.upc/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-scan.upc/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index d940120057ce0..46eb80a532853 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "SCAN.UPC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,35 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2ae71390e3725a325f9f8a1cdfab55786a7f5a1e3ecf969385600d304ccef3b9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 851c199a54f682a2faad4fe4311eb1c51e27d209ad64358f9afa5fcd193f1b5c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-affyio - - 'bioconductor-biobase >=2.6.0' - - bioconductor-biostrings - - bioconductor-geoquery - - bioconductor-iranges - - bioconductor-oligo - - bioconductor-sva + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-foreach - r-mass run: - - bioconductor-affy - - bioconductor-affyio - - 'bioconductor-biobase >=2.6.0' - - bioconductor-biostrings - - bioconductor-geoquery - - bioconductor-iranges - - bioconductor-oligo - - bioconductor-sva + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-foreach - r-mass @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: MIT summary: 'SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.' - extra: identifiers: - biotools:scan.upc diff --git a/recipes/bioconductor-scater-scripts/conda_build_config.yaml b/recipes/bioconductor-scater-scripts/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-scater-scripts/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-scater-scripts/meta.yaml b/recipes/bioconductor-scater-scripts/meta.yaml index a809d7394236e..a2702ed146784 100644 --- a/recipes/bioconductor-scater-scripts/meta.yaml +++ b/recipes/bioconductor-scater-scripts/meta.yaml @@ -41,3 +41,4 @@ about: ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages. license_family: GPL + diff --git a/recipes/bioconductor-scater/conda_build_config.yaml b/recipes/bioconductor-scater/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-scater/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-scater/meta.yaml b/recipes/bioconductor-scater/meta.yaml index 5bc78dec3cbc7..f7baac2012b38 100644 --- a/recipes/bioconductor-scater/meta.yaml +++ b/recipes/bioconductor-scater/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.4" %} {% set name = "scater" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,70 +8,73 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 35f2c47392514afeb8b4b59dddf81b0eb1d7d224d93a0bb3f01dc66a9dffa886 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 266cef66bf96fc94c94abc46886e612611d2fae40170dd3bb91a3ba1d575749c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-edger - - bioconductor-limma - - bioconductor-rhdf5 - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-tximport - - bioconductor-rhdf5lib # not specified - - bioconductor-beachmat # not specified + - 'bioconductor-beachmat >=1.2.1,<1.4.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-tximport >=1.8.0,<1.10.0' - r-base - r-data.table - r-dplyr - r-ggbeeswarm - r-ggplot2 - r-matrix - - r-matrixstats - r-plyr - - r-rcpp + - 'r-rcpp >=0.12.14' - r-reshape2 - r-rjson - r-shiny - r-shinydashboard - r-viridis run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-edger - - bioconductor-limma - - bioconductor-rhdf5 - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-tximport - - bioconductor-rhdf5lib # not specified - - bioconductor-beachmat # not specified + - 'bioconductor-beachmat >=1.2.1,<1.4.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-tximport >=1.8.0,<1.10.0' - r-base - r-data.table - r-dplyr - r-ggbeeswarm - r-ggplot2 - r-matrix - - r-matrixstats - r-plyr - - r-rcpp + - 'r-rcpp >=0.12.14' - r-reshape2 - r-rjson - r-shiny - r-shinydashboard - r-viridis + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -79,7 +82,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.' - extra: identifiers: - biotools:scater diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml index a2eab4eb32fc8..7545cdc79ac71 100644 --- a/recipes/bioconductor-scde/meta.yaml +++ b/recipes/bioconductor-scde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "scde" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 226c6ac1699c507546144313027b844280092e311da1fb4cb10b288d6854aa33 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 11f1a4b9a343e70023364f92a89ead50bfa0f490c9e4c21174d7b1ac47aab7ad build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-pcamethods + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-pcamethods >=1.72.0,<1.74.0' - r-base - r-cairo - r-extremes - - r-flexmix <=2.3_13 + - r-flexmix - r-mass - r-mgcv - r-nnet @@ -36,17 +35,14 @@ requirements: - r-rjson - r-rmtstat - r-rook - - xorg-libxrender 0.9.* - - xorg-libsm 1.2.* - - xorg-libxext 1.3.* run: - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-pcamethods + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-pcamethods >=1.72.0,<1.74.0' - r-base - r-cairo - r-extremes - - r-flexmix <=2.3_13 + - r-flexmix - r-mass - r-mgcv - r-nnet @@ -57,10 +53,10 @@ requirements: - r-rjson - r-rmtstat - r-rook - - xorg-libxrender 0.9.* - - xorg-libsm 1.2.* - - xorg-libxext 1.3.* - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -68,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).' - extra: identifiers: - biotools:scde diff --git a/recipes/bioconductor-scisi/meta.yaml b/recipes/bioconductor-scisi/meta.yaml index 4d64b703b23e7..c15b753dea266 100644 --- a/recipes/bioconductor-scisi/meta.yaml +++ b/recipes/bioconductor-scisi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "ScISI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7c5b88be7704a0fcfbafda5954898ad58f72d3fc4ce598b207e42bb6c4e85e6b + sha256: 52d824983f017feeb7703a091d81256abcc278015a648dfae83649af9c80d145 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-apcomplex - - bioconductor-go.db - - bioconductor-org.sc.sgd.db - - bioconductor-rpsixml + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-apcomplex >=2.46.0,<2.48.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' + - 'bioconductor-rpsixml >=2.22.0,<2.24.0' - r-base run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-apcomplex - - bioconductor-go.db - - bioconductor-org.sc.sgd.db - - bioconductor-rpsixml + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-apcomplex >=2.46.0,<2.48.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' + - 'bioconductor-rpsixml >=2.22.0,<2.24.0' - r-base test: commands: @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Package to create In Silico Interactomes' - extra: identifiers: - biotools:scisi diff --git a/recipes/bioconductor-scnorm/conda_build_config.yaml b/recipes/bioconductor-scnorm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-scnorm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-scnorm/meta.yaml b/recipes/bioconductor-scnorm/meta.yaml index 3b76cdca8f465..0ba12d20c39d8 100644 --- a/recipes/bioconductor-scnorm/meta.yaml +++ b/recipes/bioconductor-scnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "SCnorm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,17 +10,19 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2657577e53a2b41000863c9d5f104b196f267e28242dddc30bb5c1f58a62fc6e + sha256: f91e137b6037bbbbd3b5e3ce3fa11a54a3c9e4c1af3583145f88c83f986b8d19 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ +# note the conda_build_config.yaml requirements: host: - - bioconductor-biocparallel - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-cluster - r-data.table @@ -29,9 +31,10 @@ requirements: - r-moments - r-quantreg run: - - bioconductor-biocparallel - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-cluster - r-data.table @@ -46,3 +49,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements SCnorm — a method to normalize single-cell RNA-seq data.' + + diff --git a/recipes/bioconductor-scpipe/build.sh b/recipes/bioconductor-scpipe/build.sh index da43ce2168312..79225b632eebb 100644 --- a/recipes/bioconductor-scpipe/build.sh +++ b/recipes/bioconductor-scpipe/build.sh @@ -1,4 +1,12 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file +# We need gcc >= 4.9 and the Makevars are just getting ignored +if [[ $target_platform =~ linux.* ]] ; then + foo=`which g++` + rm $foo + ln -s $GXX $foo + ln -s ${PREFIX}/lib/libgfortran.so.3 ${PREFIX}/lib/libgfortran.so + export LIBRARY_PATH=${PREFIX}/lib +fi +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-scpipe/conda_build_config.yaml b/recipes/bioconductor-scpipe/conda_build_config.yaml new file mode 100644 index 0000000000000..cf49bdd148cd7 --- /dev/null +++ b/recipes/bioconductor-scpipe/conda_build_config.yaml @@ -0,0 +1,8 @@ +r_base: + - 3.5.1 +c_compiler: + - gcc # [linux] + - clang # [osx] +cxx_compiler: + - gxx # [linux] + - clangxx # [osx] diff --git a/recipes/bioconductor-scpipe/meta.yaml b/recipes/bioconductor-scpipe/meta.yaml index d18b766f8a537..cd6c82def0b49 100644 --- a/recipes/bioconductor-scpipe/meta.yaml +++ b/recipes/bioconductor-scpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "scPipe" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9f95d574b379194d82a6b3864f239d41878f8ab22b6a3c3709e690d7cda2a1de + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ae2c9d2c00b750e95fbf735e031bfc0055568a9c6506db1cbb38083ac0e5d89a build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-rhtslib - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-ggally - r-ggplot2 @@ -35,12 +38,16 @@ requirements: - r-robustbase - r-scales run: - - bioconductor-biocgenerics - - bioconductor-biomart - - bioconductor-rhtslib - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rhtslib >=1.12.1,<1.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-ggally - r-ggplot2 @@ -50,10 +57,17 @@ requirements: - r-reshape - r-robustbase - r-scales + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'to process single cell RNA-seq data from fastq to gene counting matrix. it can process data generated by CEL-seq, MARS-seq, Drop-seq and SMART-seq.' + summary: 'A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.' + + diff --git a/recipes/bioconductor-scran/conda_build_config.yaml b/recipes/bioconductor-scran/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-scran/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-scran/meta.yaml b/recipes/bioconductor-scran/meta.yaml index e52f4391fc2c6..8b6b93b8cb024 100644 --- a/recipes/bioconductor-scran/meta.yaml +++ b/recipes/bioconductor-scran/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.4" %} {% set name = "scran" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,72 +8,74 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 944e5af670ceb9fc742b65d9c30c687d364eb49b6932d006424e972ce67a1b15 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d288b0413d7235b40a71483e6dfbc97587f4474fd5f28b5925f64c95d64e789f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-scater - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-rhdf5lib # not specified - - bioconductor-beachmat # not specified + - 'bioconductor-beachmat >=1.2.1,<1.4.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-scater >=1.8.4,<1.10.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dt - r-dynamictreecut - r-fnn - r-ggplot2 - r-igraph - - r-mass - r-matrix - - r-rcpp + - 'r-rcpp >=0.12.14' - r-shiny - r-statmod - r-viridis - - r-zoo run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-limma - - bioconductor-s4vectors - - bioconductor-scater - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-rhdf5lib # not specified - - bioconductor-beachmat # not specified + - 'bioconductor-beachmat >=1.2.1,<1.4.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-scater >=1.8.4,<1.10.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dt - r-dynamictreecut - r-fnn - r-ggplot2 - r-igraph - - r-mass - r-matrix - - r-rcpp + - 'r-rcpp >=0.12.14' - r-shiny - r-statmod - r-viridis - - r-zoo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.' - + summary: 'Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, correction of batch effects, identification of marker genes, and other common tasks in single-cell analysis workflows.' extra: identifiers: - biotools:scran diff --git a/recipes/bioconductor-segmentseq/meta.yaml b/recipes/bioconductor-segmentseq/meta.yaml index 3ba0bdd9f73a8..3b7cda06cbccf 100644 --- a/recipes/bioconductor-segmentseq/meta.yaml +++ b/recipes/bioconductor-segmentseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "segmentSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c42c3729bcae59b3c581ada10db74a26a517d32e5ea9ca4e340eaa9e7f6b0d4b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 28d8d72b03d540e5c5d3edfa6f734e70ef345d353788e0fc41e7265ba57c7c27 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-bayseq >=2.9.0' - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-shortread + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-abind - r-base run: - - 'bioconductor-bayseq >=2.9.0' - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-shortread + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' - r-abind - r-base test: @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.' - extra: identifiers: - biotools:segmentseq diff --git a/recipes/bioconductor-semdist/meta.yaml b/recipes/bioconductor-semdist/meta.yaml index 0c92f9651349e..926d87c2a4e3b 100644 --- a/recipes/bioconductor-semdist/meta.yaml +++ b/recipes/bioconductor-semdist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SemDist" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ab089efa87bbc74541cced051c07fc35f1e10d7a1a991e91105d0703c96874c0 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ef8dd578f134b7161a5d737fe41d4d6c35015f8cb760673a2f072202c1f1c17e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.' - extra: identifiers: - biotools:semdist diff --git a/recipes/bioconductor-semisup/meta.yaml b/recipes/bioconductor-semisup/meta.yaml index 5075a1119f7cd..6dcbf1d1b427d 100644 --- a/recipes/bioconductor-semisup/meta.yaml +++ b/recipes/bioconductor-semisup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "semisup" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f92014660213a5baa9302a603be9b5ac42964d9a0845ce35f29964a4d0b80293 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 569f50fb9511417bce439881e31cc0c87c45ca514ab98b63ab79f3527f3cc90d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-vgam run: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-vgam test: @@ -31,3 +32,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in distribution between some individuals in one group and all other individuals, it possibly has an interactive effect. Implicitly, the membership probabilities may suggest potential interacting variables.' + + diff --git a/recipes/bioconductor-sepa/meta.yaml b/recipes/bioconductor-sepa/meta.yaml index 451db67be7e52..b2464a2b75eab 100644 --- a/recipes/bioconductor-sepa/meta.yaml +++ b/recipes/bioconductor-sepa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SEPA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,27 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 47a54229d8b74413e4d392f8b22ae3b016741c597835407e4d7721ab1fc70f3c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 827977cece3573fc600d90bfc7cd17f4ebadd02e0dde494ad6dfac1077efc391 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-org.hs.eg.db - - bioconductor-org.mm.eg.db - - bioconductor-topgo + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-ggplot2 - r-reshape2 - r-segmented - r-shiny run: - - bioconductor-org.hs.eg.db - - bioconductor-org.mm.eg.db - - bioconductor-topgo + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-ggplot2 - r-reshape2 @@ -41,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.' - extra: identifiers: - biotools:sepa diff --git a/recipes/bioconductor-seq2pathway.data/meta.yaml b/recipes/bioconductor-seq2pathway.data/meta.yaml index d63cccd78b10b..7e842531f579b 100644 --- a/recipes/bioconductor-seq2pathway.data/meta.yaml +++ b/recipes/bioconductor-seq2pathway.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "seq2pathway.data" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 05e0c471f23e6f4825b0b5ab67fc0efd24d37864ff672ec77e7c3d7115ec0606 + sha256: c54109592ef4eef69c86a2c4491c6f89c21afafc31916db917d13baa360b3a64 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project.' + + diff --git a/recipes/bioconductor-seq2pathway.data/post-link.sh b/recipes/bioconductor-seq2pathway.data/post-link.sh index fc43f1a15cd25..194d777896700 100644 --- a/recipes/bioconductor-seq2pathway.data/post-link.sh +++ b/recipes/bioconductor-seq2pathway.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="seq2pathway.data_1.10.0.tar.gz" +FN="seq2pathway.data_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/seq2pathway.data_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/seq2pathway.data_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.10.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/seq2pathway.data_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/seq2pathway.data_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.12.0_src_all.tar.gz" ) -MD5="da2fa3ca1002b4216301cfc2b97c03f3" +MD5="b8290b0259648264b2194867c624224f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-seq2pathway/meta.yaml b/recipes/bioconductor-seq2pathway/meta.yaml index 66ee66681478f..928575e1981e5 100644 --- a/recipes/bioconductor-seq2pathway/meta.yaml +++ b/recipes/bioconductor-seq2pathway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "seq2pathway" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6f214c150bf1bd389a07a8f40f7da9ce71ca2a4ed7d579af0e827fb127e9e973 + sha256: 9edd3eec43f9c9b33cbb04cc52c3ef6af2c32230f8a65a846e41fb227ca37bea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-genomicranges - - bioconductor-seq2pathway.data + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-seq2pathway.data >=1.12.0,<1.14.0' - r-base - r-gsa - r-nnet - r-wgcna run: - - bioconductor-biomart - - bioconductor-genomicranges - - bioconductor-seq2pathway.data + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-seq2pathway.data >=1.12.0,<1.14.0' - r-base - r-gsa - r-nnet @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.' - extra: identifiers: - biotools:seq2pathway diff --git a/recipes/bioconductor-seqgsea/meta.yaml b/recipes/bioconductor-seqgsea/meta.yaml index 9368b6a6745fa..ab98655ac3229 100644 --- a/recipes/bioconductor-seqgsea/meta.yaml +++ b/recipes/bioconductor-seqgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SeqGSEA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4aac943601f218adca968c80d34e337e5623ae89e3f3f42d5eb7f33da55158ed + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 72bf104155765f009f1c92d6aba534d8219a20c35de6ea2463c67e889e1ef11c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-deseq + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' - r-base - r-doparallel run: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-deseq + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' - r-base - r-doparallel test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively.' - extra: identifiers: - biotools:seqgsea diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index 0c5089251e25f..a27cc278e70d0 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "seqLogo" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 78069ef80ea0addd9c8738c8e121d648bfda3f6283e1361252c148d037c184e2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 81459d392504a00a520f501282aa2c246be7ad893de68aaadca9473b1bc3bb9b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).' - extra: identifiers: - biotools:seqlogo diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 4b3c4489fe6e4..8378daf104e40 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "seqPattern" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f59e54dcd136b30ebdaf3f797c8d35cca05ff023d7dba337d8801f3c102f95cd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7c5c0e62021cfeafa31682277e88aa343969650cfdd28eef5e1138e61af58037 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-kernsmooth - r-plotrix run: - - bioconductor-biostrings - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-kernsmooth - r-plotrix @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.' - extra: identifiers: - biotools:seqpattern diff --git a/recipes/bioconductor-seqtools/meta.yaml b/recipes/bioconductor-seqtools/meta.yaml index 823b5ee9e1467..abac7db3f8112 100644 --- a/recipes/bioconductor-seqtools/meta.yaml +++ b/recipes/bioconductor-seqtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "seqTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: da16ce53c9b838c08aa1e9bb364eb2cdd392925960d8c793e5bf8e9bdaeac9d4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cbc433c0f1c72b7f4bb494b8006d80c56638f843a67c8f9726dc276ea3cd9611 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-zlibbioc + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - bioconductor-zlibbioc + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.' - extra: identifiers: - biotools:seqtools diff --git a/recipes/bioconductor-sgseq/meta.yaml b/recipes/bioconductor-sgseq/meta.yaml index 9a40a13b7504e..21422e3ce1169 100644 --- a/recipes/bioconductor-sgseq/meta.yaml +++ b/recipes/bioconductor-sgseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SGSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,43 +8,44 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 98a4ddc705f2566bf427d50b920f7a9e1ef175040a20189853534e6649f67c71 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e61fb11182dcbaf177f882b46ff4df73e58d77e2cfdf94aee5f8ed473179c387 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.23.21' - - bioconductor-iranges - - bioconductor-rsamtools - - 'bioconductor-rtracklayer >=1.37.2' - - 'bioconductor-s4vectors >=0.9.39' - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-igraph - r-runit run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.23.21' - - bioconductor-iranges - - bioconductor-rsamtools - - 'bioconductor-rtracklayer >=1.37.2' - - 'bioconductor-s4vectors >=0.9.39' - - bioconductor-summarizedexperiment + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-igraph - r-runit @@ -55,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.' - extra: identifiers: - biotools:sgseq diff --git a/recipes/bioconductor-shinymethyl/meta.yaml b/recipes/bioconductor-shinymethyl/meta.yaml index 26086ffd9312f..7ae3455afe4e0 100644 --- a/recipes/bioconductor-shinymethyl/meta.yaml +++ b/recipes/bioconductor-shinymethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "shinyMethyl" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8ad7d8daacd56dafb9c7ae199a7a3b089f9d57caefa319831fbc68921fd4879f + sha256: 1ca469110677b1a38683a16fa24c17224853996fe01676e482375dcdc02ce7cd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-illuminahumanmethylation450kmanifest - - 'bioconductor-minfi >=1.18.2' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - r-matrixstats - r-rcolorbrewer - 'r-shiny >=0.13.2' run: - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-illuminahumanmethylation450kmanifest - - 'bioconductor-minfi >=1.18.2' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' + - 'bioconductor-minfi >=1.26.2,<1.28.0' - r-base - r-matrixstats - r-rcolorbrewer @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.' - extra: identifiers: - biotools:shinymethyl diff --git a/recipes/bioconductor-shortread/build.sh b/recipes/bioconductor-shortread/build.sh index f34d4d94635a0..da43ce2168312 100644 --- a/recipes/bioconductor-shortread/build.sh +++ b/recipes/bioconductor-shortread/build.sh @@ -1,6 +1,4 @@ #!/bin/bash -export CFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index 173424b828f4c..962a36d424c53 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ShortRead" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,46 +8,54 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9f7dbec9d74f16a67403a0f801024fceb637c5ddef2ad97e5716925635b5b31a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cb058f83d68937dc1ec1d6662d2597c65bbdfc943a24ffe5bbab7085cf1f1f0d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.23.3' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.37.1' - - 'bioconductor-genomeinfodb >=1.1.19' - - 'bioconductor-genomicalignments >=1.5.4' - - 'bioconductor-genomicranges >=1.21.6' - - 'bioconductor-iranges >=2.3.7' - - 'bioconductor-rsamtools >=1.21.4' - - 'bioconductor-s4vectors >=0.13.8' - - bioconductor-zlibbioc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-hwriter - r-lattice - r-latticeextra run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.23.3' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.37.1' - - 'bioconductor-genomeinfodb >=1.1.19' - - 'bioconductor-genomicalignments >=1.5.4' - - 'bioconductor-genomicranges >=1.21.6' - - 'bioconductor-iranges >=2.3.7' - - 'bioconductor-rsamtools >=1.21.4' - - 'bioconductor-s4vectors >=0.13.8' - - bioconductor-zlibbioc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-hwriter - r-lattice - r-latticeextra + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -55,7 +63,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.' - extra: identifiers: - biotools:shortread diff --git a/recipes/bioconductor-sigar/meta.yaml b/recipes/bioconductor-sigar/meta.yaml index f23ec90251ac5..fa7335cd03280 100644 --- a/recipes/bioconductor-sigar/meta.yaml +++ b/recipes/bioconductor-sigar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "sigaR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b380854cbbf25afb685d2ce56e768dae6f12e58451a4425bdd29e2ecd290d2a4 + sha256: bab613194873b70ba0a6e8cde7e550bad897593bc546667a59f20bf6f7f8d7ce build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-cghbase - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - 'r-corpcor >=1.6.2' - r-igraph @@ -31,10 +31,10 @@ requirements: - r-quadprog - r-snowfall run: - - bioconductor-biobase - - bioconductor-cghbase - - bioconductor-limma - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - 'r-corpcor >=1.6.2' - r-igraph @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Facilitates the joint analysis of high-throughput data from multiple molecular levels. Contains functions for manipulation of objects, various analysis types, and some visualization.' - extra: identifiers: - biotools:sigar diff --git a/recipes/bioconductor-sigfuge/meta.yaml b/recipes/bioconductor-sigfuge/meta.yaml index b83dfa07d1753..f38afb479468d 100644 --- a/recipes/bioconductor-sigfuge/meta.yaml +++ b/recipes/bioconductor-sigfuge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SigFuge" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8ee467fc7f4e44d6c035bd2c8728f8a774cf25e4aa5c03e0d3af80e5d532be35 + sha256: 1fff662907729e3b68c90232d7443b634b3b371763be5b15a43d6ad508742996 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust run: - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-base - r-ggplot2 - r-matlab @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Algorithm for testing significance of clustering in RNA-seq data.' - extra: identifiers: - biotools:sigfuge diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index 2ab6729cb69f2..dfc816069b8cf 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "siggenes" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bcba6cba0673211b0a534dcd3ce277b0c420b1e627848667f355cf3bd4cb08bd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 1e9b945bfdcefbe5357f2d7169af27d4f4d45a90842d623488c1a489909d2f5c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base run: - - bioconductor-biobase - - bioconductor-multtest + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).' - extra: identifiers: - biotools:siggenes diff --git a/recipes/bioconductor-sights/meta.yaml b/recipes/bioconductor-sights/meta.yaml index fe79c88a8cbac..b1ea4e4c27bf6 100644 --- a/recipes/bioconductor-sights/meta.yaml +++ b/recipes/bioconductor-sights/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "sights" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ba37ff6904e7e930e421de5fb634710be314b36f8bc6a79f247bbfad52dfdfc2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e40ca2d70559fe57a5fdd6f68aac764a76591964e69c855e3a6d5156bbceb981 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-qvalue >=2.2' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' - 'r-mass >=7.3' - 'r-reshape2 >=1.4' run: - - 'bioconductor-qvalue >=2.2' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | file LICENSE' summary: 'SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.' - extra: identifiers: - biotools:sights diff --git a/recipes/bioconductor-signer/meta.yaml b/recipes/bioconductor-signer/meta.yaml index 03867da896d5c..db608430b0b0b 100644 --- a/recipes/bioconductor-signer/meta.yaml +++ b/recipes/bioconductor-signer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "signeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,38 +8,43 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1628d75b3c6a728e43c97d67b1740a63cef07e56f68709eb5e495f73a1e4ad66 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 109d1cf32259ea818750d2377a4e8f8711f991b7b87358a857ab4f26f654a630 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - 'bioconductor-bsgenome >=1.36.3' - - bioconductor-genomicranges - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-class - - r-rcpparmadillo # not listed - r-nloptr - r-nmf - r-pmcmr + - r-rcpp + - 'r-rcpparmadillo >=0.7.100' run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - 'bioconductor-bsgenome >=1.36.3' - - bioconductor-genomicranges - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-class - - r-rcpparmadillo # not listed - r-nloptr - r-nmf - r-pmcmr + - r-rcpp + - 'r-rcpparmadillo >=0.7.100' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +52,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' - extra: identifiers: - biotools:signer diff --git a/recipes/bioconductor-sigpathway/meta.yaml b/recipes/bioconductor-sigpathway/meta.yaml index f1a1c6b0dffa4..ce3a7f2d33e80 100644 --- a/recipes/bioconductor-sigpathway/meta.yaml +++ b/recipes/bioconductor-sigpathway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "sigPathway" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5f4c88ae565e7160d27ce4b5aeeae1dcf2b0b4a5a0e6163618bf1df36e3ed6a2 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 202a3e4d2ea17945fffb67c3bb6ba484dd64c4285ae35656e1da27f84168f5be build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,9 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005)' - extra: identifiers: - biotools:sigpathway diff --git a/recipes/bioconductor-sim/meta.yaml b/recipes/bioconductor-sim/meta.yaml index 5c67ebdd9868d..4f00a02f0df17 100644 --- a/recipes/bioconductor-sim/meta.yaml +++ b/recipes/bioconductor-sim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "SIM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cecad837161de40bc56dc745e3fb1776f3804f77fa5eb44b285bb4160b3f40d8 + sha256: ad883a0998f04b9f446c12603f9d6abbe8a502ba6612394ba7a43fd5ba28bc3e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-globaltest - - bioconductor-quantsmooth + - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' - r-base - r-quantreg run: - - bioconductor-globaltest - - bioconductor-quantsmooth + - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' - r-base - r-quantreg - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Finds associations between two human genomic datasets.' - extra: identifiers: - biotools:sim diff --git a/recipes/bioconductor-simat/meta.yaml b/recipes/bioconductor-simat/meta.yaml index 7863bd9807cae..ee44840af4264 100644 --- a/recipes/bioconductor-simat/meta.yaml +++ b/recipes/bioconductor-simat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "SIMAT" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 10a494cbeea8d62ad4472fbfa1c6b52bddd65ebfd7b7e73bb03c3839d14da93d + sha256: 4ba6cf05252f63457d121e064b0dda6412d3fd93ae1d849469d9e350534f02c3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - - bioconductor-mzr + - 'bioconductor-mzr >=2.17.0,<2.19.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' - r-reshape2 run: - - bioconductor-mzr + - 'bioconductor-mzr >=2.17.0,<2.19.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: - '$R -e "library(''{{ name }}'')"' @@ -38,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.' - extra: identifiers: - biotools:simat diff --git a/recipes/bioconductor-simbindprofiles/conda_build_config.yaml b/recipes/bioconductor-simbindprofiles/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-simbindprofiles/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-simbindprofiles/meta.yaml b/recipes/bioconductor-simbindprofiles/meta.yaml index d5cda7e3aabcb..c607ae9e18623 100644 --- a/recipes/bioconductor-simbindprofiles/meta.yaml +++ b/recipes/bioconductor-simbindprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SimBindProfiles" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 02a93e3f96f80e7376577d7b32e2757340fb15d2a7eb2a710155cf42393a6d4a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2f3f0ce9098781eb8a6af8134b48a40b610e830212f2328590a430672dab8af4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-ringo + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-ringo >=1.44.0,<1.46.0' - r-base - r-mclust run: - - bioconductor-biobase - - bioconductor-limma - - bioconductor-ringo + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-ringo >=1.44.0,<1.46.0' - r-base - r-mclust test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'SimBindProfiles identifies common and unique binding regions in genome tiling array data. This package does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding.' - extra: identifiers: - biotools:simbindprofiles diff --git a/recipes/bioconductor-similarpeak/meta.yaml b/recipes/bioconductor-similarpeak/meta.yaml index 3b844b56ab768..2bc7afdf3a48d 100644 --- a/recipes/bioconductor-similarpeak/meta.yaml +++ b/recipes/bioconductor-similarpeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "similaRpeak" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ce8c0c3897fb3a1ab3a45c066d16d08f22cd005c25e6c0c5e4fa498101619590 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6a6e60857eaec4a37142a3ddb9cfa0fa112c7e7f55cbd876f4bc8e341e5bac4b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package calculates metrics which assign a level of similarity between ChIP-Seq profiles.' - extra: identifiers: - biotools:similarpeak diff --git a/recipes/bioconductor-simlr/meta.yaml b/recipes/bioconductor-simlr/meta.yaml index 4df427c84211e..03cabe1551c15 100644 --- a/recipes/bioconductor-simlr/meta.yaml +++ b/recipes/bioconductor-simlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SIMLR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ca5d129229aea762916dd09d9b80861ccf5dd757b31b2082429ea7d1b018cde9 + sha256: 872490b56557dd4752197508c4c995b5c9961c1503fa1f4c7459ccb573266eeb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-matrix @@ -33,15 +31,17 @@ requirements: - r-rcpp - r-rcppannoy - r-rspectra - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' - summary: ' Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical to identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. SIMLR is capable of separating known subpopulations more accurately in single-cell data sets than do existing dimension reduction methods. Additionally, SIMLR demonstrates high sensitivity and accuracy on high-throughput peripheral blood mononuclear cells (PBMC) data sets generated by the GemCode single-cell technology from 10x Genomics.' - + summary: ' In this package we provide implementations of both SIMLR and CIMLR. These methods were originally applied to single-cell and cancer genomic data, but they are in principle capable of effectively and efficiently learning similarities in all the contexts where diverse and heterogeneous statistical characteristics of the data make the problem harder for standard approaches.' extra: identifiers: - biotools:simlr diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml index 966c456518953..53b7e77c9f865 100644 --- a/recipes/bioconductor-simpintlists/meta.yaml +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "simpIntLists" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 74576f1b355473e76fd8f402a0e2f674821b8deaa3d3381187fc6d3ffa62b5e9 + sha256: 650cb3b0db9a7c139f5f318e07c2da0c55c274919af2492e37a66245027b2706 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it.' + + diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh index abc34406da8e7..a8b63176d1126 100644 --- a/recipes/bioconductor-simpintlists/post-link.sh +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="simpIntLists_1.14.0.tar.gz" +FN="simpIntLists_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/simpIntLists_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/simpIntLists_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/simpIntLists_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/simpIntLists_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.16.0_src_all.tar.gz" ) -MD5="38c2b32e4e24ca6b2761abf5a55e1d88" +MD5="7a876bfa3d4e4ae339b90c3f64934a51" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-simpleaffy/conda_build_config.yaml b/recipes/bioconductor-simpleaffy/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-simpleaffy/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-simpleaffy/meta.yaml b/recipes/bioconductor-simpleaffy/meta.yaml index 24f4f98b26e49..928eccd768d38 100644 --- a/recipes/bioconductor-simpleaffy/meta.yaml +++ b/recipes/bioconductor-simpleaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.54.0" %} +{% set version = "2.56.0" %} {% set name = "simpleaffy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cf3e8b25a2876f6cc24957bb1af086ecb0985b28497004365f3918fc3485212d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 66370f3b505208b22130c23e7e62aba8fb59e5a0441866536cfd28a5322d8f04 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-affy >=1.33.6' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.12' - - bioconductor-gcrma - - bioconductor-genefilter + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base run: - - 'bioconductor-affy >=1.33.6' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.1.12' - - bioconductor-gcrma - - bioconductor-genefilter + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...' - extra: identifiers: - biotools:simpleaffy diff --git a/recipes/bioconductor-sincell/meta.yaml b/recipes/bioconductor-sincell/meta.yaml index e810c6eb2fd7b..17ca23f32c6f2 100644 --- a/recipes/bioconductor-sincell/meta.yaml +++ b/recipes/bioconductor-sincell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "sincell" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,13 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5d352b3a64e1a9f806b1aca691feda5ef85adf9b08f7bfd29f84f7cfd364e21e + sha256: 68e2a512cbb5a77cbfa031a55e08310290d1265709c77dff08c3b214cb751bdf build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - r-cluster @@ -51,7 +49,10 @@ requirements: - r-scatterplot3d - r-statmod - r-tsp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -59,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.' - extra: identifiers: - biotools:sincell diff --git a/recipes/bioconductor-singlecellexperiment-scripts/conda_build_config.yaml b/recipes/bioconductor-singlecellexperiment-scripts/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-singlecellexperiment-scripts/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-singlecellexperiment-scripts/meta.yaml b/recipes/bioconductor-singlecellexperiment-scripts/meta.yaml index b1e860b05b0f4..71b784c0ba17f 100644 --- a/recipes/bioconductor-singlecellexperiment-scripts/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment-scripts/meta.yaml @@ -38,3 +38,4 @@ about: variety of software packages. license_family: GPL + diff --git a/recipes/bioconductor-singlecellexperiment/conda_build_config.yaml b/recipes/bioconductor-singlecellexperiment/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-singlecellexperiment/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-singlecellexperiment/meta.yaml b/recipes/bioconductor-singlecellexperiment/meta.yaml index 09f7e85d3fc43..b5e9632f7df0e 100644 --- a/recipes/bioconductor-singlecellexperiment/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SingleCellExperiment" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3a2be57963077d8fac43f40b7213489aae23e713259947db2e8a187e523447e4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6a5ea60b8a9dc442cf1dd9650803677711e6cac6ac6484cd461b14a12264e357 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base test: commands: diff --git a/recipes/bioconductor-sispa/meta.yaml b/recipes/bioconductor-sispa/meta.yaml index de642e164ca26..ceabed2786819 100644 --- a/recipes/bioconductor-sispa/meta.yaml +++ b/recipes/bioconductor-sispa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SISPA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,25 +8,26 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ebaef0d7c08d3a878adb616833b8b890c2d056c7163a14a223b05f42077768a3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 950d1bbe7d213f495c19433d33a862b2e1558effebe8e87b29bccfd38552e1fd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genefilter - - bioconductor-gsva + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' - r-base - r-changepoint - r-data.table - r-ggplot2 - r-plyr run: - - bioconductor-genefilter - - bioconductor-gsva + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-gsva >=1.28.0,<1.30.0' - r-base - r-changepoint - r-data.table @@ -39,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Sample Integrated Set Profile Analysis (SISPA) is a method designed to define sample groups with similar gene set enrichment profiles.' - extra: identifiers: - biotools:sispa diff --git a/recipes/bioconductor-sizepower/meta.yaml b/recipes/bioconductor-sizepower/meta.yaml index 9676c7d0235d4..af8d5ac95ec15 100644 --- a/recipes/bioconductor-sizepower/meta.yaml +++ b/recipes/bioconductor-sizepower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "sizepower" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7755439657156d01b428758b00ff6a751ebdcf7359a76fb87285922bd7c539a5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: bbd46a7d95922be2e6cff6c257ac8eec1a4cd1f7b577f59fca905747d4bc5fda build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice.' - extra: identifiers: - biotools:sizepower diff --git a/recipes/bioconductor-slgi/meta.yaml b/recipes/bioconductor-slgi/meta.yaml index 413b5468c5b02..1f982153c5fc5 100644 --- a/recipes/bioconductor-slgi/meta.yaml +++ b/recipes/bioconductor-slgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SLGI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 52a40f4cd475d29b4f6c4049b0711accda2842375327aeedb540a0ffebe714dc + sha256: 2ec40935be1e95ac7d750a2de571528b7f97a4a07e0c057dce35ab156c53d8e9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-go.db - - bioconductor-scisi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-scisi >=1.52.0,<1.54.0' - r-base - r-lattice run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-go.db - - bioconductor-scisi + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-scisi >=1.52.0,<1.54.0' - r-base - r-lattice test: @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A variety of data files and functions for the analysis of genetic interactions' - extra: identifiers: - biotools:slgi diff --git a/recipes/bioconductor-slqpcr/meta.yaml b/recipes/bioconductor-slqpcr/meta.yaml index 3e76b825d2210..b5cb3178ae120 100644 --- a/recipes/bioconductor-slqpcr/meta.yaml +++ b/recipes/bioconductor-slqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "SLqPCR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6b8ad2b5698c5bb7f808f8d5509f66eed454c58da08c352c2b8dc8b0a2d67b9a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6c1bf37f7be3fa85175cce64752102e0fda6f0f84ddf29a68b1d50315f8ae624 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH' - extra: identifiers: - biotools:slqpcr diff --git a/recipes/bioconductor-smap/meta.yaml b/recipes/bioconductor-smap/meta.yaml index 75f15270df20f..304ace1d4174f 100644 --- a/recipes/bioconductor-smap/meta.yaml +++ b/recipes/bioconductor-smap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "SMAP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b899716d625c4db5bffe1b2c90be62de38cbc5ed5fe5fa63eb394db0220e4e58 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a1b36f66d00d3d682cfcc1f4878fec0607bb49018664476e7ebe8a7470dc2362 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,9 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions and classes for DNA copy number profiling of array-CGH data' - extra: identifiers: - biotools:smap diff --git a/recipes/bioconductor-smite/meta.yaml b/recipes/bioconductor-smite/meta.yaml index 171747356cf01..df3db0fd1bd43 100644 --- a/recipes/bioconductor-smite/meta.yaml +++ b/recipes/bioconductor-smite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "SMITE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aa02ec7b0bf853fb2abbac77a20fd7b47b7ab492eb95d0363429a183dcd3afe8 + sha256: 8330f34bffd4221b8a60a0ea53604a8cbce6d0451588d324dfa14e2760e88947 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-bionet - - bioconductor-genelendatabase - - bioconductor-genomicranges - - bioconductor-goseq - - bioconductor-iranges - - bioconductor-kegg.db - - bioconductor-org.hs.eg.db - - bioconductor-reactome.db - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-bionet >=1.40.0,<1.42.0' + - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-goseq >=1.32.0,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-reactome.db >=1.64.0,<1.66.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-hmisc @@ -36,17 +36,17 @@ requirements: - r-plyr - r-scales run: - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-bionet - - bioconductor-genelendatabase - - bioconductor-genomicranges - - bioconductor-goseq - - bioconductor-iranges - - bioconductor-kegg.db - - bioconductor-org.hs.eg.db - - bioconductor-reactome.db - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-bionet >=1.40.0,<1.42.0' + - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-goseq >=1.32.0,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-reactome.db >=1.64.0,<1.66.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-ggplot2 - r-hmisc @@ -60,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.' - extra: identifiers: - biotools:smite diff --git a/recipes/bioconductor-snagee/meta.yaml b/recipes/bioconductor-snagee/meta.yaml index 8352c0ddb083d..8b63b25f65f3c 100644 --- a/recipes/bioconductor-snagee/meta.yaml +++ b/recipes/bioconductor-snagee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SNAGEE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 46c44312600bb877e6226a7d8af8f4dd25056794d59672b5ff2906411bea250c + sha256: 49e2489d1a3cbafe8a9896cd81407749ae9048d269acc7e169a8a9543bb6468c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-snageedata + - 'bioconductor-snageedata >=1.16.0,<1.18.0' - r-base run: - - bioconductor-snageedata + - 'bioconductor-snageedata >=1.16.0,<1.18.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.' - extra: identifiers: - biotools:snagee diff --git a/recipes/bioconductor-snageedata/meta.yaml b/recipes/bioconductor-snageedata/meta.yaml index dbca2d37bc470..26809aa617059 100644 --- a/recipes/bioconductor-snageedata/meta.yaml +++ b/recipes/bioconductor-snageedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SNAGEEdata" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7f4e18d174aa5a0f0021d75c94d9d55eed38339c4cbcbcb1fa2c9b0151c8be22 + sha256: a1fce00836421a20c84b5dc382f5b7b3d23cd1c26c8f82f79e566796a2128f3d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'SNAGEE data - gene list and correlation matrix' + + diff --git a/recipes/bioconductor-snageedata/post-link.sh b/recipes/bioconductor-snageedata/post-link.sh index 534261371438b..26e907605f770 100644 --- a/recipes/bioconductor-snageedata/post-link.sh +++ b/recipes/bioconductor-snageedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SNAGEEdata_1.14.0.tar.gz" +FN="SNAGEEdata_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/SNAGEEdata_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/SNAGEEdata_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/SNAGEEdata_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNAGEEdata_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.16.0_src_all.tar.gz" ) -MD5="874670b6d85d05def116df8b13ab806a" +MD5="a87c42dcdca6e1ea225cf906ceeda44d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-snm/meta.yaml b/recipes/bioconductor-snm/meta.yaml index e64e13189b1c1..72a0e8fc39d9d 100644 --- a/recipes/bioconductor-snm/meta.yaml +++ b/recipes/bioconductor-snm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "snm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 40e7c2f178af8c286e8807e2d1b11013334eaddccacead9cc3e3980307edd791 + sha256: 54c5b8e4ae9e7cc567208406e8269173e8b3ff21277bc5a6d3883323770cb50c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.' - extra: identifiers: - biotools:snm diff --git a/recipes/bioconductor-snpchip/conda_build_config.yaml b/recipes/bioconductor-snpchip/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-snpchip/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-snpchip/meta.yaml b/recipes/bioconductor-snpchip/meta.yaml index 20b14be1cd198..0e9602ec9a597 100644 --- a/recipes/bioconductor-snpchip/meta.yaml +++ b/recipes/bioconductor-snpchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "SNPchip" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,33 +8,34 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 809256fc6b445ef9f990bec0e05f7a183f40bdf0846cdcaa5409268b330207fc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9b28bd2c43d69308e4bb02714f877614d67e562384f48029b56ad22cf6e3a30a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-oligoclasses >=1.31.1' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-foreach - r-lattice run: - - bioconductor-biobase - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-oligoclasses >=1.31.1' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-foreach - r-lattice @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Functions for plotting SNP array data; maintained for historical reasons' - extra: identifiers: - biotools:snpchip diff --git a/recipes/bioconductor-snpediar/meta.yaml b/recipes/bioconductor-snpediar/meta.yaml index 829fa99791de7..93198cba2dacf 100644 --- a/recipes/bioconductor-snpediar/meta.yaml +++ b/recipes/bioconductor-snpediar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SNPediaR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89f5437c3a1c27750fee938f628acf3d6d230cd9ef9493362a65f4531629a9fe + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ffc3328dc2359af63ceca0bfa09d0173babf3c99cc12347255524436d1a442f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'SNPediaR provides some tools for downloading and parsing data from the SNPedia web site . The implemented functions allow users to import the wiki text available in SNPedia pages and to extract the most relevant information out of them. If some information in the downloaded pages is not automatically processed by the library functions, users can easily implement their own parsers to access it in an efficient way.' - extra: identifiers: - biotools:snpediar diff --git a/recipes/bioconductor-snphood/meta.yaml b/recipes/bioconductor-snphood/meta.yaml index a0193961a18f2..c33a948a3294f 100644 --- a/recipes/bioconductor-snphood/meta.yaml +++ b/recipes/bioconductor-snphood/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SNPhood" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f9c0ca9c14cf1c3c22152654058f19a7145a800a28ea384617f671d97ee54e20 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6a9e530c54fb6cec5107f81a85490dc596fc6986d546797ba2506d4ec9d2de82 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-deseq2 - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-checkmate - r-cluster @@ -39,17 +40,17 @@ requirements: - r-reshape2 - r-scales run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-deseq2 - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-checkmate - r-cluster @@ -67,7 +68,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly *Bioconductor* R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest.' - extra: identifiers: - biotools:snphood diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml index fa5a21da49508..722cb62101b4c 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: b6c6ae8d3a866501146e325d40dc1695b26b522c6f9d063218fc6466bbd5b57b build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - 'bioconductor-bsgenome >=1.43.4' - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base run: - - bioconductor-biocgenerics - - 'bioconductor-bsgenome >=1.43.4' - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - wget test: @@ -40,3 +41,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' + + diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index d3652c33a2a71..9e2167869d148 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "SNPRelate" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7166a26e89d9dfd300e3fb6d6a2beed21946c5832015ac1393dbcfbfbc94a017 + sha256: 994975539df83f04af7fbda4eb0bad506138c755c453016090e545738e100f39 build: - number: 1 - skip: True # [osx] + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - 'bioconductor-gdsfmt >=1.8.3' + - 'bioconductor-gdsfmt >=1.16.0,<1.18.0' - r-base run: - - 'bioconductor-gdsfmt >=1.8.3' + - 'bioconductor-gdsfmt >=1.16.0,<1.18.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,3 +34,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.' + + diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index e9a1a49aaa2ac..254d4206a503f 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -21,17 +21,20 @@ build: requirements: host: - - bioconductor-biocgenerics - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-matrix - r-survival run: - - bioconductor-biocgenerics - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-matrix - r-survival + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.' - extra: identifiers: - biotools:snpstats diff --git a/recipes/bioconductor-soggi/meta.yaml b/recipes/bioconductor-soggi/meta.yaml index de1e30dde35df..6d08f6f42acd6 100644 --- a/recipes/bioconductor-soggi/meta.yaml +++ b/recipes/bioconductor-soggi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "soGGi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,45 +8,46 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b14bc2fb1e11b666ac3b9402eaff3b3b925a992e53d864aba558f9550af6974a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f675d48906f055f72a0665b1dad087d7e500176e2e40c640288a12a6166e949b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-chipseq - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-reshape2 run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-chipseq - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-preprocesscore - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-reshape2 @@ -57,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.' - extra: identifiers: - biotools:soggi diff --git a/recipes/bioconductor-somaticsignatures/conda_build_config.yaml b/recipes/bioconductor-somaticsignatures/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-somaticsignatures/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-somaticsignatures/meta.yaml b/recipes/bioconductor-somaticsignatures/meta.yaml index fd4906efdc720..3f809c2eba1e1 100644 --- a/recipes/bioconductor-somaticsignatures/meta.yaml +++ b/recipes/bioconductor-somaticsignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "SomaticSignatures" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,39 +8,40 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 102d737f91b4f47189c8d7391667bf2494c2d7ec4b5f4c9ddab713efe69cfe80 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: dfb8755b115406e213873fae3241c9422a0c15ad17596a9c859177e8f24a8c95 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-iranges - - bioconductor-pcamethods - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-pcamethods >=1.72.0,<1.74.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 run: - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-ggbio - - bioconductor-iranges - - bioconductor-pcamethods - - bioconductor-s4vectors - - bioconductor-variantannotation + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-ggbio >=1.28.5,<1.30.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-pcamethods >=1.72.0,<1.74.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-ggplot2 - r-nmf @@ -53,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.' - extra: identifiers: - biotools:somaticsignatures diff --git a/recipes/bioconductor-spacepac/meta.yaml b/recipes/bioconductor-spacepac/meta.yaml index 65a5fd74dac33..279c23646d8c5 100644 --- a/recipes/bioconductor-spacepac/meta.yaml +++ b/recipes/bioconductor-spacepac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.3" %} {% set name = "SpacePAC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d6cc73719fb06dec064fac3fb91f88c077e90ef573fc2e58eed4d83f8df988b5 + sha256: 7a156227d40dc50a8451b2df4b5960b0d3b6cfde00c53c128046ad00819049be build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-ipac + - 'bioconductor-ipac >=1.24.2,<1.26.0' - r-base run: - - bioconductor-ipac + - 'bioconductor-ipac >=1.24.2,<1.26.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein''s tertiary structure.' - extra: identifiers: - biotools:spacepac diff --git a/recipes/bioconductor-specl/meta.yaml b/recipes/bioconductor-specl/meta.yaml index 7ab9e6cc055d1..5660b9c77d7a6 100644 --- a/recipes/bioconductor-specl/meta.yaml +++ b/recipes/bioconductor-specl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "specL" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,38 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3746570731e14d2ee38a6409a92c7f4f6d374efb060acc0fa1d2b43b3e80730d + sha256: e65998f7276f9d1b3680ff60a8c71a00faa1624ffe81138ee75d394d056767fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('cxx') }} host: - r-base - 'r-dbi >=0.5.1' - - 'r-protviz >=0.2.31' - - 'r-rcpp >=0.12.4' + - 'r-protviz >=0.2.45' - 'r-rsqlite >=1.1.2' - 'r-seqinr >=3.3.3' run: - r-base - 'r-dbi >=0.5.1' - - 'r-protviz >=0.2.31' - - 'r-rcpp >=0.12.4' + - 'r-protviz >=0.2.45' - 'r-rsqlite >=1.1.2' - 'r-seqinr >=3.3.3' - - libcxx # [osx] test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'specL provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.' - + summary: 'provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.' extra: identifiers: - biotools:specl diff --git a/recipes/bioconductor-specond/meta.yaml b/recipes/bioconductor-specond/meta.yaml index 4e55b0fc78d38..a476f0f28821c 100644 --- a/recipes/bioconductor-specond/meta.yaml +++ b/recipes/bioconductor-specond/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SpeCond" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5d13f7c93dcebe3f36c8f7697dd0306b27a9f8ec524373ba85da112164ffa4cc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f5d050e5f6e4a17dcd52277e03d92448285a15350ef4ae2ae366b725d6ea750b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.15.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-fields - 'r-hwriter >=1.1' - 'r-mclust >=3.3.1' - r-rcolorbrewer run: - - 'bioconductor-biobase >=1.15.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-fields - 'r-hwriter >=1.1' @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>=2)' summary: 'This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.' - extra: identifiers: - biotools:specond diff --git a/recipes/bioconductor-spem/meta.yaml b/recipes/bioconductor-spem/meta.yaml index e1aa6cd1ef9d5..019cb05cb94d5 100644 --- a/recipes/bioconductor-spem/meta.yaml +++ b/recipes/bioconductor-spem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SPEM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aa144c35fc6c5d1bff35cfd00fad9e5e4bb426a6579bb698ec88c7e95d90f715 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e8b912777376c86f0cf4de3e6a292a8a4c54cbb70b15b5a5ff46f74779308640 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rsolnp run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-rsolnp test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package can optimize the parameter in S-system models given time series data' - extra: identifiers: - biotools:spem diff --git a/recipes/bioconductor-spia/meta.yaml b/recipes/bioconductor-spia/meta.yaml index 911b995613da3..9eba2082d3379 100644 --- a/recipes/bioconductor-spia/meta.yaml +++ b/recipes/bioconductor-spia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "SPIA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 03f7906c3e07165c1f3021652ea2a015a564fde28b6629384aed6d20bfd95b54 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ad6fbe3f4aa9bb5c10e466f7689f8914d4bcf99a8ad008e0cd1f872ea92dec09 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-kegggraph + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - r-base run: - - bioconductor-kegggraph + - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.' - extra: identifiers: - biotools:spia diff --git a/recipes/bioconductor-spidermir/meta.yaml b/recipes/bioconductor-spidermir/meta.yaml index 00f9047d42963..b9f9c572f598b 100644 --- a/recipes/bioconductor-spidermir/meta.yaml +++ b/recipes/bioconductor-spidermir/meta.yaml @@ -1,31 +1,28 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "SpidermiR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 310f133714be1cbd942fae6bc17be663ccedac5575a44dadc46cb1526e769990 - + sha256: 92b0a36ebdbd3e0224ec23c72788a1db35e7087bc4b9ee30325882f5d12c0b1f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-mirnatap - - bioconductor-mirnatap.db - - bioconductor-org.hs.eg.db - - bioconductor-tcgabiolinks + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-mirnatap >=1.14.0,<1.16.0' + - 'bioconductor-mirnatap.db >=0.99.10,<0.101.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' - r-base - r-gdata - r-ggplot2 @@ -38,11 +35,11 @@ requirements: - r-networkd3 - r-visnetwork run: - - bioconductor-annotationdbi - - bioconductor-mirnatap - - bioconductor-mirnatap.db - - bioconductor-org.hs.eg.db - - bioconductor-tcgabiolinks + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-mirnatap >=1.14.0,<1.16.0' + - 'bioconductor-mirnatap.db >=0.99.10,<0.101.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' - r-base - r-gdata - r-ggplot2 @@ -54,16 +51,13 @@ requirements: - r-latticeextra - r-networkd3 - r-visnetwork - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miR2Disease,miRTar, miRTarBase, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).' - extra: identifiers: - biotools:spidermir diff --git a/recipes/bioconductor-spikeli/meta.yaml b/recipes/bioconductor-spikeli/meta.yaml index 6c8caab80e36c..4dc518da45595 100644 --- a/recipes/bioconductor-spikeli/meta.yaml +++ b/recipes/bioconductor-spikeli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "spikeLI" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 48bc37515e4f782493a179b924831c45e91206889c86a71f06d5c92b13edd101 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 58d8c8f0d44e49d4970ca194fa389c5c26f832a79e1b92f3e2b5b6b16c96875f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).' - extra: identifiers: - biotools:spikeli diff --git a/recipes/bioconductor-spktools/meta.yaml b/recipes/bioconductor-spktools/meta.yaml index 3b4b7638da413..b95e943dc4696 100644 --- a/recipes/bioconductor-spktools/meta.yaml +++ b/recipes/bioconductor-spktools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "spkTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c7f2cb4d096282f8f652942d44a890a2bf04e5c9b186f459c6a830c3d0d9fe6e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0c82ed79e6abd6f2ff8224e37e9afff7fe98e7b0392ec6a9a94221dc89b791ab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-gtools - r-rcolorbrewer @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains functions that can be used to compare expression measures on different array platforms.' - extra: identifiers: - biotools:spktools diff --git a/recipes/bioconductor-splatter/conda_build_config.yaml b/recipes/bioconductor-splatter/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-splatter/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml index 74b6f1c22a5ee..23c6dd1df438e 100644 --- a/recipes/bioconductor-splatter/meta.yaml +++ b/recipes/bioconductor-splatter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.3" %} {% set name = "splatter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,39 +8,42 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: af641527ae3fb21966d11201fa227bf0934973c6b5cfcb38bac52a576b485745 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5f163d95e7e1e143c7ad453bbe21e04903cc783a87aa1547e35ac9583ee558a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-scater - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-scater >=1.8.4,<1.10.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-akima - r-base - r-checkmate + - r-crayon - r-fitdistrplus - r-ggplot2 - r-locfit - r-matrixstats - r-scales run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-scater - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-scater >=1.8.4,<1.10.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-akima - r-base - r-checkmate + - r-crayon - r-fitdistrplus - r-ggplot2 - r-locfit @@ -53,3 +56,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.' + + diff --git a/recipes/bioconductor-splicegear/meta.yaml b/recipes/bioconductor-splicegear/meta.yaml index a2494d1f5d0a3..8be060082d104 100644 --- a/recipes/bioconductor-splicegear/meta.yaml +++ b/recipes/bioconductor-splicegear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "splicegear" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a4926dd0bf30255bcdd04c8917b8f6551db505a588a59e1f53449f7343a28744 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a72f0374a574a265bb22dc66fe9e0c02d316347aaad8d7ba166b6ff57b9cd08d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-xml run: - - bioconductor-annotate - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-xml test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'A set of tools to work with alternative splicing' - extra: identifiers: - biotools:splicegear diff --git a/recipes/bioconductor-splicer/meta.yaml b/recipes/bioconductor-splicer/meta.yaml index 34fbc14e4a442..dcb44cf4bd7f5 100644 --- a/recipes/bioconductor-splicer/meta.yaml +++ b/recipes/bioconductor-splicer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "spliceR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ed29da566b588cf326070cce746d6165e5eed22afe49415c2341138719917cea + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9106991819b538b1dda7b1861cd41b1a169ff9bc59f94cfc4c913f4c440a1a91 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cummerbund - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-cummerbund >=2.22.0,<2.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-plyr - r-rcolorbrewer - r-venndiagram run: - - bioconductor-cummerbund - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer + - 'bioconductor-cummerbund >=2.22.0,<2.24.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - r-base - r-plyr - r-rcolorbrewer - r-venndiagram + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.' - extra: identifiers: - biotools:splicer diff --git a/recipes/bioconductor-splicinggraphs/meta.yaml b/recipes/bioconductor-splicinggraphs/meta.yaml index 277b0ef2a833f..d8191c6608540 100644 --- a/recipes/bioconductor-splicinggraphs/meta.yaml +++ b/recipes/bioconductor-splicinggraphs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SplicingGraphs" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,37 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 03437c1db8bc082586863c37566709c00458e0a2d4f967d5ad443159d81671df + sha256: 3e530ab3b49b1894739a1ade79535d625d95aa276fa78a69514fbe255be6eb15 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=1.1.22' - - 'bioconductor-genomicfeatures >=1.17.13' - - 'bioconductor-genomicranges >=1.23.21' - - bioconductor-graph - - 'bioconductor-iranges >=2.3.21' - - 'bioconductor-rgraphviz >=2.3.7' - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-igraph run: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - 'bioconductor-genomicalignments >=1.1.22' - - 'bioconductor-genomicfeatures >=1.17.13' - - 'bioconductor-genomicranges >=1.23.21' - - bioconductor-graph - - 'bioconductor-iranges >=2.3.21' - - 'bioconductor-rgraphviz >=2.3.7' - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-igraph test: @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.' - extra: identifiers: - biotools:splicinggraphs diff --git a/recipes/bioconductor-splinetimer/meta.yaml b/recipes/bioconductor-splinetimer/meta.yaml index 829216d53b3d0..8180d9741c187 100644 --- a/recipes/bioconductor-splinetimer/meta.yaml +++ b/recipes/bioconductor-splinetimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "splineTimeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 248c8319bd027297f9de66784e59cafffa6b936d30fe6585213076f4d9a7a18b + sha256: 99cd3c02d5683045e4530a7cdafb75d87a26de1587e018671b96c3fb900d086d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-fis - - bioconductor-gseabase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-fis >=1.8.0,<1.10.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - 'r-genenet >=1.2.13' - r-gtools - r-igraph - 'r-longitudinal >=1.1.12' run: - - bioconductor-biobase - - bioconductor-fis - - bioconductor-gseabase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-fis >=1.8.0,<1.10.0' + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - 'r-genenet >=1.2.13' - r-gtools @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.' - extra: identifiers: - biotools:splinetimer diff --git a/recipes/bioconductor-splinter/meta.yaml b/recipes/bioconductor-splinter/meta.yaml index e17d930a110ee..ab98d9950ae06 100644 --- a/recipes/bioconductor-splinter/meta.yaml +++ b/recipes/bioconductor-splinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SPLINTER" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,41 +8,42 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89a6a4e0b505b36857f8ffd096abc041c0e94b7b9f0f86ac91fc52ce76acaa1b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5ca730f8563121515a26a6654a67a4c97b3eab20e5f6b664a7fe6104e5e18d4d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome.mmusculus.ucsc.mm9 - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-seqlogo + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-base - r-ggplot2 - r-plyr run: - - bioconductor-biomart - - bioconductor-biostrings - - bioconductor-bsgenome.mmusculus.ucsc.mm9 - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-seqlogo + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - r-base - r-ggplot2 - r-plyr @@ -53,7 +54,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.' - extra: identifiers: - biotools:splinter diff --git a/recipes/bioconductor-splots/meta.yaml b/recipes/bioconductor-splots/meta.yaml index 133227196ec29..d84a97b861743 100644 --- a/recipes/bioconductor-splots/meta.yaml +++ b/recipes/bioconductor-splots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "splots" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f6e64339078804c72563e9c2e218b04080eb0e816587d840317ee43a6872ec27 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 840dcb623410683d24adea404f1cfb0285ad6f41c9c653af010d09dbbbc0e204 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The splots package provides the plotScreen function for visualising data in microtitre plate or slide format.' - extra: identifiers: - biotools:splots diff --git a/recipes/bioconductor-spotsegmentation/meta.yaml b/recipes/bioconductor-spotsegmentation/meta.yaml index d5183a963ff77..0e641adcf0490 100644 --- a/recipes/bioconductor-spotsegmentation/meta.yaml +++ b/recipes/bioconductor-spotsegmentation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "spotSegmentation" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b782a3e1088d2447d8e3d912888b80deeb53a1336a74ec287426287bc67cb04a + sha256: 3646b09ff82756759bd871ededbec0888770985df612969b884afbc629eaa0d9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington.' - extra: identifiers: - biotools:spotsegmentation diff --git a/recipes/bioconductor-squadd/meta.yaml b/recipes/bioconductor-squadd/meta.yaml index a2151ae316793..ba17fc24d9cdd 100644 --- a/recipes/bioconductor-squadd/meta.yaml +++ b/recipes/bioconductor-squadd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "SQUADD" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a6fd241bf951747ed80541bab0948aba5d451b6ab63395da7e04abd5c14d23fc + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 26ae39028e1b9e5d181377f13b029fbd865a3dfc469c2a75d7534cb04700c58b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package SQUADD is a SQUAD add-on. It permits to generate SQUAD simulation matrix, prediction Heat-Map and Correlation Circle from PCA analysis.' - extra: identifiers: - biotools:squadd diff --git a/recipes/bioconductor-sradb/meta.yaml b/recipes/bioconductor-sradb/meta.yaml index 09c4bcc68d35d..0f402afd60a59 100644 --- a/recipes/bioconductor-sradb/meta.yaml +++ b/recipes/bioconductor-sradb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.37.0" %} +{% set version = "1.42.2" %} {% set name = "SRAdb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3573abf8ed55a0e639196e02a15c96b41d965fd0527b890500c4803fa12c88c8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8a2e6401e9df35bc644c2d5e16ba2bc53c6b7fcbd01570939e236c9ceedb3190 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-geoquery - - bioconductor-graph + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-rcurl - r-rsqlite run: - - bioconductor-geoquery - - bioconductor-graph + - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-rcurl - r-rsqlite @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.' - extra: identifiers: - biotools:sradb diff --git a/recipes/bioconductor-srap/meta.yaml b/recipes/bioconductor-srap/meta.yaml index 75fbbd372e8bb..fddf335ce2a6d 100644 --- a/recipes/bioconductor-srap/meta.yaml +++ b/recipes/bioconductor-srap/meta.yaml @@ -1,48 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sRAP" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: babcb47f63435eb590d1be5d165ee49520ff3e7c78a2abb7409e854cad50017a - + sha256: 3dcc600558319df54168bbd97db299ea3f34d17a1d2f0b24b46d6d7405ef7a02 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-qvalue + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-gplots - r-pls - r-rocr - r-writexls run: - - bioconductor-qvalue + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-gplots - r-pls - r-rocr - r-writexls - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.' - extra: identifiers: - biotools:srap diff --git a/recipes/bioconductor-sscore/conda_build_config.yaml b/recipes/bioconductor-sscore/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-sscore/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-sscore/meta.yaml b/recipes/bioconductor-sscore/meta.yaml index b80d9480d47ba..907bc53922241 100644 --- a/recipes/bioconductor-sscore/meta.yaml +++ b/recipes/bioconductor-sscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "sscore" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 08c026fd36801a55c4f2fb4ef9cd669256bd7aea2529c97dd810e86b964b7a47 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 54a2d21ec56869fa581999cb2567df7e501f8f132e7005e122822b084a42dc5f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-affyio + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' - r-base run: - - bioconductor-affy - - bioconductor-affyio + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affyio >=1.50.0,<1.52.0' - r-base test: commands: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains an implementation of the S-Score algorithm as described by Zhang et al (2002).' - extra: identifiers: - biotools:sscore diff --git a/recipes/bioconductor-sscu/meta.yaml b/recipes/bioconductor-sscu/meta.yaml index 8605e077bdd93..2825e28952ffa 100644 --- a/recipes/bioconductor-sscu/meta.yaml +++ b/recipes/bioconductor-sscu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "sscu" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7a970ddf0409e67e5f92b641cafe4bc563f3493d1320b1ff4e36f68e324344a9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d6f279121057630315716894488f8120bcd1f7d2e6811db2079189144bfb0361 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.16.1' - - 'bioconductor-biostrings >=2.36.4' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - 'r-seqinr >=3.1-3' run: - - 'bioconductor-biocgenerics >=0.16.1' - - 'bioconductor-biostrings >=2.36.4' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - r-base - 'r-seqinr >=3.1-3' test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp''s method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) The package can detect the strength of translational accuracy selection by Akashi''s test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi''s test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function low_frequency_op in the package. The function try to find the low frequency optimal codons, among all the optimal codons identified by the op_highly function.' - extra: identifiers: - biotools:sscu diff --git a/recipes/bioconductor-sseq/meta.yaml b/recipes/bioconductor-sseq/meta.yaml index 140903f3034aa..c449af14c3bb0 100644 --- a/recipes/bioconductor-sseq/meta.yaml +++ b/recipes/bioconductor-sseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "sSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9062aea637fa7946e3f8f334b6b8307b51923c64db1b2919dc1f2fdf52bc4a22 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2a7f6504753c39258268fe006ef413117e1e75919e924cc432e7bf63189fba8b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.' - extra: identifiers: - biotools:sseq diff --git a/recipes/bioconductor-ssize/meta.yaml b/recipes/bioconductor-ssize/meta.yaml index 4e96754c526cd..ba90dc500f9cf 100644 --- a/recipes/bioconductor-ssize/meta.yaml +++ b/recipes/bioconductor-ssize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "ssize" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 235713dc8643e1facf6bde9aefe81e25f2b7b65850bd0c66494e1b46287f8109 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0645ada9237bfa91449bdeb168e6c3c08b822cdfe5fbe28f6b11b31e58002417 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions for computing and displaying sample size information for gene expression arrays.' - extra: identifiers: - biotools:ssize diff --git a/recipes/bioconductor-sspa/meta.yaml b/recipes/bioconductor-sspa/meta.yaml index bc841d8803c1a..2c0ba527c4efc 100644 --- a/recipes/bioconductor-sspa/meta.yaml +++ b/recipes/bioconductor-sspa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "SSPA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d23f7b85e64117c173a01512d0c2fb666f1021aa0d0f0708e6e5499f92900437 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c7f1ac6c3727cfe580c91d59fcbace4336332cce7bb86f87961465d9a3af8c06 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-lattice run: - - bioconductor-limma - - bioconductor-qvalue + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-lattice + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'General Sample size and power analysis for microarray and next-generation sequencing data.' - extra: identifiers: - biotools:sspa diff --git a/recipes/bioconductor-ssviz/meta.yaml b/recipes/bioconductor-ssviz/meta.yaml index 6ac347bfff719..62cc52e8dd8c0 100644 --- a/recipes/bioconductor-ssviz/meta.yaml +++ b/recipes/bioconductor-ssviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ssviz" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bc231bc2c7314f07d698931cf855eb05302bd1ba1d483191aace478b2fde10e1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: bfde64c8c08255da4c4a84b208667a08edd6e472bdd7b585f12944d1bc686eb3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biostrings - - bioconductor-rsamtools + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape run: - - bioconductor-biostrings - - bioconductor-rsamtools + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-ggplot2 - r-rcolorbrewer @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Small RNA sequencing viewer' - extra: identifiers: - biotools:ssviz diff --git a/recipes/bioconductor-stan/meta.yaml b/recipes/bioconductor-stan/meta.yaml index 5ad467ad10604..65c4e1673b180 100644 --- a/recipes/bioconductor-stan/meta.yaml +++ b/recipes/bioconductor-stan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "STAN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,37 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 57f631c2de8398df6292654cfd66ee1d873afa1845e6d9cc657b353daea14a25 + sha256: 2c148979f22929c741fabc0068c60e2f154d9d3ebaeb47fde168ec22b2b71fed build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-poilog - r-rsolnp run: - - bioconductor-biocgenerics - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-poilog - r-rsolnp - - libcxx # [osx] + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. STAN (genomic STate ANnotation) implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data (e.g. continuous, discrete, binary). STAN de novo learns and annotates the genome into a given number of ''genomic states''. The ''genomic states'' may for instance reflect distinct genome-associated protein complexes (e.g. ''transcription states'') or describe recurring patterns of chromatin features (referred to as ''chromatin states''). Unlike other tools, STAN also allows for the integration of strand-specific (e.g. RNA) and non-strand-specific data (e.g. ChIP).' - extra: identifiers: - biotools:stan diff --git a/recipes/bioconductor-starank/conda_build_config.yaml b/recipes/bioconductor-starank/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-starank/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-starank/meta.yaml b/recipes/bioconductor-starank/meta.yaml index cd57271e50d66..136824680ce8b 100644 --- a/recipes/bioconductor-starank/meta.yaml +++ b/recipes/bioconductor-starank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "staRank" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fee509074b9608bb595ebf4ae34f8281efbf977eb462a29841b3b7c2b4a1f838 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 74c3206b29d28d3ff9e3d1df58db7e4f9449968ac4f851098ae2dd47dfcbb2fa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cellhts2 + - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' - r-base run: - - bioconductor-cellhts2 + - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' - r-base test: commands: @@ -29,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.' - extra: identifiers: - biotools:starank diff --git a/recipes/bioconductor-starbiotrek/meta.yaml b/recipes/bioconductor-starbiotrek/meta.yaml index 427de084b928f..b39ddd34a254e 100644 --- a/recipes/bioconductor-starbiotrek/meta.yaml +++ b/recipes/bioconductor-starbiotrek/meta.yaml @@ -1,52 +1,47 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "StarBioTrek" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d28e761fcbaa9a7d5e7737d798d5fe3502bf8a70a3ffb32a454d8adf3728fe8c - + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: eb4b648ac31d9fbe67f6197360aa1f3b33d37d91be427c3fddd3994524993d0f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-annotationdbi - - bioconductor-keggrest - - bioconductor-org.hs.eg.db - - bioconductor-spidermir + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-spidermir >=1.10.0,<1.12.0' - r-base - r-e1071 - r-igraph - r-rocr run: - - bioconductor-annotationdbi - - bioconductor-keggrest - - bioconductor-org.hs.eg.db - - bioconductor-spidermir + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-spidermir >=1.10.0,<1.12.0' - r-base - r-e1071 - r-igraph - r-rocr - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.' - extra: identifiers: - biotools:starbiotrek diff --git a/recipes/bioconductor-starr/conda_build_config.yaml b/recipes/bioconductor-starr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-starr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-starr/meta.yaml b/recipes/bioconductor-starr/meta.yaml index f97b678e277d7..24007b43c89f6 100644 --- a/recipes/bioconductor-starr/meta.yaml +++ b/recipes/bioconductor-starr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Starr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,30 +8,35 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d8a982b3c45dd15a5a8a0b9b28ae9a29f84fcb2ecee381ed125e47b151ba0c73 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 07cf29e78ad186d057937032b59679424e8032656641cd75992783e205cdb474 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affxparser - - bioconductor-affy - - bioconductor-ringo - - bioconductor-zlibbioc + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-ringo >=1.44.0,<1.46.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-mass - r-pspline run: - - bioconductor-affxparser - - bioconductor-affy - - bioconductor-ringo - - bioconductor-zlibbioc + - 'bioconductor-affxparser >=1.52.0,<1.54.0' + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-ringo >=1.44.0,<1.46.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-mass - r-pspline + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.' - extra: identifiers: - biotools:starr diff --git a/recipes/bioconductor-stategra/conda_build_config.yaml b/recipes/bioconductor-stategra/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-stategra/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-stategra/meta.yaml b/recipes/bioconductor-stategra/meta.yaml index ecc42576f937b..b437decc66f9f 100644 --- a/recipes/bioconductor-stategra/meta.yaml +++ b/recipes/bioconductor-stategra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.1" %} {% set name = "STATegRa" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6572a7923392e7d43ece9c388039bf785c9def605f9a107b17f23e5622646222 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a86d2272b62d2a5d1bd50688d3eacbdd53d41a40ec5c19e9a74e6900d070e48a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-calibrate - r-foreach @@ -29,10 +30,10 @@ requirements: - r-gridextra - r-mass run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-calibrate - r-foreach @@ -47,7 +48,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Classes and tools for multi-omics data integration.' - extra: identifiers: - biotools:stategra diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml index e850f106cd04d..dfe27af2b3ef6 100644 --- a/recipes/bioconductor-stemhypoxia/meta.yaml +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "stemHypoxia" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 883e0099b7dafeb1d58e254315b228346b5f7d5afba360f0ebf99db44277d650 + sha256: 5ad7114a399dfbeeee2d5500c515cced17c6953c54cbdb2d682e4a3fa9e66b5c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -29,3 +29,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Expression profiling using microarray technology to prove if ''Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium'' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761.' + + diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh index e0cbfd5b6d955..5d9b756714bf1 100644 --- a/recipes/bioconductor-stemhypoxia/post-link.sh +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="stemHypoxia_1.14.0.tar.gz" +FN="stemHypoxia_1.16.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/stemHypoxia_1.14.0.tar.gz" - "https://bioarchive.galaxyproject.org/stemHypoxia_1.14.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.14.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/stemHypoxia_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/stemHypoxia_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.16.0_src_all.tar.gz" ) -MD5="ce1e542ac7f851642c8f55e25da1312a" +MD5="b26a9742c2c354c375fb4231b922d439" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-stepnorm/meta.yaml b/recipes/bioconductor-stepnorm/meta.yaml index d2337cac14154..5139543063c1b 100644 --- a/recipes/bioconductor-stepnorm/meta.yaml +++ b/recipes/bioconductor-stepnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "stepNorm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ae1a2aa19b69e4f6f78621880c2299fcc03654d86b8444132624797c8730cd81 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 62e942c1cd6b34c3f172d383f3db4efc3def651d9b0af7dc68ec8934fcde91fb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-marray + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-mass run: - - bioconductor-marray + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-mass test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Stepwise normalization functions for cDNA microarray data.' - extra: identifiers: - biotools:stepnorm diff --git a/recipes/bioconductor-streamer/meta.yaml b/recipes/bioconductor-streamer/meta.yaml index f9dbc4437704d..a357d7ebfc547 100644 --- a/recipes/bioconductor-streamer/meta.yaml +++ b/recipes/bioconductor-streamer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "Streamer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,28 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 984ed60ddf88c7c8c0f8bd42cc637ab96c592f277c3ee71c8015a745c5dbb2ae + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7a5de406c952a62b86152fb5a853a51dfe1248ba84d6815b9a8826166676b201 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-graph - - bioconductor-rbgl + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -33,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is ''streamed'' from disk into R via a `producer'' and through a series of `consumers'' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.' - extra: identifiers: - biotools:streamer diff --git a/recipes/bioconductor-stringdb/meta.yaml b/recipes/bioconductor-stringdb/meta.yaml index db73c8b468ad5..51e651b670956 100644 --- a/recipes/bioconductor-stringdb/meta.yaml +++ b/recipes/bioconductor-stringdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "STRINGdb" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6e1de815279199136df7efd8acac0d0f6ddd945780fb0799b85fd0cb48973043 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 89c2e5c96083c388526f3dd254e3085fe3b9e185965cf67d691b0264b37df05d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The STRINGdb package provides a R interface to the STRING protein-protein interactions database (http://www.string-db.org).' - extra: identifiers: - biotools:stringdb diff --git a/recipes/bioconductor-subseq/meta.yaml b/recipes/bioconductor-subseq/meta.yaml index 0f47b410907f9..efdd54ab5bb7c 100644 --- a/recipes/bioconductor-subseq/meta.yaml +++ b/recipes/bioconductor-subseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "subSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 64d462fe68a6858a4aeae7b47c8884a0bd9a0310d17d92c965db5a4899e338fd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d06f05a1dbe1ba52e25dc1a46b2feff337542b632e049108d9488984442525d3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-qvalue >=1.99' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-data.table - r-digest @@ -27,8 +28,8 @@ requirements: - r-magrittr - r-tidyr run: - - bioconductor-biobase - - 'bioconductor-qvalue >=1.99' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-data.table - r-digest @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Subsampling of high throughput sequencing count data for use in experiment design and analysis.' - extra: identifiers: - biotools:subseq diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index 1979b7c706be7..abe39b1aeeec0 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "SummarizedExperiment" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,33 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aeeec5e6a5caacb209ba11e245dc5f454d7359eb04d615860482a00928ca2180 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 81dacf10280d5f6e79a5eed84c1ccaac7cf536a47f5b569e4a676bcc12ed7f6c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - 'bioconductor-delayedarray >=0.3.20' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.17' - - 'bioconductor-s4vectors >=0.13.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-matrix run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - 'bioconductor-delayedarray >=0.3.20' - - 'bioconductor-genomeinfodb >=1.13.1' - - 'bioconductor-genomicranges >=1.29.14' - - 'bioconductor-iranges >=2.11.17' - - 'bioconductor-s4vectors >=0.13.13' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-matrix test: @@ -43,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.' - extra: identifiers: - biotools:summarizedexperiment diff --git a/recipes/bioconductor-suprahex/meta.yaml b/recipes/bioconductor-suprahex/meta.yaml index 1760ef78cdeb3..1e444251f9a83 100644 --- a/recipes/bioconductor-suprahex/meta.yaml +++ b/recipes/bioconductor-suprahex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "supraHex" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7614a20ab8ad0c7c4e658ada33eef194f7873d62bd366aae0de98eb1286c9082 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3f02f75500f78197af715e1be91a0ce0d3c3748ee2d5ef9ee769ee086a12dde7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics input data. The supraHex is able to carry out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. So with supraHex, it is also possible to carry out multilayer omics data comparisons. Newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships. Uniquely to this package, users can ultrafastly understand any tabular omics data, both scientifically and artistically, especially in a sample-specific fashion but without loss of information on large genes.' - extra: identifiers: - biotools:suprahex diff --git a/recipes/bioconductor-survcomp/meta.yaml b/recipes/bioconductor-survcomp/meta.yaml index 2cd3f1dab321e..55e6313a11b0e 100644 --- a/recipes/bioconductor-survcomp/meta.yaml +++ b/recipes/bioconductor-survcomp/meta.yaml @@ -1,23 +1,21 @@ -{% set version = "1.28.4" %} +{% set version = "1.30.0" %} {% set name = "survcomp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 80fbdd9d0027ccf69217e7e0bdd9eb0c909e86ef01bfe57a28797f77b34eb3a0 - + sha256: 12915ec5ca42bd2fcc7f019b0282c0d64624bc1aaffd1eacba2e598b23af1691 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - r-base @@ -39,16 +37,17 @@ requirements: - r-suppdists - r-survival - r-survivalroc - + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Assessment and Comparison for Performance of Risk Prediction (Survival) Models.' - extra: identifiers: - biotools:survcomp diff --git a/recipes/bioconductor-sushi/meta.yaml b/recipes/bioconductor-sushi/meta.yaml index b3a4ae595026b..c689e09d1b3d7 100644 --- a/recipes/bioconductor-sushi/meta.yaml +++ b/recipes/bioconductor-sushi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Sushi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ef20f3d099688a7b02bd4b189623b9416dc535a8bcbf46c5020d7d8048c5aa2b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8150007890d74ca563a7e070dc27706af5d36191ae17633dd41083495e8525d4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biomart + - 'bioconductor-biomart >=2.36.1,<2.38.0' - r-base - r-zoo run: - - bioconductor-biomart + - 'bioconductor-biomart >=2.36.1,<2.38.0' - r-base - r-zoo test: @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures' - extra: identifiers: - biotools:sushi diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 91f442c080aa9..3e1f6ce761d32 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.26.0" %} +{% set version = "3.28.0" %} {% set name = "sva" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fcdd6155277cb0e090acbc6eab694831fc7a8f51b5ec999187cc32c79159bd60 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 5a142ac9faa2ffbf1030b4e5db7963d8038214abd7e1296dee325c09fec27228 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel - - bioconductor-genefilter - - bioconductor-limma + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-matrixstats - r-mgcv run: - - bioconductor-biocparallel - - bioconductor-genefilter - - bioconductor-limma + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-matrixstats - r-mgcv + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).' - extra: identifiers: - biotools:sva diff --git a/recipes/bioconductor-svaplsseq/meta.yaml b/recipes/bioconductor-svaplsseq/meta.yaml index 1cfa5ffe0ee58..313c2634fd00f 100644 --- a/recipes/bioconductor-svaplsseq/meta.yaml +++ b/recipes/bioconductor-svaplsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "SVAPLSseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,25 +10,25 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b68c8261e389d02fb7df0825314a2f7c7bc107e5775c9e148520a01c291919a4 + sha256: 79005f67f72335851a4ac1f711b3ef0dc7175b6c44d0d184bcfad525ad06034c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-edger - - bioconductor-limma - - bioconductor-summarizedexperiment + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-lmtest - r-pls run: - - bioconductor-edger - - bioconductor-limma - - bioconductor-summarizedexperiment + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-ggplot2 - r-lmtest @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package contains functions that are intended for extracting the signatures of latent variation in RNAseq data and using them to perform an improved differential expression analysis for a set of features (genes, transcripts) between two specified biological groups.' - extra: identifiers: - biotools:svaplsseq diff --git a/recipes/bioconductor-swath2stats/meta.yaml b/recipes/bioconductor-swath2stats/meta.yaml index bdeecf0f30a7e..70c2cb33e1263 100644 --- a/recipes/bioconductor-swath2stats/meta.yaml +++ b/recipes/bioconductor-swath2stats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.2" %} {% set name = "SWATH2stats" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 698ce8bca8dda57c5ea2d7522730073ae5539d56807fd253133ba02b567fa4c1 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 333f5e0deaefb3fcd69d696eed715a05580cccc0e154b645b7d08cd5860623b6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.' - extra: identifiers: - biotools:swath2stats diff --git a/recipes/bioconductor-swathxtend/meta.yaml b/recipes/bioconductor-swathxtend/meta.yaml index e0d26be304e7d..209e4f329d0d4 100644 --- a/recipes/bioconductor-swathxtend/meta.yaml +++ b/recipes/bioconductor-swathxtend/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "SwathXtend" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ae8f58708b2de9f96f6b4d3a250e0c4e6ccd86a53f4d7ef565039402068d15ed + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0ad178da7a9f9a1d043a87dbfe72595c42bedcdcf85e945a46cbe96dc644a93e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data.' - extra: identifiers: - biotools:swathxtend diff --git a/recipes/bioconductor-swimr/meta.yaml b/recipes/bioconductor-swimr/meta.yaml index 990d0db4c0890..135b5bdb2f166 100644 --- a/recipes/bioconductor-swimr/meta.yaml +++ b/recipes/bioconductor-swimr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SwimR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,9 +10,9 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ff478a104c366d31248875cf1cfc770ede95b7033f1ebb9ba2d8d879d780700c + sha256: ff895a68334d1787be3a24797f395d0ca67d46cb64e0d159df436807e5ccfe64 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -36,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'SwimR is an R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is input to SwipR from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker.' - extra: identifiers: - biotools:swimr diff --git a/recipes/bioconductor-switchbox/meta.yaml b/recipes/bioconductor-switchbox/meta.yaml index 9356ff609ee86..c84d1645e3f1e 100644 --- a/recipes/bioconductor-switchbox/meta.yaml +++ b/recipes/bioconductor-switchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "switchBox" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 62ed7e6b6d8d08c9c77d04d2374692487bd34d5b4e594442d0638fc639711356 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cb6b004c77d7064b43f836e1ee7eccb44b80a1b75022815917c1def0c3778ed2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -24,6 +25,10 @@ requirements: - r-base - r-gplots - r-proc + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -31,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).' - extra: identifiers: - biotools:switchbox diff --git a/recipes/bioconductor-switchde/conda_build_config.yaml b/recipes/bioconductor-switchde/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-switchde/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-switchde/meta.yaml b/recipes/bioconductor-switchde/meta.yaml index 8c1db20e92744..d78ef5dcda6de 100644 --- a/recipes/bioconductor-switchde/meta.yaml +++ b/recipes/bioconductor-switchde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "switchde" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c62b0c0d0e306bd7a10a82842e0cef4049874daaec56ce8a56183f095a78ad3b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 87142bb58a4816a104bfd7067b971b3ad31eb571230ff0dbc48d02d3f61c2449 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dplyr - r-ggplot2 run: - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-dplyr - r-ggplot2 @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.' - extra: identifiers: - biotools:switchde diff --git a/recipes/bioconductor-synapter/meta.yaml b/recipes/bioconductor-synapter/meta.yaml index 16c85449864ad..59070bbe143ce 100644 --- a/recipes/bioconductor-synapter/meta.yaml +++ b/recipes/bioconductor-synapter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.1" %} {% set name = "synapter" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2cfe793f9ea5621c5b8e3b796dffcc9946a1c8438e03ef632e8ba351db153ad5 + sha256: 34650a2b53e157ef1fb2a488fdbd73b80117369a07817c02771b77e8a0404479 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biostrings - - 'bioconductor-cleaver >=1.3.3' - - 'bioconductor-msnbase >=2.1.2' - - bioconductor-multtest - - bioconductor-qvalue + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-cleaver >=1.18.0,<1.20.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-knitr - r-lattice @@ -31,12 +31,12 @@ requirements: - 'r-readr >=0.2' - 'r-rmarkdown >=1.0' run: - - bioconductor-biobase - - bioconductor-biostrings - - 'bioconductor-cleaver >=1.3.3' - - 'bioconductor-msnbase >=2.1.2' - - bioconductor-multtest - - bioconductor-qvalue + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-cleaver >=1.18.0,<1.20.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' - r-base - r-knitr - r-lattice @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.' - extra: identifiers: - biotools:synapter diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index c65cdfafbbe1f..3165ccbbe8bab 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "synergyfinder" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,14 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89da2f717294077eab04cbd791d6235a63ca3e74686139796548ff59a2d9524d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ecc6b18511a9204ffb34b425fd8292c44fb072612278829c9e1791e69960e1af build: - number: 1 - - # "Error in dyn.load(file, DLLpath = DLLpath, ...) : ..../nloptr/libs/nloptr.so". - # Adding llvm did not solve the issue. - skip: True # [osx] + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -45,9 +42,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic License 2.0' + license: 'Mozilla Public License 2.0 + file LICENSE' summary: 'Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix.' - extra: identifiers: - biotools:synergyfinder diff --git a/recipes/bioconductor-synlet/meta.yaml b/recipes/bioconductor-synlet/meta.yaml index 27be999618829..b27115cfb8716 100644 --- a/recipes/bioconductor-synlet/meta.yaml +++ b/recipes/bioconductor-synlet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "synlet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b2a8eb12ac9ef36b6f1ae3c5af0ab717037e1e0da2d08067e89b8dc78d8190dd + sha256: 91ee2e3059dc637f5bb1da82ae5ac62d5503d3ffc6f725fb36d1ab30b2a1198c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-rankprod + - 'bioconductor-rankprod >=3.6.0,<3.8.0' - r-base - r-doby - r-dplyr @@ -27,7 +27,7 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - bioconductor-rankprod + - 'bioconductor-rankprod >=3.6.0,<3.8.0' - r-base - r-doby - r-dplyr @@ -42,7 +42,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.' - extra: identifiers: - biotools:synlet diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index b406315b2994a..5d6a4cdeb2fad 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "systemPipeR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,49 +8,50 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9b1110f37b2a7a6c3f6dbfcc36c71d713b72f6bf4fd58dcc2942ee82e545b286 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 95963a20ac6c26c195b3c36c1ec8091f4f12dc3fd1de3adf067ed63a4cbba094 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-gostats - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-shortread - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-batchjobs - r-ggplot2 - r-pheatmap - r-rjson run: - - bioconductor-annotate - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-go.db - - bioconductor-gostats - - bioconductor-limma - - bioconductor-rsamtools - - bioconductor-shortread - - bioconductor-summarizedexperiment - - bioconductor-variantannotation + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-gostats >=2.46.0,<2.48.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-batchjobs - r-ggplot2 @@ -63,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.' - extra: identifiers: - biotools:systempiper diff --git a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml new file mode 100644 index 0000000000000..945663410a614 --- /dev/null +++ b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.6.1" %} +{% set name = "targetscan.Hs.eg.db" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c4f55d11e7e95e437ef40f1fe7b2cd0cbd6184494befc4f93455b460a19724dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'TargetScan miRNA target predictions for human assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3'' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites.' + + diff --git a/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh b/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh new file mode 100644 index 0000000000000..d52c0fb2a2121 --- /dev/null +++ b/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="targetscan.Hs.eg.db_0.6.1.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz" + "https://bioarchive.galaxyproject.org/targetscan.Hs.eg.db_0.6.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz" +) +MD5="d10569315400f6c1b95ad2688632b6de" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-targetscan.hs.eg.db/pre-unlink.sh b/recipes/bioconductor-targetscan.hs.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..93fc2e0802f03 --- /dev/null +++ b/recipes/bioconductor-targetscan.hs.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ targetscan.Hs.eg.db diff --git a/recipes/bioconductor-targetscore/meta.yaml b/recipes/bioconductor-targetscore/meta.yaml index 4d2a0c675e4b7..978883618388a 100644 --- a/recipes/bioconductor-targetscore/meta.yaml +++ b/recipes/bioconductor-targetscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TargetScore" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8741ee1142fe1474a85b408429bb47c7949a0e94b6fedb1a491e7d0c59815bb5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ea8824a908c345ee7b92c5a1ddd3619832c69b05fa78a2f8e6c6ef1aa95935e2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.' - extra: identifiers: - biotools:targetscore diff --git a/recipes/bioconductor-tarseqqc/meta.yaml b/recipes/bioconductor-tarseqqc/meta.yaml index 9521c1dc9d2c8..762b6645a094c 100644 --- a/recipes/bioconductor-tarseqqc/meta.yaml +++ b/recipes/bioconductor-tarseqqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TarSeqQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f742e53c07265fb893effdeac55268a71899ba2be2fb11eb9e4069700895fa76 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e2d70634d99666fec6b80209bb8cfdef7a35f76ddfbfd806751d70e74aad9047 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.20.4' - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-cowplot - r-ggplot2 @@ -34,15 +35,15 @@ requirements: - r-plyr - r-reshape2 run: - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.20.4' - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-cowplot - r-ggplot2 @@ -57,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.' - extra: identifiers: - biotools:tarseqqc diff --git a/recipes/bioconductor-tcc/meta.yaml b/recipes/bioconductor-tcc/meta.yaml index 22e0cec688178..943ba7aaaaee4 100644 --- a/recipes/bioconductor-tcc/meta.yaml +++ b/recipes/bioconductor-tcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "TCC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,27 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a50aa4a3238127e273f982e6a2faf4918b9c67d7d4ae3d5296054d838e82d582 + sha256: 8915a72bf5c1c05c9e2c0c01d653851c516c2e1121a02c02c2d3a498ad8bbe30 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bayseq - - bioconductor-deseq - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-roc + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - - r-samr run: - - bioconductor-bayseq - - bioconductor-deseq - - bioconductor-deseq2 - - bioconductor-edger - - bioconductor-roc + - 'bioconductor-bayseq >=2.14.0,<2.16.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - - r-samr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -40,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.' - extra: identifiers: - biotools:tcc diff --git a/recipes/bioconductor-tcgabiolinks/meta.yaml b/recipes/bioconductor-tcgabiolinks/meta.yaml index 6e85275e1d9dc..ebd252fd3ea85 100644 --- a/recipes/bioconductor-tcgabiolinks/meta.yaml +++ b/recipes/bioconductor-tcgabiolinks/meta.yaml @@ -1,40 +1,37 @@ -{% set version = "2.6.11" %} +{% set version = "2.8.4" %} {% set name = "TCGAbiolinks" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9ddf81188e0d2c4df1e6f084e723c24ade8873735b086ed8132689afe6031cfc - + sha256: fbe2b4bf27934055452be731c42c1a21f77f2702eb1b341a89eb77757d8cb8fe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-biomart - - 'bioconductor-complexheatmap >=1.10.2' - - bioconductor-consensusclusterplus - - 'bioconductor-edaseq >=2.0.0' - - 'bioconductor-edger >=3.0.0' - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.4.0' - - bioconductor-sva + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-edaseq >=2.14.1,<2.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-circlize - r-data.table @@ -63,20 +60,20 @@ requirements: - 'r-xml >=3.98.0' - r-xml2 run: - - bioconductor-biomart - - 'bioconductor-complexheatmap >=1.10.2' - - bioconductor-consensusclusterplus - - 'bioconductor-edaseq >=2.0.0' - - 'bioconductor-edger >=3.0.0' - - bioconductor-genefilter - - bioconductor-genomeinfodb - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-limma - - bioconductor-s4vectors - - 'bioconductor-summarizedexperiment >=1.4.0' - - bioconductor-sva + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-edaseq >=2.14.1,<2.16.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-circlize - r-data.table @@ -104,16 +101,13 @@ requirements: - r-tibble - 'r-xml >=3.98.0' - r-xml2 - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.' - extra: identifiers: - biotools:tcgabiolinks diff --git a/recipes/bioconductor-tdaracne/meta.yaml b/recipes/bioconductor-tdaracne/meta.yaml index d0ee784255886..5ffbc48bbfc2d 100644 --- a/recipes/bioconductor-tdaracne/meta.yaml +++ b/recipes/bioconductor-tdaracne/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "TDARACNE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4e26fc89d0aa2914846c772c47c2aa825608a070aea46fdf3444f934febbff29 + sha256: e69fc502f8d3010247d0e455bfa5762a32c4642d13d473a6bf34a61332a1754d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-rgraphviz + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-genkern run: - - bioconductor-biobase - - bioconductor-rgraphviz + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - r-base - r-genkern test: @@ -34,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'To infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.' - extra: identifiers: - biotools:tdaracne diff --git a/recipes/bioconductor-teqc/meta.yaml b/recipes/bioconductor-teqc/meta.yaml index 601f3972b60c3..33a6167550d35 100644 --- a/recipes/bioconductor-teqc/meta.yaml +++ b/recipes/bioconductor-teqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.18.0" %} +{% set version = "4.2.0" %} {% set name = "TEQC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,27 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f25a1d51a487c94390425c59a5337158be202a6e2f31c807178ec173cca4d866 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5266dd24cf9da014c564eb510f06a7a65efc9c83d76cfa143f92a5b80eaefb69 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-iranges >=1.13.5' - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-hwriter run: - - 'bioconductor-biobase >=2.15.1' - - 'bioconductor-biocgenerics >=0.1.0' - - 'bioconductor-iranges >=1.13.5' - - bioconductor-rsamtools + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - r-base - r-hwriter test: @@ -37,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.' - extra: identifiers: - biotools:teqc diff --git a/recipes/bioconductor-ternarynet/meta.yaml b/recipes/bioconductor-ternarynet/meta.yaml index 3e5814957a2f4..b101bb94d691d 100644 --- a/recipes/bioconductor-ternarynet/meta.yaml +++ b/recipes/bioconductor-ternarynet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ternarynet" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4a355846843fec2f2f961a34b66c89285b14e1852f9607270f2d662f7f181acd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a13713ab4400a022d71ea22afb03893270742257367c0412a3bba59a39dbd4f7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,10 @@ requirements: run: - r-base - r-igraph + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A computational Bayesian approach to ternary gene regulatory network estimation from gene perturbation experiments.' - extra: identifiers: - biotools:ternarynet diff --git a/recipes/bioconductor-tfbstools/meta.yaml b/recipes/bioconductor-tfbstools/meta.yaml index 3feac314388a8..d6a9992a9b727 100644 --- a/recipes/bioconductor-tfbstools/meta.yaml +++ b/recipes/bioconductor-tfbstools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TFBSTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,29 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1e12d49fac35d5f9fed0b14ff43bb49bdd95b0f4be95fa7d64fa165ef1da3b6a + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d15e80f4ab53ffe240b52a64cf00b82895bb6f9e8d414741fc07364c9ebb6bb8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.28' - - 'bioconductor-biocgenerics >=0.14.0' - - 'bioconductor-biocparallel >=1.2.21' - - 'bioconductor-biostrings >=2.36.4' - - 'bioconductor-bsgenome >=1.36.3' - - 'bioconductor-cner >=1.4.0' - - 'bioconductor-dirichletmultinomial >=1.10.0' - - 'bioconductor-genomeinfodb >=1.6.1' - - 'bioconductor-genomicranges >=1.20.6' - - 'bioconductor-iranges >=2.2.7' - - 'bioconductor-rtracklayer >=1.28.10' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-seqlogo >=1.34.0' - - 'bioconductor-xvector >=0.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-cner >=1.16.1,<1.18.0' + - 'bioconductor-dirichletmultinomial >=1.22.0,<1.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -39,20 +40,20 @@ requirements: - 'r-tfmpvalue >=0.0.5' - 'r-xml >=3.98-1.3' run: - - 'bioconductor-biobase >=2.28' - - 'bioconductor-biocgenerics >=0.14.0' - - 'bioconductor-biocparallel >=1.2.21' - - 'bioconductor-biostrings >=2.36.4' - - 'bioconductor-bsgenome >=1.36.3' - - 'bioconductor-cner >=1.4.0' - - 'bioconductor-dirichletmultinomial >=1.10.0' - - 'bioconductor-genomeinfodb >=1.6.1' - - 'bioconductor-genomicranges >=1.20.6' - - 'bioconductor-iranges >=2.2.7' - - 'bioconductor-rtracklayer >=1.28.10' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-seqlogo >=1.34.0' - - 'bioconductor-xvector >=0.8.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-cner >=1.16.1,<1.18.0' + - 'bioconductor-dirichletmultinomial >=1.22.0,<1.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -60,6 +61,9 @@ requirements: - 'r-rsqlite >=1.0.0' - 'r-tfmpvalue >=0.0.5' - 'r-xml >=3.98-1.3' + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -67,7 +71,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.' - extra: identifiers: - biotools:tfbstools diff --git a/recipes/bioconductor-tigre/meta.yaml b/recipes/bioconductor-tigre/meta.yaml index 35941671bf41c..49ea21d441d79 100644 --- a/recipes/bioconductor-tigre/meta.yaml +++ b/recipes/bioconductor-tigre/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "tigre" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f00ed6ec40c6d38be249dd6a13c7e4b26929e181a9e4b691a61a610689b4f400 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ce2d3f680a61019347c94d83e6f35826ee208505eaef7bd1faf72bca6e2b0a4b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-dbi - r-gplots - r-rsqlite run: - - bioconductor-annotate - - bioconductor-annotationdbi - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-annotate >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-dbi - r-gplots - r-rsqlite + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.' - extra: identifiers: - biotools:tigre diff --git a/recipes/bioconductor-timecourse/meta.yaml b/recipes/bioconductor-timecourse/meta.yaml index d196a490eee29..c6a6d5a5ea2e6 100644 --- a/recipes/bioconductor-timecourse/meta.yaml +++ b/recipes/bioconductor-timecourse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "timecourse" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,25 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f92e36c8c550c15e488dddfa489fc0cb31410dfe27732e4095b80a14bdfd2453 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a93caaa2e211c1ca0b51c8b691fd0d54a0d13b8d11517a7f4b5b425dbb782572 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - 'bioconductor-limma >=1.8.6' - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-mass run: - - bioconductor-biobase - - 'bioconductor-limma >=1.8.6' - - bioconductor-marray + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-mass test: @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions for data analysis and graphical displays for developmental microarray time course data.' - extra: identifiers: - biotools:timecourse diff --git a/recipes/bioconductor-tin/meta.yaml b/recipes/bioconductor-tin/meta.yaml index 878a6ace23b8b..e1dcb9f794391 100644 --- a/recipes/bioconductor-tin/meta.yaml +++ b/recipes/bioconductor-tin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TIN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,15 +10,15 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: eda55f4b183ef45dd885a2d23d5c7ca6b8d06aa455d4b0c054eb0f2dc93c9b9a + sha256: ff3aa08c7673d3c45fc8926e07cdbef9ea518765171a6b5f5ed31c50c2dc291a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-aroma.affymetrix - r-base - r-data.table @@ -26,7 +26,7 @@ requirements: - r-stringr - r-wgcna run: - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-aroma.affymetrix - r-base - r-data.table @@ -40,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.' - extra: identifiers: - biotools:tin diff --git a/recipes/bioconductor-tissueenrich/build.sh b/recipes/bioconductor-tissueenrich/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-tissueenrich/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tissueenrich/conda_build_config.yaml b/recipes/bioconductor-tissueenrich/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-tissueenrich/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-tissueenrich/meta.yaml b/recipes/bioconductor-tissueenrich/meta.yaml new file mode 100644 index 0000000000000..ee1dfab840e01 --- /dev/null +++ b/recipes/bioconductor-tissueenrich/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.7" %} +{% set name = "TissueEnrich" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c910cdf72450093540ea05ed7bdd95733812ca18103f68f21c56f7496669e314 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' + - r-base + - 'r-dplyr >=0.7.3' + - 'r-ensurer >=1.1.0' + - 'r-ggplot2 >=2.2.1' + - 'r-tidyr >=0.8.0' + run: + - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' + - r-base + - 'r-dplyr >=0.7.3' + - 'r-ensurer >=1.1.0' + - 'r-ggplot2 >=2.2.1' + - 'r-tidyr >=0.8.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.' diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 8a6c97fe2e5d5..53161790bf015 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -18,7 +18,6 @@ build: - lib/ requirements: host: - - r-base 3.4.1 - perl # for adding in correct path references to scripts - 'bioconductor-genomeinfodb >=1.8.7' - 'bioconductor-genomicranges >=1.24.3' @@ -40,12 +39,9 @@ requirements: - 'bioconductor-rsamtools >=1.24.0' - 'bioconductor-variantannotation >=1.18.7' - 'r-foreach >=1.4.3' - - r-data.table - - r-dplyr - - r-optparse - - r-domc - - bioconductor-snpchip - - r-stringr + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 3b9ebe0f6ebb5..194350d0528f9 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "topGO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,31 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bf0d474056f75bc94333eef2e44655b64c8c5e01e08c2b77ebf49d8bcb770ec3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 81f758e507ac28ec341ecad1a8d67e50b6619e4b2e8254274dfc2dd4e2b4dd17 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.7.19' - - 'bioconductor-biobase >=2.0.0' - - 'bioconductor-biocgenerics >=0.13.6' - - 'bioconductor-go.db >=2.3.0' - - 'bioconductor-graph >=1.14.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-dbi - r-lattice - r-matrixstats - 'r-sparsem >=0.73' run: - - 'bioconductor-annotationdbi >=1.7.19' - - 'bioconductor-biobase >=2.0.0' - - 'bioconductor-biocgenerics >=0.13.6' - - 'bioconductor-go.db >=2.3.0' - - 'bioconductor-graph >=1.14.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - r-dbi - r-lattice @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.' - extra: identifiers: - biotools:topgo diff --git a/recipes/bioconductor-tracktables/meta.yaml b/recipes/bioconductor-tracktables/meta.yaml index 06329a7b9870f..2db160ec4d36c 100644 --- a/recipes/bioconductor-tracktables/meta.yaml +++ b/recipes/bioconductor-tracktables/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "tracktables" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c3a5d1ea7538ef104a1d2a4f7c89434e4dcde3c5107a69db2c2f7ebe34b1850a + sha256: 36442889139f0c5395be2704a132414b281061e91d6f277fc8bc331599e7b902 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-xvector + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml run: - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-xvector + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base - r-rcolorbrewer - r-stringr @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.' - extra: identifiers: - biotools:tracktables diff --git a/recipes/bioconductor-trackviewer/conda_build_config.yaml b/recipes/bioconductor-trackviewer/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-trackviewer/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-trackviewer/meta.yaml b/recipes/bioconductor-trackviewer/meta.yaml index bd2cab8411ede..d8e7b4674ace4 100644 --- a/recipes/bioconductor-trackviewer/meta.yaml +++ b/recipes/bioconductor-trackviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.1" %} {% set name = "trackViewer" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,44 +10,52 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c6c040d0920347432eb93f51b28c22a3b7ad59af4c98e9718d43f49484733e09 + sha256: 42d8d513d099d29764505ae646148b5954cc8cde5837e01af89a1970bba5eead build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-interactionset >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-grimport - r-htmlwidgets - - r-pbapply + - r-plotrix - r-scales run: - - bioconductor-annotationdbi - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - bioconductor-gviz - - bioconductor-iranges - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-interactionset >=1.8.0,<1.10.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-grimport - r-htmlwidgets - - r-pbapply + - r-plotrix - r-scales test: commands: @@ -56,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.' - extra: identifiers: - biotools:trackviewer diff --git a/recipes/bioconductor-transcriptr/meta.yaml b/recipes/bioconductor-transcriptr/meta.yaml index 1aa7692e64fbd..d06d2de828545 100644 --- a/recipes/bioconductor-transcriptr/meta.yaml +++ b/recipes/bioconductor-transcriptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "transcriptR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,24 +10,24 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5a4cebeaf09ba6bebd7abc7ebfe0a311d43370f2c8ee86eb0aa26ec287825455 + sha256: c83546052cd55ff2093f298f9a32c5c9491eaeb3155e24ce36a5bed16f1f2095 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-chipseq - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.11.15' - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-caret - r-e1071 @@ -35,16 +35,16 @@ requirements: - r-proc - r-reshape2 run: - - bioconductor-biocgenerics - - bioconductor-chipseq - - bioconductor-genomeinfodb - - bioconductor-genomicalignments - - bioconductor-genomicfeatures - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.11.15' - - bioconductor-rsamtools - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-chipseq >=1.30.0,<1.32.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-caret - r-e1071 @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample.' - extra: identifiers: - biotools:transcriptr diff --git a/recipes/bioconductor-translatome/meta.yaml b/recipes/bioconductor-translatome/meta.yaml index 45cdcf2dc77b7..0ef9481e811d6 100644 --- a/recipes/bioconductor-translatome/meta.yaml +++ b/recipes/bioconductor-translatome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.5" %} {% set name = "tRanslatome" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,53 +10,50 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b2c7868125e956a40f15440deeb691b4bc36a03a3a376474d4184aa466e916f2 + sha256: ba3713d72b18f107b2849c536790d80093e47aa769e2e899b313054f4a3c1749 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-anota - - bioconductor-biobase - - bioconductor-deseq - - bioconductor-edger - - bioconductor-gosemsim - - bioconductor-heatplus - - bioconductor-limma - - bioconductor-org.hs.eg.db - - bioconductor-rankprod - - bioconductor-sigpathway - - bioconductor-topgo + - 'bioconductor-anota >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-heatplus >=2.26.0,<2.28.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rankprod >=3.6.0,<3.8.0' + - 'bioconductor-sigpathway >=1.48.0,<1.50.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-gplots - r-plotrix - - r-samr run: - - bioconductor-anota - - bioconductor-biobase - - bioconductor-deseq - - bioconductor-edger - - bioconductor-gosemsim - - bioconductor-heatplus - - bioconductor-limma - - bioconductor-org.hs.eg.db - - bioconductor-rankprod - - bioconductor-sigpathway - - bioconductor-topgo + - 'bioconductor-anota >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-heatplus >=2.26.0,<2.28.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-rankprod >=3.6.0,<3.8.0' + - 'bioconductor-sigpathway >=1.48.0,<1.50.0' + - 'bioconductor-topgo >=2.32.0,<2.34.0' - r-base - r-gplots - r-plotrix - - r-samr test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.' - + summary: 'Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.' extra: identifiers: - biotools:translatome diff --git a/recipes/bioconductor-transview/meta.yaml b/recipes/bioconductor-transview/meta.yaml index f267bdceee457..8be74d39e4033 100644 --- a/recipes/bioconductor-transview/meta.yaml +++ b/recipes/bioconductor-transview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TransView" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 06bf31f483f56642ae2935b8926a2433526f0b9a99b81a95eda5593845a0068c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 49007bacd52ae273fa3216f399b9e32e3d2441c44011b2b8600a96b8a2da48a5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.19.38' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-gplots run: - - bioconductor-biocgenerics - - bioconductor-genomicranges - - bioconductor-iranges - - 'bioconductor-rsamtools >=1.19.38' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-gplots + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.' - extra: identifiers: - biotools:transview diff --git a/recipes/bioconductor-traser/meta.yaml b/recipes/bioconductor-traser/meta.yaml index 03bb178b90638..f049012fbe3bf 100644 --- a/recipes/bioconductor-traser/meta.yaml +++ b/recipes/bioconductor-traser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "traseR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,23 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1e50028e3029fca41f3c5fe1bae709b0357757d8f18c90e5df82f18bf8f90cff + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 293f445a6729a71b7074a78bda52e092f54321262f847b73e71d07599d6da6cb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base run: - - bioconductor-bsgenome.hsapiens.ucsc.hg19 - - bioconductor-genomicranges - - bioconductor-iranges + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base test: commands: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.' - extra: identifiers: - biotools:traser diff --git a/recipes/bioconductor-treeio/meta.yaml b/recipes/bioconductor-treeio/meta.yaml index 533de51d5c30b..7b76ddbf81d52 100644 --- a/recipes/bioconductor-treeio/meta.yaml +++ b/recipes/bioconductor-treeio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.3" %} {% set name = "treeio" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9de664155c482be466a0089cf4757288bd672ee92958e07f49cfde641b9666d4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b546ef1c71b4029f8c5ae10311e78cb14f695355c043912dac288afbbf4b4256 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -19,21 +20,29 @@ requirements: host: - r-ape - r-base - - r-ggplot2 + - r-dplyr - r-jsonlite - r-magrittr + - r-rlang - r-rvcheck + - r-tibble + - 'r-tidytree >=0.1.7' run: - r-ape - r-base - - r-ggplot2 + - r-dplyr - r-jsonlite - r-magrittr + - r-rlang - r-rvcheck + - r-tibble + - 'r-tidytree >=0.1.7' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Base classes and functions for parsing and exporting phylogenetic trees.' + summary: 'Base classes and functions for parsing and exporting phylogenetic trees. ''treeio'' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file.' + + diff --git a/recipes/bioconductor-triform/meta.yaml b/recipes/bioconductor-triform/meta.yaml index e161cbaf163e8..d15165779c502 100644 --- a/recipes/bioconductor-triform/meta.yaml +++ b/recipes/bioconductor-triform/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "triform" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 862cf8cbd93b2f95c18c63b86f457697940d41144a2e2683dd60bebff2b41426 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 79365c1345b1a6c4a62407afe2a9299b033da3c0e78aeefb8d492c0a3026fd17 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - 'bioconductor-iranges >=2.5.27' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-yaml run: - - bioconductor-biocgenerics - - 'bioconductor-iranges >=2.5.27' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' - r-base - r-yaml test: @@ -33,7 +34,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.' - extra: identifiers: - biotools:triform diff --git a/recipes/bioconductor-trigger/meta.yaml b/recipes/bioconductor-trigger/meta.yaml index 05f668c264aa8..8de0588dbbef5 100644 --- a/recipes/bioconductor-trigger/meta.yaml +++ b/recipes/bioconductor-trigger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "trigger" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,28 +10,28 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3c13c33f305e1200ab4251908ac358b9dfe7ad09c540963ef5eb9ee13958279b + sha256: 267ab711df8e70684ab6d7cfa8f49225840fd3dbf3df811ff9df44d48557644f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-qvalue - - bioconductor-sva + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-corpcor - r-qtl run: - - bioconductor-qvalue - - bioconductor-sva + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-sva >=3.28.0,<3.30.0' - r-base - r-corpcor - r-qtl - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.' - extra: identifiers: - biotools:trigger diff --git a/recipes/bioconductor-trio/meta.yaml b/recipes/bioconductor-trio/meta.yaml index 465422ba6671f..0597a5a9e0c7f 100644 --- a/recipes/bioconductor-trio/meta.yaml +++ b/recipes/bioconductor-trio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.16.0" %} +{% set version = "3.18.0" %} {% set name = "trio" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e794a54a9461b6a7bab2375074f0f8649cd83cb148261fb179f5675c926780af + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 9d5d4c09b6c57a1c26a4d8c123e9f77218979a33fa0ed324171dd0f327a83621 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.' - extra: identifiers: - biotools:trio diff --git a/recipes/bioconductor-triplex/meta.yaml b/recipes/bioconductor-triplex/meta.yaml index db810fb79f58a..163d96ef16113 100644 --- a/recipes/bioconductor-triplex/meta.yaml +++ b/recipes/bioconductor-triplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "triplex" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bd198fb9493d72b5acd53f127f3f1f36184e41026ab5f97e566b4139f1f4e474 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 3113d1456d357332296f12585a65cf403165fff660b17f5319b82ad98d026c38 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings >=2.39.10' - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.5.27' - - 'bioconductor-s4vectors >=0.5.14' - - 'bioconductor-xvector >=0.11.6' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base run: - - 'bioconductor-biostrings >=2.39.10' - - bioconductor-genomicranges - - 'bioconductor-iranges >=2.5.27' - - 'bioconductor-s4vectors >=0.5.14' - - 'bioconductor-xvector >=0.11.6' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.' - extra: identifiers: - biotools:triplex diff --git a/recipes/bioconductor-tscan/meta.yaml b/recipes/bioconductor-tscan/meta.yaml index cb5c3d46fb64b..2b3ade7f20423 100644 --- a/recipes/bioconductor-tscan/meta.yaml +++ b/recipes/bioconductor-tscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TSCAN" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: af5b980ef06ad1455d91ef433d0ff1e22dec9099d9fdeacd442a1bf27cc90855 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5c9007f51d20b908f737381ab300396572553c709d2073fb2141649d67180db1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'TSCAN enables users to easily construct and tune pseudotemporal cell ordering as well as analyzing differentially expressed genes. TSCAN comes with a user-friendly GUI written in shiny. More features will come in the future.' - extra: identifiers: - biotools:tscan diff --git a/recipes/bioconductor-tspair/meta.yaml b/recipes/bioconductor-tspair/meta.yaml index 89744554256a6..4d8efbc29440d 100644 --- a/recipes/bioconductor-tspair/meta.yaml +++ b/recipes/bioconductor-tspair/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "tspair" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dc602daff9a7ddb1cc5017123fd7a3060a0202118fc3ba9970ad74b345903c1d + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 8509a2f8003b33df8d9027fdaae15de28077fa76316f52b634d5500c31ac0409 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.4.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=2.4.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This "top scoring pair" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of classifying samples based on only the relative rank of a pair of genes is (a) the classifiers are much simpler and often more interpretable than more complicated classification schemes and (b) if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples. See the references for the tspcalc() function for references regarding TSP classifiers.' - extra: identifiers: - biotools:tspair diff --git a/recipes/bioconductor-tssi/meta.yaml b/recipes/bioconductor-tssi/meta.yaml index 37de0761ab6f5..69e357607c2a4 100644 --- a/recipes/bioconductor-tssi/meta.yaml +++ b/recipes/bioconductor-tssi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "TSSi" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,32 +8,36 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aaf374afd5b95706a6d751e1f66e4296a6f8b2f6fc3ef451f757c265b1b5270e + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 51c7131ed78586561100307e31a75ad592fe18c02a5b70ccec7322ca5c9a00ac build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=0.3.2' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-hmisc - r-minqa - r-plyr run: - - 'bioconductor-biobase >=0.3.2' - - 'bioconductor-biocgenerics >=0.3.2' - - bioconductor-iranges - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-hmisc - r-minqa - r-plyr + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +45,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identify and normalize transcription start sites in high-throughput sequencing data.' - extra: identifiers: - biotools:tssi diff --git a/recipes/bioconductor-turbonorm/conda_build_config.yaml b/recipes/bioconductor-turbonorm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-turbonorm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-turbonorm/meta.yaml b/recipes/bioconductor-turbonorm/meta.yaml index 4c0f81ad26c34..087840bcee23e 100644 --- a/recipes/bioconductor-turbonorm/meta.yaml +++ b/recipes/bioconductor-turbonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "TurboNorm" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,30 +10,30 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4d0bb6762f3790b288c37cd9042195281e8d64df227d2475481e1d5b7c1dd62b + sha256: 7e381ff66918cfbe2a1f277fa7f8f6c569e8efb31d52088402c261a91c52dd89 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy - - bioconductor-convert - - 'bioconductor-limma >=1.7.0' - - bioconductor-marray + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-convert >=1.56.0,<1.58.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-lattice run: - - bioconductor-affy - - bioconductor-convert - - 'bioconductor-limma >=1.7.0' - - bioconductor-marray + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-convert >=1.56.0,<1.58.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-marray >=1.58.0,<1.60.0' - r-base - r-lattice - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -41,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.' - extra: identifiers: - biotools:turbonorm diff --git a/recipes/bioconductor-tvtb/meta.yaml b/recipes/bioconductor-tvtb/meta.yaml index 46cc1ae828478..654c040847fa5 100644 --- a/recipes/bioconductor-tvtb/meta.yaml +++ b/recipes/bioconductor-tvtb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TVTB" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,49 +10,49 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ab04eefb68671c170966d35b29e7c0ed32128f4cb930ca8317d0e9caa43c26dc + sha256: 4a30a085640cb5e77ef9bbf9f32f8e0033d94146cfd3912790749f1937fbcca2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationfilter - - 'bioconductor-biocgenerics >=0.19.1' - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-ensembldb - - bioconductor-ensemblvep - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gviz - - 'bioconductor-iranges >=2.7.1' - - bioconductor-limma - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.11.11' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.19.9' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-ensemblvep >=1.22.0,<1.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-ggally - r-ggplot2 - r-reshape2 run: - - bioconductor-annotationfilter - - 'bioconductor-biocgenerics >=0.19.1' - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-ensembldb - - bioconductor-ensemblvep - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gviz - - 'bioconductor-iranges >=2.7.1' - - bioconductor-limma - - bioconductor-rsamtools - - 'bioconductor-s4vectors >=0.11.11' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.19.9' + - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-ensemblvep >=1.22.0,<1.24.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-ggally - r-ggplot2 @@ -64,7 +64,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).' - extra: identifiers: - biotools:tvtb diff --git a/recipes/bioconductor-tweedeseq/meta.yaml b/recipes/bioconductor-tweedeseq/meta.yaml index 7104610377afc..b6157c637c7d5 100644 --- a/recipes/bioconductor-tweedeseq/meta.yaml +++ b/recipes/bioconductor-tweedeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "tweeDEseq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 239dbe88f40f9a3d87a3b0b5ea69932520e9c2d2339e10aaeaf3a95e96be49d7 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 55bc0add0f651ef5fc66f7b34b073ca691694b6b786c0e16edf380b1abc4fef8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-cqn - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-cqn >=1.26.0,<1.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-mass run: - - bioconductor-cqn - - bioconductor-edger - - bioconductor-limma + - 'bioconductor-cqn >=1.26.0,<1.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-mass + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.' - extra: identifiers: - biotools:tweedeseq diff --git a/recipes/bioconductor-twilight/meta.yaml b/recipes/bioconductor-twilight/meta.yaml index f994bf450bada..20fcc784cf5dd 100644 --- a/recipes/bioconductor-twilight/meta.yaml +++ b/recipes/bioconductor-twilight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "twilight" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,24 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a3c03646fd5944e2ae665a8cb6e3ac4e0837a4ba3b77ccffc324a0217833f32c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 76db531c1798882fdf620232a767869ba855293a56358d360565fd8014c4bb4d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=1.12.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=1.12.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -29,7 +33,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package ''twilight'' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.' - extra: identifiers: - biotools:twilight diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index 157dbe1f69f6f..12834a2b54fa9 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.2" %} +{% set version = "3.4.3" %} {% set name = "TxDb.Celegans.UCSC.ce11.refGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4331555a7214d576dbbae002dcfa121596c341dcf44f8307de5a6e5c4d2e943c + sha256: 89873961267cd0a6e729ff3c09eb6eb3617cae61d707fb940e8ad423916ec8e0 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.29.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.29.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh index 39861d72448db..645ce9de9f796 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.2.tar.gz" +FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.2.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.2_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.3_src_all.tar.gz" ) -MD5="db249f10830c9e547852ae2996afb420" +MD5="62144dbefc0beb1bb1c2e0db3757179c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index 12a524241b0cd..faec0530fa0ae 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Celegans.UCSC.ce6.ensGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 20c51a06664f1135500b3ce1b9eeacf5154995ab4847217524beb131d4bef7e9 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh index ffceae30a4b53..49215dd6fd9b2 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz" ) MD5="215c2edd440a3df8229fe6a75b431aa8" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index 2b4ad33de5997..95519a3675bbe 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm3.ensGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 879d366e7c6ca9734a059c060e0b36019e11f32c42e83a90fa31d69687e8678c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh index 525d0ecd5cfc3..160fc4fc37928 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz" ) MD5="46b7ffe0c516edf8a2a3b5d78e0d8b67" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index 29def453c3b79..436dc9fc1b551 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.1" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm6.ensGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 01cc6196b2660348d6ec3c7eb707966b07f803c0a40bef63958e1234d703bc69 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.27.13' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.27.13' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh index 119489492bc63..d47728c075d58 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.1_src_all.tar.gz" ) MD5="539737dcb0b3d6d0134f5fe2ecf4e835" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index 5ff8ce245061e..3529a953fda80 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.2" %} +{% set version = "3.4.3" %} {% set name = "TxDb.Drerio.UCSC.danRer10.refGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 740cf7e249e19afe47119564aee3515728e0b9056779a013b43f4bb1e93e0cb3 + sha256: 794989712cfc2f6d9cc0cca6216326b8536c2e2215643a39a62f24bc448c5c0d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.29.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.29.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh index 859f850f0c474..4bbb49e809b76 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.2.tar.gz" +FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.2.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.2_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.3_src_all.tar.gz" ) -MD5="fc024ebcd884f44f52adeb552347ad0a" +MD5="db746342bff2cd07c9e02b5f5840fb2b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 58ba54fad0148..262094f36a3c9 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg18.knownGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: bc9ca40b4eab87f5ca64a4b876d42502b9b8e9f5983d745bfe0ee349d97b69fa build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh index 1b7a768dc32e9..6c561280b58d5 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz" ) MD5="e8b32a672e87345c72bb30be73d1e2d6" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index b71c90a9c71b2..84572b048ae3e 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.knownGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh index b08268c2a79d7..4fa0165f6ef81 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz" ) MD5="61be88a81433958571b57d0952be48a0" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index ba7f70cf589ca..4539913ea4b2e 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 4f68ee75c1722b53de4a5382a455730673dab8c0fd7585f86771efe6e7b9ab2e build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh index 58182b405cbac..0d715bcfcac5c 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz" ) MD5="a0d61cd90639c40b3d0bb6bdb043cf12" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index 1e4a131f0e1e3..1e040d4da4789 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.knownGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: c5e6ebd84690e00eed966e4569dbd5abccf478b60dcb1842ca0310cb2ae01d44 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.25.18' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.25.18' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh index ba93622aea1ef..fe0d79fd8e074 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.0_src_all.tar.gz" ) MD5="1d5e07631ea58e96b11905d39e76ca6e" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index 03a8b46afb156..be309abb5459d 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.ensGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 3abd4f50b358ed1d1996da6c894ab82b13b247b33e07bf9d46a3f1d85c885d69 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.25.17' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.25.17' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh index 77637db4d313e..d6bf203d9f539 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz" ) MD5="88d65b714d1f86b456aee2b8524e9d84" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index 292d7ca2f0b2b..79984396f0ef9 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.knownGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6b2e9ce3b2050cb770cca989b14b09c50e20ef88568b19cac7ec6ecd93daea21 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.25.17' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.25.17' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh index 1e901ec810f27..4f47f3f82d372 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.0_src_all.tar.gz" ) MD5="86b7dca1b7d0d957c1794d261fc5bb81" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index b325fb58ad575..04299049e5603 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Mmusculus.UCSC.mm9.knownGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: a2d760206336d0c1ba48108ba3e23b201aa429a6b88a19437270980180ef7299 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh index 33271b56804a3..7bb559a168511 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz" ) MD5="cb72af039b011033477363bda8ed9104" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 109ecfaeeae57..5596886011a4d 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn4.ensGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 15325d09a9da4292678768164e1850a78595dd96351970553844f5eeac5f683f build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh index 2bebb77c1dd24..5eef393d3801f 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz" ) MD5="6bf2ebc522c2828c036e52b2028792c1" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index 1dfff54ff8545..99f5e1d42c333 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.2" %} +{% set version = "3.4.3" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn5.refGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 336e90a3c5be255fd2340b268c3b22b953fb91efd6757f09ef52d60644dedd87 + sha256: 82a9597c56c1181f26363601f9618fa203c50f04a5a3386c0f66c137747af34a build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.29.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.29.10' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh index fa048c2878fab..090cc1bacd076 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2.tar.gz" +FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.2_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.3_src_all.tar.gz" ) -MD5="194a3f04725e7ac39bd0e68efdffbc6a" +MD5="4dafbc7e60e8fb947d40571fa3812699" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 37da5b05940d5..4d68f80fb327b 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.1" %} +{% set version = "3.4.3" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.refGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 53a75972d28eb3a7681512e1618e1d21fc4e091951b6b5beba05abc2d2118423 + sha256: 4325ad6b56fe6de8f17eae445327f4cac8731530a46e5fa4775d242bfb730296 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.27.13' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.27.13' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh index 70ff47b58391d..3b8b82daa4d17 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1.tar.gz" +FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.1_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.3_src_all.tar.gz" ) -MD5="4128d06fb48a78aad08da3765fe55234" +MD5="502c29bc0eb476938794a01c2d8ce269" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index 026537e184538..1e70b4eab380b 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: eaf35b5a3e4706328e7a5b89d7de846055f5ac0aa34109d305a6ffbd2067af50 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh index 5d03d154e4917..616af4ba2ab51 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz" ) MD5="8ce83ef2ba6cfc69f9b4435a0a047819" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index 29f9d2c2d5f5a..58ff21afdd9af 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,21 +8,22 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 6dac0b4f88ce54c8543bb0ce236507cd46dd78ff7b3e3457ef7fd0b1dca15cea build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base run: - - bioconductor-annotationdbi - - 'bioconductor-genomicfeatures >=1.21.30' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - r-base - wget test: @@ -32,3 +33,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + + diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh index 1682d0a078cf1..a3773b0b6b287 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" + "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz" ) MD5="afb23b3265730b9e59c2f07ab37cc3a0" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index feacb7b4f2221..8d527f4c0b7cd 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tximport" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 505c8d721b09897519cfa0e82fabbfe97a536ce0587c86e59be175185265d8bf + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 375224ca34750e5064bb3db0e0f7347d84af2c2633dd2cd9be8cfd96a03a4ce2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.' - extra: identifiers: - biotools:tximport diff --git a/recipes/bioconductor-undo/meta.yaml b/recipes/bioconductor-undo/meta.yaml index c7285ae1f6bcb..d547ca9ea0f4e 100644 --- a/recipes/bioconductor-undo/meta.yaml +++ b/recipes/bioconductor-undo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "UNDO" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,23 +10,23 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ddb838222b1d86b91a05d146c4e2fba2de847d24ac84e94ec959d54a0e6b1d44 + sha256: b92e02e3ef692d7a40c4e5fe7aaf7443004765b45df439e8afeb23d28dd71698 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-boot - r-mass - r-nnls run: - - bioconductor-biobase - - bioconductor-biocgenerics + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base - r-boot - r-mass @@ -38,7 +38,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.' - extra: identifiers: - biotools:undo diff --git a/recipes/bioconductor-unifiedwmwqpcr/conda_build_config.yaml b/recipes/bioconductor-unifiedwmwqpcr/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-unifiedwmwqpcr/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml index e51c6b8de012e..b8f1ad179ae73 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml +++ b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "unifiedWMWqPCR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2a4b62e69543176674d1a4daf704986d777b1a888ed33b2ea43933d3ce84d3b4 + sha256: 6ba1920b69895745d5b7cc0a85ef2ec957fd628f01f912019737fe5fec856268 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-htqpcr + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-htqpcr >=1.34.0,<1.36.0' - r-base run: - - bioconductor-biocgenerics - - bioconductor-htqpcr + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-htqpcr >=1.34.0,<1.36.0' - r-base test: commands: @@ -32,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.' - extra: identifiers: - biotools:unifiedwmwqpcr diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml index 5975b8de8dd67..dd14915f1daec 100644 --- a/recipes/bioconductor-uniprot.ws/meta.yaml +++ b/recipes/bioconductor-uniprot.ws/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.4" %} {% set name = "UniProt.ws" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,24 +8,29 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dc652b6480badda24c895284f573915d904733e16667ccfb521c152f01ab381c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 38f80df3370c7beb0de96666b5df08efddbb66bd91c2a58aed2ac20d7dfa60ab build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-annotationdbi - - 'bioconductor-biocgenerics >=0.13.8' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base + - r-rappdirs - r-rcurl - r-rsqlite run: - - bioconductor-annotationdbi - - 'bioconductor-biocgenerics >=0.13.8' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - r-base + - r-rappdirs - r-rcurl - r-rsqlite test: @@ -35,7 +40,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic License 2.0' summary: 'A collection of functions for retrieving, processing and repackaging the UniProt web services.' - extra: identifiers: - biotools:uniprot.ws diff --git a/recipes/bioconductor-uniquorn/meta.yaml b/recipes/bioconductor-uniquorn/meta.yaml index c09cf960f77a5..40a0105686389 100644 --- a/recipes/bioconductor-uniquorn/meta.yaml +++ b/recipes/bioconductor-uniquorn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "2.0.0" %} {% set name = "Uniquorn" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,27 +10,33 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f02c3e45e5eb249455ae0e276a166e3b89a318834ac72a7b6e6561c29d4f9e15 + sha256: 2b82752fc5f2ec01bba3e71e9fa1fdda65db22ad5e598b1eb91f7fd10de997eb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocparallel + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - - r-dbi + - r-data.table + - r-doparallel + - r-foreach - r-r.utils - - r-rsqlite - r-stringr - r-writexls run: - - bioconductor-biocparallel + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - - r-dbi + - r-data.table + - r-doparallel + - r-foreach - r-r.utils - - r-rsqlite - r-stringr - r-writexls test: @@ -39,8 +45,7 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Identifies cancer cell lines with their small variant fingerprint. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations or loci of somatic and germline mutations or variations. The input format is vcf and the files have to contain a single cancer cell line sample. The implemented method is optimized for the Next-generation whole exome and whole genome DNA-sequencing technology. RNA-seq data is very likely to work as well but hasn''t been rigiously tested yet. Panel-seq will require manual adjustment of thresholds.' - + summary: 'This packages enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file). The implemented method is optimized for the Next-generation whole exome and whole genome DNA-sequencing technology. RNA-seq data is very likely to work as well but hasn''t been rigiously tested yet. Panel-seq will require manual adjustment of thresholds' extra: identifiers: - biotools:uniquorn diff --git a/recipes/bioconductor-vanillaice/conda_build_config.yaml b/recipes/bioconductor-vanillaice/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-vanillaice/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml index aa805d05bb8a8..d6c6e57f8bf1d 100644 --- a/recipes/bioconductor-vanillaice/meta.yaml +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.4" %} {% set name = "VanillaICE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,48 +10,48 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e2d6f62714c6da9341072bb89c6a17b6fddd6769dc695cff40c594b89da05c93 + sha256: 0f744caf4e2dcceb4d25dccfcf06147e479db8145289c27eb204a73893fb3763 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.6' - - bioconductor-bsgenome.hsapiens.ucsc.hg18 - - bioconductor-crlmm - - 'bioconductor-genomeinfodb >=1.11.4' - - 'bioconductor-genomicranges >=1.27.6' - - 'bioconductor-iranges >=1.14.0' - - 'bioconductor-oligoclasses >=1.31.1' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-summarizedexperiment >=1.5.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.1000,<1.5.0' + - 'bioconductor-crlmm >=1.38.0,<1.40.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-foreach - r-lattice - r-matrixstats run: - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.6' - - bioconductor-bsgenome.hsapiens.ucsc.hg18 - - bioconductor-crlmm - - 'bioconductor-genomeinfodb >=1.11.4' - - 'bioconductor-genomicranges >=1.27.6' - - 'bioconductor-iranges >=1.14.0' - - 'bioconductor-oligoclasses >=1.31.1' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-summarizedexperiment >=1.5.3' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.1000,<1.5.0' + - 'bioconductor-crlmm >=1.38.0,<1.40.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-foreach - r-lattice - r-matrixstats - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -59,7 +59,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.' - extra: identifiers: - biotools:vanillaice diff --git a/recipes/bioconductor-variancepartition/meta.yaml b/recipes/bioconductor-variancepartition/meta.yaml index 6c47ab79df825..bc8a8f6312176 100644 --- a/recipes/bioconductor-variancepartition/meta.yaml +++ b/recipes/bioconductor-variancepartition/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.4" %} {% set name = "variancePartition" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,17 +8,18 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bd8381a9e0b1153a7a249101769bc9a91f76e9134e234f4f8c38b536e4b93a22 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 24a6bc59c65bc97d0818010c489bd16eb7c746d9c45f0c53b90e581e9fbc5b2f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-colorramps - r-doparallel @@ -27,12 +28,14 @@ requirements: - r-gplots - r-iterators - 'r-lme4 >=1.1-10' + - r-lmertest - r-mass - 'r-pbkrtest >=0.4-4' - r-reshape2 + - r-scales run: - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-colorramps - r-doparallel @@ -41,17 +44,18 @@ requirements: - r-gplots - r-iterators - 'r-lme4 >=1.1-10' + - r-lmertest - r-mass - 'r-pbkrtest >=0.4-4' - r-reshape2 + - r-scales test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.' - + summary: 'Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.' extra: identifiers: - biotools:variancepartition diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index aaa70bed632af..ceb5276d433cd 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.1" %} {% set name = "VariantAnnotation" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,50 +8,54 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f6b030d73691eb96db5446c4bcc6a08fa011052a94dc3ece5672b42ad4f353b8 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 59a2859fddc9ed6ddc98969bd2e6df65c6643c73768ee3370e48b650529ca5e4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-annotationdbi >=1.27.9' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - 'bioconductor-biostrings >=2.33.5' - - 'bioconductor-bsgenome >=1.37.6' - - 'bioconductor-genomeinfodb >=1.11.4' - - 'bioconductor-genomicfeatures >=1.27.4' - - 'bioconductor-genomicranges >=1.27.6' - - 'bioconductor-iranges >=2.3.25' - - 'bioconductor-rsamtools >=1.23.10' - - 'bioconductor-rtracklayer >=1.25.16' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.5.3' - - 'bioconductor-xvector >=0.5.6' - - bioconductor-zlibbioc + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.27.9' - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.15.3' - - 'bioconductor-biostrings >=2.33.5' - - 'bioconductor-bsgenome >=1.37.6' - - 'bioconductor-genomeinfodb >=1.11.4' - - 'bioconductor-genomicfeatures >=1.27.4' - - 'bioconductor-genomicranges >=1.27.6' - - 'bioconductor-iranges >=2.3.25' - - 'bioconductor-rsamtools >=1.23.10' - - 'bioconductor-rtracklayer >=1.25.16' - - 'bioconductor-s4vectors >=0.13.13' - - 'bioconductor-summarizedexperiment >=1.5.3' - - 'bioconductor-xvector >=0.5.6' - - bioconductor-zlibbioc + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base - r-dbi + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -59,7 +63,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Annotate variants, compute amino acid coding changes, predict coding outcomes.' - extra: identifiers: - biotools:variantannotation diff --git a/recipes/bioconductor-variantfiltering/conda_build_config.yaml b/recipes/bioconductor-variantfiltering/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-variantfiltering/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-variantfiltering/meta.yaml b/recipes/bioconductor-variantfiltering/meta.yaml index abf111bce2ad6..891040a80c2d2 100644 --- a/recipes/bioconductor-variantfiltering/meta.yaml +++ b/recipes/bioconductor-variantfiltering/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "VariantFiltering" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,60 +10,68 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4b450c8f7c7dd8ea25f43bf3bfbd56528a754324ae0f8ef29731621fd34b25f1 + sha256: 96013d7fde2454ac565a36fd01ef9593c338b0f6d25ed2ac491810350c801395 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.33.11' - - bioconductor-bsgenome - - 'bioconductor-genomeinfodb >=1.3.6' - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.19.13' - - 'bioconductor-genomicscores >=1.0.0' - - bioconductor-graph - - bioconductor-gviz - - 'bioconductor-iranges >=2.3.23' - - bioconductor-rbgl - - 'bioconductor-rsamtools >=1.17.8' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.13.29' - - bioconductor-xvector + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base + - r-dt - r-shiny + - r-shinyjs + - r-shinythemes + - r-shinytree run: - - bioconductor-annotationdbi - - bioconductor-biobase - - 'bioconductor-biocgenerics >=0.13.8' - - bioconductor-biocparallel - - 'bioconductor-biostrings >=2.33.11' - - bioconductor-bsgenome - - 'bioconductor-genomeinfodb >=1.3.6' - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.19.13' - - 'bioconductor-genomicscores >=1.0.0' - - bioconductor-graph - - bioconductor-gviz - - 'bioconductor-iranges >=2.3.23' - - bioconductor-rbgl - - 'bioconductor-rsamtools >=1.17.8' - - 'bioconductor-s4vectors >=0.9.25' - - bioconductor-summarizedexperiment - - 'bioconductor-variantannotation >=1.13.29' - - bioconductor-xvector + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicscores >=1.4.1,<1.6.0' + - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-gviz >=1.24.0,<1.26.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-xvector >=0.20.0,<0.22.0' - r-base + - r-dt - r-shiny - - libcxx # [osx] + - r-shinyjs + - r-shinythemes + - r-shinytree + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -71,7 +79,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.' - extra: identifiers: - biotools:variantfiltering diff --git a/recipes/bioconductor-varianttools/meta.yaml b/recipes/bioconductor-varianttools/meta.yaml index af1e82fcb51fd..f4d29d38804ca 100644 --- a/recipes/bioconductor-varianttools/meta.yaml +++ b/recipes/bioconductor-varianttools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "VariantTools" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,44 +8,45 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5ee327fd15427b4895e231ffd62372e5b98d947589a2cae42bca006393c641d5 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 945d1d7f611094b7cfebf46583ebe431b644af071c385be5481e2cc8e78570f4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - 'bioconductor-genomicfeatures >=1.17.13' - - 'bioconductor-genomicranges >=1.17.7' - - 'bioconductor-iranges >=1.99.2' - - 'bioconductor-rsamtools >=1.17.6' - - 'bioconductor-rtracklayer >=1.25.3' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-variantannotation >=1.11.16' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-matrix run: - - bioconductor-biobase - - bioconductor-biocgenerics - - bioconductor-biocparallel - - bioconductor-biostrings - - bioconductor-bsgenome - - bioconductor-genomeinfodb - - 'bioconductor-genomicfeatures >=1.17.13' - - 'bioconductor-genomicranges >=1.17.7' - - 'bioconductor-iranges >=1.99.2' - - 'bioconductor-rsamtools >=1.17.6' - - 'bioconductor-rtracklayer >=1.25.3' - - 'bioconductor-s4vectors >=0.9.25' - - 'bioconductor-variantannotation >=1.11.16' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-matrix test: @@ -55,7 +56,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Explore, diagnose, and compare variant calls using filters.' - extra: identifiers: - biotools:varianttools diff --git a/recipes/bioconductor-vbmp/meta.yaml b/recipes/bioconductor-vbmp/meta.yaml index 5a26386a35270..4b91eeadddd3b 100644 --- a/recipes/bioconductor-vbmp/meta.yaml +++ b/recipes/bioconductor-vbmp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "vbmp" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 77a4058129bd3dcffd917143730be3e19c14b880e41277054c1b9675659b7f05 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 6e0eaa285699b910c8f7dc3da040d774dc1b04c170d74884e0c73f14e556e8df build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.' - extra: identifiers: - biotools:vbmp diff --git a/recipes/bioconductor-vega/meta.yaml b/recipes/bioconductor-vega/meta.yaml index c9f115bbbecde..95dfbfd56add3 100644 --- a/recipes/bioconductor-vega/meta.yaml +++ b/recipes/bioconductor-vega/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Vega" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cd97a242b61e24629494aeb41c9dbc3f26f2249ff6cead073ded10d50f3ccacf + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fb8f664b4b98bf2143bf215fa949fde00a8906915c9b9d004f6c242ff931f78c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,9 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +31,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Vega (Variational Estimator for Genomic Aberrations) is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected.' - extra: identifiers: - biotools:vega diff --git a/recipes/bioconductor-vegamc/meta.yaml b/recipes/bioconductor-vegamc/meta.yaml index 006ae23a7c851..a276db1b721e2 100644 --- a/recipes/bioconductor-vegamc/meta.yaml +++ b/recipes/bioconductor-vegamc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.16.0" %} +{% set version = "3.18.0" %} {% set name = "VegaMC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,26 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 71180a4a3c184c82519d9fd260242f2cdaf73c545740f2c5eeae59459caaafd2 + sha256: 4abeb54d7a68466198c47961c6bed5ae0b7699cf3f039a9db203e911b1caa711 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-genoset + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genoset >=1.36.0,<1.38.0' - r-base run: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-genoset + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-genoset >=1.36.0,<1.38.0' - r-base - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +37,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.' - extra: identifiers: - biotools:vegamc diff --git a/recipes/bioconductor-viper/meta.yaml b/recipes/bioconductor-viper/meta.yaml index 977e87e1e66d8..f4b14539805cb 100644 --- a/recipes/bioconductor-viper/meta.yaml +++ b/recipes/bioconductor-viper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "viper" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,22 +8,23 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 35156e299bee35c08442ac75e281f0cf1fd6d5d4a10290ae2a2f6c10c0773ecd + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: afb1a611e36c40cd3b1b58ae2f1bcd20df028bee9e01981788d735283c348203 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-e1071 - r-kernsmooth - r-mixtools run: - - bioconductor-biobase + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - r-e1071 - r-kernsmooth @@ -35,7 +36,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms' - extra: identifiers: - biotools:viper diff --git a/recipes/bioconductor-vsn/conda_build_config.yaml b/recipes/bioconductor-vsn/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-vsn/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index 17e89f28c9e30..1b40a9a5e68cb 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.46.0" %} +{% set version = "3.48.1" %} {% set name = "vsn" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,28 +8,32 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d270edb3a08bb03e0164101f6e541c62d6e5b90c84966dde2b47e6f8e115c6a3 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: f0948b5041b216e92af04571de5150a210ebc88bbbf630ae720bfff10654d54c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-ggplot2 - r-lattice run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-limma + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' - r-base - r-ggplot2 - r-lattice + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -37,7 +41,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.' - extra: identifiers: - biotools:vsn diff --git a/recipes/bioconductor-watermelon/conda_build_config.yaml b/recipes/bioconductor-watermelon/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-watermelon/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml index b9878ac3007f1..3ee7290b89461 100644 --- a/recipes/bioconductor-watermelon/meta.yaml +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "wateRmelon" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,31 +10,31 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b0d82f5016e87a12cd7568391a6ae0684a11a1b198c1a22fe56db6ad26e78380 + sha256: 01a311de4db43001c9fa0f2695fe6737aee266f67672dcd5fa3dab9f9ddc2db4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 - - bioconductor-illuminaio - - bioconductor-limma - - bioconductor-lumi - - bioconductor-methylumi - - bioconductor-roc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - r-matrixstats run: - - bioconductor-biobase - - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 - - bioconductor-illuminaio - - bioconductor-limma - - bioconductor-lumi - - bioconductor-methylumi - - bioconductor-roc + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' + - 'bioconductor-illuminaio >=0.22.0,<0.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-lumi >=2.32.0,<2.34.0' + - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-roc >=1.56.0,<1.58.0' - r-base - r-matrixstats test: @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: '15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.' - extra: identifiers: - biotools:watermelon diff --git a/recipes/bioconductor-wavcluster/meta.yaml b/recipes/bioconductor-wavcluster/meta.yaml index df31e05bf1656..30637d195e8d4 100644 --- a/recipes/bioconductor-wavcluster/meta.yaml +++ b/recipes/bioconductor-wavcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.11.0" %} +{% set version = "2.14.0" %} {% set name = "wavClusteR" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,22 +10,22 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b1fab2c4a4814e8b19f776801ed1129662a43dbe72222cb50719fba40a993438 + sha256: f5076a5fa67e32d22faa10e696558dc5b9bd251bac83070ba8ef8ebca8ab8526 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-foreach - r-ggplot2 @@ -35,14 +35,14 @@ requirements: - r-stringr - r-wmtsa run: - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-genomicfeatures - - 'bioconductor-genomicranges >=1.23.16' - - 'bioconductor-iranges >=2.5.27' - - bioconductor-rsamtools - - bioconductor-rtracklayer - - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-foreach - r-ggplot2 @@ -58,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).' - extra: identifiers: - biotools:wavcluster diff --git a/recipes/bioconductor-wavetiling/conda_build_config.yaml b/recipes/bioconductor-wavetiling/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-wavetiling/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-wavetiling/meta.yaml b/recipes/bioconductor-wavetiling/meta.yaml index ce139fb77808f..a136d9d3c44f3 100644 --- a/recipes/bioconductor-wavetiling/meta.yaml +++ b/recipes/bioconductor-wavetiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "waveTiling" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,40 +10,40 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4f9e350f0cc50ad17bbefdf8063808c84271a529b2325d4bf85959b911299fb6 + sha256: 771257e7925bf8ae57b042f6885eb251184c285149d81e9c374fed49bdf82fb1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} host: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-genomegraphs - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-oligo - - bioconductor-oligoclasses - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-waveslim run: - - bioconductor-affy - - bioconductor-biobase - - bioconductor-biostrings - - bioconductor-genomegraphs - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-oligo - - bioconductor-oligoclasses - - bioconductor-preprocesscore + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-base - r-waveslim - - libcxx # [osx] + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +51,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.' - extra: identifiers: - biotools:wavetiling diff --git a/recipes/bioconductor-weaver/meta.yaml b/recipes/bioconductor-weaver/meta.yaml index 9274b838bc4e9..8291f6e4ab46a 100644 --- a/recipes/bioconductor-weaver/meta.yaml +++ b/recipes/bioconductor-weaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "weaver" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c6ef9230ec22c6519a919d8e29dfff98e4f0739edc65997c5caa8afbc847cf19 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d87b51bf4c5b15c2c17f9c4310b535b7eb3abe9d2ee2918167e7193543e025cc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -31,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.' - extra: identifiers: - biotools:weaver diff --git a/recipes/bioconductor-webbioc/conda_build_config.yaml b/recipes/bioconductor-webbioc/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-webbioc/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-webbioc/meta.yaml b/recipes/bioconductor-webbioc/meta.yaml index 26bd9d9bad769..593165c34993e 100644 --- a/recipes/bioconductor-webbioc/meta.yaml +++ b/recipes/bioconductor-webbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "webbioc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ad2a0cf3b4b0fe9f5a9de9515941482ea01bf971a262d36fbdfe240ced55e6cd + sha256: 89dee6b8f11fa13f49f128a629fa0dc101b3f9ffdfba186a533e4c4b943d697c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-affy - - bioconductor-annaffy - - bioconductor-biobase - - bioconductor-biocinstaller - - bioconductor-gcrma - - bioconductor-multtest - - bioconductor-qvalue - - bioconductor-vsn + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base run: - - bioconductor-affy - - bioconductor-annaffy - - bioconductor-biobase - - bioconductor-biocinstaller - - bioconductor-gcrma - - bioconductor-multtest - - bioconductor-qvalue - - bioconductor-vsn + - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' + - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-vsn >=3.48.1,<3.50.0' - r-base test: commands: @@ -44,7 +44,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)' - extra: identifiers: - biotools:webbioc diff --git a/recipes/bioconductor-wiggleplotr/meta.yaml b/recipes/bioconductor-wiggleplotr/meta.yaml index 2ce8025ac5315..1c4eb374b3e83 100644 --- a/recipes/bioconductor-wiggleplotr/meta.yaml +++ b/recipes/bioconductor-wiggleplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "wiggleplotr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,20 +8,21 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c25604d9375e49e279a91a60c628a11cdd437ef248b94d7140cc781360dd98e9 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a1996015e41c68a01d2985c6f0447426d1cff870489c7ec3240fb0c9e2c819ea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-assertthat - r-base - r-cowplot @@ -29,11 +30,11 @@ requirements: - 'r-ggplot2 >=2.2.0' - r-purrr run: - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-iranges - - bioconductor-rtracklayer - - bioconductor-s4vectors + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-assertthat - r-base - r-cowplot @@ -47,3 +48,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Apache License 2.0' summary: 'Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.' + + diff --git a/recipes/bioconductor-xbseq/meta.yaml b/recipes/bioconductor-xbseq/meta.yaml index 5e39c1328f684..01f4735da943e 100644 --- a/recipes/bioconductor-xbseq/meta.yaml +++ b/recipes/bioconductor-xbseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "XBSeq" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,18 +8,19 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 245a06e94e1341f0ce530acd877ad6ff6cda066a40a99984a4878ec6031b221c + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3d566b6c678dbd5a3fa93100a24d4ec43b9e8a5c5ae1ad538a355fd2a8abd3ea build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-deseq2 - - bioconductor-roar + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-roar >=1.16.0,<1.18.0' - r-base - r-dplyr - r-ggplot2 @@ -28,9 +29,9 @@ requirements: - r-matrixstats - r-pracma run: - - bioconductor-biobase - - bioconductor-deseq2 - - bioconductor-roar + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' + - 'bioconductor-roar >=1.16.0,<1.18.0' - r-base - r-dplyr - r-ggplot2 @@ -45,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.' - extra: identifiers: - biotools:xbseq diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index f439ecf6a19a3..a5f8e3b32d408 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "3.0.0" %} +{% set version = "3.2.0" %} {% set name = "xcms" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: 'https://depot.galaxyproject.org/software/bioconductor-xcms/bioconductor-xcms_3.0.0_src_all.tar.gz' - sha256: a0e7e3fb25eefa4976577cbf862504239eaeb15c28dfcc11c5e040a88f2fc47b + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: af86ad398169f2ed955bb5fbfea86ca3913fda3431cbaac59ec0ca7b99e91a77 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-biocparallel >=1.8.0' - - 'bioconductor-massspecwavelet >=1.5.2' - - 'bioconductor-msnbase >=2.3.11' - - bioconductor-multtest - - 'bioconductor-mzr >=1.1.6' - - bioconductor-protgenerics - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-lattice - r-plyr - r-rann - r-rcolorbrewer run: - - bioconductor-biobase - - bioconductor-biocgenerics - - 'bioconductor-biocparallel >=1.8.0' - - 'bioconductor-massspecwavelet >=1.5.2' - - 'bioconductor-msnbase >=2.3.11' - - bioconductor-multtest - - 'bioconductor-mzr >=1.1.6' - - bioconductor-protgenerics - - bioconductor-s4vectors + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' + - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - r-base - r-lattice - r-plyr - r-rann - r-rcolorbrewer + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -51,7 +58,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.' - extra: identifiers: - biotools:xcms diff --git a/recipes/bioconductor-xde/meta.yaml b/recipes/bioconductor-xde/meta.yaml index 4da993117d5c1..93feaccbceff3 100644 --- a/recipes/bioconductor-xde/meta.yaml +++ b/recipes/bioconductor-xde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "XDE" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,36 +8,41 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b70888f962a6556afaa95096b30890c799abfafb1556100e1ee03ae5ec27e785 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a9e0c589824eecc5b5c2d8a7b2032c20922987ed7bcabd68b8317c02d8889929 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-genemeta - - bioconductor-mergemaid - - bioconductor-siggenes + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genemeta >=1.52.0,<1.54.0' + - 'bioconductor-mergemaid >=2.52.0,<2.54.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' - r-base - r-gtools - r-mvtnorm - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.5.5' - - bioconductor-biocgenerics - - bioconductor-genefilter - - bioconductor-genemeta - - bioconductor-mergemaid - - bioconductor-siggenes + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genemeta >=1.52.0,<1.54.0' + - 'bioconductor-mergemaid >=2.52.0,<2.54.0' + - 'bioconductor-siggenes >=1.54.0,<1.56.0' - r-base - r-gtools - r-mvtnorm - r-rcolorbrewer + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -45,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'Multi-level model for cross-study detection of differential gene expression.' - extra: identifiers: - biotools:xde diff --git a/recipes/bioconductor-xmapbridge/meta.yaml b/recipes/bioconductor-xmapbridge/meta.yaml index 36c40f39d1f83..183a1b3bfdb2f 100644 --- a/recipes/bioconductor-xmapbridge/meta.yaml +++ b/recipes/bioconductor-xmapbridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "xmapbridge" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1e43753f3716ca2f6191258fe48e20516910f4c85324be8299530e28df3c604b + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b07cc4776287820b8ef16153a1265a071c285711056043e653051c116f1bc09f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -27,7 +28,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.' - extra: identifiers: - biotools:xmapbridge diff --git a/recipes/bioconductor-xvector/meta.yaml b/recipes/bioconductor-xvector/meta.yaml index 0f2585e3e6274..f383693a09647 100644 --- a/recipes/bioconductor-xvector/meta.yaml +++ b/recipes/bioconductor-xvector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.18.0" %} +{% set version = "0.20.0" %} {% set name = "XVector" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,26 +8,30 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b36e985344cc3d033d567e2206029e272e1fc23dc5e0ce66c8149ddcdb1c91c4 + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6e5c1a3b9f5ff1319082165bdc7e5e33a121b8d70c1514b4040f7a4d138454fe build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.19.2' - - 'bioconductor-iranges >=2.9.18' - - 'bioconductor-s4vectors >=0.15.14' - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base run: - - 'bioconductor-biocgenerics >=0.19.2' - - 'bioconductor-iranges >=2.9.18' - - 'bioconductor-s4vectors >=0.15.14' - - bioconductor-zlibbioc + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +39,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).' - extra: identifiers: - biotools:xvector diff --git a/recipes/bioconductor-yamss/meta.yaml b/recipes/bioconductor-yamss/meta.yaml index 5a90f7c4241aa..3df1a082d05a5 100644 --- a/recipes/bioconductor-yamss/meta.yaml +++ b/recipes/bioconductor-yamss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "yamss" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,32 +10,32 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2987fc9b2c0665adba4e720bb93eee903d53a13b6184c998e206b9788403b822 + sha256: 0ed9549260a45ad3063d4ff19186c744de7c3279c8666aa1fa692ea9cfceff61 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-ebimage - - bioconductor-iranges - - bioconductor-limma - - bioconductor-mzr - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocgenerics >=0.15.3' - - bioconductor-ebimage - - bioconductor-iranges - - bioconductor-limma - - bioconductor-mzr - - bioconductor-s4vectors - - bioconductor-summarizedexperiment + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-data.table - r-matrix @@ -46,7 +46,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.' - extra: identifiers: - biotools:yamss diff --git a/recipes/bioconductor-yapsa/conda_build_config.yaml b/recipes/bioconductor-yapsa/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-yapsa/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-yapsa/meta.yaml b/recipes/bioconductor-yapsa/meta.yaml index 2888914123c8b..8a08240bdc742 100644 --- a/recipes/bioconductor-yapsa/meta.yaml +++ b/recipes/bioconductor-yapsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "YAPSA" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,21 +10,21 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9ccf72d8810f9e55fe2e501bc8d14cf61f73fc64a6da1138446b65dc3a20694b + sha256: 85fb250a2badf2975347257691b2371000ab12476525bdf196c3a090a40a7042 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-complexheatmap - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gtrellis - - bioconductor-keggrest - - bioconductor-somaticsignatures - - bioconductor-variantannotation + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gtrellis >=1.12.1,<1.14.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-circlize - r-corrplot @@ -36,13 +36,13 @@ requirements: - r-pmcmr - r-reshape2 run: - - bioconductor-complexheatmap - - bioconductor-genomeinfodb - - bioconductor-genomicranges - - bioconductor-gtrellis - - bioconductor-keggrest - - bioconductor-somaticsignatures - - bioconductor-variantannotation + - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' + - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-gtrellis >=1.12.1,<1.14.0' + - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' + - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - r-base - r-circlize - r-corrplot @@ -60,7 +60,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.' - extra: identifiers: - biotools:yapsa diff --git a/recipes/bioconductor-yaqcaffy/conda_build_config.yaml b/recipes/bioconductor-yaqcaffy/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-yaqcaffy/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-yaqcaffy/meta.yaml b/recipes/bioconductor-yaqcaffy/meta.yaml index 42320f18ef458..fb26cdb8ad613 100644 --- a/recipes/bioconductor-yaqcaffy/meta.yaml +++ b/recipes/bioconductor-yaqcaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "yaqcaffy" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8f8203525852860d439f58e7f2afd035e83480dad7a46c60d93b437570fa9390 + sha256: ebb25aba1d352aedc41c94267536d6914d2107a753e426e58cb0f4c27956a7a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-simpleaffy >=2.19.3' + - 'bioconductor-simpleaffy >=2.56.0,<2.58.0' - r-base run: - - 'bioconductor-simpleaffy >=2.19.3' + - 'bioconductor-simpleaffy >=2.56.0,<2.58.0' - r-base test: commands: @@ -30,7 +30,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.' - extra: identifiers: - biotools:yaqcaffy diff --git a/recipes/bioconductor-yarn/meta.yaml b/recipes/bioconductor-yarn/meta.yaml index 7c68449449e47..2cb61bab40931 100644 --- a/recipes/bioconductor-yarn/meta.yaml +++ b/recipes/bioconductor-yarn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "yarn" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,20 +10,20 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3b62b4a2c8fc4740f4d518d210837901bfb9cec0a640bebed9ff3e7421b727bf + sha256: 10760732a1437ca8e94773e452fbc49ed96a44ac6ff1a5c71b0e751136b39e3b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-edger - - bioconductor-limma - - bioconductor-preprocesscore - - bioconductor-quantro + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-quantro >=1.14.0,<1.16.0' - r-base - r-downloader - r-gplots @@ -31,12 +31,12 @@ requirements: - r-rcolorbrewer - r-readr run: - - bioconductor-biobase - - bioconductor-biomart - - bioconductor-edger - - bioconductor-limma - - bioconductor-preprocesscore - - bioconductor-quantro + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-quantro >=1.14.0,<1.16.0' - r-base - r-downloader - r-gplots @@ -50,7 +50,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.' - extra: identifiers: - biotools:yarn diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml index 3051c2ebdc02a..3401987270c8a 100644 --- a/recipes/bioconductor-yeastcc/meta.yaml +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "yeastCC" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,18 +10,18 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d166f00c91828632439753a814f6c63237efda363a3d12b5bc7c1161a39da0e2 + sha256: 1098741155fb624a2a02d1f74874d307882842dfcbb79937bd64f9120ed6602f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base run: - - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-biobase >=2.40.0,<2.42.0' - r-base - wget test: @@ -31,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment' + + diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh index 07c2425ad12da..0c62ebc7b5b9b 100644 --- a/recipes/bioconductor-yeastcc/post-link.sh +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastCC_1.18.0.tar.gz" +FN="yeastCC_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/yeastCC_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastCC_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.18.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/yeastCC_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastCC_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.20.0_src_all.tar.gz" ) -MD5="676bd01ca703f018cd36a8b7a2f37989" +MD5="01c7f1799dc44282f802e6e05cc6b730" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index 2af1c5ca2f33e..8203b9957f8fb 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.24.0" %} +{% set version = "0.26.0" %} {% set name = "yeastExpData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,19 +8,20 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2d6e269b91945c9957e1c4a3bc2ff06c26f759451b8a68969be8ce63580069a7 + sha256: 07e0e11fbf2c30f393c72e0f0363fa331e616441d39575fa90837b5b52fa45e0 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-graph >=1.9.26' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base run: - - 'bioconductor-graph >=1.9.26' + - 'bioconductor-graph >=1.58.0,<1.60.0' - r-base - wget test: @@ -30,3 +31,5 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL summary: 'A collection of different sets of experimental data from yeast.' + + diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index 01ead60b635d4..a5991bfbe185b 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="yeastExpData_0.24.0.tar.gz" +FN="yeastExpData_0.26.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/yeastExpData_0.24.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.24.0_src_all.tar.gz" + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/yeastExpData_0.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastExpData_0.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.26.0_src_all.tar.gz" ) -MD5="0f210bd46c16fd7b10ce38ecda8ad37a" +MD5="43d0c9935427e1b2d7c35ff5fbb3d5fc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -42,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-zfpkm/meta.yaml b/recipes/bioconductor-zfpkm/meta.yaml index 8c27fb8759706..b4ae1d7a49a2d 100644 --- a/recipes/bioconductor-zfpkm/meta.yaml +++ b/recipes/bioconductor-zfpkm/meta.yaml @@ -1,45 +1,42 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "zFPKM" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3ba04bf9b972bfb0f71eb350ac17e756f8e418e9a199740830dbee086a5042ae - + sha256: e96ab54765a5198bb135eed7d31ac835f62aa1dfbd5167e089d579fab37571da build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: host: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr run: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr - test: commands: - '$R -e "library(''{{ name }}'')"' - about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | file LICENSE' summary: 'Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.' + + diff --git a/recipes/bioconductor-zinbwave/conda_build_config.yaml b/recipes/bioconductor-zinbwave/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-zinbwave/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index e7ef7e0c7f251..5dbf4df5aa581 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "zinbwave" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,7 +10,7 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2ac640227b3adc489086fa7f9c797d595fce3ad0e8ef79c80533af7334cced64 + sha256: a01299397b8cd8bc4d1e6818b3006f25cf9da2a4a482703e703ee63159ab819a build: number: 0 skip: true # [osx] @@ -19,22 +19,22 @@ build: - lib/ requirements: build: - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-genefilter - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.0,<1.16.0' + - 'bioconductor-edger >=3.22.0,<3.24.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' - r-base - r-copula - r-glmnet - r-softimpute - gsl >=2.4 run: - - bioconductor-biocparallel - - bioconductor-edger - - bioconductor-genefilter - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment + - 'bioconductor-biocparallel >=1.14.0,<1.16.0' + - 'bioconductor-edger >=3.22.0,<3.24.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' - r-base - r-copula - r-glmnet diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index f04d8c6e16f3d..95d1e203c029d 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "zlibbioc" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -8,10 +8,11 @@ package: source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 22f9bb05a415ae3ce828a904abc0f290aede5ae5fdb212fc75f4c152e08229ff + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ff9d472e7505f049f291285bc276e48fa40aab24712b1d0116e12814590599e7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ @@ -20,6 +21,10 @@ requirements: - r-base run: - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -27,7 +32,6 @@ about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 + file LICENSE' summary: 'This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.' - extra: identifiers: - biotools:zlibbioc diff --git a/recipes/dnp-diprofile/build.sh b/recipes/dnp-diprofile/build.sh index b89115bfc4cc5..4bea5decc0b49 100644 --- a/recipes/dnp-diprofile/build.sh +++ b/recipes/dnp-diprofile/build.sh @@ -1,5 +1,4 @@ #!/bin/bash -env sed 's/CPROGNAME/diprofile/g' CMakeLists.template > CMakeLists.txt mkdir -p build diff --git a/recipes/genenotebook/build.sh b/recipes/genenotebook/build.sh index 25663b089fd18..360efc995f30e 100644 --- a/recipes/genenotebook/build.sh +++ b/recipes/genenotebook/build.sh @@ -2,12 +2,8 @@ set -exo pipefail -echo ${CXX} - outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} mkdir -p $outdir $PREFIX/bin - -pwd ls -l . npm install --unsafe-perm METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index f2e821ec21ac1..31494fe13b885 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -32,4 +32,4 @@ about: home: https://genenotebook.github.io license: AGPL-3.0 license_file: LICENSE - summary: A colleborative notebook for comparative genomics \ No newline at end of file + summary: A colleborative notebook for comparative genomics diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 570e5c209e4a2..a16d2a1b79a23 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -24,7 +24,6 @@ source: url: http://genesis.ugent.be/maven2/eu/isas/peptideshaker/{{ name }}/{{ version }}/{{ name }}-{{ version }}.zip sha256: 7086bf35b9f0ac0ad52d940f782373cd05f0b5cac638d3e696311939de980602 - requirements: host: run: diff --git a/recipes/phame/meta.yaml b/recipes/phame/meta.yaml index d7a2f45765b80..99e21c20496f9 100644 --- a/recipes/phame/meta.yaml +++ b/recipes/phame/meta.yaml @@ -2,7 +2,6 @@ {% set version = "1.0.3" %} {% set hash = "026b5c54ff9fe121fefd222dc2f9912da34a9395a04d26f7e468aca5adcd1703" %} - package: name: {{ name }} version: "{{ version }}" diff --git a/recipes/r-DGEclustering/build.sh b/recipes/r-DGEclustering/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-DGEclustering/build.sh +++ b/recipes/r-DGEclustering/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-DGEclustering/meta.yaml b/recipes/r-DGEclustering/meta.yaml index daec07cbe3614..105b4c5f94f02 100644 --- a/recipes/r-DGEclustering/meta.yaml +++ b/recipes/r-DGEclustering/meta.yaml @@ -12,6 +12,7 @@ source: build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ @@ -51,4 +52,12 @@ about: home: https://github.com/reneechou123/DGEclustering license: "MIT" summary: "DGEclustering is an R package for multidimensional clustering of differential gene expression datasets, and it integrates GO annotations to improve the clustering result." - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-adegenet/build.sh b/recipes/r-adegenet/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-adegenet/build.sh +++ b/recipes/r-adegenet/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-adegenet/meta.yaml b/recipes/r-adegenet/meta.yaml index ad22970e0cdda..4c90f835212b6 100644 --- a/recipes/r-adegenet/meta.yaml +++ b/recipes/r-adegenet/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.1.0' %} +{% set version = '2.1.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-adegenet @@ -6,20 +9,29 @@ package: source: url: - - https://cran.r-project.org/src/contrib/adegenet_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/adegenet/adegenet_{{ version }}.tar.gz - sha256: 7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a + - {{ cran_mirror }}/src/contrib/adegenet_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/adegenet/adegenet_{{ version }}.tar.gz + sha256: 3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -38,6 +50,7 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-mass - r-ade4 - r-ape @@ -53,7 +66,9 @@ requirements: test: commands: - - $R -e "library('adegenet')" + + - $R -e "library('adegenet')" # [not win] + - "\"%R%\" -e \"library('adegenet')\"" # [win] about: home: https://github.com/thibautjombart/adegenet @@ -67,3 +82,12 @@ about: A range of both empirical and simulated datasets is also provided to illustrate various methods. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-adephylo/build.sh b/recipes/r-adephylo/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-adephylo/build.sh +++ b/recipes/r-adephylo/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-adephylo/meta.yaml b/recipes/r-adephylo/meta.yaml index 83dcdb975db42..397436edc6348 100644 --- a/recipes/r-adephylo/meta.yaml +++ b/recipes/r-adephylo/meta.yaml @@ -1,26 +1,36 @@ {% set version = '1.1-11' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-adephylo version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/adephylo_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/adephylo/adephylo_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/adephylo_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/adephylo/adephylo_{{ version }}.tar.gz sha256: 154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ - requirements: - build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -31,6 +41,7 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-ade4 >=1.7_10 - r-adegenet - r-ape @@ -38,11 +49,22 @@ requirements: test: commands: - - $R -e "library('adephylo')" + + - $R -e "library('adephylo')" # [not win] + - "\"%R%\" -e \"library('adephylo')\"" # [win] about: home: https://CRAN.R-project.org/package=adephylo - license: 'GPL (>= 2)' + license: GPL (>= 2) summary: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-alakazam/build.sh b/recipes/r-alakazam/build.sh deleted file mode 100755 index af6547bf3c22e..0000000000000 --- a/recipes/r-alakazam/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$R CMD INSTALL --build . diff --git a/recipes/r-alakazam/meta.yaml b/recipes/r-alakazam/meta.yaml deleted file mode 100644 index ccc324e359ec8..0000000000000 --- a/recipes/r-alakazam/meta.yaml +++ /dev/null @@ -1,60 +0,0 @@ -{% set version = '0.2.10' %} - -package: - name: r-alakazam - version: {{ version|replace("-", "_") }} - -source: - url: - - https://cran.r-project.org/src/contrib/alakazam_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/alakazam/alakazam_{{ version }}.tar.gz - sha256: d9fe93736b7ec0a38774f8a31df04461bee45ca71d31e45703b242b6f261d82d - -build: - number: 1 - skip: true # [osx] - - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - {{ compiler('cxx') }} - - host: - - r-base - - r-rcpp - - r-dplyr >=0.5.0 - - r-ggplot2 >=2.0.0 - - r-igraph >=1.0.0 - - r-lazyeval - - r-progress - - r-readr - - r-scales - - r-seqinr - - r-stringi - - run: - - r-base - - r-rcpp - - r-dplyr >=0.5.0 - - r-ggplot2 >=2.0.0 - - r-igraph >=1.0.0 - - r-lazyeval - - r-progress - - r-readr - - r-scales - - r-seqinr - - r-stringi - -test: - commands: - - $R -e "library('alakazam')" - -about: - home: http://alakazam.readthedocs.org - license: CC BY-SA 4.0 - summary: Provides immunoglobulin (Ig) sequence lineage reconstruction, diversity profiling, - and amino acid property analysis. - license_family: OTHER diff --git a/recipes/r-ampvis/build.sh b/recipes/r-ampvis/build.sh index d5c1a4cb4bbdc..506aa0793f132 100644 --- a/recipes/r-ampvis/build.sh +++ b/recipes/r-ampvis/build.sh @@ -1,6 +1,3 @@ - #!/bin/bash - - # R refuses to build packages that mark themselves as Priority: Recommended mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION diff --git a/recipes/r-ampvis/meta.yaml b/recipes/r-ampvis/meta.yaml index 3849d18461aa7..7bb30dc8fbbb1 100644 --- a/recipes/r-ampvis/meta.yaml +++ b/recipes/r-ampvis/meta.yaml @@ -12,7 +12,6 @@ source: build: number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -65,4 +64,12 @@ about: home: https://github.com/MadsAlbertsen/ampvis license: AGPL-3 summary: 'A package to visualise amplicon data' - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-annotables/build.sh b/recipes/r-annotables/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-annotables/build.sh +++ b/recipes/r-annotables/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-annotables/meta.yaml b/recipes/r-annotables/meta.yaml index abb8185140819..e98e5a8f28ab3 100644 --- a/recipes/r-annotables/meta.yaml +++ b/recipes/r-annotables/meta.yaml @@ -6,7 +6,6 @@ package: version: {{ version|replace("-", "_") }} source: - fn: {{ version }}.tar.gz url: - https://github.com/stephenturner/{{ name }}/archive/{{ version }}.tar.gz sha256: a2a0e929cc2682c72032337aac3775733a68163ed7a6d72c25cc316f9f9c5c47 @@ -17,7 +16,6 @@ build: - lib/R/lib/ - lib/ - requirements: build: - r-base @@ -35,7 +33,17 @@ about: license: 'GPL-3' summary: Provides tables for converting and annotating Ensembl Gene IDs. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] extra: identifiers: - doi:10.5281/zenodo.996854 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-aptreeshape/build.sh b/recipes/r-aptreeshape/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-aptreeshape/build.sh +++ b/recipes/r-aptreeshape/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-aptreeshape/meta.yaml b/recipes/r-aptreeshape/meta.yaml index 840bbf4a3c66c..edbad01298f9c 100644 --- a/recipes/r-aptreeshape/meta.yaml +++ b/recipes/r-aptreeshape/meta.yaml @@ -1,26 +1,32 @@ -{% set name = 'apTreeshape' %} {% set version = '1.5-0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: - name: r-{{ name|lower }} + name: r-aptreeshape version: {{ version|replace("-", "_") }} source: - fn: {{ name }}_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/apTreeshape_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/apTreeshape/apTreeshape_{{ version }}.tar.gz sha256: 2f6619fe793d084e3cf97c12adfa4c1cb562e1a34db12da7bda79453c26cde56 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ - requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-ape - r-coda @@ -38,17 +44,27 @@ requirements: test: commands: - - $R -e "library('apTreeshape')" + + - $R -e "library('apTreeshape')" # [not win] + - "\"%R%\" -e \"library('apTreeshape')\"" # [win] about: home: https://CRAN.R-project.org/package=apTreeshape - license: 'GPL (>= 2)' + license: GPL (>= 2) summary: Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can - be converted easily. Implements methods described in Bortolussi et al. (2005) - and Maliet et al. (2017). + be converted easily. Implements methods described in Bortolussi et al. (2005) + and Maliet et al. (2017) . license_family: GPL3 - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-argumentcheck/build.sh b/recipes/r-argumentcheck/build.sh index be092347e8f41..5bf492ab9fc06 100644 --- a/recipes/r-argumentcheck/build.sh +++ b/recipes/r-argumentcheck/build.sh @@ -1,17 +1 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# diff --git a/recipes/r-argumentcheck/meta.yaml b/recipes/r-argumentcheck/meta.yaml index 41e08fb4675aa..ad31bd5dbe1ea 100644 --- a/recipes/r-argumentcheck/meta.yaml +++ b/recipes/r-argumentcheck/meta.yaml @@ -1,24 +1,31 @@ {% set version = '0.10.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-argumentcheck version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/ArgumentCheck_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ArgumentCheck/ArgumentCheck_{{ version }}.tar.gz - - + - {{ cran_mirror }}/src/contrib/ArgumentCheck_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ArgumentCheck/ArgumentCheck_{{ version }}.tar.gz sha256: 6c4222bc7e9cefbdabdc2e4336d851f3939b22d01b26c77ab49e8bb77e3dfd55 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -27,7 +34,9 @@ requirements: test: commands: - - $R -e "library('ArgumentCheck')" # [not win] + + - $R -e "library('ArgumentCheck')" # [not win] + - "\"%R%\" -e \"library('ArgumentCheck')\"" # [win] about: home: https://github.com/nutterb/ArgumentCheck @@ -38,3 +47,14 @@ about: argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-aroma.affymetrix/build.sh b/recipes/r-aroma.affymetrix/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-aroma.affymetrix/build.sh +++ b/recipes/r-aroma.affymetrix/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index c0c7220eaff49..75eabf5fe8ba4 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '3.1.0' %} +{% set version = '3.1.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-aroma.affymetrix @@ -6,51 +9,59 @@ package: source: url: - - https://cran.r-project.org/src/contrib/aroma.affymetrix_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/aroma.affymetrix/aroma.affymetrix_{{ version }}.tar.gz - sha256: 03c0d30c2e636409d527c0d4253d792218bba133681d5d334d19350c32ae8bea + - {{ cran_mirror }}/src/contrib/aroma.affymetrix_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/aroma.affymetrix/aroma.affymetrix_{{ version }}.tar.gz + sha256: 5c896d3e6ef45d11b7e2df6dff51d07d277d565b36cb537c93ecc0bd54e354f4 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-mass - - r-r.cache >=0.12.0 + - r-r.cache >=0.13.0 - r-r.devices >=2.15.1 - r-r.filesets >=2.11.0 - r-r.methodss3 >=1.7.1 - r-r.oo >=1.21.0 - - r-r.utils >=2.5.0 + - r-r.utils >=2.6.0 - r-aroma.apd >=0.6.0 - - r-aroma.core >=3.1.0 + - r-aroma.core >=3.1.1 - r-future - r-listenv - - r-matrixstats >=0.51.0 + - r-matrixstats >=0.52.2 run: - r-base - r-mass - - r-r.cache >=0.12.0 + - r-r.cache >=0.13.0 - r-r.devices >=2.15.1 - r-r.filesets >=2.11.0 - r-r.methodss3 >=1.7.1 - r-r.oo >=1.21.0 - - r-r.utils >=2.5.0 + - r-r.utils >=2.6.0 - r-aroma.apd >=0.6.0 - - r-aroma.core >=3.1.0 + - r-aroma.core >=3.1.1 - r-future - r-listenv - - r-matrixstats >=0.51.0 + - r-matrixstats >=0.52.2 test: commands: - - $R -e "library('aroma.affymetrix')" + + - $R -e "library('aroma.affymetrix')" # [not win] + - "\"%R%\" -e \"library('aroma.affymetrix')\"" # [win] about: home: http://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.affymetrix @@ -61,3 +72,12 @@ about: Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. license_family: LGPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-aroma.core/build.sh b/recipes/r-aroma.core/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-aroma.core/build.sh +++ b/recipes/r-aroma.core/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index 60f40a196a408..001eaeefd06bc 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '3.1.1' %} +{% set version = '3.1.3' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-aroma.core @@ -6,55 +9,72 @@ package: source: url: - - https://cran.r-project.org/src/contrib/aroma.core_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/aroma.core/aroma.core_{{ version }}.tar.gz - sha256: 615af96ace9ce276e0277d76637417508ea0d6f15e907732332ea28a029a7055 + - {{ cran_mirror }}/src/contrib/aroma.core_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/aroma.core/aroma.core_{{ version }}.tar.gz + sha256: 387cc6914188e0bd3aa1fb790c30666d913fa3bae800b0de04c03a0c078b337e build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - - r-pscbs >=0.62.0 - - r-r.cache >=0.12.0 + - r-pscbs >=0.63.0 + - r-r.cache >=0.13.0 - r-r.devices >=2.15.1 - - r-r.filesets >=2.11.0 + - r-r.filesets >=2.12.1 - r-r.methodss3 >=1.7.1 - - r-r.oo >=1.21.0 - - r-r.rsp >=0.40.0 - - r-r.utils >=2.5.0 + - r-r.oo >=1.22.0 + - r-r.rsp >=0.42.0 + - r-r.utils >=2.6.0 - r-rcolorbrewer >=1.1_2 - r-future - r-listenv - - r-matrixstats >=0.52.2 + - r-matrixstats >=0.53.1 run: - r-base - - r-pscbs >=0.62.0 - - r-r.cache >=0.12.0 + - r-pscbs >=0.63.0 + - r-r.cache >=0.13.0 - r-r.devices >=2.15.1 - - r-r.filesets >=2.11.0 + - r-r.filesets >=2.12.1 - r-r.methodss3 >=1.7.1 - - r-r.oo >=1.21.0 - - r-r.rsp >=0.40.0 - - r-r.utils >=2.5.0 + - r-r.oo >=1.22.0 + - r-r.rsp >=0.42.0 + - r-r.utils >=2.6.0 - r-rcolorbrewer >=1.1_2 - r-future - r-listenv - - r-matrixstats >=0.52.2 + - r-matrixstats >=0.53.1 test: commands: - - $R -e "library('aroma.core')" + + - $R -e "library('aroma.core')" # [not win] + - "\"%R%\" -e \"library('aroma.core')\"" # [win] about: home: https://github.com/HenrikBengtsson/aroma.core, http://www.aroma-project.org/ license: LGPL (>= 2.1) - summary: Core methods and classes used by higher-level aroma.* packages part of the Aroma Project, - e.g. aroma.affymetrix and aroma.cn. + summary: Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma + Project, e.g. 'aroma.affymetrix' and 'aroma.cn'. license_family: LGPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-asics/build.sh b/recipes/r-asics/build.sh index 6864ae6daf614..5bf492ab9fc06 100644 --- a/recipes/r-asics/build.sh +++ b/recipes/r-asics/build.sh @@ -1,8 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - diff --git a/recipes/r-asics/meta.yaml b/recipes/r-asics/meta.yaml index 479b8f575629a..9539e6c0d7bad 100644 --- a/recipes/r-asics/meta.yaml +++ b/recipes/r-asics/meta.yaml @@ -14,12 +14,10 @@ source: build: number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown requirements: host: - r-base @@ -50,4 +48,12 @@ about: in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) . ' - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-basejump/build.sh b/recipes/r-basejump/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-basejump/build.sh +++ b/recipes/r-basejump/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 9c4a757c7c79d..1a303844a152e 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -1,7 +1,6 @@ package: name: r-basejump - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. + version: "0.7.2" source: @@ -10,7 +9,8 @@ source: build: number: 0 - # This is required to make R link correctly on Linux. + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ @@ -94,3 +94,12 @@ about: home: https://github.com/steinbaugh/basejump license: MIT summary: Base functions for bioinformatics and R package development. +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-bcbiobase/build.sh b/recipes/r-bcbiobase/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-bcbiobase/build.sh +++ b/recipes/r-bcbiobase/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-bcbiobase/meta.yaml b/recipes/r-bcbiobase/meta.yaml index d7093b96bd7d1..93638978693fc 100644 --- a/recipes/r-bcbiobase/meta.yaml +++ b/recipes/r-bcbiobase/meta.yaml @@ -10,6 +10,7 @@ source: build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -80,3 +81,12 @@ about: summary: Base functions and generics for bcbio R packages. license_family: MIT dev_url: https://github.com/hbc/bcbioBase +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-bcbiornaseq/build.sh b/recipes/r-bcbiornaseq/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-bcbiornaseq/build.sh +++ b/recipes/r-bcbiornaseq/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-bcbiornaseq/conda_build_config.yaml b/recipes/r-bcbiornaseq/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/r-bcbiornaseq/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml index d527481d49e67..5835ae77d6364 100644 --- a/recipes/r-bcbiornaseq/meta.yaml +++ b/recipes/r-bcbiornaseq/meta.yaml @@ -1,7 +1,6 @@ package: name: r-bcbiornaseq - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. + version: "0.2.7" source: @@ -10,7 +9,8 @@ source: build: number: 0 - # This is required to make R link correctly on Linux. + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ @@ -22,7 +22,7 @@ requirements: - 'r-bcbiobase >=0.2.17' - bioconductor-deseq2 - bioconductor-degreport - - bioconductor-edger + - bioconductobioconductor-edger - r-ggrepel - r-pbapply - bioconductor-tximport @@ -36,7 +36,7 @@ requirements: - 'r-bcbiobase >=0.2.17' - bioconductor-deseq2 - bioconductor-degreport - - bioconductor-edger + - bioconductobioconductor-edger - r-ggrepel - r-pbapply - bioconductor-tximport @@ -44,7 +44,6 @@ requirements: - r-rmarkdown - r-tidyverse - test: commands: - $R -e "library('bcbioRNASeq')" @@ -53,3 +52,12 @@ about: home: https://github.com/hbc/bcbioRNASeq license: MIT summary: Quality control and differential expression for bcbio RNA-seq experiments. +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-bio3d/build.sh b/recipes/r-bio3d/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-bio3d/build.sh +++ b/recipes/r-bio3d/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-bio3d/meta.yaml b/recipes/r-bio3d/meta.yaml index 797543aa7ac7f..7662b6cc064ed 100644 --- a/recipes/r-bio3d/meta.yaml +++ b/recipes/r-bio3d/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.3-3' %} +{% set version = '2.3-4' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-bio3d @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/bio3d_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/bio3d/bio3d_{{ version }}.tar.gz - sha256: f4b45847eb8a4175dacea659f30a8075769ec1ae19daec6842b0d72227b48633 + - {{ cran_mirror }}/src/contrib/bio3d_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/bio3d/bio3d_{{ version }}.tar.gz + sha256: f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,7 +25,14 @@ build: requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -27,11 +40,14 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-rcpp test: commands: - - $R -e "library('bio3d')" + + - $R -e "library('bio3d')" # [not win] + - "\"%R%\" -e \"library('bio3d')\"" # [win] about: home: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d @@ -47,3 +63,14 @@ about: graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-biodb/build.sh b/recipes/r-biodb/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-biodb/build.sh +++ b/recipes/r-biodb/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-biodb/meta.yaml b/recipes/r-biodb/meta.yaml index cfea18064dfec..a1715fa14623e 100644 --- a/recipes/r-biodb/meta.yaml +++ b/recipes/r-biodb/meta.yaml @@ -49,3 +49,12 @@ about: license: AGPL-3.0 summary: 'An R package for connecting to chemical and biological databases.' home: https://github.com/pkrog/biodb +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-biom/build.sh b/recipes/r-biom/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-biom/build.sh +++ b/recipes/r-biom/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-biom/meta.yaml b/recipes/r-biom/meta.yaml index bfe4064ace04e..53ad5decab0b6 100644 --- a/recipes/r-biom/meta.yaml +++ b/recipes/r-biom/meta.yaml @@ -1,7 +1,6 @@ package: name: r-biom - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. + version: "0.3.12" source: @@ -12,12 +11,10 @@ source: build: number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) requirements: host: - r-base @@ -33,17 +30,20 @@ requirements: test: commands: - # You can put additional test commands to be run here. + - $R -e "library('biom')" # [not win] - "\"%R%\" -e \"library('biom')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://github.com/joey711/biom/, http://biom-format.org/ license: GPL-2 summary: This is an R package for interfacing with the BIOM format. +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-biomark/build.sh b/recipes/r-biomark/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-biomark/build.sh +++ b/recipes/r-biomark/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-biomark/meta.yaml b/recipes/r-biomark/meta.yaml index 16b63f54c7d44..08eac7590e961 100644 --- a/recipes/r-biomark/meta.yaml +++ b/recipes/r-biomark/meta.yaml @@ -1,28 +1,38 @@ {% set version = '0.4.5' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-biomark version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/BioMark_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/BioMark/BioMark_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/BioMark_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/BioMark/BioMark_{{ version }}.tar.gz sha256: 754c5d7696155264c7639035a57ea0e71b1d01fd184b45e3fa6a78af9638ccc5 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-mass - r-glmnet - r-pls - r-st >=1.1.6 + run: - r-base - r-mass @@ -32,7 +42,9 @@ requirements: test: commands: - - $R -e "library('BioMark')" + + - $R -e "library('BioMark')" # [not win] + - "\"%R%\" -e \"library('BioMark')\"" # [win] about: home: https://CRAN.R-project.org/package=BioMark @@ -41,4 +53,16 @@ about: net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.' + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-bipartite/build.sh b/recipes/r-bipartite/build.sh index da7badcd783a9..fba88e4b0a09e 100644 --- a/recipes/r-bipartite/build.sh +++ b/recipes/r-bipartite/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-bipartite/meta.yaml b/recipes/r-bipartite/meta.yaml index d090625e8f156..6dba2662caf08 100644 --- a/recipes/r-bipartite/meta.yaml +++ b/recipes/r-bipartite/meta.yaml @@ -1,26 +1,38 @@ {% set version = '2.11' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-bipartite version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/bipartite_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/bipartite_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/bipartite/bipartite_{{ version }}.tar.gz sha256: e2b8231055bc766ce3764ac889bf986eea091c7df718676b622d20f44c3216aa build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-mass @@ -29,8 +41,10 @@ requirements: - r-permute - r-sna - r-vegan + run: - r-base + - {{native}}gcc-libs # [win] - r-mass - r-fields - r-igraph @@ -40,7 +54,9 @@ requirements: test: commands: - - $R -e "library('bipartite')" + + - $R -e "library('bipartite')" # [not win] + - "\"%R%\" -e \"library('bipartite')\"" # [win] about: home: https://github.com/biometry/bipartite @@ -50,13 +66,15 @@ about: e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web''s topology. ' + license_family: GPL extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr - johanneskoester - bgruening - daler - jdblischak - - cbrueffer diff --git a/recipes/r-blockfest/build.sh b/recipes/r-blockfest/build.sh index b2875d8f102ac..cb4df2c15e8d6 100644 --- a/recipes/r-blockfest/build.sh +++ b/recipes/r-blockfest/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-blockfest/meta.yaml b/recipes/r-blockfest/meta.yaml index 351d3963dc975..10a4febc2f9b9 100644 --- a/recipes/r-blockfest/meta.yaml +++ b/recipes/r-blockfest/meta.yaml @@ -1,6 +1,7 @@ {% set version = '1.6' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-blockfest @@ -13,25 +14,38 @@ source: sha256: 458d137f638905578a4aeec28b3a7aa33bc71d3672d1c3947cabdba355514742 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-basix + run: - r-base + - {{native}}gcc-libs # [win] - r-basix test: commands: - - $R -e "library('BlockFeST')" + + - $R -e "library('BlockFeST')" # [not win] + - "\"%R%\" -e \"library('BlockFeST')\"" # [win] about: home: https://CRAN.R-project.org/package=BlockFeST @@ -42,7 +56,6 @@ about: regions, genes, or gene sets containing one or more SNPs that evolved under directional selection. license_family: GPL2 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: identifiers: diff --git a/recipes/r-boutroslabplottinggeneral/build.sh b/recipes/r-boutroslabplottinggeneral/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-boutroslabplottinggeneral/build.sh +++ b/recipes/r-boutroslabplottinggeneral/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-boutroslabplottinggeneral/meta.yaml b/recipes/r-boutroslabplottinggeneral/meta.yaml index 4869fafee8dc8..1270bd57ba849 100644 --- a/recipes/r-boutroslabplottinggeneral/meta.yaml +++ b/recipes/r-boutroslabplottinggeneral/meta.yaml @@ -62,4 +62,14 @@ test: - '$R -e "library(''BoutrosLab.plotting.general'')"' about: home: https://labs.oicr.on.ca/boutros-lab/software/bpg - license: GPL-2 \ No newline at end of file + license: GPL-2extra + +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-canopy/build.sh b/recipes/r-canopy/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-canopy/build.sh +++ b/recipes/r-canopy/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-canopy/meta.yaml b/recipes/r-canopy/meta.yaml index 5e8ff523b7405..937dbd9d96f58 100644 --- a/recipes/r-canopy/meta.yaml +++ b/recipes/r-canopy/meta.yaml @@ -9,32 +9,32 @@ package: source: url: - - https://cran.r-project.org/src/contrib/Canopy_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/Canopy/Canopy_{{ version }}.tar.gz - - + - {{ cran_mirror }}/src/contrib/Canopy_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/Canopy/Canopy_{{ version }}.tar.gz sha256: 8d87184ee99efdcec58dc8199aacbed5398be88050832ec3d9c4c10fef85e924 build: - # If this is a new build for the same version, increment the build number. - number: 1 + merge_build_host: True # [win] + + number: 2 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ - requirements: + build: + - {{posix}}zip # [win] + host: - - r-base >=3.4 + - r-base - r-ape - r-fields - r-pheatmap - r-scatterplot3d run: - - r-base >=3.4 + - r-base - r-ape - r-fields - r-pheatmap @@ -42,11 +42,12 @@ requirements: test: commands: - - $R -e "library('Canopy')" # [not win] + + - $R -e "library('Canopy')" # [not win] - "\"%R%\" -e \"library('Canopy')\"" # [win] about: - home: https://cran.r-project.org/web/packages/Canopy/index.html + home: https://github.com/yuchaojiang/Canopy license: GPL-2 summary: A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring @@ -60,3 +61,12 @@ about: evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment. license_family: GPL2 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-chbutils/build.sh b/recipes/r-chbutils/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-chbutils/build.sh +++ b/recipes/r-chbutils/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-chbutils/meta.yaml b/recipes/r-chbutils/meta.yaml index 1fa9d5fa5dfc5..24b045cdb2e00 100644 --- a/recipes/r-chbutils/meta.yaml +++ b/recipes/r-chbutils/meta.yaml @@ -1,7 +1,6 @@ package: name: r-chbutils - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. + version: "0.1_2015_12_21" source: @@ -11,7 +10,7 @@ source: build: number: 1 skip: True # [osx] - # This is required to make R link correctly on Linux. + rpaths: - lib/R/lib/ - lib/ @@ -35,3 +34,12 @@ about: home: https://github.com/hbc/CHBUtils license: MIT summary: Useful utility functions used at the Harvard Chan School Bioinformatics core +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-cimpl/build.sh b/recipes/r-cimpl/build.sh index 5ef31338aa3c7..5bf492ab9fc06 100644 --- a/recipes/r-cimpl/build.sh +++ b/recipes/r-cimpl/build.sh @@ -1,8 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . diff --git a/recipes/r-cimpl/meta.yaml b/recipes/r-cimpl/meta.yaml index 00b2eb7bf74e9..861d3c320aa7a 100644 --- a/recipes/r-cimpl/meta.yaml +++ b/recipes/r-cimpl/meta.yaml @@ -33,3 +33,12 @@ about: summary: 'An analysis package for multi sample insertional mutagenesis data (including viral- and transposon-based systems) using Gaussian kernel convolution to identify common insertion sites.' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-cnogpro/build.sh b/recipes/r-cnogpro/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-cnogpro/build.sh +++ b/recipes/r-cnogpro/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-cnogpro/meta.yaml b/recipes/r-cnogpro/meta.yaml index d4f35534b39cc..fa8bd80f95644 100644 --- a/recipes/r-cnogpro/meta.yaml +++ b/recipes/r-cnogpro/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-cnogpro version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/CNOGpro_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/CNOGpro/CNOGpro_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/CNOGpro_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/CNOGpro/CNOGpro_{{ version }}.tar.gz sha256: 889aba7c5201bda7edc369798e5fb9043ffb73c54b310394dee1d18c1dac3abb build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-seqinr @@ -27,7 +36,9 @@ requirements: test: commands: - - $R -e "library('CNOGpro')" + + - $R -e "library('CNOGpro')" # [not win] + - "\"%R%\" -e \"library('CNOGpro')\"" # [win] about: home: https://CRAN.R-project.org/package=CNOGpro @@ -35,8 +46,17 @@ about: summary: Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms. license_family: GPL2 - + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] extra: identifiers: - biotools:cnogpro - doi:10.1093/bioinformatics/btv070 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-coenocliner/build.sh b/recipes/r-coenocliner/build.sh index 06cff3b76e604..74f176ad34376 100644 --- a/recipes/r-coenocliner/build.sh +++ b/recipes/r-coenocliner/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-coenocliner/meta.yaml b/recipes/r-coenocliner/meta.yaml index bfe7c5914dd2b..fc5a487884213 100644 --- a/recipes/r-coenocliner/meta.yaml +++ b/recipes/r-coenocliner/meta.yaml @@ -1,39 +1,55 @@ {% set version = '0.2-2' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-coenocliner version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/coenocliner_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/coenocliner_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/coenocliner/coenocliner_{{ version }}.tar.gz sha256: ae558be071d6362e48e942658bff35c21c80ac5c4af12b6b67a189ad46069064 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + host: - r-base + run: - r-base test: commands: - - $R -e "library('coenocliner')" + + - $R -e "library('coenocliner')" # [not win] + - "\"%R%\" -e \"library('coenocliner')\"" # [win] about: home: https://github.com/gavinsimpson/coenocliner/ license: GPL-2 summary: Simulate species occurrence and abundances (counts) along gradients. license_family: GPL2 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-coloc/build.sh b/recipes/r-coloc/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-coloc/build.sh +++ b/recipes/r-coloc/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-coloc/meta.yaml b/recipes/r-coloc/meta.yaml index 9e78b6cabea95..0b224f6cafb87 100644 --- a/recipes/r-coloc/meta.yaml +++ b/recipes/r-coloc/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.3-1' %} +{% set version = '3.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-coloc @@ -6,37 +9,60 @@ package: source: url: - - https://cran.r-project.org/src/contrib/coloc_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/coloc/coloc_{{ version }}.tar.gz - sha256: c0bc7850364091189f49d10a69b429d468b30a9a1b7b3456fc0bd4799d4a75c8 + - {{ cran_mirror }}/src/contrib/coloc_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/coloc/coloc_{{ version }}.tar.gz + sha256: 882ae56514e93839bd2d9c630a6eb5dc0e146062a46ad1583e7687cfcb31418c build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-bma - - r-mass - - r-colorspace + - r-flashclust + - r-ggplot2 + - r-reshape + - bioconductor-snpstats + - r-speedglm run: - r-base - r-bma - - r-mass - - r-colorspace + - r-flashclust + - r-ggplot2 + - r-reshape + - bioconductor-snpstats + - r-speedglm test: commands: - - $R -e "library('coloc')" + + - $R -e "library('coloc')" # [not win] + - "\"%R%\" -e \"library('coloc')\"" # [win] about: - home: https://github.com/chr1swallace/coloc + home: https://CRAN.R-project.org/package=coloc license: GPL - summary: Performs the colocalisation tests described in Plagnol et al (2009), Wallace et al - (2013) and Giambartolomei et al (2013). + summary: Performs the colocalisation tests described in Plagnol et al (2009) , + Wallace et al (2013) and Giambartolomei et al (2013) . license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-dartr/build.sh b/recipes/r-dartr/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-dartr/build.sh +++ b/recipes/r-dartr/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-dartr/meta.yaml b/recipes/r-dartr/meta.yaml index 535b2cc759d4d..0f49f950535aa 100644 --- a/recipes/r-dartr/meta.yaml +++ b/recipes/r-dartr/meta.yaml @@ -1,31 +1,38 @@ -{% set version = '1.0' %} +{% set version = '1.0.5' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-dartr - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/dartR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/dartR/dartR_{{ version }}.tar.gz - sha256: 4c3bf15a9460204491cb4e16f73e3127cf7bbbdadc4fdb871293e8cd771ae7de + - {{ cran_mirror }}/src/contrib/dartR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/dartR/dartR_{{ version }}.tar.gz + sha256: fc2b5643ef222ac20e62c5899f8f36b5ba92bf9146b7a5e25457d7ac789fb3f5 build: - number: 1 - skip: True # [osx] + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - - bioconductor-qvalue - - bioconductor-snprelate - - libgdal 2.2.4 # Force libgdal from conda-forge - r-base - r-dbi - r-demerelate - r-mass + - bioconductor-snprelate - r-snpassoc - r-stampp - r-adegenet >=2.0.0 @@ -42,6 +49,7 @@ requirements: - r-plotly - r-plyr - r-quadprog + - bioconductor-qvalue - r-reshape2 - r-rgdal - r-rgl @@ -52,13 +60,11 @@ requirements: - r-vegan run: - - bioconductor-qvalue - - bioconductor-snprelate - - libgdal 2.2.4 # Force libgdal from conda-forge - r-base - r-dbi - r-demerelate - r-mass + - bioconductor-snprelate - r-snpassoc - r-stampp - r-adegenet >=2.0.0 @@ -75,6 +81,7 @@ requirements: - r-plotly - r-plyr - r-quadprog + - bioconductor-qvalue - r-reshape2 - r-rgdal - r-rgl @@ -86,24 +93,34 @@ requirements: test: commands: - - $R -e "library('dartR')" + + - $R -e "library('dartR')" # [not win] + - "\"%R%\" -e \"library('dartR')\"" # [win] about: home: https://CRAN.R-project.org/package=dartR license: GPL-2 + summary: Functions are provided that facilitate the import and analysis of SNP (single nucleotide + polymorphism) and silicodart (presence/absence) data. The main focus is on data + generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment + presence/absence data from any source is imported into a genlight object many of + the functions can be used. Functions are available for input and output of SNP and + silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, + Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is + based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions + are available for visualization after PCoA (Principle Coordinate Analysis), or to + facilitate transfer of data between genlight/genind objects and newhybrids, related, + phylip, structure, faststructure packages. license_family: GPL2 - summary: Functions are provided that facilitate the import and analysis of snp and silicodart - (presence/absence) data. The main focus is on data generated by DarT (Diversity - Arrays Technology). However, once SNP or related fragment presence/absence data - from any source is imported into a genlight object many of the functions can be - used. Functions are available for input and output of SNP and silicodart data, for - reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, - maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium - and HWE. Other functions are available for visualization after PCoA, or to facilitate - transfer of data between genlight/genind objects and newhybrids, related, phylip - packages etc. - extra: container: # needed for libGL.so.1 extended-base: true + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-data.table/build.sh b/recipes/r-data.table/build.sh new file mode 100644 index 0000000000000..638885d473c4b --- /dev/null +++ b/recipes/r-data.table/build.sh @@ -0,0 +1,9 @@ +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/data.table + mv * $PREFIX/lib/R/library/data.table +fi diff --git a/recipes/r-data.table/meta.yaml b/recipes/r-data.table/meta.yaml new file mode 100644 index 0000000000000..7bb39ee002e15 --- /dev/null +++ b/recipes/r-data.table/meta.yaml @@ -0,0 +1,64 @@ +{% set version = '1.11.6' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-data.table + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/data.table_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/data.table/data.table_{{ version }}.tar.gz + sha256: ac6783c18e94d1bc05702ddec9fd87c542c744f640132f5ffc373348be84d9e9 + +build: + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + + run: + - r-base + - {{native}}gcc-libs # [win] + +test: + commands: + + - $R -e "library('data.table')" # [not win] + - "\"%R%\" -e \"library('data.table')\"" # [win] + +about: + home: http://r-datatable.com + license: MPL-2.0 + summary: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete + of columns by group using no copies at all, list columns, friendly and fast character-separated-value + read/write. Offers a natural and flexible syntax, for faster development. + license_family: OTHER +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-dbchip/build.sh b/recipes/r-dbchip/build.sh index 4bc8e1853b492..5bf492ab9fc06 100644 --- a/recipes/r-dbchip/build.sh +++ b/recipes/r-dbchip/build.sh @@ -1,3 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . diff --git a/recipes/r-dbchip/meta.yaml b/recipes/r-dbchip/meta.yaml index bc08069051279..52af556671841 100644 --- a/recipes/r-dbchip/meta.yaml +++ b/recipes/r-dbchip/meta.yaml @@ -10,7 +10,6 @@ build: number: 2 skip: True # [osx] - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -19,12 +18,12 @@ requirements: host: - r-base - bioconductor-deseq - - bioconductor-edger + - bioconductobioconductor-edger run: - r-base - bioconductor-deseq - - bioconductor-edger + - bioconductobioconductor-edger test: commands: @@ -39,3 +38,11 @@ extra: identifiers: - biotools:dbchip - doi:10.1093/bioinformatics/btr605 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-deconstructsigs/build.sh b/recipes/r-deconstructsigs/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-deconstructsigs/build.sh +++ b/recipes/r-deconstructsigs/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-deconstructsigs/meta.yaml b/recipes/r-deconstructsigs/meta.yaml index eda4d2f74f2ea..b2776c5564a3e 100644 --- a/recipes/r-deconstructsigs/meta.yaml +++ b/recipes/r-deconstructsigs/meta.yaml @@ -1,5 +1,8 @@ {% set version = '1.8.0.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-deconstructsigs version: {{ version|replace("-", "_") }} @@ -19,6 +22,8 @@ build: - lib/ requirements: + build: + - {{posix}}zip # [win] host: - r-base - bioconductor-bsgenome @@ -34,12 +39,23 @@ requirements: test: commands: - - $R -e "library('deconstructSigs')" + + - $R -e "library('deconstructSigs')" # [not win] + - "\"%R%\" -e \"library('deconstructSigs')\"" # [win] about: - home: https + home: https://github.com/raerose01/deconstructSigs license: GPL (>= 2) summary: Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-deoptimr/build.sh b/recipes/r-deoptimr/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-deoptimr/build.sh +++ b/recipes/r-deoptimr/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-deoptimr/meta.yaml b/recipes/r-deoptimr/meta.yaml index 95c80725c7e45..1e279cf9d13c0 100644 --- a/recipes/r-deoptimr/meta.yaml +++ b/recipes/r-deoptimr/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.0-8' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-deoptimr version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/DEoptimR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/DEoptimR/DEoptimR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/DEoptimR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/DEoptimR/DEoptimR_{{ version }}.tar.gz sha256: 846911c1b2561a9fae73a8c60a21a5680963ebb0050af3c1f1147ae9a121e5ef build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('DEoptimR')" + + - $R -e "library('DEoptimR')" # [not win] + - "\"%R%\" -e \"library('DEoptimR')\"" # [win] about: home: https://CRAN.R-project.org/package=DEoptimR @@ -36,3 +47,14 @@ about: and (3) can be efficiently implemented directly in the R language. Currently, it only provides an implementation of the 'jDE' algorithm by Brest et al. (2006) . license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-diptest/build.sh b/recipes/r-diptest/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-diptest/build.sh +++ b/recipes/r-diptest/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-diptest/meta.yaml b/recipes/r-diptest/meta.yaml index e0945796e946f..6ac969d641d5d 100644 --- a/recipes/r-diptest/meta.yaml +++ b/recipes/r-diptest/meta.yaml @@ -1,34 +1,49 @@ {% set version = '0.75-7' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-diptest version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/diptest_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/diptest/diptest_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/diptest_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/diptest/diptest_{{ version }}.tar.gz sha256: 462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base run: - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('diptest')" + + - $R -e "library('diptest')" # [not win] + - "\"%R%\" -e \"library('diptest')\"" # [win] about: home: https://CRAN.R-project.org/package=diptest @@ -37,3 +52,14 @@ about: a test with simulation based p-values, where the original public code has been corrected. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-dpeak/build.sh b/recipes/r-dpeak/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-dpeak/build.sh +++ b/recipes/r-dpeak/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-dpeak/meta.yaml b/recipes/r-dpeak/meta.yaml index 6a8b5a82f2146..d8ff3f2884a28 100644 --- a/recipes/r-dpeak/meta.yaml +++ b/recipes/r-dpeak/meta.yaml @@ -1,7 +1,6 @@ package: name: r-dpeak - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. + version: "2.0.1" source: @@ -11,7 +10,6 @@ source: build: number: 2 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -37,10 +35,19 @@ requirements: test: commands: - # You can put additional test commands to be run here. + - $R -e "library('dpeak')" about: home: http://dongjunchung.github.io/dpeak/ license: GPL (>= 2) summary: This package provides functions for fitting dPeak, a statistical framework to deconvolve ChIP-seq peaks. +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-drc/build.sh b/recipes/r-drc/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-drc/build.sh +++ b/recipes/r-drc/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-drc/meta.yaml b/recipes/r-drc/meta.yaml index 6e4f71440ef22..aaa89b61efac5 100644 --- a/recipes/r-drc/meta.yaml +++ b/recipes/r-drc/meta.yaml @@ -1,22 +1,31 @@ {% set version = '3.0-1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-drc version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/drc_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/drc/drc_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/drc_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/drc/drc_{{ version }}.tar.gz sha256: 3ec01182895e8ec9b13bcdfed6a812800ad02d732634e4213802ff1b33b21d31 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-mass @@ -26,9 +35,6 @@ requirements: - r-plotrix - r-scales - # from prev version - #- r-nloptr - run: - r-base - r-mass @@ -38,12 +44,11 @@ requirements: - r-plotrix - r-scales - # from prev version - # - r-nloptr - test: commands: - - $R -e "library('drc')" + + - $R -e "library('drc')" # [not win] + - "\"%R%\" -e \"library('drc')\"" # [win] about: home: http://www.r-project.org, http://www.bioassay.dk @@ -51,3 +56,14 @@ about: summary: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions. license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-dynamictreecut/build.sh b/recipes/r-dynamictreecut/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-dynamictreecut/build.sh +++ b/recipes/r-dynamictreecut/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-dynamictreecut/meta.yaml b/recipes/r-dynamictreecut/meta.yaml index 9acb51c042f3f..9f57ff02d9b23 100644 --- a/recipes/r-dynamictreecut/meta.yaml +++ b/recipes/r-dynamictreecut/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.63-1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-dynamictreecut version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/dynamicTreeCut_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/dynamicTreeCut/dynamicTreeCut_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/dynamicTreeCut_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/dynamicTreeCut/dynamicTreeCut_{{ version }}.tar.gz sha256: 831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,10 +34,23 @@ requirements: test: commands: - - $R -e "library('dynamicTreeCut')" + + - $R -e "library('dynamicTreeCut')" # [not win] + - "\"%R%\" -e \"library('dynamicTreeCut')\"" # [win] about: home: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/ license: GPL (>= 2) summary: Contains methods for detection of clusters in hierarchical clustering dendrograms. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ecodist/build.sh b/recipes/r-ecodist/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-ecodist/build.sh +++ b/recipes/r-ecodist/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-ecodist/meta.yaml b/recipes/r-ecodist/meta.yaml index 49e434ff99982..0ad952a40896d 100644 --- a/recipes/r-ecodist/meta.yaml +++ b/recipes/r-ecodist/meta.yaml @@ -1,38 +1,62 @@ {% set version = '2.0.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-ecodist version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/ecodist_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ecodist/ecodist_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/ecodist_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ecodist/ecodist_{{ version }}.tar.gz sha256: afb099c4484dbeef913bd187cb23ce805df56958431bffc27e392db244d9f112 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base run: - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('ecodist')" + + - $R -e "library('ecodist')" # [not win] + - "\"%R%\" -e \"library('ecodist')\"" # [win] about: home: https://CRAN.R-project.org/package=ecodist - license: 'GPL (>= 2)' + license: GPL (>= 2) summary: Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-empiricalfdr.deseq2/build.sh b/recipes/r-empiricalfdr.deseq2/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-empiricalfdr.deseq2/build.sh +++ b/recipes/r-empiricalfdr.deseq2/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-empiricalfdr.deseq2/meta.yaml b/recipes/r-empiricalfdr.deseq2/meta.yaml index 70e52da5c684f..d6451c057b914 100644 --- a/recipes/r-empiricalfdr.deseq2/meta.yaml +++ b/recipes/r-empiricalfdr.deseq2/meta.yaml @@ -1,36 +1,46 @@ {% set version = '1.0.3' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-empiricalfdr.deseq2 version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/empiricalFDR.DESeq2_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/empiricalFDR.DESeq2/empiricalFDR.DESeq2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/empiricalFDR.DESeq2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/empiricalFDR.DESeq2/empiricalFDR.DESeq2_{{ version }}.tar.gz sha256: 831be77d3b40fcc41e70c0dadcb50871fda6093de3130d6c334c8d4d78635540 build: - # prev version skipped osx - #skip: True # [osx] - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - bioconductor-deseq2 - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + run: - r-base - bioconductor-deseq2 - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' test: commands: - - $R -e "library('empiricalFDR.DESeq2')" + + - $R -e "library('empiricalFDR.DESeq2')" # [not win] + - "\"%R%\" -e \"library('empiricalFDR.DESeq2')\"" # [win] about: home: https://CRAN.R-project.org/package=empiricalFDR.DESeq2 @@ -40,3 +50,12 @@ about: and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-exomedepth/build.sh b/recipes/r-exomedepth/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-exomedepth/build.sh +++ b/recipes/r-exomedepth/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-exomedepth/meta.yaml b/recipes/r-exomedepth/meta.yaml index c03376436fa51..1f3c876b3755a 100644 --- a/recipes/r-exomedepth/meta.yaml +++ b/recipes/r-exomedepth/meta.yaml @@ -1,17 +1,22 @@ {% set version = '1.1.10' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-exomedepth version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/ExomeDepth_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ExomeDepth/ExomeDepth_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/ExomeDepth_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ExomeDepth/ExomeDepth_{{ version }}.tar.gz sha256: 2678ff4c4d024e08a843f08cb932707a11ce7274ab48bfc2632669ca930d8f86 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,31 +24,41 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - bioconductor-biostrings - - bioconductor-genomicalignments - - bioconductor-genomicranges >=1.23.0 + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-rsamtools >=1.32.0,<1.34.0' - r-vgam >=0.8.4 - r-aod run: - r-base - - bioconductor-biostrings - - bioconductor-genomicalignments - - bioconductor-genomicranges >=1.23.0 + - {{native}}gcc-libs # [win] + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - bioconductor-iranges - - bioconductor-rsamtools + - 'bioconductor-rsamtools >=1.32.0,<1.34.0' - r-vgam >=0.8.4 - r-aod test: commands: - - $R -e "library('ExomeDepth')" + + - $R -e "library('ExomeDepth')" # [not win] + - "\"%R%\" -e \"library('ExomeDepth')\"" # [win] about: home: https://CRAN.R-project.org/package=ExomeDepth @@ -51,7 +66,14 @@ about: summary: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. license_family: GPL3 - extra: identifiers: - biotools:exomedepth + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-fastqcr/build.sh b/recipes/r-fastqcr/build.sh index c4125008f30f7..5bf492ab9fc06 100644 --- a/recipes/r-fastqcr/build.sh +++ b/recipes/r-fastqcr/build.sh @@ -1,11 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-fastqcr/meta.yaml b/recipes/r-fastqcr/meta.yaml index 5876c387c6f3e..9729b1c5d67ee 100644 --- a/recipes/r-fastqcr/meta.yaml +++ b/recipes/r-fastqcr/meta.yaml @@ -9,21 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/fastqcr_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/fastqcr/fastqcr_{{ version }}.tar.gz - + - {{ cran_mirror }}/src/contrib/fastqcr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/fastqcr/fastqcr_{{ version }}.tar.gz sha256: 2abf81eae7de1c521879dcdc37fc8830e079997a76e2b8065c601ead8cb9f443 build: - number: 0 + merge_build_host: True # [win] + + number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-dplyr - r-ggplot2 @@ -53,7 +56,8 @@ requirements: test: commands: - - $R -e "library('fastqcr')" # [not win] + + - $R -e "library('fastqcr')" # [not win] - "\"%R%\" -e \"library('fastqcr')\"" # [win] about: @@ -68,33 +72,12 @@ about: ''Multi-QC'' report, as well as, a ''one-sample'' report with result interpretations.' license_family: GPL2 - -# The original CRAN metadata for this package was: - -# Package: fastqcr -# Type: Package -# Title: Quality Control of Sequencing Data -# Version: 0.1.0 -# Date: 2017-04-12 -# Authors@R: c( person("Alboukadel", "Kassambara", role = c("aut", "cre"), email = "alboukadel.kassambara@gmail.com") ) -# Description: 'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing data. It produces, for each sample, an html report and a compressed file containing the raw data. If you have hundreds of samples, you are not going to open up each 'HTML' page. You need some way of looking at these data in aggregate. 'fastqcr' Provides helper functions to easily parse, aggregate and analyze 'FastQC' reports for large numbers of samples. It provides a convenient solution for building a 'Multi-QC' report, as well as, a 'one-sample' report with result interpretations. -# License: GPL-2 -# Encoding: UTF-8 -# LazyData: true -# Depends: R (>= 3.1.2) -# Imports: dplyr, grid, gridExtra, ggplot2, magrittr, readr, rmarkdown(>= 1.4), rvest, tibble, tidyr, scales, stats, utils, xml2 -# Suggests: knitr -# URL: http://www.sthda.com/english/rpkgs/fastqcr/ -# BugReports: https://github.com/kassambara/fastqcr/issues -# RoxygenNote: 6.0.1 -# Collate: 'utilities.R' 'fastqc.R' 'fastqc_install.R' 'qc_aggregate.R' 'qc_plot.R' 'qc_problems.R' 'qc_read.R' 'qc_report.R' 'qc_unzip.R' -# NeedsCompilation: no -# Packaged: 2017-04-11 10:31:32 UTC; kassambara -# Author: Alboukadel Kassambara [aut, cre] -# Maintainer: Alboukadel Kassambara -# Repository: CRAN -# Date/Publication: 2017-04-11 10:43:29 UTC - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-fateid/build.sh b/recipes/r-fateid/build.sh index 6cb8c0aafc3ee..bc73e236735ef 100644 --- a/recipes/r-fateid/build.sh +++ b/recipes/r-fateid/build.sh @@ -1,5 +1,3 @@ -#!/bin/bash - if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 mv DESCRIPTION DESCRIPTION.old diff --git a/recipes/r-fateid/meta.yaml b/recipes/r-fateid/meta.yaml index 3c922253d4f07..784a2fd4973bf 100644 --- a/recipes/r-fateid/meta.yaml +++ b/recipes/r-fateid/meta.yaml @@ -14,19 +14,18 @@ source: sha256: 1e168ccdef75b6a4229976740e60704d75e2f1d5c3f6757f9fb7798c727f7fec build: - # If this is a new build for the same version, increment the build number. - number: 0 - # rgl issues on OSX - skip: True # [osx] + merge_build_host: True # [win] + + number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: DESeq2, destiny, knitr, rmarkdown requirements: build: + - {{posix}}zip # [win] + host: - r-base - r-rcolorbrewer @@ -53,19 +52,29 @@ requirements: test: commands: + - $R -e "library('FateID')" # [not win] + - "\"%R%\" -e \"library('FateID')\"" # [win] about: home: https://CRAN.R-project.org/package=FateID license: GPL-3 summary: "Application of 'FateID' allows computation and visualization of cell fate bias for - multi-lineage single cell transcriptome data." + multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Gr\xFCn D. (2017) + ." license_family: GPL3 - extra: identifiers: - doi:10.1038/nmeth.4662 container: # needed for libGL.so.1 extended-base: true + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-fmsb/build.sh b/recipes/r-fmsb/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-fmsb/build.sh +++ b/recipes/r-fmsb/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-fmsb/meta.yaml b/recipes/r-fmsb/meta.yaml index 7675e30297150..0c7ae6602c7ee 100644 --- a/recipes/r-fmsb/meta.yaml +++ b/recipes/r-fmsb/meta.yaml @@ -1,17 +1,22 @@ {% set version = '0.6.3' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-fmsb version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/fmsb_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/fmsb/fmsb_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/fmsb_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/fmsb/fmsb_{{ version }}.tar.gz sha256: 4503998d2fd90f5ee62587594dc2adeaf022355d2e294dc5bcfb0271bd5d49d8 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,7 +24,7 @@ build: requirements: build: - - {{ compiler('c') }} + - {{posix}}zip # [win] host: - r-base @@ -29,7 +34,9 @@ requirements: test: commands: - - $R -e "library('fmsb')" + + - $R -e "library('fmsb')" # [not win] + - "\"%R%\" -e \"library('fmsb')\"" # [win] about: home: http://minato.sip21c.org/msb/ @@ -38,3 +45,12 @@ about: Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-funrar/build.sh b/recipes/r-funrar/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-funrar/build.sh +++ b/recipes/r-funrar/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-funrar/meta.yaml b/recipes/r-funrar/meta.yaml index fb59c6618f32e..f89c46e7e0ba8 100644 --- a/recipes/r-funrar/meta.yaml +++ b/recipes/r-funrar/meta.yaml @@ -1,24 +1,32 @@ {% set version = '1.2.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-funrar version: {{ version|replace("-", "_") }} source: - fn: funrar_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/funrar_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/funrar/funrar_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/funrar_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/funrar/funrar_{{ version }}.tar.gz sha256: 1458d848593212ce293a4cd406814b006e5cb295bf9e90ac6861903639ec339d build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-cluster - r-dplyr >=0.4.3 @@ -30,15 +38,28 @@ requirements: test: commands: - - $R -e "library('funrar')" + + - $R -e "library('funrar')" # [not win] + - "\"%R%\" -e \"library('funrar')\"" # [win] about: - home: https + home: https://github.com/Rekyt/funrar license: GPL (>= 2) - summary: Computes functional rarity indices as proposed by Violle et al. (2017) - license_family: GPL3 + summary: "Computes functional rarity indices as proposed by Violle et al. (2017) . + Various indices can be computed using both regional and local information. Functional + Rarity combines both the functional aspect of rarity as well as the extent aspect + of rarity. 'funrar' is presented in Greni\xE9 et al. (2017) ." + license_family: GPL3 extra: identifiers: - doi:10.1016/j.tree.2017.02.002 - doi:10.1111/ddi.12629 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gam/build.sh b/recipes/r-gam/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-gam/build.sh +++ b/recipes/r-gam/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-gam/meta.yaml b/recipes/r-gam/meta.yaml index 08a36979837da..0297c36faf80f 100644 --- a/recipes/r-gam/meta.yaml +++ b/recipes/r-gam/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.14-4' %} +{% set version = '1.16' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-gam @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/gam_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/gam/gam_{{ version }}.tar.gz - sha256: 6a65d7f707c4833bf2f0b51f959e1bf05d83a75848884b65f6b40787e737aa8e + - {{ cran_mirror }}/src/contrib/gam_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/gam/gam_{{ version }}.tar.gz + sha256: 020532e49e59b8691dbbdd44fdaee6c0cf7334708b3080c24706140edf238f2e build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,8 +25,14 @@ build: requirements: build: - # need fortran as well for osx - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('fortran') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -28,11 +40,14 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-foreach test: commands: - - $R -e "library('gam')" + + - $R -e "library('gam')" # [not win] + - "\"%R%\" -e \"library('gam')\"" # [win] about: home: https://CRAN.R-project.org/package=gam @@ -41,3 +56,14 @@ about: chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990). license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gbm/build.sh b/recipes/r-gbm/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-gbm/build.sh +++ b/recipes/r-gbm/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-gbm/meta.yaml b/recipes/r-gbm/meta.yaml index 88bdee6d13d31..c8034f3b7cd4f 100644 --- a/recipes/r-gbm/meta.yaml +++ b/recipes/r-gbm/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.1.3' %} +{% set version = '2.1.4' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-gbm @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/gbm_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/gbm/gbm_{{ version }}.tar.gz - sha256: eaf24be931d762f1ccca4f90e15997719d01005f152160a3d20d858a0bbed92b + - {{ cran_mirror }}/src/contrib/gbm_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/gbm/gbm_{{ version }}.tar.gz + sha256: 91fe50345f94a42a75a789cc2c05e489610c109508896479725df810920ee152 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,28 +25,52 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base + - r-gridextra - r-lattice - r-survival run: - r-base + - {{native}}gcc-libs # [win] + - r-gridextra - r-lattice - r-survival test: commands: - - $R -e "library('gbm')" + + - $R -e "library('gbm')" # [not win] + - "\"%R%\" -e \"library('gbm')\"" # [win] about: - home: http://code.google.com/p/gradientboostedmodels/ + home: https://github.com/gbm-developers/gbm license: GPL (>= 2) - summary: An implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's - gradient boosting machine. Includes regression methods for least squares, absolute - loss, t-distribution loss, quantile regression, logistic, multinomial logistic, - Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, - Huberized hinge loss, and Learning to Rank measures (LambdaMart). + summary: An implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's + gradient boosting machine. Includes regression methods for least squares, absolute + loss, t-distribution loss, quantile regression, logistic, multinomial logistic, + Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, + Huberized hinge loss, and Learning to Rank measures (LambdaMart). Originally developed + by Greg Ridgeway. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-geiger/build.sh b/recipes/r-geiger/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-geiger/build.sh +++ b/recipes/r-geiger/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-geiger/meta.yaml b/recipes/r-geiger/meta.yaml index 5764f53282b5e..c8f18a2bc188c 100644 --- a/recipes/r-geiger/meta.yaml +++ b/recipes/r-geiger/meta.yaml @@ -1,24 +1,39 @@ {% set version = '2.0.6' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-geiger version: {{ version|replace("-", "_") }} source: - fn: geiger_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/geiger_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/geiger/geiger_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/geiger_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/geiger/geiger_{{ version }}.tar.gz sha256: e13b2c526378eaf9356b00bbe21b3c2c956327f8062fed638ccc1f49591c3eff build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: - r-base - r-mass - r-rcpp >=0.9.0 @@ -30,10 +45,10 @@ requirements: - r-mvtnorm - r-ncbit - r-subplex - - gcc run: - r-base + - {{native}}gcc-libs # [win] - r-mass - r-rcpp >=0.9.0 - r-ape >=3.0_6 @@ -47,10 +62,21 @@ requirements: test: commands: - - $R -e "library('geiger')" + + - $R -e "library('geiger')" # [not win] + - "\"%R%\" -e \"library('geiger')\"" # [win] about: - home: http + home: http://www.webpages.uidaho.edu/~lukeh/software.html license: GPL (>= 2) summary: Methods for fitting macroevolutionary models to phylogenetic trees. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-genabel.data/build.sh b/recipes/r-genabel.data/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-genabel.data/build.sh +++ b/recipes/r-genabel.data/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-genabel.data/meta.yaml b/recipes/r-genabel.data/meta.yaml index f569594aa0d08..ffc859dae82c2 100644 --- a/recipes/r-genabel.data/meta.yaml +++ b/recipes/r-genabel.data/meta.yaml @@ -32,3 +32,14 @@ about: license: GPL (>= 2) summary: GenABEL.data package consists of a data set used by GenABEL functions license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-genabel/build.sh b/recipes/r-genabel/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-genabel/build.sh +++ b/recipes/r-genabel/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-genabel/meta.yaml b/recipes/r-genabel/meta.yaml index 47bb107603845..e56191aa26832 100644 --- a/recipes/r-genabel/meta.yaml +++ b/recipes/r-genabel/meta.yaml @@ -40,3 +40,14 @@ about: summary: 'A package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs). ' license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-genenet/build.sh b/recipes/r-genenet/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-genenet/build.sh +++ b/recipes/r-genenet/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-genenet/meta.yaml b/recipes/r-genenet/meta.yaml index e65b2623c43cc..5297a4676cddb 100644 --- a/recipes/r-genenet/meta.yaml +++ b/recipes/r-genenet/meta.yaml @@ -1,23 +1,31 @@ {% set version = '1.2.13' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-genenet version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/GeneNet_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/GeneNet/GeneNet_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/GeneNet_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/GeneNet/GeneNet_{{ version }}.tar.gz sha256: 3798caac3bef7dc87f97b3628eb29eb12365d571ce0837b5b6285b0be655a270 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-corpcor >=1.6.8 @@ -32,7 +40,9 @@ requirements: test: commands: - - $R -e "library('GeneNet')" + + - $R -e "library('GeneNet')" # [not win] + - "\"%R%\" -e \"library('GeneNet')\"" # [win] about: home: http://strimmerlab.org/software/genenet/ @@ -43,3 +53,14 @@ about: networks (including assignment of putative directions). ' license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-genometricorr/build.sh b/recipes/r-genometricorr/build.sh index 1ad9046d759c2..aea5b12eaa821 100644 --- a/recipes/r-genometricorr/build.sh +++ b/recipes/r-genometricorr/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - R CMD INSTALL --build . diff --git a/recipes/r-genometricorr/meta.yaml b/recipes/r-genometricorr/meta.yaml index f1dd50a66e577..787b8851399c6 100644 --- a/recipes/r-genometricorr/meta.yaml +++ b/recipes/r-genometricorr/meta.yaml @@ -53,4 +53,13 @@ about: summary: Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets. extra: - doi: doi.org/10.1371/journal.pcbi.1002529 + identifiers: + - doi: doi.org/10.1371/journal.pcbi.1002529 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-geoaxe/build.sh b/recipes/r-geoaxe/build.sh index 695ef87bd4ada..5bf492ab9fc06 100644 --- a/recipes/r-geoaxe/build.sh +++ b/recipes/r-geoaxe/build.sh @@ -1,4 +1 @@ -#!/bin/bash $R CMD INSTALL --build . - - diff --git a/recipes/r-geoaxe/meta.yaml b/recipes/r-geoaxe/meta.yaml index 67765a1de7ff6..2e5ec78ac857c 100644 --- a/recipes/r-geoaxe/meta.yaml +++ b/recipes/r-geoaxe/meta.yaml @@ -1,17 +1,22 @@ {% set version = '0.1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-geoaxe version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/geoaxe_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/geoaxe/geoaxe_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/geoaxe_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/geoaxe/geoaxe_{{ version }}.tar.gz sha256: 7ba4e5285670e67e307224222fcee5f7d6b67b6c1a5f7b8f34e64222d63c7e10 build: - number: 2 + merge_build_host: True # [win] + + number: 3 rpaths: - lib/R/lib/ @@ -19,24 +24,40 @@ build: requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-jsonlite - - r-rgeos >=0.3_28 + - r-rgeos - r-sp + - geos run: - r-base - r-jsonlite - - r-rgeos >=0.3_28 + - r-rgeos - r-sp + - geos test: commands: - - $R -e "library('geoaxe')" + + - $R -e "library('geoaxe')" # [not win] + - "\"%R%\" -e \"library('geoaxe')\"" # [win] about: home: https://github.com/ropenscilabs/geoaxe - license: MIT + file LICENSE + license: MIT summary: Split 'geospatial' objects into pieces. Includes support for some spatial object inputs, 'Well-Known Text', and 'GeoJSON'. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-george/build.sh b/recipes/r-george/build.sh index bea0cb7ce0b86..5bf492ab9fc06 100644 --- a/recipes/r-george/build.sh +++ b/recipes/r-george/build.sh @@ -1,11 +1 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# - diff --git a/recipes/r-george/meta.yaml b/recipes/r-george/meta.yaml index faa1c0e343857..8871572b9fd88 100644 --- a/recipes/r-george/meta.yaml +++ b/recipes/r-george/meta.yaml @@ -30,3 +30,12 @@ about: home: https://github.com/jcapelladesto/geoRge/README.md license: 'GPL (>= 2)' summary: 'geoRge, a computational tool for stable isotope labelling detection in LC/MS-based untargeted metabolomics' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ggrasp/build.sh b/recipes/r-ggrasp/build.sh index 50bee029a649a..8ff6b134030ee 100644 --- a/recipes/r-ggrasp/build.sh +++ b/recipes/r-ggrasp/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-ggrasp/meta.yaml b/recipes/r-ggrasp/meta.yaml index 320ba7929db6a..bca34f749abc1 100644 --- a/recipes/r-ggrasp/meta.yaml +++ b/recipes/r-ggrasp/meta.yaml @@ -1,23 +1,31 @@ {% set version = '1.0' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-ggrasp version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/ggrasp_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/ggrasp_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ggrasp/ggrasp_{{ version }}.tar.gz sha256: 0133019df762cd19d7daf1b5f2b353c43568124ade6e34fa04837656138a3652 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + host: - r-base - r-ape @@ -25,6 +33,7 @@ requirements: - r-colorspace - r-ggplot2 - r-mixtools + run: - r-base - r-ape @@ -35,7 +44,9 @@ requirements: test: commands: - - $R -e "library('ggrasp')" + + - $R -e "library('ggrasp')" # [not win] + - "\"%R%\" -e \"library('ggrasp')\"" # [win] about: home: https://CRAN.R-project.org/package=ggrasp @@ -46,11 +57,16 @@ about: out as a list or a new phylogeny with graphs of the trees and distance distributions also available. For detailed introduction see: Thomas H Clarke, Lauren M Brinkac, Granger Sutton, and Derrick E Fouts (2018), GGRaSP: a R-package for selecting representative - genomes using Gaussian mixture models, Bioinformatics, bty300, - .' + genomes using Gaussian mixture models, Bioinformatics, bty300, .' + license_family: GPL2 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-giant/build.sh b/recipes/r-giant/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-giant/build.sh +++ b/recipes/r-giant/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-giant/meta.yaml b/recipes/r-giant/meta.yaml index e56e9ac8bc79e..2d8c9acef6a33 100644 --- a/recipes/r-giant/meta.yaml +++ b/recipes/r-giant/meta.yaml @@ -34,3 +34,12 @@ about: summary: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets. license_family: OTHER +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gkmsvm/build.sh b/recipes/r-gkmsvm/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-gkmsvm/build.sh +++ b/recipes/r-gkmsvm/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-gkmsvm/meta.yaml b/recipes/r-gkmsvm/meta.yaml index 64b57c7201b1f..6ceccf3d2350e 100644 --- a/recipes/r-gkmsvm/meta.yaml +++ b/recipes/r-gkmsvm/meta.yaml @@ -11,27 +11,31 @@ source: url: - https://cran.r-project.org/src/contrib/gkmSVM_{{ version }}.tar.gz - https://cran.r-project.org/src/contrib/Archive/gkmSVM/gkmSVM_{{ version }}.tar.gz - - sha256: e36b4a25f7dcb00cddf206bd22972bb61950eef27b3b5233f954b9edde9aaa11 build: number: 0 - rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - bioconductor-biocgenerics - - bioconductor-biostrings + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - bioconductor-genomeinfodb - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - bioconductor-iranges - r-rocr - r-rcpp @@ -42,10 +46,11 @@ requirements: run: - r-base - - bioconductor-biocgenerics - - bioconductor-biostrings + - {{native}}gcc-libs # [win] + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biostrings >=2.48.0,<2.50.0' - bioconductor-genomeinfodb - - bioconductor-genomicranges + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - bioconductor-iranges - r-rocr - r-rcpp @@ -56,14 +61,23 @@ requirements: test: commands: - - $R -e "library('gkmSVM')" # [not win] + + - $R -e "library('gkmSVM')" # [not win] - "\"%R%\" -e \"library('gkmSVM')\"" # [win] about: home: https://CRAN.R-project.org/package=gkmSVM license: GPL (>= 2) - summary: 'Imports the ''gkmSVM'' v2.0 functionalities into R (www.beerlab.org/gkmsvm). It also - uses the ''kernlab'' library (separate R package by different authors) for various - SVM algorithms. ' - + summary: Imports the 'gkmSVM' v2.0 functionalities into R + It also uses the 'kernlab' library (separate R package by different authors) for + various SVM algorithms. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gprofiler/build.sh b/recipes/r-gprofiler/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-gprofiler/build.sh +++ b/recipes/r-gprofiler/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-gprofiler/meta.yaml b/recipes/r-gprofiler/meta.yaml index af27a1e71d277..fb78ae8d3fcc6 100644 --- a/recipes/r-gprofiler/meta.yaml +++ b/recipes/r-gprofiler/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '0.6.1' %} +{% set version = '0.6.6' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-gprofiler @@ -6,17 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/gProfileR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/gProfileR/gProfileR_{{ version }}.tar.gz - sha256: 17edad1d2f61f84b443b3b322972c5e4d94a12ad5c31cadad536290e5a093de2 + - {{ cran_mirror }}/src/contrib/gProfileR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/gProfileR/gProfileR_{{ version }}.tar.gz + sha256: f161dabaeb425345fac2d0b221ee2019c470256d847ab853274b80204590ccd8 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-rcurl @@ -29,11 +39,24 @@ requirements: test: commands: - - $R -e "library('gProfileR')" + + - $R -e "library('gProfileR')" # [not win] + - "\"%R%\" -e \"library('gProfileR')\"" # [win] about: home: https://CRAN.R-project.org/package=gProfileR license: GPL (>= 2) summary: Functional enrichment analysis, gene identifier conversion and mapping homologous - genes across related organisms via the 'g:Profiler' toolkit (http://biit.cs.ut.ee/gprofiler/). + genes across related organisms via the 'g:Profiler' toolkit (). license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gpseq/build.sh b/recipes/r-gpseq/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-gpseq/build.sh +++ b/recipes/r-gpseq/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-gpseq/meta.yaml b/recipes/r-gpseq/meta.yaml index ba0ec96f76bf8..7fe237d000b9d 100644 --- a/recipes/r-gpseq/meta.yaml +++ b/recipes/r-gpseq/meta.yaml @@ -34,7 +34,17 @@ about: to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons. license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] extra: identifiers: - biotools:gpseq + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-grimport/build.sh b/recipes/r-grimport/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-grimport/build.sh +++ b/recipes/r-grimport/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-grimport/meta.yaml b/recipes/r-grimport/meta.yaml index c0a562c2c55c1..e741d434211b1 100644 --- a/recipes/r-grimport/meta.yaml +++ b/recipes/r-grimport/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '0.9-0' %} +{% set version = '0.9-1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-grimport @@ -6,18 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/grImport_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/grImport/grImport_{{ version }}.tar.gz - sha256: 813bde85ee4db0edb63240c3f29de0d4e750240e79362c7364476201ca690eb5 + - {{ cran_mirror }}/src/contrib/grImport_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/grImport/grImport_{{ version }}.tar.gz + sha256: 5b5664163cb43e5c102c0a1fb6da91e7abb703e3edb17d190f1c3b1f79e11ee2 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-xml @@ -28,10 +37,23 @@ requirements: test: commands: - - $R -e "library('grImport')" + + - $R -e "library('grImport')" # [not win] + - "\"%R%\" -e \"library('grImport')\"" # [win] about: home: https://CRAN.R-project.org/package=grImport license: GPL (>= 2) summary: Functions for converting, importing, and drawing PostScript pictures in R plots. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gsalib/build.sh b/recipes/r-gsalib/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-gsalib/build.sh +++ b/recipes/r-gsalib/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-gsalib/meta.yaml b/recipes/r-gsalib/meta.yaml index 4ad8c599e5c13..2f0c7cbad16c8 100644 --- a/recipes/r-gsalib/meta.yaml +++ b/recipes/r-gsalib/meta.yaml @@ -1,22 +1,31 @@ {% set version = '2.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-gsalib version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/gsalib_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/gsalib/gsalib_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/gsalib_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/gsalib/gsalib_{{ version }}.tar.gz sha256: e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('gsalib')" + + - $R -e "library('gsalib')" # [not win] + - "\"%R%\" -e \"library('gsalib')\"" # [win] about: home: https://CRAN.R-project.org/package=gsalib @@ -34,3 +45,12 @@ about: to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gsmoothr/build.sh b/recipes/r-gsmoothr/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-gsmoothr/build.sh +++ b/recipes/r-gsmoothr/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-gsmoothr/meta.yaml b/recipes/r-gsmoothr/meta.yaml index ff8e94a0fc5d2..974043535d5c0 100644 --- a/recipes/r-gsmoothr/meta.yaml +++ b/recipes/r-gsmoothr/meta.yaml @@ -1,37 +1,61 @@ {% set version = '0.1.7' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-gsmoothr version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/gsmoothr_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/gsmoothr/gsmoothr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/gsmoothr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/gsmoothr/gsmoothr_{{ version }}.tar.gz sha256: b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base run: - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('gsmoothr')" + + - $R -e "library('gsmoothr')" # [not win] + - "\"%R%\" -e \"library('gsmoothr')\"" # [win] about: home: https://CRAN.R-project.org/package=gsmoothr license: LGPL (>= 2.0) summary: Tools rewritten in C for various smoothing tasks license_family: LGPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-gwpcr/build.sh b/recipes/r-gwpcr/build.sh index 4bc8e1853b492..5bf492ab9fc06 100644 --- a/recipes/r-gwpcr/build.sh +++ b/recipes/r-gwpcr/build.sh @@ -1,3 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . diff --git a/recipes/r-gwpcr/meta.yaml b/recipes/r-gwpcr/meta.yaml index 2a6871fd0d149..e30a1042cb27f 100644 --- a/recipes/r-gwpcr/meta.yaml +++ b/recipes/r-gwpcr/meta.yaml @@ -42,3 +42,12 @@ about: The model is based on a mechanistic model of PCR amplification as a Galton-Watson branching process, and on Poissonan sampling to model high-throughput sequencing.' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-haplo.stats/build.sh b/recipes/r-haplo.stats/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-haplo.stats/build.sh +++ b/recipes/r-haplo.stats/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-haplo.stats/meta.yaml b/recipes/r-haplo.stats/meta.yaml index db09db0f8fc4c..214156a355946 100644 --- a/recipes/r-haplo.stats/meta.yaml +++ b/recipes/r-haplo.stats/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.7.7' %} +{% set version = '1.7.9' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-haplo.stats @@ -6,19 +9,29 @@ package: source: url: - - https://cran.r-project.org/src/contrib/haplo.stats_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/haplo.stats/haplo.stats_{{ version }}.tar.gz - sha256: 9318467aa304e49ff826e7de554e3295293b3b2b9cb7a00a3f28238fb5104fe5 + - {{ cran_mirror }}/src/contrib/haplo.stats_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/haplo.stats/haplo.stats_{{ version }}.tar.gz + sha256: bd0adec41cc0ab45eb2674f6f7c40ffe0011e5198883dedb071f178c99567da6 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -26,11 +39,14 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-rms test: commands: - - $R -e "library('haplo.stats')" + + - $R -e "library('haplo.stats')" # [not win] + - "\"%R%\" -e \"library('haplo.stats')\"" # [win] about: home: http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software @@ -40,4 +56,16 @@ about: unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.' + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-hemdag/build.sh b/recipes/r-hemdag/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-hemdag/build.sh +++ b/recipes/r-hemdag/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-hemdag/meta.yaml b/recipes/r-hemdag/meta.yaml index 354ee908c5554..56605a8b82220 100644 --- a/recipes/r-hemdag/meta.yaml +++ b/recipes/r-hemdag/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.1.3' %} +{% set version = '2.2.5' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-hemdag @@ -6,42 +9,62 @@ package: source: url: - - https://cran.r-project.org/src/contrib/HEMDAG_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/HEMDAG/HEMDAG_{{ version }}.tar.gz - - - sha256: 3c62a2c0295bc839d0eec757d31bc731abe3baa6d758860bdc784704fc190c84 + - {{ cran_mirror }}/src/contrib/HEMDAG_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/HEMDAG/HEMDAG_{{ version }}.tar.gz + sha256: dc8d65aa533c9e304dd8a3d312fa83424dc563bfff6dba1ff28ae90b29c29f48 build: - number: 2 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - - r-perfmeas - bioconductor-rbgl + - r-doparallel + - r-foreach - bioconductor-graph + - r-iterators + - r-plyr - r-precrec - - bioconductor-preprocesscore + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' run: - r-base - - r-perfmeas + - {{native}}gcc-libs # [win] - bioconductor-rbgl + - r-doparallel + - r-foreach - bioconductor-graph + - r-iterators + - r-plyr - r-precrec - - bioconductor-preprocesscore + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' test: commands: - - $R -e "library('HEMDAG')" + + - $R -e "library('HEMDAG')" # [not win] + - "\"%R%\" -e \"library('HEMDAG')\"" # [win] about: - home: https://CRAN.R-project.org/package=HEMDAG + home: https://hemdag-tutorials.readthedocs.io, https://github.com/marconotaro/HEMDAG license: GPL (>= 3) summary: An implementation of Hierarchical Ensemble Methods for Directed Acyclic Graphs (DAGs). The 'HEMDAG' package can be used to enhance the predictions of virtually any flat @@ -51,5 +74,14 @@ about: (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco - Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) doi:10.1186/s12859-017-1854-y + Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) ). license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-histonehmm/build.sh b/recipes/r-histonehmm/build.sh index 54a048c046461..5bf492ab9fc06 100644 --- a/recipes/r-histonehmm/build.sh +++ b/recipes/r-histonehmm/build.sh @@ -1,4 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . - diff --git a/recipes/r-histonehmm/meta.yaml b/recipes/r-histonehmm/meta.yaml index 278a4cb55f675..10c2e4e003ade 100644 --- a/recipes/r-histonehmm/meta.yaml +++ b/recipes/r-histonehmm/meta.yaml @@ -9,7 +9,6 @@ package: source: url: https://github.com/matthiasheinig/histoneHMM/archive/a02036a0f541f2c870a880f954c8e2a9432d1433.zip sha256: {{ hash }} -# patches: loghmm.patch build: number: 1 @@ -51,3 +50,12 @@ about: with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-htssip/build.sh b/recipes/r-htssip/build.sh index 6b12898290847..ae301d0bcd14d 100644 --- a/recipes/r-htssip/build.sh +++ b/recipes/r-htssip/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-htssip/meta.yaml b/recipes/r-htssip/meta.yaml index 0fc6632db2279..f0e97a969f92b 100644 --- a/recipes/r-htssip/meta.yaml +++ b/recipes/r-htssip/meta.yaml @@ -1,26 +1,34 @@ {% set version = '1.4.0' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-htssip version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/HTSSIP_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/HTSSIP_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/HTSSIP/HTSSIP_{{ version }}.tar.gz sha256: db93fe66ac3cbde74816cd4c1354e450b398f190fb291b9369b2e753e2e28e13 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + host: - r-base - - bioconductor-deseq2 >=1.16.1 + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - r-ape >=4.1 - r-coenocliner >=0.2.2 - r-dplyr >=0.7.4 @@ -33,9 +41,10 @@ requirements: - r-stringr >=1.2.0 - r-tidyr >=0.7.2 - r-vegan >=2.4.0 + run: - r-base - - bioconductor-deseq2 >=1.16.1 + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - r-ape >=4.1 - r-coenocliner >=0.2.2 - r-dplyr >=0.7.4 @@ -51,18 +60,26 @@ requirements: test: commands: - - $R -e "library('HTSSIP')" + + - $R -e "library('HTSSIP')" # [not win] + - "\"%R%\" -e \"library('HTSSIP')\"" # [win] about: home: https://CRAN.R-project.org/package=HTSSIP license: GPL-2 - summary: 'Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) + summary: 'Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window - high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope - probing (q-SIP).' + high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope + probing (q-SIP). ' + license_family: GPL2 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ic10/build.sh b/recipes/r-ic10/build.sh index a6a73f234c13d..5bf492ab9fc06 100644 --- a/recipes/r-ic10/build.sh +++ b/recipes/r-ic10/build.sh @@ -1,4 +1 @@ -#!/bin/sh -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-ic10/meta.yaml b/recipes/r-ic10/meta.yaml index 94c1d894bfc82..7369bc4530e25 100644 --- a/recipes/r-ic10/meta.yaml +++ b/recipes/r-ic10/meta.yaml @@ -1,26 +1,37 @@ -{% set version = '1.1.3' %} +{% set version = '1.4.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-ic10 - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/iC10_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/iC10/iC10_{{ version }}.tar.gz - sha256: b02f4f1e4cedd894eec2b5f807b94f0f61ec92c2453bf9777dadfe4324cfb4a5 + - {{ cran_mirror }}/src/contrib/iC10_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/iC10/iC10_{{ version }}.tar.gz + sha256: 86075b562b78d609f0ddf729f4d624f35e8fc2e907deadd51a15bbe5a1c6fd5c build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-ic10trainingdata - r-pamr + run: - r-base - r-ic10trainingdata @@ -28,14 +39,25 @@ requirements: test: commands: - - $R -e "library('iC10')" + + - $R -e "library('iC10')" # [not win] + - "\"%R%\" -e \"library('iC10')\"" # [win] about: home: https://CRAN.R-project.org/package=iC10 license: GPL-3 summary: Implementation of the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., - Genome Biology 2014). It uses copy number and/or expression from breast cancer data, + Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ic10trainingdata/build.sh b/recipes/r-ic10trainingdata/build.sh index a6a73f234c13d..5bf492ab9fc06 100644 --- a/recipes/r-ic10trainingdata/build.sh +++ b/recipes/r-ic10trainingdata/build.sh @@ -1,4 +1 @@ -#!/bin/sh -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-ic10trainingdata/meta.yaml b/recipes/r-ic10trainingdata/meta.yaml index 21a0488b1c3f0..ae3d60045213c 100644 --- a/recipes/r-ic10trainingdata/meta.yaml +++ b/recipes/r-ic10trainingdata/meta.yaml @@ -1,30 +1,43 @@ -{% set version = '1.0.1' %} +{% set version = '1.3.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-ic10trainingdata - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/iC10TrainingData_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/iC10TrainingData/iC10TrainingData_{{ version }}.tar.gz - sha256: c4627844b65cc749ed31f6e2dbf2a1f74111920e7bd5292ae487a615637f33f4 + - {{ cran_mirror }}/src/contrib/iC10TrainingData_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/iC10TrainingData/iC10TrainingData_{{ version }}.tar.gz + sha256: 41a2d27f8e41680fd1676a2f3f4cbf51473d7dd6d78c094d12a90c3856acbe9c build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base + run: - r-base test: commands: - - $R -e "library('iC10TrainingData')" + + - $R -e "library('iC10TrainingData')" # [not win] + - "\"%R%\" -e \"library('iC10TrainingData')\"" # [win] about: home: https://CRAN.R-project.org/package=iC10TrainingData @@ -36,3 +49,14 @@ about: available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ichorcna/build.sh b/recipes/r-ichorcna/build.sh index 36961fecb275f..b64b76c3ef41a 100644 --- a/recipes/r-ichorcna/build.sh +++ b/recipes/r-ichorcna/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash $R CMD INSTALL --build . outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM @@ -9,9 +8,6 @@ mkdir -p $PREFIX/bin perl -pi -e 'print "#!/opt/anaconda1anaconda2anaconda3/bin/Rscript\n" if $. == 1' scripts/runIchorCNA.R perl -pi -e 'print "#!/opt/anaconda1anaconda2anaconda3/bin/Rscript\n" if $. == 1' scripts/createPanelOfNormals.R -mv scripts/runIchorCNA.R $outdir/scripts/runIchorCNA.R -mv scripts/createPanelOfNormals.R $outdir/scripts/ichorCNA_createPanelOfNormals.R - chmod a+x $outdir/scripts/*.R ln -s $outdir/scripts/runIchorCNA.R $PREFIX/bin ln -s $outdir/scripts/ichorCNA_createPanelOfNormals.R $PREFIX/bin diff --git a/recipes/r-ichorcna/meta.yaml b/recipes/r-ichorcna/meta.yaml index 606b5a1bac5c3..77ebf18111e16 100644 --- a/recipes/r-ichorcna/meta.yaml +++ b/recipes/r-ichorcna/meta.yaml @@ -12,6 +12,7 @@ source: build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ @@ -40,3 +41,12 @@ about: home: https://github.com/broadinstitute/ichorCNA license: GPL-3 summary: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-icluster/build.sh b/recipes/r-icluster/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-icluster/build.sh +++ b/recipes/r-icluster/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-icluster/meta.yaml b/recipes/r-icluster/meta.yaml index 08b44187fcd2a..74bffe4e2d5af 100644 --- a/recipes/r-icluster/meta.yaml +++ b/recipes/r-icluster/meta.yaml @@ -1,22 +1,31 @@ {% set version = '2.1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-icluster version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/iCluster_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/iCluster/iCluster_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/iCluster_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/iCluster/iCluster_{{ version }}.tar.gz sha256: d97cdcba3b53cf10160c333976d2244c2ad5abb8154e194b1568b48376374326 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-catools @@ -35,7 +44,9 @@ requirements: test: commands: - - $R -e "library('iCluster')" + + - $R -e "library('iCluster')" # [not win] + - "\"%R%\" -e \"library('iCluster')\"" # [win] about: home: https://CRAN.R-project.org/package=iCluster @@ -43,3 +54,14 @@ about: summary: Integrative clustering of multiple genomic data types using a joint latent variable model. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-idr/build.sh b/recipes/r-idr/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-idr/build.sh +++ b/recipes/r-idr/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-idr/meta.yaml b/recipes/r-idr/meta.yaml index 07e818aa99ae9..076ca87c96fe3 100644 --- a/recipes/r-idr/meta.yaml +++ b/recipes/r-idr/meta.yaml @@ -1,22 +1,32 @@ {% set version = '1.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-idr version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/idr_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/idr/idr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/idr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/idr/idr_{{ version }}.tar.gz sha256: 8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +35,9 @@ requirements: test: commands: - - $R -e "library('idr')" + + - $R -e "library('idr')" # [not win] + - "\"%R%\" -e \"library('idr')\"" # [win] about: home: https://CRAN.R-project.org/package=idr @@ -35,3 +47,14 @@ about: of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel ' license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-inlinedocs/build.sh b/recipes/r-inlinedocs/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-inlinedocs/build.sh +++ b/recipes/r-inlinedocs/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-inlinedocs/meta.yaml b/recipes/r-inlinedocs/meta.yaml index 9d0888bdbd6cf..6869cf378ae0d 100644 --- a/recipes/r-inlinedocs/meta.yaml +++ b/recipes/r-inlinedocs/meta.yaml @@ -1,22 +1,31 @@ {% set version = '2013.9.3' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-inlinedocs version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/inlinedocs_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/inlinedocs/inlinedocs_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/inlinedocs_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/inlinedocs/inlinedocs_{{ version }}.tar.gz sha256: 599135152779b26864c258e8d10144462a885ddfb5bbf2c376940f71d236738f build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('inlinedocs')" + + - $R -e "library('inlinedocs')" # [not win] + - "\"%R%\" -e \"library('inlinedocs')\"" # [win] about: home: http://inlinedocs.r-forge.r-project.org @@ -35,3 +46,14 @@ about: argument names are not repeated in comments, and (3) examples are defined in R code, not comments. It is also easy to define a new syntax. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-intego/build.sh b/recipes/r-intego/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-intego/build.sh +++ b/recipes/r-intego/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-intego/meta.yaml b/recipes/r-intego/meta.yaml index 5e67b3398370f..37451d83ccc0a 100644 --- a/recipes/r-intego/meta.yaml +++ b/recipes/r-intego/meta.yaml @@ -12,6 +12,7 @@ source: build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ @@ -37,3 +38,11 @@ about: extra: identifiers: - doi:10.1186/1471-2105-14-42 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-kinship2/build.sh b/recipes/r-kinship2/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-kinship2/build.sh +++ b/recipes/r-kinship2/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-kinship2/meta.yaml b/recipes/r-kinship2/meta.yaml index bfafac3028855..6e3f6a659b881 100644 --- a/recipes/r-kinship2/meta.yaml +++ b/recipes/r-kinship2/meta.yaml @@ -1,24 +1,32 @@ {% set version = '1.6.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-kinship2 version: {{ version|replace("-", "_") }} source: - fn: kinship2_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/kinship2_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/kinship2/kinship2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/kinship2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/kinship2/kinship2_{{ version }}.tar.gz sha256: d2a76aee1a07acf0503acfbe155eeb783d83ee9d8e4428449adf0ea455f123a7 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-matrix - r-quadprog @@ -30,10 +38,12 @@ requirements: test: commands: - - $R -e "library('kinship2')" + + - $R -e "library('kinship2')" # [not win] + - "\"%R%\" -e \"library('kinship2')\"" # [win] about: - home: https://CRAN.R-project.org/package=kinship2 + home: http://r-forge.r-project.org license: GPL (>= 2) summary: Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship @@ -43,3 +53,12 @@ about: include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-km.ci/build.sh b/recipes/r-km.ci/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-km.ci/build.sh +++ b/recipes/r-km.ci/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-km.ci/meta.yaml b/recipes/r-km.ci/meta.yaml index 4a2ee990f0ac8..b766e7d7b2103 100644 --- a/recipes/r-km.ci/meta.yaml +++ b/recipes/r-km.ci/meta.yaml @@ -1,22 +1,31 @@ {% set version = '0.5-2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-km.ci version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/km.ci_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/km.ci/km.ci_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/km.ci_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/km.ci/km.ci_{{ version }}.tar.gz sha256: 1bb9c60e27ba42ea773407dcc438b4a630f53877eb16e6054041a97b25e2d3d0 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-survival @@ -27,7 +36,9 @@ requirements: test: commands: - - $R -e "library('km.ci')" + + - $R -e "library('km.ci')" # [not win] + - "\"%R%\" -e \"library('km.ci')\"" # [win] about: home: https://CRAN.R-project.org/package=km.ci @@ -37,3 +48,14 @@ about: the simultaneous confidence bands by Nair and Hall and Wellner.' license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-kmsurv/build.sh b/recipes/r-kmsurv/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-kmsurv/build.sh +++ b/recipes/r-kmsurv/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-kmsurv/meta.yaml b/recipes/r-kmsurv/meta.yaml index aaa7902d6976c..cce330ce9e774 100644 --- a/recipes/r-kmsurv/meta.yaml +++ b/recipes/r-kmsurv/meta.yaml @@ -1,22 +1,31 @@ {% set version = '0.1-5' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-kmsurv version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/KMsurv_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/KMsurv/KMsurv_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/KMsurv_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/KMsurv/KMsurv_{{ version }}.tar.gz sha256: 55627bc301245e0a4d6be04565fbaabd9cc360e2e5e4bc1e38341354e6de2542 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('KMsurv')" + + - $R -e "library('KMsurv')" # [not win] + - "\"%R%\" -e \"library('KMsurv')\"" # [win] about: home: https://CRAN.R-project.org/package=KMsurv @@ -33,3 +44,14 @@ about: summary: Data sets and functions for Klein and Moeschberger (1997), "Survival Analysis, Techniques for Censored and Truncated Data", Springer. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-kriging/build.sh b/recipes/r-kriging/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-kriging/build.sh +++ b/recipes/r-kriging/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-kriging/meta.yaml b/recipes/r-kriging/meta.yaml index 01432d07ebdce..24abcc4f2a30f 100644 --- a/recipes/r-kriging/meta.yaml +++ b/recipes/r-kriging/meta.yaml @@ -1,17 +1,22 @@ {% set version = '1.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-kriging version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/kriging_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/kriging/kriging_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/kriging_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/kriging/kriging_{{ version }}.tar.gz sha256: bc20a08af3e6175836985cb0763cca20faf32f4190e6b779a656b8fcc8c87d11 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,20 +24,40 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base run: - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('kriging')" + + - $R -e "library('kriging')" # [not win] + - "\"%R%\" -e \"library('kriging')\"" # [win] about: home: https://CRAN.R-project.org/package=kriging license: GPL-2 summary: Simple and highly optimized ordinary kriging algorithm to plot geographical data license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-lme4qtl/build.sh b/recipes/r-lme4qtl/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-lme4qtl/build.sh +++ b/recipes/r-lme4qtl/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-lme4qtl/meta.yaml b/recipes/r-lme4qtl/meta.yaml index 04b864593a072..b9dd44329dbf2 100644 --- a/recipes/r-lme4qtl/meta.yaml +++ b/recipes/r-lme4qtl/meta.yaml @@ -1,12 +1,10 @@ {% set version = '0.1.10' %} - package: name: r-lme4qtl version: {{ version|replace("-", "_") }} source: - fn: {{ version }}.tar.gz url: - https://github.com/variani/lme4qtl/archive/{{ version }}.tar.gz sha256: 59ae1e4aac83b55794cebdcda5529bdabab53a716213b964e6728468d8d594e8 @@ -46,3 +44,14 @@ about: summary: Linear mixed models (lme4) with flexible covariance structure for qtl and association analysis. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-lsd/build.sh b/recipes/r-lsd/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-lsd/build.sh +++ b/recipes/r-lsd/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-lsd/meta.yaml b/recipes/r-lsd/meta.yaml index de5a121a515c5..0a060e047f80a 100644 --- a/recipes/r-lsd/meta.yaml +++ b/recipes/r-lsd/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '3.0' %} +{% set version = '4.0-0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-lsd @@ -6,17 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/LSD_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/LSD/LSD_{{ version }}.tar.gz - sha256: 733c298d7d0df3d7d5cb9b334832c7d2537e8ee2689d25d09d9147c3d5183719 + - {{ cran_mirror }}/src/contrib/LSD_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/LSD/LSD_{{ version }}.tar.gz + sha256: 038a9cc692c67141da066251110e326faf6e1751dd9b367f4d2c5a9bf91d573b build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,11 +35,21 @@ requirements: test: commands: - - $R -e "library('LSD')" + + - $R -e "library('LSD')" # [not win] + - "\"%R%\" -e \"library('LSD')\"" # [win] about: home: https://CRAN.R-project.org/package=LSD license: Unlimited - summary: Create lots of colorful plots in a plethora of variations (try the LSD demotour() - ) + summary: Create lots of colorful plots in a plethora of variations. Try the LSD demotour(). license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-maldiquant/build.sh b/recipes/r-maldiquant/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-maldiquant/build.sh +++ b/recipes/r-maldiquant/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-maldiquant/meta.yaml b/recipes/r-maldiquant/meta.yaml index dade8217cd09d..0b43f17bc81f8 100644 --- a/recipes/r-maldiquant/meta.yaml +++ b/recipes/r-maldiquant/meta.yaml @@ -1,43 +1,69 @@ {% set version = '1.18' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-maldiquant version: {{ version|replace("-", "_") }} source: - url: https://cran.r-project.org/src/contrib/MALDIquant_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/MALDIquant_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MALDIquant/MALDIquant_{{ version }}.tar.gz sha256: 46c1744ead86dc782c410b0be8bf2e95dbef01af53a6f3d665b36bd94910d4a2 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base + run: - r-base - - libgfortran-ng + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('MALDIquant')" + + - $R -e "library('MALDIquant')" # [not win] + - "\"%R%\" -e \"library('MALDIquant')\"" # [win] about: - home: https://github.com/sgibb/MALDIquant/ + home: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquant/ license: GPL (>= 3) - license_family: GPL3 - summary: | - A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight + summary: A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions. + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-maldiquantforeign/build.sh b/recipes/r-maldiquantforeign/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-maldiquantforeign/build.sh +++ b/recipes/r-maldiquantforeign/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-maldiquantforeign/meta.yaml b/recipes/r-maldiquantforeign/meta.yaml index 3d9a00bfb6266..bb56331b4b9ac 100644 --- a/recipes/r-maldiquantforeign/meta.yaml +++ b/recipes/r-maldiquantforeign/meta.yaml @@ -1,23 +1,31 @@ {% set version = '0.11.5' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-maldiquantforeign version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/MALDIquantForeign_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/MALDIquantForeign/MALDIquantForeign_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/MALDIquantForeign_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MALDIquantForeign/MALDIquantForeign_{{ version }}.tar.gz sha256: 31422da4ab767132bd045c3961e54f11aa4e8e704bcbc2ccc74785095bddd863 build: - number: 0 + merge_build_host: True # [win] + + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-maldiquant >=1.16.4 @@ -26,6 +34,7 @@ requirements: - r-digest - r-readbrukerflexdata >=1.7 - r-readmzxmldata >=2.7 + run: - r-base - r-maldiquant >=1.16.4 @@ -37,12 +46,23 @@ requirements: test: commands: - - $R -e "library('MALDIquantForeign')" + + - $R -e "library('MALDIquantForeign')" # [not win] + - "\"%R%\" -e \"library('MALDIquantForeign')\"" # [win] about: home: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquantForeign/ license: GPL (>= 3) - license_family: GPL3 summary: Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from 'MALDIquant' objects. + license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-maldirppa/build.sh b/recipes/r-maldirppa/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-maldirppa/build.sh +++ b/recipes/r-maldirppa/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-maldirppa/meta.yaml b/recipes/r-maldirppa/meta.yaml index 92b12eec9cf4d..c10101e4623d3 100644 --- a/recipes/r-maldirppa/meta.yaml +++ b/recipes/r-maldirppa/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.0.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-maldirppa version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/MALDIrppa_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/MALDIrppa/MALDIrppa_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/MALDIrppa_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MALDIrppa/MALDIrppa_{{ version }}.tar.gz sha256: 0ea6f65ef546130e399caac95f37cea5618acabc958eace5ff7be2cd8ac956f8 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-maldiquant @@ -35,7 +44,9 @@ requirements: test: commands: - - $R -e "library('MALDIrppa')" + + - $R -e "library('MALDIrppa')" # [not win] + - "\"%R%\" -e \"library('MALDIrppa')\"" # [win] about: home: https://CRAN.R-project.org/package=MALDIrppa @@ -43,3 +54,12 @@ about: summary: Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-matrixeqtl/build.sh b/recipes/r-matrixeqtl/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-matrixeqtl/build.sh +++ b/recipes/r-matrixeqtl/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-matrixeqtl/meta.yaml b/recipes/r-matrixeqtl/meta.yaml index e12f3de496907..528875312c34a 100644 --- a/recipes/r-matrixeqtl/meta.yaml +++ b/recipes/r-matrixeqtl/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.1.1' %} +{% set version = '2.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-matrixeqtl @@ -6,17 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/MatrixEQTL_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/MatrixEQTL/MatrixEQTL_{{ version }}.tar.gz - sha256: 3316fbfd2c538ee89632bbbed87a665db5b8cebd4cde190a7efa86bae1876eaf + - {{ cran_mirror }}/src/contrib/MatrixEQTL_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MatrixEQTL/MatrixEQTL_{{ version }}.tar.gz + sha256: 6a6df3ef019c7a7ee228c0e1801d300b8c9c098e5cddda441ee848557a970588 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,15 +35,26 @@ requirements: test: commands: - - $R -e "library('MatrixEQTL')" + + - $R -e "library('MatrixEQTL')" # [not win] + - "\"%R%\" -e \"library('MatrixEQTL')\"" # [win] about: home: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ license: LGPL-3 summary: Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can - test for association between genotype and gene expression using linear regression with + test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery - rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. + rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. license_family: LGPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-metalonda/build.sh b/recipes/r-metalonda/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-metalonda/build.sh +++ b/recipes/r-metalonda/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-metalonda/meta.yaml b/recipes/r-metalonda/meta.yaml index 627e82302d5ad..23130d6c3f9c1 100644 --- a/recipes/r-metalonda/meta.yaml +++ b/recipes/r-metalonda/meta.yaml @@ -1,26 +1,34 @@ {% set version = '1.1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-metalonda version: {{ version|replace("-", "_") }} source: - fn: MetaLonDA_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/MetaLonDA_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/MetaLonDA/MetaLonDA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/MetaLonDA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MetaLonDA/MetaLonDA_{{ version }}.tar.gz sha256: 802fe2956c49aec9054c086ec464404297e9edc0366b6e0a4c02e3569cc1ab5e build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - - bioconductor-deseq2 + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - r-catools - r-doparallel - bioconductor-edger @@ -31,7 +39,7 @@ requirements: run: - r-base - - bioconductor-deseq2 + - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - r-catools - r-doparallel - bioconductor-edger @@ -42,11 +50,22 @@ requirements: test: commands: - - $R -e "library('MetaLonDA')" + + - $R -e "library('MetaLonDA')" # [not win] + - "\"%R%\" -e \"library('MetaLonDA')\"" # [win] about: - home: https - license: MIT + file LICENSE + home: https://github.com/aametwally/MetaLonDA + license: MIT summary: Identify time intervals of differentially abundant metagenomics features in longitudinal studies. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-metama/build.sh b/recipes/r-metama/build.sh index ef53d70dd563d..5309021553b07 100644 --- a/recipes/r-metama/build.sh +++ b/recipes/r-metama/build.sh @@ -1,8 +1,3 @@ -#!/bin/bash - export DISABLE_AUTOBREW=1 -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - diff --git a/recipes/r-metama/meta.yaml b/recipes/r-metama/meta.yaml index 2118574a280de..e3343095d7e00 100644 --- a/recipes/r-metama/meta.yaml +++ b/recipes/r-metama/meta.yaml @@ -1,23 +1,31 @@ {% set version = '3.1.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-metama version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/metaMA_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/metaMA/metaMA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/metaMA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/metaMA/metaMA_{{ version }}.tar.gz sha256: 01851d9632cdf1988d6a43ba44500e51477b9b25d5df1e1da488cd800df85ed6 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-smvar @@ -30,7 +38,9 @@ requirements: test: commands: - - $R -e "library('metaMA')" + + - $R -e "library('metaMA')" # [not win] + - "\"%R%\" -e \"library('metaMA')\"" # [win] about: home: https://CRAN.R-project.org/package=metaMA @@ -38,3 +48,12 @@ about: summary: Combines either p-values or modified effect sizes from different studies to find differentially expressed genes license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-metarnaseq/build.sh b/recipes/r-metarnaseq/build.sh index ef53d70dd563d..5309021553b07 100644 --- a/recipes/r-metarnaseq/build.sh +++ b/recipes/r-metarnaseq/build.sh @@ -1,8 +1,3 @@ -#!/bin/bash - export DISABLE_AUTOBREW=1 -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - diff --git a/recipes/r-metarnaseq/meta.yaml b/recipes/r-metarnaseq/meta.yaml index f2869b3415c46..2e90ca31b5322 100644 --- a/recipes/r-metarnaseq/meta.yaml +++ b/recipes/r-metarnaseq/meta.yaml @@ -1,23 +1,31 @@ {% set version = '1.0.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-metarnaseq version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/metaRNASeq_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/metaRNASeq/metaRNASeq_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/metaRNASeq_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/metaRNASeq/metaRNASeq_{{ version }}.tar.gz sha256: 0affd7f4eb25635b2410110f381809b751655a7f3709f2bc1183e0eb8f6be7f7 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -26,7 +34,9 @@ requirements: test: commands: - - $R -e "library('metaRNASeq')" + + - $R -e "library('metaRNASeq')" # [not win] + - "\"%R%\" -e \"library('metaRNASeq')\"" # [win] about: home: https://CRAN.R-project.org/package=metaRNASeq @@ -35,5 +45,12 @@ about: A vignette is provided to explain how to perform a meta-analysis from two independent RNA-seq experiments. license_family: GPL - - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-metstat/build.sh b/recipes/r-metstat/build.sh index 5a931c2ee7c04..ad2681297b08d 100644 --- a/recipes/r-metstat/build.sh +++ b/recipes/r-metstat/build.sh @@ -1,5 +1,3 @@ -#!/bin/bash - if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 mv DESCRIPTION DESCRIPTION.old diff --git a/recipes/r-metstat/meta.yaml b/recipes/r-metstat/meta.yaml index 7e128c066eee5..ca46e1f6e9eaf 100644 --- a/recipes/r-metstat/meta.yaml +++ b/recipes/r-metstat/meta.yaml @@ -1,5 +1,8 @@ {% set version = '1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-metstat version: {{ version|replace("-", "_") }} @@ -12,16 +15,16 @@ source: build: merge_build_host: True # [win] - # If this is a new build for the same version, increment the build number. - number: 0 - # This is required to make R link correctly on Linux. + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] host: - r-base @@ -37,38 +40,21 @@ requirements: test: commands: - # You can put additional test commands to be run here. - - $R -e "library('MetStaT')" - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - # requires: - # Put any additional test requirements here. + - $R -e "library('MetStaT')" # [not win] + - "\"%R%\" -e \"library('MetStaT')\"" # [win] about: home: https://CRAN.R-project.org/package=MetStaT license: Apache License (== 2.0) summary: A diverse collection of metabolomics related statistical tools. license_family: APACHE - -# The original CRAN metadata for this package was: - -# Package: MetStaT -# Type: Package -# Title: Statistical metabolomics tools -# Version: 1.0 -# Date: 2012-12-10 -# Author: Tim Dorscheidt -# Maintainer: Gooitzen Zwanenburg -# Depends: MASS, abind, pls -# Description: A diverse collection of metabolomics related statistical tools. -# License: Apache License (== 2.0) -# Packaged: 2013-11-18 08:31:40 UTC; gzwanen1 -# NeedsCompilation: no -# Repository: CRAN -# Date/Publication: 2013-11-18 10:09:08 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-micropan/build.sh b/recipes/r-micropan/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-micropan/build.sh +++ b/recipes/r-micropan/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-micropan/meta.yaml b/recipes/r-micropan/meta.yaml index c84fe271d6e81..bb54a870ec8b7 100644 --- a/recipes/r-micropan/meta.yaml +++ b/recipes/r-micropan/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.1.2' %} +{% set version = '1.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-micropan @@ -6,38 +9,66 @@ package: source: url: - - https://cran.r-project.org/src/contrib/micropan_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/micropan/micropan_{{ version }}.tar.gz - sha256: efb4491b04f781a99fb9180689b7788618800618c3433a8af897ee926f556a67 + - {{ cran_mirror }}/src/contrib/micropan_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/micropan/micropan_{{ version }}.tar.gz + sha256: 7ee2a31928e454defe2b37b0da65aef8e6157d76187e7186b6d2266a586970ac build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base + - r-bh + - r-rcpp >=0.12.0 - r-igraph - r-microseq run: - r-base + - {{native}}gcc-libs # [win] + - r-bh + - r-rcpp >=0.12.0 - r-igraph - r-microseq test: commands: - - $R -e "library('micropan')" + + - $R -e "library('micropan')" # [not win] + - "\"%R%\" -e \"library('micropan')\"" # [win] about: home: https://CRAN.R-project.org/package=micropan license: GPL-2 summary: A collection of functions for computations and visualizations of microbial pan-genomes. license_family: GPL2 - extra: identifiers: - biotools:micropan - doi:10.1186/s12859-015-0517-0 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-microseq/build.sh b/recipes/r-microseq/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-microseq/build.sh +++ b/recipes/r-microseq/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-microseq/meta.yaml b/recipes/r-microseq/meta.yaml index 4dabe86759682..8acdc93cec941 100644 --- a/recipes/r-microseq/meta.yaml +++ b/recipes/r-microseq/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.2' %} +{% set version = '1.2.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-microseq @@ -6,34 +9,60 @@ package: source: url: - - https://cran.r-project.org/src/contrib/microseq_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/microseq/microseq_{{ version }}.tar.gz - sha256: 9ac33165011c856bf149c0e15340a4677888844c7a3e0f5e61f949c099778193 + - {{ cran_mirror }}/src/contrib/microseq_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/microseq/microseq_{{ version }}.tar.gz + sha256: 878d5e99a3ee323533cbcf1ae6bc6153d1964f1e1a344807a919ab1c774402c1 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - r-rcpp >=0.11.1 + - r-rcpp >=0.12.0 run: - r-base - - r-rcpp >=0.11.1 + - {{native}}gcc-libs # [win] + - r-rcpp >=0.12.0 test: commands: - - $R -e "library('microseq')" + + - $R -e "library('microseq')" # [not win] + - "\"%R%\" -e \"library('microseq')\"" # [win] about: home: https://CRAN.R-project.org/package=microseq license: GPL-2 - summary: Basic functions for microbial sequence data analysis. + summary: Basic functions for microbial sequence data analysis. The idea is to use the basic + R data structures as much as possible, without building complex data types. license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-mixomics/build.sh b/recipes/r-mixomics/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-mixomics/build.sh +++ b/recipes/r-mixomics/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-mixomics/meta.yaml b/recipes/r-mixomics/meta.yaml index be4620e12c8ab..70180ee9d1075 100644 --- a/recipes/r-mixomics/meta.yaml +++ b/recipes/r-mixomics/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '6.3.1' %} +{% set version = '6.3.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-mixomics @@ -6,18 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/mixOmics_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/mixOmics/mixOmics_{{ version }}.tar.gz - sha256: 1883f0c60e4f0dfa0beb62a9b0f377624cc310efef1646b9c4ba57927a5f742f + - {{ cran_mirror }}/src/contrib/mixOmics_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/mixOmics/mixOmics_{{ version }}.tar.gz + sha256: 62c9bfe8967997c673e45433a8705dd43f6b5eb3c9fd62529461d3e6f4cb10d3 build: - number: 1 - # r-rgl not available on OSX for conda-forge - skip: true # [osx] + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-mass @@ -30,15 +39,11 @@ requirements: - r-igraph - r-lattice - r-matrixstats - - r-plyr - r-rarpack - r-reshape2 - r-rgl - r-tidyr - # prev version - - libglu # [linux] - run: - r-base - r-mass @@ -51,18 +56,16 @@ requirements: - r-igraph - r-lattice - r-matrixstats - - r-plyr - r-rarpack - r-reshape2 - r-rgl - r-tidyr - # prev version - - libglu # [linux] - test: commands: - - $R -e "library('mixOmics')" + + - $R -e "library('mixOmics')" # [not win] + - "\"%R%\" -e \"library('mixOmics')\"" # [win] about: home: http://www.mixOmics.org @@ -89,8 +92,17 @@ about: with variants of multi-group Partial Least Squares.' license_family: GPL3 - + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] extra: container: # needed for libGL.so.1 extended-base: true + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-mlgt/build.sh b/recipes/r-mlgt/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-mlgt/build.sh +++ b/recipes/r-mlgt/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-mlgt/meta.yaml b/recipes/r-mlgt/meta.yaml index cdbfeb7110144..531deebb136b9 100644 --- a/recipes/r-mlgt/meta.yaml +++ b/recipes/r-mlgt/meta.yaml @@ -1,23 +1,31 @@ {% set version = '0.16' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-mlgt version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/mlgt_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/mlgt/mlgt_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/mlgt_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/mlgt/mlgt_{{ version }}.tar.gz sha256: a93d6a2aafec41946773484a1bc5087cd56b967e4f8de3e68c69e4b7abc16ddb build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-seqinr @@ -28,7 +36,9 @@ requirements: test: commands: - - $R -e "library('mlgt')" + + - $R -e "library('mlgt')" # [not win] + - "\"%R%\" -e \"library('mlgt')\"" # [win] about: home: http://personalpages.manchester.ac.uk/staff/David.Gerrard/ @@ -38,7 +48,16 @@ about: sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. license_family: GPL3 - + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] extra: identifiers: - biotools:mlgt + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-mmgenome/build.sh b/recipes/r-mmgenome/build.sh index 0fc821f93c0a4..4684b0b86c263 100644 --- a/recipes/r-mmgenome/build.sh +++ b/recipes/r-mmgenome/build.sh @@ -1,10 +1,3 @@ -#!/bin/bash - cd mmgenome -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - - diff --git a/recipes/r-mmgenome/meta.yaml b/recipes/r-mmgenome/meta.yaml index c7c5b6b473a84..df5e3f4c8dfae 100644 --- a/recipes/r-mmgenome/meta.yaml +++ b/recipes/r-mmgenome/meta.yaml @@ -48,3 +48,12 @@ about: home: https://github.com/MadsAlbertsen/mmgenome license: AGPL-3 summary: 'Tools for extracting individual genomes from metagenomes' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-mqtl/build.sh b/recipes/r-mqtl/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-mqtl/build.sh +++ b/recipes/r-mqtl/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-mqtl/meta.yaml b/recipes/r-mqtl/meta.yaml index 58bd04bc15fe9..d30a7b4bfc4c0 100644 --- a/recipes/r-mqtl/meta.yaml +++ b/recipes/r-mqtl/meta.yaml @@ -1,26 +1,30 @@ {% set version = '1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-mqtl version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/mQTL_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/mQTL/mQTL_{{ version }}.tar.gz - - sha256: 7a36044224285354a58686dbf7ce24ee8bd8a543a56821d7b8152c90e7ee004d + - {{ cran_mirror }}/src/contrib/mQTL_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/mQTL/mQTL_{{ version }}.tar.gz + sha256: 21193861fbf2d280f2b7284ba87d68adce515e35fbe4e71821439fa8b14d1b72 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ - requirements: build: - - {{ compiler('c') }} + - {{posix}}zip # [win] host: - r-base @@ -36,7 +40,9 @@ requirements: test: commands: - - $R -e "library('mQTL')" + + - $R -e "library('mQTL')" # [not win] + - "\"%R%\" -e \"library('mQTL')\"" # [win] about: home: https://CRAN.R-project.org/package=mQTL @@ -46,3 +52,12 @@ about: dimensionality reduction using SRV approach and finally QTL mapping using R/qtl package. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-msm/build.sh b/recipes/r-msm/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-msm/build.sh +++ b/recipes/r-msm/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-msm/meta.yaml b/recipes/r-msm/meta.yaml index ab534b36bcdac..5ab519656a1f2 100644 --- a/recipes/r-msm/meta.yaml +++ b/recipes/r-msm/meta.yaml @@ -1,42 +1,58 @@ {% set version = '1.6.6' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-msm version: {{ version|replace("-", "_") }} source: - fn: msm_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/msm_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/msm/msm_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/msm_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/msm/msm_{{ version }}.tar.gz sha256: fd12512d3cdca5fab634bf6222d896482bd1876192939da475f251b3a873a71a build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: - r-base - r-expm - r-mvtnorm - r-survival - - gcc run: - r-base + - {{native}}gcc-libs # [win] - r-expm - r-mvtnorm - r-survival test: commands: - - $R -e "library('msm')" + + - $R -e "library('msm')" # [not win] + - "\"%R%\" -e \"library('msm')\"" # [win] about: - home: https + home: https://github.com/chjackson/msm license: GPL (>= 2) summary: Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. Designed for processes observed at arbitrary times in continuous @@ -44,3 +60,12 @@ about: transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-msqrob/conda_build_config.yaml b/recipes/r-msqrob/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/r-msqrob/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/r-mutoss/build.sh b/recipes/r-mutoss/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-mutoss/build.sh +++ b/recipes/r-mutoss/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-mutoss/meta.yaml b/recipes/r-mutoss/meta.yaml index 5ac807372b271..854a7af4d4f28 100644 --- a/recipes/r-mutoss/meta.yaml +++ b/recipes/r-mutoss/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '0.1-10' %} +{% set version = '0.1-12' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-mutoss @@ -6,18 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/mutoss_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/mutoss/mutoss_{{ version }}.tar.gz - sha256: 23e62c2e3fa0fb235adb47deed2502f054510661aaadfe1a8f91d9dad4c832de + - {{ cran_mirror }}/src/contrib/mutoss_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/mutoss/mutoss_{{ version }}.tar.gz + sha256: 2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-multcomp >=1.1_0 @@ -34,11 +43,23 @@ requirements: test: commands: - - $R -e "library('mutoss')" + + - $R -e "library('mutoss')" # [not win] + - "\"%R%\" -e \"library('mutoss')\"" # [win] about: - home: http://mutoss.r-forge.r-project.org/ + home: https://github.com/kornl/mutoss/ license: GPL - summary: The Mutoss package and accompanying mutossGUI package are designed to ease the application - and comparison of multiple hypothesis testing procedures. + summary: Designed to ease the application and comparison of multiple hypothesis testing procedures + for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying + 'mutossGUI'. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-nanostringnorm/build.sh b/recipes/r-nanostringnorm/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-nanostringnorm/build.sh +++ b/recipes/r-nanostringnorm/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-nanostringnorm/conda_build_config.yaml b/recipes/r-nanostringnorm/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/r-nanostringnorm/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/r-nanostringnorm/meta.yaml b/recipes/r-nanostringnorm/meta.yaml index 0a427a45d466b..219564a41d79b 100644 --- a/recipes/r-nanostringnorm/meta.yaml +++ b/recipes/r-nanostringnorm/meta.yaml @@ -1,36 +1,58 @@ -{% set version = '1.1.21' %} +{% set version = '1.2.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-nanostringnorm version: {{ version|replace("-", "_") }} source: - url: https://cran.r-project.org/src/contrib/Archive/NanoStringNorm/NanoStringNorm_{{ version }}.tar.gz - sha256: 6416dd76a84d30bf9bd7000a581fd9b7757558b86e2afb49ad433f35cb8475e5 + url: + - {{ cran_mirror }}/src/contrib/NanoStringNorm_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/NanoStringNorm/NanoStringNorm_{{ version }}.tar.gz + sha256: f2d4773a67c609a85ad12635252310e1e190444a66997d07665544def3862117 build: - number: 2 - + merge_build_host: True # [win] + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] host: - r-base + - r-xml >=3.98_1.5 - r-gdata >=2.8.2 - bioconductor-vsn >=3.22.0 run: - r-base + - r-xml >=3.98_1.5 - r-gdata >=2.8.2 - bioconductor-vsn >=3.22.0 test: commands: - - $R -e "library('NanoStringNorm')" + + - $R -e "library('NanoStringNorm')" # [not win] + - "\"%R%\" -e \"library('NanoStringNorm')\"" # [win] about: home: https://CRAN.R-project.org/package=NanoStringNorm license: GPL-2 - summary: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data. + summary: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter + data. license_family: GPL2 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-nastiseq/build.sh b/recipes/r-nastiseq/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-nastiseq/build.sh +++ b/recipes/r-nastiseq/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-nastiseq/meta.yaml b/recipes/r-nastiseq/meta.yaml index 950d5ea76a226..173514d6dbe3d 100644 --- a/recipes/r-nastiseq/meta.yaml +++ b/recipes/r-nastiseq/meta.yaml @@ -15,7 +15,6 @@ build: - lib/R/lib/ - lib/ - requirements: host: - r-base @@ -49,3 +48,11 @@ extra: identifiers: - biotools:nastiseq - doi:10.1101/gr.149310.112 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ncbit/build.sh b/recipes/r-ncbit/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-ncbit/build.sh +++ b/recipes/r-ncbit/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-ncbit/meta.yaml b/recipes/r-ncbit/meta.yaml index 169e0f97e1e99..950615356d4c7 100644 --- a/recipes/r-ncbit/meta.yaml +++ b/recipes/r-ncbit/meta.yaml @@ -1,24 +1,32 @@ {% set version = '2013.03.29' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-ncbit version: {{ version|replace("-", "_") }} source: - fn: ncbit_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/ncbit_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ncbit/ncbit_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/ncbit_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ncbit/ncbit_{{ version }}.tar.gz sha256: 4480271f14953615c8ddc2e0666866bb1d0964398ba0fab6cc29046436820738 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base run: @@ -26,10 +34,21 @@ requirements: test: commands: - - $R -e "library('ncbit')" + + - $R -e "library('ncbit')" # [not win] + - "\"%R%\" -e \"library('ncbit')\"" # [win] about: home: https://CRAN.R-project.org/package=ncbit license: GPL (>= 2) summary: making NCBI taxonomic data locally available and searchable as an R object license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ngsplot-hg19/meta.yaml b/recipes/r-ngsplot-hg19/meta.yaml index 69c3e982120c4..872762e45f99f 100644 --- a/recipes/r-ngsplot-hg19/meta.yaml +++ b/recipes/r-ngsplot-hg19/meta.yaml @@ -23,3 +23,12 @@ about: home: 'https://github.com/shenlab-sinai/ngsplot' license: GPL-2.0 summary: 'HG19 genome database for NGSplot' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ngsplot-hg38/meta.yaml b/recipes/r-ngsplot-hg38/meta.yaml index 6bc7a2125919e..52a4693133fd7 100644 --- a/recipes/r-ngsplot-hg38/meta.yaml +++ b/recipes/r-ngsplot-hg38/meta.yaml @@ -20,3 +20,12 @@ about: home: 'https://github.com/shenlab-sinai/ngsplot' license: GPL-2.0 summary: 'HG19 genome database for NGSplot' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ngsplot-mm10/meta.yaml b/recipes/r-ngsplot-mm10/meta.yaml index cbae4cf6c32d5..77088c2099117 100644 --- a/recipes/r-ngsplot-mm10/meta.yaml +++ b/recipes/r-ngsplot-mm10/meta.yaml @@ -20,3 +20,12 @@ about: home: 'https://github.com/shenlab-sinai/ngsplot' license: GPL-2.0 summary: 'MM10 genome database for NGSplot' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ngsplot/build.sh b/recipes/r-ngsplot/build.sh index 3ec522d58bca1..a0867bed641c4 100644 --- a/recipes/r-ngsplot/build.sh +++ b/recipes/r-ngsplot/build.sh @@ -1,14 +1,12 @@ -#!/bin/bash outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir mkdir -p $PREFIX/bin cp -R {bin,database,example,galaxy,lib,LICENSE} ${outdir}/ -# Set up links for + for f in ${outdir}/bin/*; do ln -s ${f} ${PREFIX}/bin done -# Patch scripts to use proper path and not depend on NGSPLOT env variable for f in "${outdir}"/bin/*.py ; do sed -Ei.bak "s|os\.environ\[\"NGSPLOT\"\]|\"${outdir}\"|g" "${f}" rm "${f}.bak" diff --git a/recipes/r-ngsplot/meta.yaml b/recipes/r-ngsplot/meta.yaml index 5661050c8679c..85b714998a7b5 100644 --- a/recipes/r-ngsplot/meta.yaml +++ b/recipes/r-ngsplot/meta.yaml @@ -38,3 +38,11 @@ about: extra: identifiers: - doi:10.1186/1471-2164-15-284 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-nodiv/build.sh b/recipes/r-nodiv/build.sh index 2c2d35b07c819..27dfbc4d6f61c 100644 --- a/recipes/r-nodiv/build.sh +++ b/recipes/r-nodiv/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-nodiv/meta.yaml b/recipes/r-nodiv/meta.yaml index f85b294a112ae..cca6ec2d2434a 100644 --- a/recipes/r-nodiv/meta.yaml +++ b/recipes/r-nodiv/meta.yaml @@ -1,23 +1,31 @@ {% set version = '1.2.0' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-nodiv version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/nodiv_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/nodiv_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/nodiv/nodiv_{{ version }}.tar.gz sha256: cb5517dcf6fd1b614891ddef0c555dabc0df07419fcc68f982c984660ba6b02d build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + host: - r-base - r-ape @@ -25,6 +33,7 @@ requirements: - r-raster - r-sp - r-vegan + run: - r-base - r-ape @@ -35,22 +44,30 @@ requirements: test: commands: - - $R -e "library('nodiv')" + + - $R -e "library('nodiv')" # [not win] + - "\"%R%\" -e \"library('nodiv')\"" # [win] about: home: https://CRAN.R-project.org/package=nodiv license: MIT summary: 'An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species - distributions. Methods in Ecology and Evolution 5(11): 1225-1235. - . + distributions. Methods in Ecology and Evolution 5(11): 1225-1235. . Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.' + license_family: MIT extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-oai/build.sh b/recipes/r-oai/build.sh index 54a048c046461..5bf492ab9fc06 100644 --- a/recipes/r-oai/build.sh +++ b/recipes/r-oai/build.sh @@ -1,4 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . - diff --git a/recipes/r-oai/meta.yaml b/recipes/r-oai/meta.yaml index a158abbc4bd8f..6306008a209f0 100644 --- a/recipes/r-oai/meta.yaml +++ b/recipes/r-oai/meta.yaml @@ -1,17 +1,22 @@ {% set version = '0.2.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-oai version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/oai_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/oai/oai_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/oai_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/oai/oai_{{ version }}.tar.gz sha256: a1eef45c7faf1b12613b1e782847cc6f8994ffe917f1b694d325de9b79123c60 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,7 +24,15 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-httr >=1.2.0 @@ -30,7 +43,7 @@ requirements: run: - r-base - - libgcc + - {{native}}gcc-libs # [win] - r-httr >=1.2.0 - r-plyr >=1.8.4 - r-stringr >=1.1.0 @@ -39,15 +52,25 @@ requirements: test: commands: - - $R -e "library('oai')" + - $R -e "library('oai')" # [not win] + - "\"%R%\" -e \"library('oai')\"" # [win] about: home: https://github.com/ropensci/oai - license: MIT + file LICENSE + license: MIT summary: 'A general purpose client to work with any ''OAI-PMH'' (Open Archives Initiative Protocol for ''Metadata'' Harvesting) service. The ''OAI-PMH'' protocol is described at . Functions are provided to work with the ''OAI-PMH'' verbs: ''GetRecord'', ''Identify'', ''ListIdentifiers'', ''ListMetadataFormats'', ''ListRecords'', and ''ListSets''.' license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-pamr/build.sh b/recipes/r-pamr/build.sh index 6a5287bec0c5c..5bf492ab9fc06 100644 --- a/recipes/r-pamr/build.sh +++ b/recipes/r-pamr/build.sh @@ -1,7 +1 @@ -#!/bin/sh - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-pamr/meta.yaml b/recipes/r-pamr/meta.yaml index 9860fac99fef3..b50bc2fa75ab9 100644 --- a/recipes/r-pamr/meta.yaml +++ b/recipes/r-pamr/meta.yaml @@ -1,25 +1,37 @@ {% set version = '1.55' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-pamr - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/pamr_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/pamr/pamr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/pamr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/pamr/pamr_{{ version }}.tar.gz sha256: ed910194937a6097ec79234d84777856fd520b111a7c79f7c86dc607169cc3c3 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: - # gcc unconditionally for Fortran - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('fortran') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -28,15 +40,29 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-cluster - r-survival test: commands: - - $R -e "library('pamr')" + + - $R -e "library('pamr')" # [not win] + - "\"%R%\" -e \"library('pamr')\"" # [win] about: home: https://CRAN.R-project.org/package=pamr license: GPL-2 summary: Some functions for sample classification in microarrays license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-patpro/build.sh b/recipes/r-patpro/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-patpro/build.sh +++ b/recipes/r-patpro/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-patpro/meta.yaml b/recipes/r-patpro/meta.yaml index f12b924ba8bab..e24524a1df54d 100644 --- a/recipes/r-patpro/meta.yaml +++ b/recipes/r-patpro/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-patpro version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/patPRO_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/patPRO/patPRO_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/patPRO_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/patPRO/patPRO_{{ version }}.tar.gz sha256: d63bfb2a673000b285d5e7106597c8fc148509461bf047f48ecf553ae933d8d0 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-rcolorbrewer @@ -35,7 +44,9 @@ requirements: test: commands: - - $R -e "library('patPRO')" + + - $R -e "library('patPRO')" # [not win] + - "\"%R%\" -e \"library('patPRO')\"" # [win] about: home: https://CRAN.R-project.org/package=patPRO @@ -43,3 +54,14 @@ about: summary: Quickly and easily visualize longitudinal microbiome profiles using standard output from the QIIME microbiome analysis toolkit (see for more information). license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-peer/build.sh b/recipes/r-peer/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-peer/build.sh +++ b/recipes/r-peer/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-peer/meta.yaml b/recipes/r-peer/meta.yaml index 82e29793166a5..228e79ab247d5 100644 --- a/recipes/r-peer/meta.yaml +++ b/recipes/r-peer/meta.yaml @@ -11,7 +11,6 @@ build: number: 1 skip: True # [osx] - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -38,3 +37,12 @@ by threefold and (iii) allowed inference of intermediate cellular traits, such as transcription factor or pathway activations. This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python. ' +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-pegas/build.sh b/recipes/r-pegas/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-pegas/build.sh +++ b/recipes/r-pegas/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-pegas/meta.yaml b/recipes/r-pegas/meta.yaml index 31bbf39af438f..3fbaac527a844 100644 --- a/recipes/r-pegas/meta.yaml +++ b/recipes/r-pegas/meta.yaml @@ -1,24 +1,37 @@ -{% set version = '0.10' %} +{% set version = '0.11' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-pegas - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/pegas_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/pegas/pegas_{{ version }}.tar.gz - sha256: eaa1bb8aaf5ecd0c26ee041bb0b40f8f4481614803ba13f1364a65fd56e742e3 + - {{ cran_mirror }}/src/contrib/pegas_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/pegas/pegas_{{ version }}.tar.gz + sha256: fdae330ea325198e217dc09dc6587816267f738272e8b9175d9bc9f5af5a4150 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -27,17 +40,31 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-adegenet - r-ape >=2.4 test: commands: - - $R -e "library('pegas')" + + - $R -e "library('pegas')" # [not win] + - "\"%R%\" -e \"library('pegas')\"" # [win] about: - home: http + home: http://ape-package.ird.fr/pegas.html license: GPL (>= 2) summary: Functions for reading, writing, plotting, analysing, and manipulating allelic and - haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites - including coalescence analyses. + haplotypic data, including from VCF files, and for the analysis of population nucleotide + sequences and micro-satellites including coalescent analyses, linkage disequilibrium, + population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum + spanning tree and network, and median-joining networks. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-perfmeas/build.sh b/recipes/r-perfmeas/build.sh index 07b4915c88fa7..5bf492ab9fc06 100644 --- a/recipes/r-perfmeas/build.sh +++ b/recipes/r-perfmeas/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - diff --git a/recipes/r-perfmeas/meta.yaml b/recipes/r-perfmeas/meta.yaml index d007ed088fb62..7478e37a0ac8c 100644 --- a/recipes/r-perfmeas/meta.yaml +++ b/recipes/r-perfmeas/meta.yaml @@ -1,28 +1,36 @@ {% set version = '1.2.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-perfmeas version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/PerfMeas_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/PerfMeas/PerfMeas_{{ version }}.tar.gz - - + - {{ cran_mirror }}/src/contrib/PerfMeas_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PerfMeas/PerfMeas_{{ version }}.tar.gz sha256: 2371d9f8949d8c570d8b772ff1c3615eebf5e825a96722b40ced07b22ab3eaf4 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ - requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -32,23 +40,31 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - bioconductor-rbgl - bioconductor-graph - bioconductor-limma test: commands: - - $R -e "library('PerfMeas')" + - $R -e "library('PerfMeas')" # [not win] + - "\"%R%\" -e \"library('PerfMeas')\"" # [win] about: home: https://CRAN.R-project.org/package=PerfMeas - license: GPL3 + license: GPL (>= 2) summary: Package that implements different performance measures for classification and ranking tasks. AUC, precision at a given recall, F-score for single and multiple classes are available. - license_family: GPL + license_family: GPL3 extra: recipe-maintainers: - - visze + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-phangorn/build.sh b/recipes/r-phangorn/build.sh index d5450b8790d6c..5bf492ab9fc06 100644 --- a/recipes/r-phangorn/build.sh +++ b/recipes/r-phangorn/build.sh @@ -1,5 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - diff --git a/recipes/r-phangorn/meta.yaml b/recipes/r-phangorn/meta.yaml index b17f5444c61c0..5e2e3ccdb96a3 100644 --- a/recipes/r-phangorn/meta.yaml +++ b/recipes/r-phangorn/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.2.0' %} +{% set version = '2.4.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-phangorn @@ -6,24 +9,36 @@ package: source: url: - - https://cran.r-project.org/src/contrib/phangorn_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/phangorn/phangorn_{{ version }}.tar.gz - sha256: 32c81a1af524284c57408a5182dd3b6fd99652ae00572e4c5c05ecd08a59210b + - {{ cran_mirror }}/src/contrib/phangorn_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/phangorn/phangorn_{{ version }}.tar.gz + sha256: 31d0ea035b48d3940013f369e514351db19f9f92b2832c53f09f752b4a998875 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ + requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - r-matrix - - r-rcpp - - r-ape >=4.1 + - r-rcpp >=0.12.0 + - r-ape >=5.0 - r-fastmatch - r-igraph >=1.0 - r-magrittr @@ -31,9 +46,10 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-matrix - - r-rcpp - - r-ape >=4.1 + - r-rcpp >=0.12.0 + - r-ape >=5.0 - r-fastmatch - r-igraph >=1.0 - r-magrittr @@ -41,12 +57,25 @@ requirements: test: commands: - - $R -e "library('phangorn')" + + - $R -e "library('phangorn')" # [not win] + - "\"%R%\" -e \"library('phangorn')\"" # [win] about: home: https://github.com/KlausVigo/phangorn license: GPL (>= 2) - summary: 'Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum - Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.' + summary: 'Package contains methods for estimation of phylogenetic trees and networks using + Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. + Allows to compare trees, models selection and offers visualizations for trees and + split networks. ' license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-phewas/build.sh b/recipes/r-phewas/build.sh index 02a04919ff792..f3e9e74d0a6e4 100644 --- a/recipes/r-phewas/build.sh +++ b/recipes/r-phewas/build.sh @@ -1,5 +1,3 @@ -#!/bin/bash - if [[ $target_platform =~ linux.* ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 mv DESCRIPTION DESCRIPTION.old diff --git a/recipes/r-phewas/meta.yaml b/recipes/r-phewas/meta.yaml index edc238d2c4ebd..d16cff71c6a57 100644 --- a/recipes/r-phewas/meta.yaml +++ b/recipes/r-phewas/meta.yaml @@ -12,6 +12,7 @@ source: build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -65,4 +66,10 @@ extra: identifiers: - doi:10.1093/bioinformatics/btu197 recipe-maintainers: - - slacalle + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-phyext2/build.sh b/recipes/r-phyext2/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-phyext2/build.sh +++ b/recipes/r-phyext2/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-phyext2/meta.yaml b/recipes/r-phyext2/meta.yaml index 89336bf3eb6a2..3ebb91fd98abf 100644 --- a/recipes/r-phyext2/meta.yaml +++ b/recipes/r-phyext2/meta.yaml @@ -1,24 +1,32 @@ {% set version = '0.0.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-phyext2 version: {{ version|replace("-", "_") }} source: - fn: phyext2_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/phyext2_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/phyext2/phyext2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/phyext2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/phyext2/phyext2_{{ version }}.tar.gz sha256: 2ba35543bf7b4bfab5d41ad4de2ff2a1ac78ce0f07c0d736a0d4a58adf0c0749 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-ape - r-phylobase @@ -30,7 +38,9 @@ requirements: test: commands: - - $R -e "library('phyext2')" + + - $R -e "library('phyext2')" # [not win] + - "\"%R%\" -e \"library('phyext2')\"" # [win] about: home: https://CRAN.R-project.org/package=phyext2 @@ -40,3 +50,12 @@ about: provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-phylobase/build.sh b/recipes/r-phylobase/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-phylobase/build.sh +++ b/recipes/r-phylobase/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-phylobase/meta.yaml b/recipes/r-phylobase/meta.yaml index c939cf38977ab..b619a80ae7351 100644 --- a/recipes/r-phylobase/meta.yaml +++ b/recipes/r-phylobase/meta.yaml @@ -1,24 +1,37 @@ {% set version = '0.8.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-phylobase version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/phylobase_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/phylobase/phylobase_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/phylobase_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/phylobase/phylobase_{{ version }}.tar.gz sha256: d7c1a972c266ffe80345c7150608a85e6e2def4a3f079ac964ad9dbce2281002 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -30,6 +43,7 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-rnexml - r-rcpp >=0.11.0 - r-ade4 @@ -38,11 +52,22 @@ requirements: test: commands: - - $R -e "library('phylobase')" + + - $R -e "library('phylobase')" # [not win] + - "\"%R%\" -e \"library('phylobase')\"" # [win] about: home: https://github.com/fmichonneau/phylobase - license: 'GPL (>= 2)' + license: GPL (>= 2) summary: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-phylomeasures/build.sh b/recipes/r-phylomeasures/build.sh index 04e18532850d4..e6eabe73e59d5 100644 --- a/recipes/r-phylomeasures/build.sh +++ b/recipes/r-phylomeasures/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-phylomeasures/meta.yaml b/recipes/r-phylomeasures/meta.yaml index 03a595f982a40..4524397a49258 100644 --- a/recipes/r-phylomeasures/meta.yaml +++ b/recipes/r-phylomeasures/meta.yaml @@ -1,36 +1,52 @@ {% set version = '2.1' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-phylomeasures version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/PhyloMeasures_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/PhyloMeasures_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PhyloMeasures/PhyloMeasures_{{ version }}.tar.gz sha256: 1982f47cb5bfa61e56f47cae78e199f13778edde49af86fa5cc183a0d1d15d05 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-ape + run: - r-base + - {{native}}gcc-libs # [win] - r-ape test: commands: - - $R -e "library('PhyloMeasures')" + + - $R -e "library('PhyloMeasures')" # [not win] + - "\"%R%\" -e \"library('PhyloMeasures')\"" # [win] about: home: https://CRAN.R-project.org/package=PhyloMeasures @@ -50,13 +66,13 @@ about: can compute exactly any statistical moment of the measure. The package supports computations under different null models, including abundance-weighted models. license_family: GPL3 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr - johanneskoester - bgruening - daler - jdblischak - - cbrueffer diff --git a/recipes/r-phylosignal/build.sh b/recipes/r-phylosignal/build.sh index 245a74880766f..4dda985dabbcf 100644 --- a/recipes/r-phylosignal/build.sh +++ b/recipes/r-phylosignal/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-phylosignal/meta.yaml b/recipes/r-phylosignal/meta.yaml index a058cd2574a95..2dfaa87fa912f 100644 --- a/recipes/r-phylosignal/meta.yaml +++ b/recipes/r-phylosignal/meta.yaml @@ -1,26 +1,38 @@ {% set version = '1.2' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-phylosignal version: {{ version|replace("-", "_") }} source: - url: {{ cran_mirror }}/src/contrib/phylosignal_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/phylosignal_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/phylosignal/phylosignal_{{ version }}.tar.gz sha256: 4b1229a75352f86978137a2108938803240a55e8865a8e3cb21c151b3679fa2a build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-dbi @@ -31,8 +43,10 @@ requirements: - r-boot - r-igraph - r-phylobase + run: - r-base + - {{native}}gcc-libs # [win] - r-dbi - r-rcpp >=0.11.0 - r-rcpparmadillo @@ -44,7 +58,9 @@ requirements: test: commands: - - $R -e "library('phylosignal')" + + - $R -e "library('phylosignal')" # [not win] + - "\"%R%\" -e \"library('phylosignal')\"" # [win] about: home: https://CRAN.R-project.org/package=phylosignal @@ -54,8 +70,13 @@ about: tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method. license_family: GPL3 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: recipe-maintainers: - - nick-youngblut + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-phytools/build.sh b/recipes/r-phytools/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-phytools/build.sh +++ b/recipes/r-phytools/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-phytools/meta.yaml b/recipes/r-phytools/meta.yaml index 292d7ad7d8fa3..cd9ee3a19c8da 100644 --- a/recipes/r-phytools/meta.yaml +++ b/recipes/r-phytools/meta.yaml @@ -1,24 +1,33 @@ -{% set version = '0.6-44' %} +{% set version = '0.6-60' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-phytools version: {{ version|replace("-", "_") }} source: - fn: phytools_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/phytools_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/phytools/phytools_{{ version }}.tar.gz - sha256: 1c11c9b87fcfe762a03121721c1623f9bf423226f82cb60911524f16f62d01f9 + - {{ cran_mirror }}/src/contrib/phytools_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/phytools/phytools_{{ version }}.tar.gz + sha256: 55cad759510d247ebbf03a53a46caddadd3bf87584ccf7fcd6dd06d44516b377 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-mass - r-animation @@ -26,9 +35,9 @@ requirements: - r-clustergeneration - r-coda - r-combinat + - r-expm - r-maps - r-mnormt - - r-msm - r-nlme - r-numderiv - r-phangorn >=2.3.1 @@ -43,9 +52,9 @@ requirements: - r-clustergeneration - r-coda - r-combinat + - r-expm - r-maps - r-mnormt - - r-msm - r-nlme - r-numderiv - r-phangorn >=2.3.1 @@ -54,10 +63,12 @@ requirements: test: commands: - - $R -e "library('phytools')" + + - $R -e "library('phytools')" # [not win] + - "\"%R%\" -e \"library('phytools')\"" # [win] about: - home: http + home: http://github.com/liamrevell/phytools license: GPL (>= 2) summary: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods @@ -76,3 +87,12 @@ about: a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-pinfsc50/build.sh b/recipes/r-pinfsc50/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-pinfsc50/build.sh +++ b/recipes/r-pinfsc50/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-pinfsc50/meta.yaml b/recipes/r-pinfsc50/meta.yaml index 028ad58ea82b4..581508238028f 100644 --- a/recipes/r-pinfsc50/meta.yaml +++ b/recipes/r-pinfsc50/meta.yaml @@ -9,21 +9,23 @@ package: source: url: - - https://cran.r-project.org/src/contrib/pinfsc50_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/pinfsc50/pinfsc50_{{ version }}.tar.gz - - + - {{ cran_mirror }}/src/contrib/pinfsc50_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/pinfsc50/pinfsc50_{{ version }}.tar.gz sha256: b6b9b6365a3f408533264d7ec820494f57eccaf362553e8478a46a8e5b474aba build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ - requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -32,7 +34,8 @@ requirements: test: commands: - - $R -e "library('pinfsc50')" # [not win] + + - $R -e "library('pinfsc50')" # [not win] - "\"%R%\" -e \"library('pinfsc50')\"" # [win] about: @@ -42,3 +45,12 @@ about: file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-plasmidprofiler/build.sh b/recipes/r-plasmidprofiler/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-plasmidprofiler/build.sh +++ b/recipes/r-plasmidprofiler/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-plasmidprofiler/meta.yaml b/recipes/r-plasmidprofiler/meta.yaml index 35ce0d8522bf6..da68e8b159c08 100644 --- a/recipes/r-plasmidprofiler/meta.yaml +++ b/recipes/r-plasmidprofiler/meta.yaml @@ -1,23 +1,31 @@ {% set version = '0.1.6' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-plasmidprofiler version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/Plasmidprofiler_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/Plasmidprofiler/Plasmidprofiler_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Plasmidprofiler_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/Plasmidprofiler/Plasmidprofiler_{{ version }}.tar.gz sha256: d37c6f7eac38aef0e525968c7caa5c82509355bece330b46cd2615f0ab9da382 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-rcolorbrewer @@ -35,9 +43,6 @@ requirements: - r-reshape2 - r-stringr - # prev version: - # - pandoc - run: - r-base - r-rcolorbrewer @@ -55,12 +60,11 @@ requirements: - r-reshape2 - r-stringr - # prev version: - # - pandoc - test: commands: - - $R -e "library('Plasmidprofiler')" + + - $R -e "library('Plasmidprofiler')" # [not win] + - "\"%R%\" -e \"library('Plasmidprofiler')\"" # [win] about: home: https://CRAN.R-project.org/package=Plasmidprofiler @@ -69,3 +73,12 @@ about: using short-read sequence typing with the results of a blast analysis against the query results. license_family: APACHE +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-pma/build.sh b/recipes/r-pma/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-pma/build.sh +++ b/recipes/r-pma/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-pma/meta.yaml b/recipes/r-pma/meta.yaml index f1b0c724a1aad..5e0c887030da3 100644 --- a/recipes/r-pma/meta.yaml +++ b/recipes/r-pma/meta.yaml @@ -1,38 +1,71 @@ {% set version = '1.0.11' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-pma version: {{ version|replace("-", "_") }} source: - fn: PMA_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/PMA_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/PMA/PMA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/PMA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PMA/PMA_{{ version }}.tar.gz sha256: ade8030475aac640a55e107330c1450fdb638cd7cf8fc32b39ed0b60a83110ed build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: - r-base - - bioconductor-impute - - gcc + - 'bioconductor-impute >=1.54.0,<1.56.0' run: - r-base - - bioconductor-impute + - {{native}}gcc-libs # [win] + - 'bioconductor-impute >=1.54.0,<1.56.0' test: commands: - - $R -e "library('PMA')" + + - $R -e "library('PMA')" # [not win] + - "\"%R%\" -e \"library('PMA')\"" # [win] about: home: https://CRAN.R-project.org/package=PMA license: GPL (>= 2) - summary: Performs Penalized Multivariate Analysis + summary: 'Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse + principal components analysis, and sparse canonical correlation analysis, described + in the following papers: (1) Witten, Tibshirani and Hastie (2009) A penalized matrix + decomposition, with applications to sparse principal components and canonical correlation + analysis. Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009) Extensions + of sparse canonical correlation analysis, with applications to genomic data. Statistical + Applications in Genetics and Molecular Biology 8(1): Article 28.' + license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-popgenome/build.sh b/recipes/r-popgenome/build.sh index 639542da531bf..74eda354eaab6 100644 --- a/recipes/r-popgenome/build.sh +++ b/recipes/r-popgenome/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash if [[ $target_platform =~ linux.* ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 $R CMD INSTALL --build . diff --git a/recipes/r-popgenome/meta.yaml b/recipes/r-popgenome/meta.yaml index 3eb228916b7ff..773062fec286b 100644 --- a/recipes/r-popgenome/meta.yaml +++ b/recipes/r-popgenome/meta.yaml @@ -1,6 +1,7 @@ {% set version = '2.6.1' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-popgenome @@ -13,26 +14,39 @@ source: sha256: 7a2922ed505fa801117a153e479d246bcf4854b91c6ab0241acc620a9d779b1c build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-ff + run: - r-base + - {{native}}gcc-libs # [win] - r-ff test: commands: - - $R -e "library('PopGenome')" + + - $R -e "library('PopGenome')" # [not win] + - "\"%R%\" -e \"library('PopGenome')\"" # [win] about: home: http://popgenome.weebly.com @@ -43,16 +57,15 @@ about: the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code. license_family: GPL3 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - doi:10.1093/molbev/msu136 recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr - johanneskoester - bgruening - daler - jdblischak - - cbrueffer - - dbast - - npavlovikj diff --git a/recipes/r-pore/build.sh b/recipes/r-pore/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-pore/build.sh +++ b/recipes/r-pore/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-pore/meta.yaml b/recipes/r-pore/meta.yaml index 4dbe7086a94c2..45d7a79df1d6b 100644 --- a/recipes/r-pore/meta.yaml +++ b/recipes/r-pore/meta.yaml @@ -40,4 +40,12 @@ about: license: BSD summary: 'An R package to enable organisation and visualisation of nanopore sequencing data' home: http://sourceforge.net/projects/rpore/ - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-precrec/build.sh b/recipes/r-precrec/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-precrec/build.sh +++ b/recipes/r-precrec/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-precrec/meta.yaml b/recipes/r-precrec/meta.yaml index fec4391d6cbc4..c4c453b5dd889 100644 --- a/recipes/r-precrec/meta.yaml +++ b/recipes/r-precrec/meta.yaml @@ -1,28 +1,41 @@ {% set version = '0.9.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-precrec version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/precrec_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/precrec/precrec_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/precrec_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/precrec/precrec_{{ version }}.tar.gz sha256: 6924fa66949d35b404239d0487ce236e6334e9b7416b5e28fd1045893aa1f74e build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - r-rcpp + - r-rcpp >=0.12.2 - r-assertthat >=0.1 - r-data.table >=1.10.4 - r-ggplot2 >=2.1.0 @@ -30,7 +43,8 @@ requirements: run: - r-base - - r-rcpp + - {{native}}gcc-libs # [win] + - r-rcpp >=0.12.2 - r-assertthat >=0.1 - r-data.table >=1.10.4 - r-ggplot2 >=2.1.0 @@ -38,10 +52,24 @@ requirements: test: commands: - - $R -e "library('precrec')" + + - $R -e "library('precrec')" # [not win] + - "\"%R%\" -e \"library('precrec')\"" # [win] about: - home: https://github.com/takayasaito/precrec + home: http://takayasaito.github.io/precrec, https://github.com/takayasaito/precrec license: GPL-3 - summary: 'Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.' + summary: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator + Characteristics) curves. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-prestor/build.sh b/recipes/r-prestor/build.sh index 4bc8e1853b492..5bf492ab9fc06 100755 --- a/recipes/r-prestor/build.sh +++ b/recipes/r-prestor/build.sh @@ -1,3 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . diff --git a/recipes/r-prestor/meta.yaml b/recipes/r-prestor/meta.yaml index dc127d0cc909d..de6e7c21be0db 100644 --- a/recipes/r-prestor/meta.yaml +++ b/recipes/r-prestor/meta.yaml @@ -59,3 +59,12 @@ about: license: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode license_family: OTHER +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-propcis/build.sh b/recipes/r-propcis/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-propcis/build.sh +++ b/recipes/r-propcis/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-propcis/meta.yaml b/recipes/r-propcis/meta.yaml index 68872aa15e335..5e80ba129c656 100644 --- a/recipes/r-propcis/meta.yaml +++ b/recipes/r-propcis/meta.yaml @@ -1,24 +1,30 @@ {% set version = '0.3-0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-propcis version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/PropCIs_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/PropCIs/PropCIs_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/PropCIs_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PropCIs/PropCIs_{{ version }}.tar.gz sha256: cd35775f4d36e642663e727450c53708f17b3c4340e1bc2c1752fd17118a9ffb build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - r-base + - {{posix}}zip # [win] host: - r-base @@ -28,10 +34,21 @@ requirements: test: commands: - - $R -e "library('PropCIs')" + + - $R -e "library('PropCIs')" # [not win] + - "\"%R%\" -e \"library('PropCIs')\"" # [win] about: home: https://github.com/shearer/PropCIs license: GPL summary: Computes two-sample confidence intervals for single, paired and independent proportions. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-pscbs/build.sh b/recipes/r-pscbs/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-pscbs/build.sh +++ b/recipes/r-pscbs/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index 3c61cbd609d52..60f3fc465fe99 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '0.63.0' %} +{% set version = '0.64.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-pscbs @@ -6,45 +9,53 @@ package: source: url: - - https://cran.r-project.org/src/contrib/PSCBS_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/PSCBS/PSCBS_{{ version }}.tar.gz - sha256: 620a4e85154e83b68ed639009a2bc7011dcddf3f817587f2eccea6b57350f05d + - {{ cran_mirror }}/src/contrib/PSCBS_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PSCBS/PSCBS_{{ version }}.tar.gz + sha256: 2196913c8dcd791c79926873de6e705d5ef4560d5fa05b4d0b91cf77e6072709 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - - bioconductor-aroma.light - - bioconductor-dnacopy + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.1 - r-r.oo >=1.21.0 - r-r.utils >=2.5.0 + - 'bioconductor-aroma.light >=3.10.0,<3.12.0' - r-future >=1.5.0 - r-listenv >=0.6.0 - r-matrixstats >=0.52.2 run: - r-base - - bioconductor-aroma.light - - bioconductor-dnacopy + - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - r-r.cache >=0.12.0 - r-r.methodss3 >=1.7.1 - r-r.oo >=1.21.0 - r-r.utils >=2.5.0 + - 'bioconductor-aroma.light >=3.10.0,<3.12.0' - r-future >=1.5.0 - r-listenv >=0.6.0 - r-matrixstats >=0.52.2 test: commands: - - $R -e "library('PSCBS')" + + - $R -e "library('PSCBS')" # [not win] + - "\"%R%\" -e \"library('PSCBS')\"" # [win] about: home: https://github.com/HenrikBengtsson/PSCBS @@ -53,3 +64,12 @@ about: abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-purbayes/build.sh b/recipes/r-purbayes/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-purbayes/build.sh +++ b/recipes/r-purbayes/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-purbayes/meta.yaml b/recipes/r-purbayes/meta.yaml index be51d08b3700d..b413746fce136 100644 --- a/recipes/r-purbayes/meta.yaml +++ b/recipes/r-purbayes/meta.yaml @@ -9,18 +9,23 @@ package: source: url: - - https://cran.r-project.org/src/contrib/PurBayes_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/PurBayes/PurBayes_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/PurBayes_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PurBayes/PurBayes_{{ version }}.tar.gz sha256: 1097eefd636ba2a71cb9b31917d75e5841cd0ccad44fb9e4e27c399e3d237559 build: - number: 1 - skip: true # [win32] + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-rjags @@ -31,7 +36,8 @@ requirements: test: commands: - - $R -e "library('PurBayes')" # [not win] + + - $R -e "library('PurBayes')" # [not win] - "\"%R%\" -e \"library('PurBayes')\"" # [win] about: @@ -40,3 +46,14 @@ about: summary: PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data. license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-qiimer/build.sh b/recipes/r-qiimer/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-qiimer/build.sh +++ b/recipes/r-qiimer/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-qiimer/meta.yaml b/recipes/r-qiimer/meta.yaml index e47e541cd4c7a..096632e90ed20 100644 --- a/recipes/r-qiimer/meta.yaml +++ b/recipes/r-qiimer/meta.yaml @@ -1,23 +1,31 @@ {% set version = '0.9.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-qiimer version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/qiimer_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/qiimer/qiimer_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/qiimer_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/qiimer/qiimer_{{ version }}.tar.gz sha256: ae9d576dc3e660fa41209e85a5dcd688af2121127462f0b47cc2c69be2d52f2b build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-pheatmap @@ -28,10 +36,23 @@ requirements: test: commands: - - $R -e "library('qiimer')" + + - $R -e "library('qiimer')" # [not win] + - "\"%R%\" -e \"library('qiimer')\"" # [win] about: home: http://www.r-project.org license: GPL (>= 2) summary: Open QIIME output files in R, compute statistics, and create plots from the data. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-qorts/build.sh b/recipes/r-qorts/build.sh index d5c1a4cb4bbdc..506aa0793f132 100644 --- a/recipes/r-qorts/build.sh +++ b/recipes/r-qorts/build.sh @@ -1,6 +1,3 @@ - #!/bin/bash - - # R refuses to build packages that mark themselves as Priority: Recommended mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION diff --git a/recipes/r-qorts/meta.yaml b/recipes/r-qorts/meta.yaml index aeb6e31074aa6..bd55f2f21b61e 100644 --- a/recipes/r-qorts/meta.yaml +++ b/recipes/r-qorts/meta.yaml @@ -12,7 +12,6 @@ source: build: number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -35,3 +34,11 @@ about: extra: notes: | This package is a requirement of the main QoRTs package; "qorts". + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-qqman/build.sh b/recipes/r-qqman/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-qqman/build.sh +++ b/recipes/r-qqman/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-qqman/meta.yaml b/recipes/r-qqman/meta.yaml index 72e93a10a5b19..474669092632e 100644 --- a/recipes/r-qqman/meta.yaml +++ b/recipes/r-qqman/meta.yaml @@ -1,23 +1,31 @@ {% set version = '0.1.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-qqman version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/qqman_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/qqman/qqman_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/qqman_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/qqman/qqman_{{ version }}.tar.gz sha256: 3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-calibrate @@ -28,10 +36,21 @@ requirements: test: commands: - - $R -e "library('qqman')" + + - $R -e "library('qqman')" # [not win] + - "\"%R%\" -e \"library('qqman')\"" # [win] about: home: https://CRAN.R-project.org/package=qqman license: GPL-3 summary: Create Q-Q and manhattan plots for GWAS data from PLINK results. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-qtl/build.sh b/recipes/r-qtl/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-qtl/build.sh +++ b/recipes/r-qtl/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-qtl/meta.yaml b/recipes/r-qtl/meta.yaml index 8ba82d4a5c137..b44b2b2447b57 100644 --- a/recipes/r-qtl/meta.yaml +++ b/recipes/r-qtl/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.41-6' %} +{% set version = '1.42-8' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-qtl @@ -6,35 +9,58 @@ package: source: url: - - https://cran.r-project.org/src/contrib/qtl_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/qtl/qtl_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/qtl_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/qtl/qtl_{{ version }}.tar.gz + sha256: 661627feb1c5ce416a3515dbd42834b72b31702635e71a0bc8b45db77943a2d0 +build: + merge_build_host: True # [win] - sha256: 4de9d406d41c2b4f9ffe85ef0af20899f004e93e0d4dd6a9b9fd8b4136f9ea18 + number: 0 + skip: true # [win32] -build: - number: 1 rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base run: - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('qtl')" + + - $R -e "library('qtl')" # [not win] + - "\"%R%\" -e \"library('qtl')\"" # [win] about: - home: http://rqtl.org + home: https://rqtl.org, https://github.com/kbroman/qtl license: GPL-3 summary: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-quorts/build.sh b/recipes/r-quorts/build.sh index d5c1a4cb4bbdc..506aa0793f132 100644 --- a/recipes/r-quorts/build.sh +++ b/recipes/r-quorts/build.sh @@ -1,6 +1,3 @@ - #!/bin/bash - - # R refuses to build packages that mark themselves as Priority: Recommended mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION diff --git a/recipes/r-quorts/meta.yaml b/recipes/r-quorts/meta.yaml index 5f5fd841551d9..8eb1fa6001fed 100644 --- a/recipes/r-quorts/meta.yaml +++ b/recipes/r-quorts/meta.yaml @@ -12,7 +12,6 @@ source: build: number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -35,3 +34,11 @@ about: extra: notes: | This package is a requirement of the main QoRTs package; "qorts". + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rBLAST/build.sh b/recipes/r-rBLAST/build.sh index f311ec01f86bd..5bf492ab9fc06 100755 --- a/recipes/r-rBLAST/build.sh +++ b/recipes/r-rBLAST/build.sh @@ -1,9 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-rBLAST/meta.yaml b/recipes/r-rBLAST/meta.yaml index 0bedcc329130f..9fc906f775d4d 100644 --- a/recipes/r-rBLAST/meta.yaml +++ b/recipes/r-rBLAST/meta.yaml @@ -26,4 +26,12 @@ about: home: https://github.com/mhahsler/rBLAST license: GPL3 summary: 'Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.' - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-raceid3/build.sh b/recipes/r-raceid3/build.sh index 43d760df3aeb1..aea5b12eaa821 100644 --- a/recipes/r-raceid3/build.sh +++ b/recipes/r-raceid3/build.sh @@ -1,4 +1 @@ -#!/bin/bash - R CMD INSTALL --build . - diff --git a/recipes/r-raceid3/meta.yaml b/recipes/r-raceid3/meta.yaml index 8380dacc13aa1..9df14e65c1b01 100644 --- a/recipes/r-raceid3/meta.yaml +++ b/recipes/r-raceid3/meta.yaml @@ -8,7 +8,8 @@ source: build: number: 0 - # rgl issues on OSX + skip: true # [win32] + skip: True # [osx] rpaths: - lib/R/lib/ @@ -63,6 +64,8 @@ about: license: GPL-3 summary: "Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the StemID2 algorithm." license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] extra: identifiers: @@ -70,3 +73,11 @@ extra: container: # needed for libGL.so.1 extended-base: true + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rapidr/build.sh b/recipes/r-rapidr/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-rapidr/build.sh +++ b/recipes/r-rapidr/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-rapidr/meta.yaml b/recipes/r-rapidr/meta.yaml index dc24e433a7333..477bec4fe3262 100644 --- a/recipes/r-rapidr/meta.yaml +++ b/recipes/r-rapidr/meta.yaml @@ -1,43 +1,54 @@ {% set version = '0.1.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-rapidr version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/RAPIDR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/RAPIDR/RAPIDR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/RAPIDR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/RAPIDR/RAPIDR_{{ version }}.tar.gz sha256: 2d286bdf13f27a040f16f8c5aa740e25fbc4b0913e3cfa4b5956152d25e19691 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - - bioconductor-biostrings - - r-data.table - - bioconductor-genomicalignments - - bioconductor-genomicranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-propcis - - bioconductor-rsamtools + - 'bioconductor-rsamtools >=1.32.0,<1.34.0' + - r-data.table run: - r-base - - bioconductor-biostrings - - r-data.table - - bioconductor-genomicalignments - - bioconductor-genomicranges + - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' + - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - r-propcis - - bioconductor-rsamtools + - 'bioconductor-rsamtools >=1.32.0,<1.34.0' + - r-data.table test: commands: - - $R -e "library('RAPIDR')" + + - $R -e "library('RAPIDR')" # [not win] + - "\"%R%\" -e \"library('RAPIDR')\"" # [win] about: home: https://CRAN.R-project.org/package=RAPIDR @@ -45,3 +56,12 @@ about: summary: Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rbison/build.sh b/recipes/r-rbison/build.sh index c51d400f352ee..5bf492ab9fc06 100644 --- a/recipes/r-rbison/build.sh +++ b/recipes/r-rbison/build.sh @@ -1,3 +1 @@ -#!/bin/bash $R CMD INSTALL --build . - diff --git a/recipes/r-rbison/meta.yaml b/recipes/r-rbison/meta.yaml index 92ef266f4ddf7..0e735d09f8a33 100644 --- a/recipes/r-rbison/meta.yaml +++ b/recipes/r-rbison/meta.yaml @@ -1,17 +1,22 @@ {% set version = '0.6.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-rbison version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/rbison_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/rbison/rbison_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/rbison_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/rbison/rbison_{{ version }}.tar.gz sha256: 30348929d2215343586e44139ca95d4e6fdd46cb0a23c95ea338686bca84ab26 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,6 +24,9 @@ build: requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-crul >=0.3.4 - r-dplyr >=0.5.0 @@ -40,14 +48,24 @@ requirements: test: commands: - - $R -e "library('rbison')" + - $R -e "library('rbison')" # [not win] + - "\"%R%\" -e \"library('rbison')\"" # [win] about: home: https://github.com/ropensci/rbison - license: MIT + file LICENSE + license: MIT summary: Interface to the 'USGS' 'BISON' () 'API', a 'database' for species occurrence data. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rcircos/build.sh b/recipes/r-rcircos/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-rcircos/build.sh +++ b/recipes/r-rcircos/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-rcircos/meta.yaml b/recipes/r-rcircos/meta.yaml index a1609b11bd4c6..5e590cf1f171e 100644 --- a/recipes/r-rcircos/meta.yaml +++ b/recipes/r-rcircos/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.2.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-rcircos version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/RCircos_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/RCircos/RCircos_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/RCircos_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/RCircos/RCircos_{{ version }}.tar.gz sha256: 7fd06e2efc33b5c30fc4ba3945b04021f255ba4ffcc394348df7488b9394444a build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('RCircos')" + + - $R -e "library('RCircos')" # [not win] + - "\"%R%\" -e \"library('RCircos')\"" # [win] about: home: http://bitbucket.org/henryhzhang/rcircos @@ -37,3 +48,14 @@ about: only R graphics package that comes with R base installation. ' license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-readbrukerflexdata/build.sh b/recipes/r-readbrukerflexdata/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-readbrukerflexdata/build.sh +++ b/recipes/r-readbrukerflexdata/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-readbrukerflexdata/meta.yaml b/recipes/r-readbrukerflexdata/meta.yaml index 0131ad3e29992..242978ff3fbfe 100644 --- a/recipes/r-readbrukerflexdata/meta.yaml +++ b/recipes/r-readbrukerflexdata/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.8.5' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-readbrukerflexdata version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/readBrukerFlexData_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/readBrukerFlexData/readBrukerFlexData_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/readBrukerFlexData_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/readBrukerFlexData/readBrukerFlexData_{{ version }}.tar.gz sha256: 35a1e2be4ce6bf57291eda5d3e220bb2d0e44404625a9b71d1a719c8bbabb1e2 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('readBrukerFlexData')" + + - $R -e "library('readBrukerFlexData')" # [not win] + - "\"%R%\" -e \"library('readBrukerFlexData')\"" # [win] about: home: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/readBrukerFlexData/ @@ -33,3 +44,14 @@ about: summary: Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-readmzxmldata/build.sh b/recipes/r-readmzxmldata/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-readmzxmldata/build.sh +++ b/recipes/r-readmzxmldata/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-readmzxmldata/meta.yaml b/recipes/r-readmzxmldata/meta.yaml index d0c8f4a81b520..55936ecf65fe2 100644 --- a/recipes/r-readmzxmldata/meta.yaml +++ b/recipes/r-readmzxmldata/meta.yaml @@ -1,22 +1,31 @@ {% set version = '2.8.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-readmzxmldata version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/readMzXmlData_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/readMzXmlData/readMzXmlData_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/readMzXmlData_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/readMzXmlData/readMzXmlData_{{ version }}.tar.gz sha256: 1c3d842d2a647020e19d42a448578e8bd48b4bbe56d8927c8d239623a582960e build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-xml @@ -31,10 +40,23 @@ requirements: test: commands: - - $R -e "library('readMzXmlData')" + + - $R -e "library('readMzXmlData')" # [not win] + - "\"%R%\" -e \"library('readMzXmlData')\"" # [win] about: home: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/readMzXmlData/ license: GPL (>= 3) summary: Functions for reading mass spectrometry data in mzXML format. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rebird/build.sh b/recipes/r-rebird/build.sh index c51d400f352ee..5bf492ab9fc06 100644 --- a/recipes/r-rebird/build.sh +++ b/recipes/r-rebird/build.sh @@ -1,3 +1 @@ -#!/bin/bash $R CMD INSTALL --build . - diff --git a/recipes/r-rebird/meta.yaml b/recipes/r-rebird/meta.yaml index af5fe79549e8f..1c4d10c0b55c8 100644 --- a/recipes/r-rebird/meta.yaml +++ b/recipes/r-rebird/meta.yaml @@ -1,42 +1,65 @@ -{% set version = '0.5.0' %} +{% set version = '1.0.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-rebird version: {{ version|replace("-", "_") }} source: - url: https://cran.r-project.org/src/contrib/rebird_{{ version }}.tar.gz - sha256: 44804ad8e63173e68c93f98b54303ddf032ab7a24ace85fca401e89cb8293c6f - + url: + - {{ cran_mirror }}/src/contrib/rebird_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/rebird/rebird_{{ version }}.tar.gz + sha256: a876ddd77692c2f7cbb48e6416699cc7443598c70eec1096d07a0f6fa453e83e build: - number: 2 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base + - r-assertthat - r-dplyr - r-httr >=1.0.0 - r-jsonlite + run: - r-base + - r-assertthat - r-dplyr - r-httr >=1.0.0 - r-jsonlite test: commands: - - $R -e "library('rebird')" + + - $R -e "library('rebird')" # [not win] + - "\"%R%\" -e \"library('rebird')\"" # [win] about: home: http://github.com/ropensci/rebird - license: MIT + file LICENSE - summary: | - A programmatic client for the eBird database, including functions for searching for + license: MIT + summary: A programmatic client for the eBird database, including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rematch2/build.sh b/recipes/r-rematch2/build.sh index af6547bf3c22e..5bf492ab9fc06 100755 --- a/recipes/r-rematch2/build.sh +++ b/recipes/r-rematch2/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-rematch2/meta.yaml b/recipes/r-rematch2/meta.yaml index 9eecf35e1cedc..8838a9730e14f 100644 --- a/recipes/r-rematch2/meta.yaml +++ b/recipes/r-rematch2/meta.yaml @@ -1,23 +1,31 @@ {% set version = '2.0.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-rematch2 version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/rematch2_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/rematch2/rematch2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/rematch2_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/rematch2/rematch2_{{ version }}.tar.gz sha256: 0612bb904334bd022ba6d1e69925b1e85f8e86b15ec65476777828776e89609a build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-tibble @@ -28,10 +36,21 @@ requirements: test: commands: - - $R -e "library('rematch2')" + + - $R -e "library('rematch2')" # [not win] + - "\"%R%\" -e \"library('rematch2')\"" # [win] about: home: https://github.com/r-lib/rematch2#readme license: MIT summary: Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rentrez/build.sh b/recipes/r-rentrez/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-rentrez/build.sh +++ b/recipes/r-rentrez/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-rentrez/meta.yaml b/recipes/r-rentrez/meta.yaml index 560157331a959..731d2f5b03e3d 100644 --- a/recipes/r-rentrez/meta.yaml +++ b/recipes/r-rentrez/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.1.0' %} +{% set version = '1.2.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-rentrez @@ -6,18 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/rentrez_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/rentrez/rentrez_{{ version }}.tar.gz - sha256: 8dd46c03cbb05d4a3e787b7fc9a1858fcbdf1bb0faf5ee438a4f2ea4dbca9d56 + - {{ cran_mirror }}/src/contrib/rentrez_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/rentrez/rentrez_{{ version }}.tar.gz + sha256: 74cf6dbe1b229518c25221534b20437b53cb663f1473cf9df5a59ca76b76ae84 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-xml @@ -32,12 +41,23 @@ requirements: test: commands: - - $R -e "library('rentrez')" + + - $R -e "library('rentrez')" # [not win] + - "\"%R%\" -e \"library('rentrez')\"" # [win] about: home: http://github.com/ropensci/rentrez license: MIT - summary: Provides an R interface to the NCBI's EUtils API allowing users to search databases - like GenBank and PubMed, process the results of those searches and pull data into - their R sessions. + summary: Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases + like 'GenBank' and 'PubMed' , + process the results of those searches and pull data into their R sessions. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rgbif/build.sh b/recipes/r-rgbif/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-rgbif/build.sh +++ b/recipes/r-rgbif/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-rgbif/meta.yaml b/recipes/r-rgbif/meta.yaml index 88df0b9e189be..acb6890de572b 100644 --- a/recipes/r-rgbif/meta.yaml +++ b/recipes/r-rgbif/meta.yaml @@ -1,20 +1,25 @@ -{% set version = '1.0.2' %} +{% set version = '1.1.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-rgbif version: {{ version|replace("-", "_") }} source: - url: https://cran.r-project.org/src/contrib/rgbif_{{ version }}.tar.gz - sha256: b79aa97b34d5895a37921c5a4906a05bd84ad2c517683d985153819a81625465 + url: + - {{ cran_mirror }}/src/contrib/rgbif_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/rgbif/rgbif_{{ version }}.tar.gz + sha256: 14feec65a16d4f71bce0fb6a702a7dd4b61ed07bc1975166c5c8a95be87dc4e6 build: - number: 2 - + number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, sp, rgeos, png, raster, vcr requirements: host: - r-base @@ -23,6 +28,7 @@ requirements: - r-geoaxe - r-ggplot2 - r-jsonlite >=0.9.16 + - r-lazyeval - r-magrittr - r-oai >=0.2.2 - r-tibble @@ -37,6 +43,7 @@ requirements: - r-geoaxe - r-ggplot2 - r-jsonlite >=0.9.16 + - r-lazyeval - r-magrittr - r-oai >=0.2.2 - r-tibble @@ -46,16 +53,28 @@ requirements: test: commands: - - $R -e "library('rgbif')" + - $R -e "library('rgbif')" # [not win] + - "\"%R%\" -e \"library('rgbif')\"" # [win] about: - home: https://github.com/ropensci/rgbif - license: MIT + file LICENSE - summary: | - A programmatic interface to the Web Service methods provided by the Global Biodiversity + home: https://github.com/ropensci/rgbif (devel) https://ropenscilabs.github.io/occurrence-manual/ + (manual) + license: MIT + summary: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; ). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on - data providers, getting species occurrence records, and getting counts of occurrence - records. + data providers, getting species occurrence records, getting counts of occurrence + records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge + amounts of data. license_family: MIT + +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-ridigbio/build.sh b/recipes/r-ridigbio/build.sh index 695ef87bd4ada..5bf492ab9fc06 100644 --- a/recipes/r-ridigbio/build.sh +++ b/recipes/r-ridigbio/build.sh @@ -1,4 +1 @@ -#!/bin/bash $R CMD INSTALL --build . - - diff --git a/recipes/r-ridigbio/meta.yaml b/recipes/r-ridigbio/meta.yaml index da0c646ee105f..2418cca62b352 100644 --- a/recipes/r-ridigbio/meta.yaml +++ b/recipes/r-ridigbio/meta.yaml @@ -1,5 +1,7 @@ {% set version = '0.3.5' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-ridigbio @@ -7,14 +9,14 @@ package: source: url: - - https://cran.r-project.org/src/contrib/ridigbio_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ridigbio/ridigbio_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/ridigbio_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ridigbio/ridigbio_{{ version }}.tar.gz sha256: e5cfb2e4dd8ddd1452a5afcf24fcc260889179d0f52eff4f41835adf99b64614 - - build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -22,6 +24,9 @@ build: requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-httr - r-jsonlite @@ -35,14 +40,25 @@ requirements: test: commands: - - $R -e "library('ridigbio')" + + - $R -e "library('ridigbio')" # [not win] + - "\"%R%\" -e \"library('ridigbio')\"" # [win] about: home: https://github.com/iDigBio/ridigbio - license: MIT + file LICENSE + license: MIT summary: An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See for information on iDigBio. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rnexml/build.sh b/recipes/r-rnexml/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-rnexml/build.sh +++ b/recipes/r-rnexml/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-rnexml/meta.yaml b/recipes/r-rnexml/meta.yaml index 30b44351b0073..2c81456bc27cc 100644 --- a/recipes/r-rnexml/meta.yaml +++ b/recipes/r-rnexml/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.1.1' %} +{% set version = '2.1.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-rnexml @@ -6,17 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/RNeXML_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/RNeXML/RNeXML_{{ version }}.tar.gz - sha256: 97f472067e42ad17a504f3ff9180f2575e47507a794735a23e7a69a54b3ddcc2 + - {{ cran_mirror }}/src/contrib/RNeXML_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/RNeXML/RNeXML_{{ version }}.tar.gz + sha256: 860dcdce074cd120a5d6cc1f253d4a409965f9d5326568310d3013e550ada52b build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-xml >=3.95 @@ -47,12 +57,23 @@ requirements: test: commands: - - $R -e "library('RNeXML')" + + - $R -e "library('RNeXML')" # [not win] + - "\"%R%\" -e \"library('RNeXML')\"" # [win] about: - home: https://CRAN.R-project.org/package=RNeXML - license: 'BSD_3_clause + file LICENSE' + home: https://github.com/ropensci/RNeXML + license: BSD_3_clause summary: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects. license_family: BSD +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-robustrankaggreg/build.sh b/recipes/r-robustrankaggreg/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-robustrankaggreg/build.sh +++ b/recipes/r-robustrankaggreg/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-robustrankaggreg/meta.yaml b/recipes/r-robustrankaggreg/meta.yaml index dd04f8bf0c38a..ac0461ccb625e 100644 --- a/recipes/r-robustrankaggreg/meta.yaml +++ b/recipes/r-robustrankaggreg/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-robustrankaggreg version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/RobustRankAggreg_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/RobustRankAggreg/RobustRankAggreg_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/RobustRankAggreg_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/RobustRankAggreg/RobustRankAggreg_{{ version }}.tar.gz sha256: 23ab88f6f1e56ae85a45bf5107ad0c37202dde275d799ed9fe214a1ab2c754df build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -25,7 +34,9 @@ requirements: test: commands: - - $R -e "library('RobustRankAggreg')" + + - $R -e "library('RobustRankAggreg')" # [not win] + - "\"%R%\" -e \"library('RobustRankAggreg')\"" # [win] about: home: https://CRAN.R-project.org/package=RobustRankAggreg @@ -36,3 +47,14 @@ about: to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking. license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rphylip/build.sh b/recipes/r-rphylip/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-rphylip/build.sh +++ b/recipes/r-rphylip/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-rphylip/meta.yaml b/recipes/r-rphylip/meta.yaml index f843f04626e8e..bb0fb59ea504c 100644 --- a/recipes/r-rphylip/meta.yaml +++ b/recipes/r-rphylip/meta.yaml @@ -1,22 +1,31 @@ {% set version = '0.1-23' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-rphylip version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/Rphylip_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/Rphylip/Rphylip_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Rphylip_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/Rphylip/Rphylip_{{ version }}.tar.gz sha256: 39bd1c9d2ce36f7a3e6c2bee12e9e064930f42de4a6d8f562427c34566acf84e build: - number: 2 + merge_build_host: True # [win] + + number: 3 rpaths: - lib/R/lib/ - lib/ + requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-ape >=3.0_10 @@ -25,12 +34,11 @@ requirements: - r-base - r-ape >=3.0_10 - # prev version: - # - phylip >=3.696 - test: commands: - - $R -e "library('Rphylip')" + + - $R -e "library('Rphylip')" # [not win] + - "\"%R%\" -e \"library('Rphylip')\"" # [win] about: home: http://www.phytools.org/Rphylip @@ -39,3 +47,14 @@ about: thus first have to install the PHYLIP phylogeny methods program package (Felsenstein 2013). See http://www.phylip.com for more information about installing PHYLIP. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-rvertnet/build.sh b/recipes/r-rvertnet/build.sh index 695ef87bd4ada..5bf492ab9fc06 100644 --- a/recipes/r-rvertnet/build.sh +++ b/recipes/r-rvertnet/build.sh @@ -1,4 +1 @@ -#!/bin/bash $R CMD INSTALL --build . - - diff --git a/recipes/r-rvertnet/meta.yaml b/recipes/r-rvertnet/meta.yaml index 9cbe9157d1991..f48560adf4e98 100644 --- a/recipes/r-rvertnet/meta.yaml +++ b/recipes/r-rvertnet/meta.yaml @@ -1,20 +1,22 @@ {% set version = '0.7.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-rvertnet version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/rvertnet_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/rvertnet/rvertnet_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/rvertnet_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/rvertnet/rvertnet_{{ version }}.tar.gz sha256: f2e1d78067bbafa0a641a0af43adf832a94bf2382151f261006907f18b8ce307 - build: - merge_build_host: True - number: 1 - noarch: generic + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -22,6 +24,9 @@ build: requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-crul >=0.5.2 - r-dplyr >=0.5.0 @@ -39,14 +44,24 @@ requirements: test: commands: - - $R -e "library('rvertnet')" + - $R -e "library('rvertnet')" # [not win] + - "\"%R%\" -e \"library('rvertnet')\"" # [win] about: home: https://github.com/ropensci/rvertnet - license: MIT + file LICENSE + license: MIT summary: Retrieve, map and summarize data from the 'VertNet.org' archives (). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-samr/build.sh b/recipes/r-samr/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-samr/build.sh +++ b/recipes/r-samr/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-samr/meta.yaml b/recipes/r-samr/meta.yaml index 9ccf0ddcb9175..9ea5b60421e8b 100644 --- a/recipes/r-samr/meta.yaml +++ b/recipes/r-samr/meta.yaml @@ -22,12 +22,12 @@ requirements: host: - r-base - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-matrixstats run: - r-base - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-matrixstats test: @@ -39,3 +39,12 @@ about: license: LGPL summary: Significance Analysis of Microarrays license_family: LGPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-sartools/build.sh b/recipes/r-sartools/build.sh index 7fe0351a83e48..5bf492ab9fc06 100644 --- a/recipes/r-sartools/build.sh +++ b/recipes/r-sartools/build.sh @@ -1,14 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. -#R -e "library(devtools); source('http://www.bioconductor.org/biocLite.R'); install_github('glibiseller/IPO') " - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-sartools/meta.yaml b/recipes/r-sartools/meta.yaml index 70406b819b329..fe2d93e920c64 100644 --- a/recipes/r-sartools/meta.yaml +++ b/recipes/r-sartools/meta.yaml @@ -20,7 +20,7 @@ requirements: - r-base - r-knitr - bioconductor-deseq2 - - bioconductor-edger + - bioconductobioconductor-edger - r-rmarkdown - r-bit64 - r-blob @@ -29,7 +29,7 @@ requirements: - r-base >=3.3.0 - r-knitr - bioconductor-deseq2 >=1.12.0 - - bioconductor-edger >=3.12.0 + - bioconductobioconductor-edger >=3.12.0 - r-rmarkdown >=1.4 - r-bit64 - r-blob @@ -47,3 +47,11 @@ about: extra: identifiers: - biotools:sartools + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-sbpiper/build.sh b/recipes/r-sbpiper/build.sh index 6cf75266b7b4c..bec411402e62f 100644 --- a/recipes/r-sbpiper/build.sh +++ b/recipes/r-sbpiper/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/r-sbpiper/meta.yaml b/recipes/r-sbpiper/meta.yaml index de9367231447a..c38556c2dedf8 100644 --- a/recipes/r-sbpiper/meta.yaml +++ b/recipes/r-sbpiper/meta.yaml @@ -1,26 +1,32 @@ -{% set name = "sbpiper" %} -{% set version = "1.9.0" %} -{% set file_ext = "tar.gz" %} +{% set version = '1.9.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: - name: 'r-{{ name|lower }}' - version: '{{ version }}' + name: r-sbpiper + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.{{ file_ext }} - - https://cran.r-project.org/src/contrib/Archive/sbpiper/{{ name }}_{{ version }}.{{ file_ext }} + - {{ cran_mirror }}/src/contrib/sbpiper_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/sbpiper/sbpiper_{{ version }}.tar.gz sha256: 8f053383eb0f73fef7809898f27882b5a662f5b2aa404b3ee52491d92342585e build: - merge_build_host: True - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-factominer - r-hmisc @@ -46,14 +52,37 @@ requirements: test: commands: - - $R -e "library('sbpiper')" + + - $R -e "library('sbpiper')" # [not win] + - "\"%R%\" -e \"library('sbpiper')\"" # [win] about: - home: https://cran.r-project.org/package=sbpiper + home: https://github.com/pdp10/sbpiper license: MIT - summary: Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation sbpiper calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation sbpiper calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. + summary: "Provides an API for analysing repetitive parameter estimations and simulations of + mathematical models. Examples of mathematical models are Ordinary Differential equations + (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for + parameter estimation 'sbpiper' calculates statistics and generates plots for parameter + density, PCA of the best fits, parameter profile likelihood estimations (PLEs), + and 2D parameter PLEs. These results can be generated using all or a subset of + the best computed parameter sets. Among the analyses for model simulation 'sbpiper' + calculates statistics and generates plots for deterministic and stochastic time + courses via cartesian and heatmap plots. Plots for the scan of one or two model + \ parameters can also be generated. This package is primarily used by the software + 'SBpipe'. Citation: Dalle Pezze P, Le Nov\xC3\xA8re N. SBpipe: a collection of + pipelines for automating repetitive simulation and analysis tasks. BMC Systems + Biology. 2017;11:46. ." + + license_family: MIT extra: - recipe-maintainers: 'Piero Dalle Pezze' identifiers: - doi:10.1186/s12918-017-0423-3 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-scimpute/build.sh b/recipes/r-scimpute/build.sh index 2dcddd52a4afd..aea5b12eaa821 100644 --- a/recipes/r-scimpute/build.sh +++ b/recipes/r-scimpute/build.sh @@ -1,8 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - R CMD INSTALL --build . - diff --git a/recipes/r-scimpute/meta.yaml b/recipes/r-scimpute/meta.yaml index 1e2012055dbd3..db91b994f4a1e 100644 --- a/recipes/r-scimpute/meta.yaml +++ b/recipes/r-scimpute/meta.yaml @@ -8,6 +8,7 @@ source: build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ @@ -50,3 +51,11 @@ about: extra: identifiers: - doi:10.1038/s41467-018-03405-7 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-scrm/build.sh b/recipes/r-scrm/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-scrm/build.sh +++ b/recipes/r-scrm/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-scrm/meta.yaml b/recipes/r-scrm/meta.yaml index 11e71216e7f54..b26e79c8f816a 100644 --- a/recipes/r-scrm/meta.yaml +++ b/recipes/r-scrm/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.7.2-0' %} +{% set version = '1.7.2-4' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-scrm @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/scrm_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/scrm/scrm_{{ version }}.tar.gz - sha256: a889b56e9107389623147539fb5a7d2160e12ba3491df63bebb523ddaa6f95c4 + - {{ cran_mirror }}/src/contrib/scrm_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/scrm/scrm_{{ version }}.tar.gz + sha256: c780450d91b671499b703588336bac23293e938ae3d33b1e54db0306091040ba build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,7 +25,14 @@ build: requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -27,11 +40,14 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-rcpp >=0.11.2 test: commands: - - $R -e "library('scrm')" + + - $R -e "library('scrm')" # [not win] + - "\"%R%\" -e \"library('scrm')\"" # [win] about: home: https://github.com/scrm/scrm-r @@ -43,3 +59,12 @@ about: data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-seqinr/build.sh b/recipes/r-seqinr/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-seqinr/build.sh +++ b/recipes/r-seqinr/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-seqinr/meta.yaml b/recipes/r-seqinr/meta.yaml index 700d7fb3c49f8..957b82472273c 100644 --- a/recipes/r-seqinr/meta.yaml +++ b/recipes/r-seqinr/meta.yaml @@ -1,24 +1,36 @@ {% set version = '3.4-5' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-seqinr version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/seqinr_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/seqinr/seqinr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/seqinr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/seqinr/seqinr_{{ version }}.tar.gz sha256: 162a347495fd52cbb62e8187a4692e7c50b9fa62123c5ef98f2744c98a05fb9f build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ + requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -27,12 +39,15 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-ade4 - r-segmented test: commands: - - $R -e "library('seqinr')" + + - $R -e "library('seqinr')" # [not win] + - "\"%R%\" -e \"library('seqinr')\"" # [win] about: home: http://seqinr.r-forge.r-project.org/ @@ -41,3 +56,14 @@ about: protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 . license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-seqminer/build.sh b/recipes/r-seqminer/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-seqminer/build.sh +++ b/recipes/r-seqminer/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-seqminer/meta.yaml b/recipes/r-seqminer/meta.yaml index 0811da6e3cead..db1cf50acf25e 100644 --- a/recipes/r-seqminer/meta.yaml +++ b/recipes/r-seqminer/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '6.0' %} +{% set version = '6.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-seqminer @@ -6,41 +9,64 @@ package: source: url: - - https://cran.r-project.org/src/contrib/seqminer_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/seqminer/seqminer_{{ version }}.tar.gz - sha256: 74e80b5ed7023fa7c7ba22b6b1ce31aba5fd05bd8ac61d55a065dcd80c0df214 + - {{ cran_mirror }}/src/contrib/seqminer_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/seqminer/seqminer_{{ version }}.tar.gz + sha256: 54e0af281977d080e130bd079a985f75bd0b800c678c85ad0c4f1ee63679d097 build: - number: 1 - # This is required to make R link correctly on Linux. + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - clangxx_osx-64 # [osx] + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}sed # [win] + - {{posix}}grep # [win] + - {{posix}}autoconf + - {{posix}}automake # [not win] + - {{posix}}automake-wrapper # [win] + - {{posix}}pkg-config + - {{posix}}make + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - gmp - - zlib - - bzip2 run: - r-base - - libcxx # [osx] - - gmp - - zlib - - bzip2 + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('seqminer')" + + - $R -e "library('seqminer')" # [not win] + - "\"%R%\" -e \"library('seqminer')\"" # [win] about: - home: https://cran.r-project.org/web/packages/seqminer/index.html - license: GPL (>= 2) - summary: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. + home: http://seqminer.genomic.codes + license: GPL + summary: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis + results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges + (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from + a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow + based on Makefile. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-seurat-scripts/build.sh b/recipes/r-seurat-scripts/build.sh index 0bb9dc2aa294d..260e8703bc0e9 100644 --- a/recipes/r-seurat-scripts/build.sh +++ b/recipes/r-seurat-scripts/build.sh @@ -1,5 +1,3 @@ -#!/usr/bin/env bash - mkdir -p $PREFIX/bin cp *.R $PREFIX/bin cp *.sh $PREFIX/bin diff --git a/recipes/r-seurat-scripts/meta.yaml b/recipes/r-seurat-scripts/meta.yaml index 53453be71dc26..dd5ffd3ed6546 100644 --- a/recipes/r-seurat-scripts/meta.yaml +++ b/recipes/r-seurat-scripts/meta.yaml @@ -10,6 +10,7 @@ source: build: number: 0 + skip: true # [win32] noarch: generic requirements: @@ -48,3 +49,12 @@ about: ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-seurat/build.sh b/recipes/r-seurat/build.sh index c51d400f352ee..5bf492ab9fc06 100644 --- a/recipes/r-seurat/build.sh +++ b/recipes/r-seurat/build.sh @@ -1,3 +1 @@ -#!/bin/bash $R CMD INSTALL --build . - diff --git a/recipes/r-seurat/meta.yaml b/recipes/r-seurat/meta.yaml index eef85c2dad22a..7c63b7e3ae125 100644 --- a/recipes/r-seurat/meta.yaml +++ b/recipes/r-seurat/meta.yaml @@ -1,130 +1,131 @@ {% set version = '2.3.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-seurat - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/Seurat_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Seurat_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/Seurat/Seurat_{{ version }}.tar.gz sha256: 0d0a92c8ecc7beebddbefbcc4d845cb1c66b7005416d9b6335e27f9b22d90b51 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - - r-ape - r-base - - r-caret + - r-hmisc + - r-mass + - r-matrix >=1.2.14 + - r-rann + - r-rcolorbrewer + - r-rocr + - r-rcpp >=0.11.0 + - r-rcppeigen + - r-rcppprogress + - r-rtsne + - r-sdmtools + - r-ape - r-cluster - r-cowplot - - r-diffusionmap - r-dosnow - r-dplyr - r-dtw - - r-fpc - r-fitdistrplus - - r-fnn - - r-hdf5r - r-foreach - - r-gdata + - r-fpc - r-ggplot2 - r-ggridges - r-gplots - - r-hmisc + - r-hdf5r + - r-httr - r-ica - r-igraph - r-irlba - r-lars - r-lmtest - - r-mass - - r-matrix >=1.2.14 - r-metap - r-mixtools - r-pbapply - r-plotly - r-png - - r-ranger - - r-rann - - r-rcolorbrewer - - r-rcpp - - r-rcppeigen - - r-rcppprogress - r-reshape2 - r-reticulate - - r-rocr - - r-rtsne - - r-sdmtools - - r-stringr - - r-tclust - r-tidyr - r-tsne - - r-vgam run: - - r-ape - r-base - - r-caret + - {{native}}gcc-libs # [win] + - r-hmisc + - r-mass + - r-matrix >=1.2.14 + - r-rann + - r-rcolorbrewer + - r-rocr + - r-rcpp >=0.11.0 + - r-rcppeigen + - r-rcppprogress + - r-rtsne + - r-sdmtools + - r-ape - r-cluster - r-cowplot - - r-diffusionmap - r-dosnow - r-dplyr - r-dtw - - r-fpc - r-fitdistrplus - - r-fnn - r-foreach - - r-hdf5r - - r-gdata + - r-fpc - r-ggplot2 - r-ggridges - r-gplots - - r-hmisc + - r-hdf5r + - r-httr - r-ica - r-igraph - r-irlba - r-lars - r-lmtest - - r-mass - - r-matrix >=1.2.14 - r-metap - r-mixtools - r-pbapply - r-plotly - r-png - - r-ranger - - r-rann - - r-rcolorbrewer - - r-rcpp - - r-rcppeigen - - r-rcppprogress - r-reshape2 - r-reticulate - - r-rocr - - r-rtsne - - r-sdmtools - - r-stringr - - r-tclust - r-tidyr - r-tsne - - r-vgam - - openjdk >=6 test: commands: - - $R -e "library('Seurat')" + + - $R -e "library('Seurat')" # [not win] + - "\"%R%\" -e \"library('Seurat')\"" # [win] about: - home: http://www.satijalab.org/seurat - dev_url: https://github.com/satijalab/seurat + home: http://www.satijalab.org/seurat, https://github.com/satijalab/seurat license: GPL-3 summary: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity @@ -132,5 +133,13 @@ about: single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , and Butler A and Satija R (2017) for more details. - license_family: GPL - + license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-shazam/build.sh b/recipes/r-shazam/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-shazam/build.sh +++ b/recipes/r-shazam/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-shazam/meta.yaml b/recipes/r-shazam/meta.yaml index 6104dd7ffbbc9..7aaeee510ee38 100644 --- a/recipes/r-shazam/meta.yaml +++ b/recipes/r-shazam/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.9' %} +{% set version = '0.1.10' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -9,25 +9,30 @@ package: source: url: - - https://cran.r-project.org/src/contrib/shazam_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/shazam/shazam_{{ version }}.tar.gz - sha256: b342aa6e5e9085de0d8fe9ac03ff185d15d28daea38f708b970a731ce828a5b6 + - {{ cran_mirror }}/src/contrib/shazam_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/shazam/shazam_{{ version }}.tar.gz + sha256: 01c5a8b3b8a9125aa6406bb957c9b6bb3d082c668012942ef988148da0140de6 build: - number: 3 - skip: true # [osx] + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-kernsmooth - r-mass - r-sdmtools - - r-alakazam >=0.2.10 + - r-alakazam >=0.2.11 - r-ape - r-diptest - r-doparallel @@ -49,7 +54,7 @@ requirements: - r-kernsmooth - r-mass - r-sdmtools - - r-alakazam >=0.2.10 + - r-alakazam >=0.2.11 - r-ape - r-diptest - r-doparallel @@ -68,15 +73,28 @@ requirements: test: commands: - - $R -e "library('shazam')" # [not win] + + - $R -e "library('shazam')" # [not win] - "\"%R%\" -e \"library('shazam')\"" # [win] about: - home: http + home: http://shazam.readthedocs.io license: CC BY-SA 4.0 - summary: Provides a computational framework for Bayesian estimation of antigen-driven selection - in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection - by quantifying the degree of selective pressure. Also provides tools to profile - mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, - and make model-dependent distance comparisons of Ig repertoires. Citations - license_family: OTHER + summary: 'Provides a computational framework for analyzing mutations in immunoglobulin (Ig) + sequences. Includes methods for Bayesian estimation of antigen-driven selection + pressure, mutational load quantification, building of somatic hypermutation (SHM) + models, and model-dependent distance calculations. Also includes empirically derived + models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et + al (2015) , Yaari, et al (2012) , Yaari, + et al (2013) , Cui, et al (2016) .' + + license_family: CC +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-sigQC/build.sh b/recipes/r-sigQC/build.sh index af6547bf3c22e..4d712504b78a2 100644 --- a/recipes/r-sigQC/build.sh +++ b/recipes/r-sigQC/build.sh @@ -1,2 +1,11 @@ #!/bin/bash -$R CMD INSTALL --build . + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/sigQC + mv * $PREFIX/lib/R/library/sigQC +fi diff --git a/recipes/r-sigQC/meta.yaml b/recipes/r-sigQC/meta.yaml index f98511a3702c4..017675fb2208e 100644 --- a/recipes/r-sigQC/meta.yaml +++ b/recipes/r-sigQC/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '0.1.14' %} +{% set version = '0.1.21' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-sigqc @@ -6,28 +9,34 @@ package: source: url: - - https://cran.r-project.org/src/contrib/sigQC_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/sigQC/sigQC_{{ version }}.tar.gz - sha256: 90678a5e52eb0813efaf32f6c225fef7c73fe5ddbcf8dadd5be321bbe6756f9f + - {{ cran_mirror }}/src/contrib/sigQC_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/sigQC/sigQC_{{ version }}.tar.gz + sha256: 1deec4c855e05bdae3fd854ae0bbb364b4b1a52df6f78bf10ba839f2e7ee241d build: - number: 1 + merge_build_host: True # [win] + # If this is a new build for the same version, increment the build number. + number: 0 + # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rmarkdown requirements: build: - - {{ compiler('c') }} + - {{posix}}zip # [win] host: - r-base - bioconductor-complexheatmap + - bioconductor-gsva - r-kernsmooth - r-mass - bioconductor-rankprod - r-biclust + - r-circlize - r-class - r-cluster - r-fmsb @@ -41,10 +50,12 @@ requirements: run: - r-base - bioconductor-complexheatmap + - bioconductor-gsva - r-kernsmooth - r-mass - bioconductor-rankprod - r-biclust + - r-circlize - r-class - r-cluster - r-fmsb @@ -57,11 +68,13 @@ requirements: test: commands: + # You can put additional test commands to be run here. - $R -e "library('sigQC')" # [not win] + - "\"%R%\" -e \"library('sigQC')\"" # [win] about: home: https://CRAN.R-project.org/package=sigQC - license: free for non-commercial users. Non-academic users MUST have requested from the author + license: file LICENSE (Restricts use) summary: Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics. diff --git a/recipes/r-sigtree/build.sh b/recipes/r-sigtree/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-sigtree/build.sh +++ b/recipes/r-sigtree/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-sigtree/meta.yaml b/recipes/r-sigtree/meta.yaml index fb4700caef585..6c4f90ce8acc6 100644 --- a/recipes/r-sigtree/meta.yaml +++ b/recipes/r-sigtree/meta.yaml @@ -1,24 +1,38 @@ {% set version = '1.10.6' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-sigtree version: {{ version|replace("-", "_") }} source: - fn: SigTree_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/SigTree_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/SigTree/SigTree_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/SigTree_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/SigTree/SigTree_{{ version }}.tar.gz sha256: 3ce57e37d1c328720bb3ffc8c1f349c62b22e4d4de132f988ce9a42cbf3af0a1 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: - r-base - r-mass - r-rcolorbrewer @@ -27,10 +41,10 @@ requirements: - r-phylobase - bioconductor-phyloseq - r-vegan - - gcc run: - r-base + - {{native}}gcc-libs # [win] - r-mass - r-rcolorbrewer - r-ape @@ -41,7 +55,9 @@ requirements: test: commands: - - $R -e "library('SigTree')" + + - $R -e "library('SigTree')" # [not win] + - "\"%R%\" -e \"library('SigTree')\"" # [win] about: home: https://CRAN.R-project.org/package=SigTree @@ -51,3 +67,12 @@ about: tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-sleuth/build.sh b/recipes/r-sleuth/build.sh index be092347e8f41..5bf492ab9fc06 100644 --- a/recipes/r-sleuth/build.sh +++ b/recipes/r-sleuth/build.sh @@ -1,17 +1 @@ - -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# diff --git a/recipes/r-sleuth/meta.yaml b/recipes/r-sleuth/meta.yaml index 60565849a0ea6..927b1a41ed814 100644 --- a/recipes/r-sleuth/meta.yaml +++ b/recipes/r-sleuth/meta.yaml @@ -6,6 +6,7 @@ source: sha256: c25158dff35416865931f7c95f02c64be764c5b2ce964fe9f40972d96150ddb2 build: number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ @@ -45,3 +46,12 @@ about: home: http://pachterlab.github.io/sleuth license: GPLv3 summary: "Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto." +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-smvar/build.sh b/recipes/r-smvar/build.sh index ef53d70dd563d..5309021553b07 100644 --- a/recipes/r-smvar/build.sh +++ b/recipes/r-smvar/build.sh @@ -1,8 +1,3 @@ -#!/bin/bash - export DISABLE_AUTOBREW=1 -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . - diff --git a/recipes/r-smvar/meta.yaml b/recipes/r-smvar/meta.yaml index 875e20733f58d..23861286dc17f 100644 --- a/recipes/r-smvar/meta.yaml +++ b/recipes/r-smvar/meta.yaml @@ -1,24 +1,31 @@ {% set version = '1.3.3' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-smvar version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/SMVar_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/SMVar/SMVar_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/SMVar_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/SMVar/SMVar_{{ version }}.tar.gz sha256: 17625e89eb8be7a6dbb77e6bd9daca1ea1acff69026049f213e30edf2325999f build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ - requirements: + build: + - {{posix}}zip # [win] + host: - r-base @@ -27,7 +34,9 @@ requirements: test: commands: - - $R -e "library('SMVar')" + + - $R -e "library('SMVar')" # [not win] + - "\"%R%\" -e \"library('SMVar')\"" # [win] about: home: https://CRAN.R-project.org/package=SMVar @@ -35,4 +44,12 @@ about: summary: Implements the structural model for variances in order to detect differentially expressed genes from gene expression data license_family: GPL - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-snpassoc/build.sh b/recipes/r-snpassoc/build.sh index b58dbca4d229f..5bf492ab9fc06 100644 --- a/recipes/r-snpassoc/build.sh +++ b/recipes/r-snpassoc/build.sh @@ -1,4 +1 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION $R CMD INSTALL --build . diff --git a/recipes/r-snpassoc/meta.yaml b/recipes/r-snpassoc/meta.yaml index b19b79f8ee0c1..3f7f071c33b83 100644 --- a/recipes/r-snpassoc/meta.yaml +++ b/recipes/r-snpassoc/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.9-2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-snpassoc version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/SNPassoc_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/SNPassoc/SNPassoc_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/SNPassoc_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/SNPassoc/SNPassoc_{{ version }}.tar.gz sha256: b08e65ddbaa287fa7f4806a4a6c1556e4cefb036a77e1c56f7ddbcf591f46b84 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-haplo.stats @@ -31,7 +40,9 @@ requirements: test: commands: - - $R -e "library('SNPassoc')" + + - $R -e "library('SNPassoc')" # [not win] + - "\"%R%\" -e \"library('SNPassoc')\"" # [win] about: home: http://www.creal.cat/jrgonzalez/software.htm @@ -43,4 +54,16 @@ about: analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. ' + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-soap-nmr/build.sh b/recipes/r-soap-nmr/build.sh index 6864ae6daf614..5bf492ab9fc06 100644 --- a/recipes/r-soap-nmr/build.sh +++ b/recipes/r-soap-nmr/build.sh @@ -1,8 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - diff --git a/recipes/r-soap-nmr/meta.yaml b/recipes/r-soap-nmr/meta.yaml index bb8a41e3d97fe..8059be8f405a2 100644 --- a/recipes/r-soap-nmr/meta.yaml +++ b/recipes/r-soap-nmr/meta.yaml @@ -38,4 +38,12 @@ about: home: https://github.com/ManonMartin/SOAP-NMR license: 'GPL2' summary: 'R package for 1H-NMR data pre-treatment ' - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-solarius/build.sh b/recipes/r-solarius/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-solarius/build.sh +++ b/recipes/r-solarius/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-solarius/meta.yaml b/recipes/r-solarius/meta.yaml index 4d33daad68107..38e57939eaec2 100644 --- a/recipes/r-solarius/meta.yaml +++ b/recipes/r-solarius/meta.yaml @@ -1,23 +1,31 @@ {% set version = '0.3.0.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-solarius version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/solarius_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/solarius/solarius_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/solarius_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/solarius/solarius_{{ version }}.tar.gz sha256: 683844028170f3311a26ddb0ef7bb2b0ee5725868e12ea3dd43d20dc6d31879d build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-data.table @@ -32,7 +40,9 @@ requirements: test: commands: - - $R -e "library('solarius')" + + - $R -e "library('solarius')" # [not win] + - "\"%R%\" -e \"library('solarius')\"" # [win] about: home: https://github.com/ugcd/solarius @@ -47,3 +57,14 @@ about: scans more efficient. See for more information about SOLAR. license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-speaq/build.sh b/recipes/r-speaq/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-speaq/build.sh +++ b/recipes/r-speaq/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-speaq/meta.yaml b/recipes/r-speaq/meta.yaml index 38116bf43a3f5..92d49693be793 100644 --- a/recipes/r-speaq/meta.yaml +++ b/recipes/r-speaq/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '2.1.0' %} +{% set version = '2.3.3' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-speaq @@ -6,18 +9,24 @@ package: source: url: - - https://cran.r-project.org/src/contrib/speaq_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/speaq/speaq_{{ version }}.tar.gz - sha256: 58c1567e02978f25d59075ce82be8748b3ceff6fe9b72239a6b5d6d23bc79caa + - {{ cran_mirror }}/src/contrib/speaq_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/speaq/speaq_{{ version }}.tar.gz + sha256: bb1aa887c93cb40baf6ee01282c5485627152363ba3f47680e3d2a2a5a4735ff build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - bioconductor-massspecwavelet @@ -52,16 +61,29 @@ requirements: test: commands: - - $R -e "library('speaq')" + + - $R -e "library('speaq')" # [not win] + - "\"%R%\" -e \"library('speaq')\"" # [win] about: home: https://CRAN.R-project.org/package=speaq license: Apache License 2.0 - summary: Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as + summary: 'Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire - analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation + analysis. ''speaq'' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed - with any number of statistical tools either included in 'speaq' or available elsewhere - on CRAN. More detail can be found in and . + with any number of statistical tools either included in ''speaq'' or available elsewhere + on CRAN. More detail can be found in Vu et al. (2011) + and Beirnaert et al. (2018) . ' + license_family: APACHE +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-spieceasi/build.sh b/recipes/r-spieceasi/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-spieceasi/build.sh +++ b/recipes/r-spieceasi/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-spieceasi/meta.yaml b/recipes/r-spieceasi/meta.yaml index 7497249e5c1f5..cab5af20a4828 100644 --- a/recipes/r-spieceasi/meta.yaml +++ b/recipes/r-spieceasi/meta.yaml @@ -35,7 +35,7 @@ test: about: home: http://github.com/EESI/themetagenomics - license: 'MIT + file LICENSE' + license: 'MIT' summary: A means to explore the structure of 16S rRNA surveys using a Structural Topic Model coupled with functional prediction. The user provides an abundance table, sample metadata, and taxonomy information, and themetagenomics infers associations between @@ -43,3 +43,12 @@ about: Functional prediction can be accomplished via Tax4Fun (for Silva references) and PICRUSt (for GreenGeenes references). license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-spocc/build.sh b/recipes/r-spocc/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-spocc/build.sh +++ b/recipes/r-spocc/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-spocc/meta.yaml b/recipes/r-spocc/meta.yaml index a17bfb30a6597..3f383680a45ac 100644 --- a/recipes/r-spocc/meta.yaml +++ b/recipes/r-spocc/meta.yaml @@ -1,35 +1,47 @@ {% set version = '0.8.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-spocc version: {{ version|replace("-", "_") }} source: - url: https://cran.r-project.org/src/contrib/spocc_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/spocc_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/spocc/spocc_{{ version }}.tar.gz sha256: 7c0d1fca1ff3b5281bdbf34e90dd3611646dcc559176370f41aab2cfa71b9503 - + build: - number: 2 + merge_build_host: True # [win] + + number: 3 rpaths: - lib/R/lib/ - lib/ +# geos isn't getting pulled in by an old version of a dependency. This is already fixed in r-rgeos requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-crul >=0.3.4 - r-data.table >=1.9.6 - r-jsonlite >=1.4 - r-lubridate >=1.5.0 - - r-rbison >=0.5.0 + - r-rbison >=0.6.0 - r-rebird >=0.3.0 - - r-rgbif >=0.9.8 + - r-rgbif >=1.0.0 - r-ridigbio >=0.3.5 - - r-rvertnet >=0.5.0 + - r-rvertnet >=0.7.0 - r-tibble >=1.2 - r-whisker >=0.3_2 - r-wicket >=0.3.0 + - geos 3.6.2 run: - r-base @@ -37,28 +49,38 @@ requirements: - r-data.table >=1.9.6 - r-jsonlite >=1.4 - r-lubridate >=1.5.0 - - r-rbison >=0.5.0 + - r-rbison >=0.6.0 - r-rebird >=0.3.0 - - r-rgbif >=0.9.8 + - r-rgbif >=1.0.0 - r-ridigbio >=0.3.5 - - r-rvertnet >=0.5.0 + - r-rvertnet >=0.7.0 - r-tibble >=1.2 - r-whisker >=0.3_2 - r-wicket >=0.3.0 + - geos 3.6.2 test: commands: - - $R -e "library('spocc')" + - $R -e "library('spocc')" # [not win] + - "\"%R%\" -e \"library('spocc')\"" # [win] about: home: https://github.com/ropensci/spocc - license: MIT + file LICENSE - summary: | - A programmatic interface to many species occurrence data sources, including Global + license: MIT + summary: A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-spp/build.sh b/recipes/r-spp/build.sh index 7117e5d9989b9..fc8b380f14d4a 100644 --- a/recipes/r-spp/build.sh +++ b/recipes/r-spp/build.sh @@ -1,4 +1,3 @@ -#!/bin/bash export BOOST_ROOT=${PREFIX} if [[ $(uname) == "Darwin" ]]; then export LDFLAGS=-L${PREFIX}/lib diff --git a/recipes/r-spp/meta.yaml b/recipes/r-spp/meta.yaml index d77277937170f..e7b2bd13f1f52 100644 --- a/recipes/r-spp/meta.yaml +++ b/recipes/r-spp/meta.yaml @@ -1,53 +1,79 @@ +{% set version = '1.15.5' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-spp - version: "1.15.2" + version: {{ version|replace("-", "_") }} source: - url: https://github.com/hms-dbmi/spp/archive/1.15.2.tar.gz - sha256: bf0d6f42d9461aeb7a20b1ddb12b57bc42d11732ca6f69ec3eb2157364cefd5b - patches: # [osx] - - Makevars.patch # [osx] + url: + - {{ cran_mirror }}/src/contrib/spp_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/spp/spp_{{ version }}.tar.gz + sha256: 1c486792ac3feb194c95efe7a8a98eab4331877ba901d774561b8839c958f924 build: - number: 1 - skip: True # [osx] + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}sed # [win] + - {{posix}}grep # [win] + - {{posix}}autoconf + - {{posix}}automake # [not win] + - {{posix}}automake-wrapper # [win] + - {{posix}}pkg-config + - {{posix}}make + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base + - r-bh >=1.66 - r-rcpp - - boost + - 'bioconductor-rsamtools >=1.32.0,<1.34.0' - r-catools - - bioconductor-rsamtools - - zlib - - bzip2 run: - r-base + - {{native}}gcc-libs # [win] + - r-bh >=1.66 - r-rcpp - - boost + - 'bioconductor-rsamtools >=1.32.0,<1.34.0' - r-catools - - bioconductor-rsamtools - - zlib - - bzip2 test: commands: - - $R -e "library(spp)" - - $R -e "library(spp); read.bam.tags(system.file(\"extdata\", \"ex1.bam\", package=\"Rsamtools\"))" -about: - license: GPL - summary: 'ChIP-seq peak caller' - home: http://compbio.med.harvard.edu/Supplements/ChIP-seq + - $R -e "library('spp')" # [not win] + - "\"%R%\" -e \"library('spp')\"" # [win] +about: + home: https://CRAN.R-project.org/package=spp + license: GPL-2 + summary: Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) ]. + license_family: GPL2 extra: identifiers: - biotools:spp - doi:10.1038/nbt.1508 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-stampp/build.sh b/recipes/r-stampp/build.sh index 81250b8ff4aaa..5bf492ab9fc06 100644 --- a/recipes/r-stampp/build.sh +++ b/recipes/r-stampp/build.sh @@ -1,7 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-stampp/meta.yaml b/recipes/r-stampp/meta.yaml index cfde6579f443e..b00111dd35ae4 100644 --- a/recipes/r-stampp/meta.yaml +++ b/recipes/r-stampp/meta.yaml @@ -1,22 +1,31 @@ {% set version = '1.5.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-stampp - version: {{ version }} + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/StAMPP_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/StAMPP/StAMPP_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/StAMPP_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/StAMPP/StAMPP_{{ version }}.tar.gz sha256: 6ebe4cadbd265953bc76ccef8def71ef0c580626eb1963d5d28cd0d199d6da7b build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-adegenet @@ -33,7 +42,9 @@ requirements: test: commands: - - $R -e "library('StAMPP')" + + - $R -e "library('StAMPP')" # [not win] + - "\"%R%\" -e \"library('StAMPP')\"" # [win] about: home: https://CRAN.R-project.org/package=StAMPP @@ -47,5 +58,15 @@ about: where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular - Ecology Resources, 13(5), 946-952. for the appropriate + citation and user manual. Thank you in advance. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-structssi/build.sh b/recipes/r-structssi/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-structssi/build.sh +++ b/recipes/r-structssi/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-structssi/meta.yaml b/recipes/r-structssi/meta.yaml index bcba7c5f7ac98..2068526a8912b 100644 --- a/recipes/r-structssi/meta.yaml +++ b/recipes/r-structssi/meta.yaml @@ -1,32 +1,35 @@ -{% set name = 'structSSI' %} {% set version = '1.1.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: - name: r-{{ name|lower }} + name: r-structssi version: {{ version|replace("-", "_") }} source: - fn: {{ name }}_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/structSSI_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/structSSI/structSSI_{{ version }}.tar.gz sha256: bbcdeac4b9eb8545217d928796b22bb7ba2e75935053b840271e13865fae3c1b build: - number: 1 + merge_build_host: True # [win] + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + host: - r-base - r-ggplot2 - r-igraph - bioconductor-multtest - r-reshape2 - r-rjson - run: - r-base - r-ggplot2 @@ -37,7 +40,8 @@ requirements: test: commands: - - $R -e "library('structSSI')" + - $R -e "library('structSSI')" # [not win] + - "\"%R%\" -e \"library('structSSI')\"" # [win] about: home: https://CRAN.R-project.org/package=structSSI @@ -45,3 +49,12 @@ about: summary: Performs multiple testing corrections that take specific structure of hypotheses into account. license_family: GPL2 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-swamp/build.sh b/recipes/r-swamp/build.sh index 6a5287bec0c5c..5bf492ab9fc06 100644 --- a/recipes/r-swamp/build.sh +++ b/recipes/r-swamp/build.sh @@ -1,7 +1 @@ -#!/bin/sh - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-swamp/meta.yaml b/recipes/r-swamp/meta.yaml index 8b61f181ae09c..92ab9b965fe81 100644 --- a/recipes/r-swamp/meta.yaml +++ b/recipes/r-swamp/meta.yaml @@ -1,43 +1,68 @@ -{% set name = 'swamp' %} {% set version = '1.4.1' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: - name: r-{{ name }} - version: {{ version }} + name: r-swamp + version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/swamp_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/swamp/swamp_{{ version }}.tar.gz sha256: a6462f4fe99837317752b6d2c8f31275414a7f3e6fb4ab2e4fd8409c4f238407 build: - number: 0 + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] + host: - r-base - r-mass - r-amap - r-gplots - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' run: - r-base - r-mass - r-amap - r-gplots - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' test: commands: - - $R -e "library('swamp')" + + - $R -e "library('swamp')" # [not win] + - "\"%R%\" -e \"library('swamp')\"" # [win] about: home: https://CRAN.R-project.org/package=swamp license: GPL (>= 2) - summary: Collection of functions to connect the structure of the data with the information on the samples. + summary: 'Collection of functions to connect the structure of the data with the information + on the samples. Three types of associations are covered: 1. linear model of principal + components. 2. hierarchical clustering analysis. 3. distribution of features-sample + annotation associations. Additionally, the inter-relation between sample annotations + can be analyzed. Simple methods are provided for the correction of batch effects + and removal of principal components.' + license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-taxa/build.sh b/recipes/r-taxa/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-taxa/build.sh +++ b/recipes/r-taxa/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-taxa/meta.yaml b/recipes/r-taxa/meta.yaml index 02bc3c4a459fa..9aff20c3ed3dd 100644 --- a/recipes/r-taxa/meta.yaml +++ b/recipes/r-taxa/meta.yaml @@ -1,24 +1,33 @@ -{% set version = '0.2.1' %} +{% set version = '0.3.1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-taxa version: {{ version|replace("-", "_") }} source: - fn: taxa_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/taxa_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/taxa/taxa_{{ version }}.tar.gz - sha256: b605fa2dbcfb710a92217d742c0bfd017ba50661e16d055b4d7d1948a58e034a + - {{ cran_mirror }}/src/contrib/taxa_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/taxa/taxa_{{ version }}.tar.gz + sha256: e718b187b7f2c8b46d9db0052e90562aab4c787c7270e9b1c67bfbbc227b6ea5 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-r6 - r-crayon @@ -50,12 +59,23 @@ requirements: test: commands: - - $R -e "library('taxa')" + + - $R -e "library('taxa')" # [not win] + - "\"%R%\" -e \"library('taxa')\"" # [win] about: - home: https://CRAN.R-project.org/package=taxa - license: MIT + file LICENSE + home: https://github.com/ropensci/taxa + license: MIT summary: Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-tcga2stat/build.sh b/recipes/r-tcga2stat/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-tcga2stat/build.sh +++ b/recipes/r-tcga2stat/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-tcga2stat/meta.yaml b/recipes/r-tcga2stat/meta.yaml index 638b03f1c4ac2..5340ff89756bd 100644 --- a/recipes/r-tcga2stat/meta.yaml +++ b/recipes/r-tcga2stat/meta.yaml @@ -1,37 +1,54 @@ {% set version = '1.2' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-tcga2stat version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/TCGA2STAT_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/TCGA2STAT/TCGA2STAT_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/TCGA2STAT_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/TCGA2STAT/TCGA2STAT_{{ version }}.tar.gz sha256: 7b46ba685839a44923d764c9c6cdbdcf87b9754eb5487e246f9db56c01a44595 build: - number: 1 + merge_build_host: True # [win] + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: + build: + - {{posix}}zip # [win] host: - r-base - - r-xml - bioconductor-cntools + - r-xml run: - r-base - - r-xml - bioconductor-cntools + - r-xml test: commands: - - $R -e "library('TCGA2STAT')" + - $R -e "library('TCGA2STAT')" # [not win] + - "\"%R%\" -e \"library('TCGA2STAT')\"" # [win] about: home: http://www.liuzlab.org/TCGA2STAT/ license: GPL-2 summary: Automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment. + license_family: GPL2 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-tfmpvalue/build.sh b/recipes/r-tfmpvalue/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-tfmpvalue/build.sh +++ b/recipes/r-tfmpvalue/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-tfmpvalue/meta.yaml b/recipes/r-tfmpvalue/meta.yaml index 8fefa976864ae..7ec6711f8ee21 100644 --- a/recipes/r-tfmpvalue/meta.yaml +++ b/recipes/r-tfmpvalue/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '0.0.6' %} +{% set version = '0.0.8' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-tfmpvalue @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/TFMPvalue_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/TFMPvalue/TFMPvalue_{{ version }}.tar.gz - sha256: cee3aa2d4e22856865d820f695e29a5f23486e5e08cd42cb95a0728f5f9522a1 + - {{ cran_mirror }}/src/contrib/TFMPvalue_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/TFMPvalue/TFMPvalue_{{ version }}.tar.gz + sha256: 6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,19 +25,29 @@ build: requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - r-rcpp + - r-rcpp >=0.11.1 run: - r-base - - r-rcpp + - {{native}}gcc-libs # [win] + - r-rcpp >=0.11.1 test: commands: - - $R -e "library('TFMPvalue')" + + - $R -e "library('TFMPvalue')" # [not win] + - "\"%R%\" -e \"library('TFMPvalue')\"" # [win] about: home: https://github.com/ge11232002/TFMPvalue @@ -39,7 +55,18 @@ about: summary: In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or - the score with given P-value. This package is an interface to code originally made - available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, - 15. + the score with given P-value. It is an interface to code originally made available + by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet + and Varre (2007) . license_family: GPL2 + license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2' # [unix] + license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2' # [win] +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-tidygenomics/build.sh b/recipes/r-tidygenomics/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-tidygenomics/build.sh +++ b/recipes/r-tidygenomics/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-tidygenomics/meta.yaml b/recipes/r-tidygenomics/meta.yaml index 2e44383c0aed3..b59eb6e25f7f1 100644 --- a/recipes/r-tidygenomics/meta.yaml +++ b/recipes/r-tidygenomics/meta.yaml @@ -1,52 +1,77 @@ {% set version = '0.1.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-tidygenomics version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/tidygenomics_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/tidygenomics/tidygenomics_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/tidygenomics_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/tidygenomics/tidygenomics_{{ version }}.tar.gz sha256: 966095c07f7f9e9e9a33585c6fa81e3e35038acd55fd6c2c536fd506bfa8d358 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base + - bioconductor-iranges - r-rcpp - r-dplyr - r-fuzzyjoin >=0.1.3 - r-purrr - r-tidyr - - bioconductor-iranges run: - r-base + - {{native}}gcc-libs # [win] + - bioconductor-iranges - r-rcpp - r-dplyr - r-fuzzyjoin >=0.1.3 - r-purrr - r-tidyr - - bioconductor-iranges test: commands: - - $R -e "library('tidygenomics')" + + - $R -e "library('tidygenomics')" # [not win] + - "\"%R%\" -e \"library('tidygenomics')\"" # [win] about: home: https://github.com/const-ae/tidygenomics license: GPL-3 - summary: Handle genomic data within data frames just as you would with 'GRanges'. This package - provides methods to deal with genomic intervals the "tidy-way" which makes it simpler + summary: Handle genomic data within data frames just as you would with 'GRanges'. This packages + provides method to deal with genomic intervals the "tidy-way" which makes it simpler to integrate in the the general data munging process. The API is inspired by the popular 'bedtools' and the genome_join() method from the 'fuzzyjoin' package. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-traminer/build.sh b/recipes/r-traminer/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-traminer/build.sh +++ b/recipes/r-traminer/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-traminer/meta.yaml b/recipes/r-traminer/meta.yaml index 81a74d045a201..bc9530e10c700 100644 --- a/recipes/r-traminer/meta.yaml +++ b/recipes/r-traminer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.0-8' %} +{% set version = '2.0-9' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -9,19 +9,30 @@ package: source: url: - - https://cran.r-project.org/src/contrib/TraMineR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/TraMineR/TraMineR_{{ version }}.tar.gz - sha256: 394d4481707dfd8a4b0e28681097948ab36934dbe4084cf0917ae5f3e0bb9774 + - {{ cran_mirror }}/src/contrib/TraMineR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/TraMineR/TraMineR_{{ version }}.tar.gz + sha256: 6e9c017ac11d131c4cfe1009ed1f33704cc9a771b5270bf10477055f5b714b07 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -32,6 +43,7 @@ requirements: run: - r-base + - {{native}}gcc-libs # [win] - r-hmisc - r-rcolorbrewer - r-boot @@ -39,10 +51,12 @@ requirements: test: commands: - - $R -e "library('TraMineR')" + + - $R -e "library('TraMineR')" # [not win] + - "\"%R%\" -e \"library('TraMineR')\"" # [win] about: - home: https://cran.r-project.org/web/packages/TraMineR + home: http://traminer.unige.ch license: GPL (>= 2) summary: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox @@ -57,3 +71,12 @@ about: discriminating ones among them. A user's guide can be found on the TraMineR web page. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-treesim/build.sh b/recipes/r-treesim/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-treesim/build.sh +++ b/recipes/r-treesim/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-treesim/meta.yaml b/recipes/r-treesim/meta.yaml index cfbe0cea86c49..9952f7de60268 100644 --- a/recipes/r-treesim/meta.yaml +++ b/recipes/r-treesim/meta.yaml @@ -1,24 +1,32 @@ {% set version = '2.3' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-treesim version: {{ version|replace("-", "_") }} source: - fn: TreeSim_{{ version }}.tar.gz url: - - https://cran.r-project.org/src/contrib/TreeSim_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/TreeSim/TreeSim_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/TreeSim_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/TreeSim/TreeSim_{{ version }}.tar.gz sha256: d05817fc4da0d050e9a1416d8f2cdbc929a3f3354d703a9fd633f50bb9a828f9 build: - number: 1 + merge_build_host: True # [win] + + number: 2 + rpaths: - lib/R/lib/ - lib/ requirements: build: + - {{posix}}zip # [win] + + host: - r-base - r-ape - r-geiger @@ -30,7 +38,9 @@ requirements: test: commands: - - $R -e "library('TreeSim')" + + - $R -e "library('TreeSim')" # [not win] + - "\"%R%\" -e \"library('TreeSim')\"" # [win] about: home: https://CRAN.R-project.org/package=TreeSim @@ -54,7 +64,17 @@ about: conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows - to simulate under epidemiological models with an exposed class. The function - sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, - and sim.genetree() simulates coalescent gene trees. + to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() + simulates coalescent gene trees within birth-death species trees, and sim.genetree() + simulates coalescent gene trees. license_family: GPL2 + +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-vcfr/build.sh b/recipes/r-vcfr/build.sh index 32bc29aa16362..5bf492ab9fc06 100644 --- a/recipes/r-vcfr/build.sh +++ b/recipes/r-vcfr/build.sh @@ -1,6 +1 @@ -#!/bin/bash - -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/r-vcfr/meta.yaml b/recipes/r-vcfr/meta.yaml index 472f48d4deb46..7720828236eb9 100644 --- a/recipes/r-vcfr/meta.yaml +++ b/recipes/r-vcfr/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.5.0' %} +{% set version = '1.8.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-vcfr @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/vcfR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/vcfR/vcfR_{{ version }}.tar.gz - sha256: 7cd7d352d72120cf6127c9ef86b5134135d66bb4f047945c75aa0b99cc741a22 + - {{ cran_mirror }}/src/contrib/vcfR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/vcfR/vcfR_{{ version }}.tar.gz + sha256: 5ffcf9980c1936b9be41b92d5887c56a7ec6e3cf197e5ef7c78aefa8aba20499 build: - number: 1 + merge_build_host: True # [win] + + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,7 +25,14 @@ build: requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base @@ -30,12 +43,13 @@ requirements: - r-memuse - r-pinfsc50 - r-stringr - - r-tidyr + - r-tibble - r-vegan - r-viridislite run: - r-base + - {{native}}gcc-libs # [win] - r-rcpp - r-ape - r-dplyr @@ -43,16 +57,18 @@ requirements: - r-memuse - r-pinfsc50 - r-stringr - - r-tidyr + - r-tibble - r-vegan - r-viridislite test: commands: - - $R -e "library('vcfR')" + + - $R -e "library('vcfR')" # [not win] + - "\"%R%\" -e \"library('vcfR')\"" # [win] about: - home: https://github.com/knausb/vcfR, https://knausb.github.io/ vcfR_documentation/ + home: https://github.com/knausb/vcfR, https://knausb.github.io/vcfR_documentation/ license: GPL summary: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser @@ -62,3 +78,12 @@ about: It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-wasabi/build.sh b/recipes/r-wasabi/build.sh index 0d6a53f143312..5bf492ab9fc06 100644 --- a/recipes/r-wasabi/build.sh +++ b/recipes/r-wasabi/build.sh @@ -1,16 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as -# "Priority: Recommended" -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# $R CMD INSTALL --build . -# -# # Add more build steps here, if they are necessary. -# -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build -# process. -# diff --git a/recipes/r-wasabi/meta.yaml b/recipes/r-wasabi/meta.yaml index 6b56663a175bc..8c2c6c0f487ec 100644 --- a/recipes/r-wasabi/meta.yaml +++ b/recipes/r-wasabi/meta.yaml @@ -28,3 +28,12 @@ about: home: https://github.com/COMBINE-lab/wasabi license: BSD-3-clause summary: "Prepare Sailfish and Salmon output for downstream analysis" +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-wgcna/build.sh b/recipes/r-wgcna/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-wgcna/build.sh +++ b/recipes/r-wgcna/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-wgcna/meta.yaml b/recipes/r-wgcna/meta.yaml index b9b70303914df..ec1c3029e84e9 100644 --- a/recipes/r-wgcna/meta.yaml +++ b/recipes/r-wgcna/meta.yaml @@ -1,4 +1,7 @@ -{% set version = '1.63' %} +{% set version = '1.64-1' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-wgcna @@ -6,12 +9,15 @@ package: source: url: - - https://cran.r-project.org/src/contrib/WGCNA_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/WGCNA/WGCNA_{{ version }}.tar.gz - sha256: 098cdfc7f8e5ccda57449e7a8ef7fa37e33f5ac3ad6b4b679dd62f642a6e4588 + - {{ cran_mirror }}/src/contrib/WGCNA_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/WGCNA/WGCNA_{{ version }}.tar.gz + sha256: 961a890cda40676ba533cd6de2b1d4f692addd16363f874c82ba8b65dd2d0db6 build: + merge_build_host: True # [win] + number: 0 + skip: true # [win32] rpaths: - lib/R/lib/ @@ -19,55 +25,73 @@ build: requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base - - bioconductor-annotationdbi - - bioconductor-go.db + - 'bioconductor-annotationdbi >=1.42.0,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-hmisc - r-rcpp >=0.11.0 - r-doparallel - r-dynamictreecut >=1.62 - r-fastcluster - r-foreach - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-matrixstats >=0.8.1 - - bioconductor-preprocesscore + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-robust - r-survival run: - r-base - - bioconductor-annotationdbi - - bioconductor-go.db + - {{native}}gcc-libs # [win] + - 'bioconductor-annotationdbi >=1.42.0,<1.44.0' + - 'bioconductor-go.db >=3.6.0,<3.8.0' - r-hmisc - r-rcpp >=0.11.0 - r-doparallel - r-dynamictreecut >=1.62 - r-fastcluster - r-foreach - - bioconductor-impute + - 'bioconductor-impute >=1.54.0,<1.56.0' - r-matrixstats >=0.8.1 - - bioconductor-preprocesscore + - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - r-robust - r-survival test: commands: - - $R -e "library('WGCNA')" + + - $R -e "library('WGCNA')" # [not win] + - "\"%R%\" -e \"library('WGCNA')\"" # [win] about: - home: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/ + home: http://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ license: GPL (>= 2) summary: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional - data. Includes functions for rudimentary data cleaning, construction of correlation - networks, module identification, summarization, and relating of variables and modules - to sample traits. Also includes a number of utility functions for data manipulation - and visualization. + data as originally described in Horvath and Zhang (2005) + and Langfelder and Horvath (2008) . Includes functions + for rudimentary data cleaning, construction of correlation networks, module identification, + summarization, and relating of variables and modules to sample traits. Also includes + a number of utility functions for data manipulation and visualization. license_family: GPL3 - extra: identifiers: - biotools:wgcna - doi:10.1186/1471-2105-9-559 + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-whopgenome/build.sh b/recipes/r-whopgenome/build.sh index 299d885ff9dcd..36091c57682e4 100644 --- a/recipes/r-whopgenome/build.sh +++ b/recipes/r-whopgenome/build.sh @@ -1,5 +1,3 @@ -#!/bin/bash - if [[ $target_platform =~ linux.* ]] || [[ $target_platform == osx-64 ]]; then export DISABLE_AUTOBREW=1 mv DESCRIPTION DESCRIPTION.old diff --git a/recipes/r-whopgenome/meta.yaml b/recipes/r-whopgenome/meta.yaml index b102191232d7a..d36eedbc46b3b 100644 --- a/recipes/r-whopgenome/meta.yaml +++ b/recipes/r-whopgenome/meta.yaml @@ -1,7 +1,7 @@ {% set version = '0.9.7' %} -{% set name = 'r-whopgenome' %} -{% set posix = '' %} -{% set native = '' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} package: name: r-whopgenome @@ -14,31 +14,37 @@ source: sha256: 58bb001a831eff64955e424f07de7775d4d463d9674fc7743a0f795b7a6a47f5 build: - number: 0 - # This is required to make R link correctly on Linux. + merge_build_host: True # [win] + + number: 1 + rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - - r-base 3.3* - - r-dbi - - bioconductor-annotationdbi - - r-rmysql + - r-base + run: - - r-base 3.3* - - r-dbi - - bioconductor-annotationdbi - - r-rmysql + - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('WhopGenome')" + + - $R -e "library('WhopGenome')" # [not win] + - "\"%R%\" -e \"library('WhopGenome')\"" # [win] about: home: https://CRAN.R-project.org/package=WhopGenome @@ -49,3 +55,12 @@ about: to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files. license_family: GPL3 +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-wicket/build.sh b/recipes/r-wicket/build.sh index 54a048c046461..5bf492ab9fc06 100644 --- a/recipes/r-wicket/build.sh +++ b/recipes/r-wicket/build.sh @@ -1,4 +1 @@ -#!/bin/bash - $R CMD INSTALL --build . - diff --git a/recipes/r-wicket/meta.yaml b/recipes/r-wicket/meta.yaml index aecff8d74fa89..d9548f027cb2c 100644 --- a/recipes/r-wicket/meta.yaml +++ b/recipes/r-wicket/meta.yaml @@ -1,17 +1,22 @@ {% set version = '0.4.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-wicket version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/wicket_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/wicket/wicket_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/wicket_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/wicket/wicket_{{ version }}.tar.gz sha256: ce76a4c8f79e7dfb9d8aadfa59b7f5cdb0de3dd9623b1426fd5caf6464fd3fd2 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,26 +24,45 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: - r-base - r-bh - r-rcpp + run: - r-base - - libgcc + - {{native}}gcc-libs # [win] - r-bh - r-rcpp test: commands: - - $R -e "library('wicket')" + - $R -e "library('wicket')" # [not win] + - "\"%R%\" -e \"library('wicket')\"" # [win] about: home: https://github.com/ropensci/wicket - license: MIT + file LICENSE + license: MIT summary: Utilities to generate bounding boxes from 'WKT' (Well-Known Text) objects and R data types, validate 'WKT' objects and convert object types from the 'sp' package into 'WKT' representations. license_family: MIT +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-workflowscriptscommon/build.sh b/recipes/r-workflowscriptscommon/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-workflowscriptscommon/build.sh +++ b/recipes/r-workflowscriptscommon/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-workflowscriptscommon/meta.yaml b/recipes/r-workflowscriptscommon/meta.yaml index 27bb666319959..14bb60d737cd8 100644 --- a/recipes/r-workflowscriptscommon/meta.yaml +++ b/recipes/r-workflowscriptscommon/meta.yaml @@ -10,6 +10,7 @@ source: build: number: 0 + skip: true # [win32] noarch: generic rpaths: - lib/R/lib/ @@ -35,3 +36,12 @@ about: package is used by other packages (e.g. r-seurat-scripts) to add sets of simple wrappers with robust argument parsing. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-xmlrpc/build.sh b/recipes/r-xmlrpc/build.sh index 0c37df6e8efec..5bf492ab9fc06 100644 --- a/recipes/r-xmlrpc/build.sh +++ b/recipes/r-xmlrpc/build.sh @@ -1,13 +1 @@ -#!/bin/bash - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/r-xmlrpc/meta.yaml b/recipes/r-xmlrpc/meta.yaml index 7392769172948..2fc30e4376fbf 100644 --- a/recipes/r-xmlrpc/meta.yaml +++ b/recipes/r-xmlrpc/meta.yaml @@ -1,30 +1,19 @@ package: name: r-xmlrpc - # Note that conda versions cannot contain -, so any -'s in the version have - # been replaced with _'s. + version: "0.2_4" source: url: - http://download.r-forge.r-project.org/src/contrib/XMLRPC_0.2-4.tar.gz - - # You can add a hash for the file here, like md5 or sha1 - # md5: 49448ba4863157652311cc5ea4fea3ea - # sha1: 3bcfbee008276084cbb37a2b453963c61176a322 - # patches: - # List any patch files here - # - fix.patch - build: number: 1 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ -# Suggests: parallel requirements: host: - r-base @@ -38,39 +27,20 @@ requirements: test: commands: - # You can put additional test commands to be run here. + - $R -e "library('XMLRPC')" # [not win] - "\"%R%\" -e \"library('XMLRPC')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: https://r-forge.r-project.org license: BSD summary: A simple implementation of XML-RPC for R. - -# The original rforge metadata for this package was: - -# Package: XMLRPC -# Version: 0.2-4 -# Title: Remote Procedure Call (RPC) via XML in R -# Description: A simple implementation of XML-RPC for R. -# Imports: methods, RCurl, XML -# License: BSD -# Author: Duncan Temple Lang -# Maintainer: Duncan Temple Lang -# References: http://en.wikipedia.org/wiki/Xml-rpc -# Packaged: 2014-04-22 19:37:21 UTC; rforge -# Repository: R-Forge -# Repository/R-Forge/Project: rmetrics -# Repository/R-Forge/Revision: 5846 -# Repository/R-Forge/DateTimeStamp: 2014-04-22 13:36:14 -# Date/Publication: 2014-04-22 13:36:14 - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-xnomial/build.sh b/recipes/r-xnomial/build.sh index af6547bf3c22e..5bf492ab9fc06 100644 --- a/recipes/r-xnomial/build.sh +++ b/recipes/r-xnomial/build.sh @@ -1,2 +1 @@ -#!/bin/bash $R CMD INSTALL --build . diff --git a/recipes/r-xnomial/meta.yaml b/recipes/r-xnomial/meta.yaml index fd9c6898963a2..521575b74123d 100644 --- a/recipes/r-xnomial/meta.yaml +++ b/recipes/r-xnomial/meta.yaml @@ -1,17 +1,22 @@ {% set version = '1.0.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + package: name: r-xnomial version: {{ version|replace("-", "_") }} source: url: - - https://cran.r-project.org/src/contrib/XNomial_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/XNomial/XNomial_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/XNomial_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/XNomial/XNomial_{{ version }}.tar.gz sha256: e6237f79d96f02bb30af1cf055ae9f70541abba34ce045a9d4359b5304189dd7 build: - number: 1 + merge_build_host: True # [win] + + number: 2 rpaths: - lib/R/lib/ @@ -19,17 +24,26 @@ build: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] host: - r-base run: - r-base + - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('XNomial')" + + - $R -e "library('XNomial')" # [not win] + - "\"%R%\" -e \"library('XNomial')\"" # [win] about: home: https://CRAN.R-project.org/package=XNomial @@ -44,3 +58,12 @@ about: A histogram of the test statistic can also be plotted and compared with the asymptotic curve. license_family: GPL +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/r-zerone/build.sh b/recipes/r-zerone/build.sh index ef1470016dcb4..782ed3d992867 100644 --- a/recipes/r-zerone/build.sh +++ b/recipes/r-zerone/build.sh @@ -1,3 +1 @@ -#!/bin/bash $R CMD INSTALL --build ZeroneRPackage - diff --git a/recipes/r-zerone/meta.yaml b/recipes/r-zerone/meta.yaml index c6089aa0f72f8..e20aab9d4dd2b 100644 --- a/recipes/r-zerone/meta.yaml +++ b/recipes/r-zerone/meta.yaml @@ -34,4 +34,12 @@ about: license: GPL-3 summary: Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. license_family: GPL - +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak diff --git a/recipes/sambamba/meta.yaml b/recipes/sambamba/meta.yaml index 0fd332afa350d..96388c7d5481b 100644 --- a/recipes/sambamba/meta.yaml +++ b/recipes/sambamba/meta.yaml @@ -10,7 +10,7 @@ source: md5: unused build: - number: 1 + number: 0 # ldc provides run time libraries as well as a compiler. # The version needs to be pinned @@ -18,7 +18,7 @@ requirements: build: - {{ compiler('c') }} host: - - ldc =1.11.0 + - ldc - bzip2 - htslib - zlib diff --git a/recipes/seq-seq-pan/1.0.0/build.sh b/recipes/seq-seq-pan/1.0.0/build.sh new file mode 100755 index 0000000000000..b3dabae16b6a1 --- /dev/null +++ b/recipes/seq-seq-pan/1.0.0/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +mkdir -p $PREFIX/opt/seq-seq-pan/ + + +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-consensus +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-wga +sed -i "s|\${BASH_SOURCE%/\*}|$PREFIX/opt/seq-seq-pan|g" seq-seq-pan-genomedescription + +cp -r * $PREFIX/opt/seq-seq-pan/ +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan $PREFIX/bin +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-consensus $PREFIX/bin +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-wga $PREFIX/bin +ln -s $PREFIX/opt/seq-seq-pan/seq-seq-pan-genomedescription $PREFIX/bin diff --git a/recipes/seq-seq-pan/1.0.0/meta.yaml b/recipes/seq-seq-pan/1.0.0/meta.yaml new file mode 100644 index 0000000000000..e5597545f04e8 --- /dev/null +++ b/recipes/seq-seq-pan/1.0.0/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} + +package: + name: seq-seq-pan + version: {{ version }} + +source: + url: https://gitlab.com/chrjan/seq-seq-pan/repository/v{{ version }}/archive.tar.gz + md5: 7a0c00d8de984f7129c7bcbe4fa26892 + +build: + number: 2 + skip: True # [osx or py27] + +requirements: + run: + - python + - biopython ==1.69 + - blat ==35 + - snakemake ==4.3 + - openjdk + - argparse + - progressivemauve ==snapshot-2015-02-13 + +test: + commands: + - seq-seq-pan -h > /dev/null + - seq-seq-pan-wga --no-hooks --config workdir=$PREFIX/opt/seq-seq-pan/example/minimal genomefile=genome_list.txt outfilename=ssp_example -n > /dev/null + - java -jar $PREFIX/opt/seq-seq-pan/java/XMFAConsensus/XMFAconsensus_majorityvote.jar -h > /dev/null + - seq-seq-pan-consensus -h > /dev/null + - seq-seq-pan-genomedescription -h >/dev/null + +about: + home: https://gitlab.com/chrjan/seq-seq-pan + license: FreeBSDLicense + summary: seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment. diff --git a/recipes/seq-seq-pan/meta.yaml b/recipes/seq-seq-pan/meta.yaml index 9cc56efc2e081..7e833dfe3a09a 100644 --- a/recipes/seq-seq-pan/meta.yaml +++ b/recipes/seq-seq-pan/meta.yaml @@ -9,7 +9,7 @@ source: md5: 3d2b2c835d9a7f8412551e9462202c60 build: - number: 0 + number: 1 skip: True # [osx or py27] requirements: diff --git a/recipes/trumicount/meta.yaml b/recipes/trumicount/meta.yaml index 65592a4f0113e..afbf61c44dc86 100644 --- a/recipes/trumicount/meta.yaml +++ b/recipes/trumicount/meta.yaml @@ -16,6 +16,8 @@ requirements: host: - r-base - r-docopt + - r-data.table + - r-gwpcr >=0.9.9 run: - gawk >=4.0.0 - r-base diff --git a/recipes/xtail/meta.yaml b/recipes/xtail/meta.yaml index 3122d6d6bfc0a..dd6988ea4a47c 100644 --- a/recipes/xtail/meta.yaml +++ b/recipes/xtail/meta.yaml @@ -18,7 +18,7 @@ build: requirements: host: - bioconductor-genefilter - - 'bioconductor-deseq2 ==1.18.1' + - 'bioconductor-deseq2 >=1.18.1' - r-base - 'r-rcpp >=0.11.0' - r-rcpparmadillo @@ -32,7 +32,7 @@ requirements: - bioconductor-iranges - 'bioconductor-s4vectors >=0.9.25' - 'bioconductor-summarizedexperiment >=1.8.0' - - 'bioconductor-deseq2 ==1.18.1' + - 'bioconductor-deseq2 >=1.18.1' - r-base - r-ggplot2 - r-hmisc From 05e9458a1cf79ee10debd79b81ab25dc661f7b55 Mon Sep 17 00:00:00 2001 From: Maux82 Date: Wed, 31 Oct 2018 17:40:02 +0100 Subject: [PATCH 002/546] Update Moff to 2.0 (#11726) * ver. 2.0 * ver. 2.0 * fixing pymzml * moff2.0 recipe * Update meta.yaml * Update meta.yaml --- recipes/moff/build.sh | 2 -- recipes/moff/meta.yaml | 42 +++++++++++++++++++++++------------------- 2 files changed, 23 insertions(+), 21 deletions(-) diff --git a/recipes/moff/build.sh b/recipes/moff/build.sh index 38262fccd09ed..37c7df18385e6 100644 --- a/recipes/moff/build.sh +++ b/recipes/moff/build.sh @@ -4,6 +4,4 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir cp -r * $outdir -ln -s $outdir/moff_mbr.py $PREFIX/bin/moff_mbr.py -ln -s $outdir/moff.py $PREFIX/bin/moff.py ln -s $outdir/moff_all.py $PREFIX/bin/moff_all.py diff --git a/recipes/moff/meta.yaml b/recipes/moff/meta.yaml index 6f34ebbbe7c41..d0bd424099135 100644 --- a/recipes/moff/meta.yaml +++ b/recipes/moff/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "2.0.1" %} package: name: moff @@ -6,38 +6,42 @@ package: source: url: https://github.com/compomics/moFF/archive/{{ version }}.tar.gz - md5: 02cb8e42928337f27e2bf66a363991ff + md5: cd8176137643087622554efb2ef265ed build: - number: 1 - skip: True # [not py27] + number: 0 + skip: True # [py27 or py35] requirements: host: - - python - - pandas 0.20.* - - numpy >1.10.0 - - argparse >1.2.1 - - scikit-learn >0.18 - - pymzml >0.7.7 + - python + - pandas >=0.23.* + - numpy >=1.15.* + - scipy >=1.1.* + - scikit-learn >=0.19 + - pymzml - mono - - simplejson + - simplejson >=3.16.1 + - brain-isotopic-distribution + - pyteomics >=3.5 + - pymzml >=2.0.5 run: - python - - pandas 0.20.* - - numpy >1.10.0 - - argparse >1.2.1 - - scikit-learn >0.18 - - pymzml >0.7.7 + - pandas >=0.23.* + - numpy >=1.15.* + - scipy >=1.1.* + - scikit-learn >0.19 + - pymzml - mono - - simplejson + - simplejson >=3.16.1 + - brain-isotopic-distribution + - pyteomics >=3.5 + - pymzml >=2.0.5 test: commands: - - 'moff.py -h' - 'moff_all.py -h' - - 'moff_mbr.py -h' about: home: https://github.com/compomics/moFF From 656c17df01fbc42654114ce364c773968fadd5fb Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:50:08 -0600 Subject: [PATCH 003/546] Update pyensembl to 1.7.2 (#11685) --- recipes/pyensembl/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 1de08e41ffba1..c3d8cc76b3a9d 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "1.2.6" %} -{% set sha256 = "28a5b7dcd0c15ba3fbffb2e13120394d0f95f6968cbf6314ec71afebb3d981e7" %} +{% set version = "1.7.2" %} +{% set sha256 = "0e40b0963d0e2a2e54adf90e414d459edd4d5c623d5c0827d44a1365d2beb845" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: noarch: python - number: 2 + number: 0 script: python -m pip install --no-deps --ignore-installed . entry_points: - pyensembl = pyensembl.shell:run From d6ece5873c0d9111c71cab4a92d780ace397b876 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:51:25 -0600 Subject: [PATCH 004/546] Update arvados-python-client to 1.2.0.20180905185317 (#11684) --- recipes/arvados-python-client/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index e5038827ee385..44e74758c3246 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.1.20171211211613" %} +{% set version="1.2.0.20180905185317" %} package: name: arvados-python-client @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - md5: 192786588a3d82957c6ee3ee7f05574f + sha256: 87d79e15cbeb1659d4a44c3d844455c697a191d6fb9e3cef6c5eaf9a3af6ccc3 build: - number: 1 + number: 0 skip: True # [not py27] requirements: From 6b66632c2110a13a70e339a0874b6e28777e92a2 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:51:39 -0600 Subject: [PATCH 005/546] Update fitter to 1.0.8 (#11683) --- recipes/fitter/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/fitter/meta.yaml b/recipes/fitter/meta.yaml index 06a347b4cdb88..6f180d2a0314c 100644 --- a/recipes/fitter/meta.yaml +++ b/recipes/fitter/meta.yaml @@ -1,14 +1,14 @@ package: name: fitter - version: "1.0.4" + version: "1.0.8" source: - url: https://pypi.python.org/packages/source/f/fitter/fitter-1.0.4.tar.gz - md5: f9a5b0dea365750168ad08c94cf7ce10 + url: https://pypi.python.org/packages/source/f/fitter/fitter-1.0.8.tar.gz + sha256: 81ae27322a1644db239e56c9c30448d9b743a70962ebf8ac4544bdee07e65034 build: noarch: python - number: 1 + number: 0 requirements: host: From 66c4a0faa62e4f809424dcc00065b9da43ac1fe8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:51:49 -0600 Subject: [PATCH 006/546] Update atropos to 1.1.19 (#11681) --- recipes/atropos/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/atropos/meta.yaml b/recipes/atropos/meta.yaml index 3722e4aa804ba..ae12fcb123c4d 100644 --- a/recipes/atropos/meta.yaml +++ b/recipes/atropos/meta.yaml @@ -1,6 +1,6 @@ {% set name = "atropos" %} -{% set version = "1.1.18" %} -{% set hash = "424f10592db82da2503ff3709f05423cc110b249b0537152da245769ac3caab9" %} +{% set version = "1.1.19" %} +{% set hash = "297513f59574a5570a7477b9aacf9abe389790c144738bad93cf744b5099b010" %} package: name: {{ name }} @@ -16,7 +16,7 @@ about: summary: 'trim adapters from high-throughput sequencing reads' build: - number: 1 + number: 0 script: python -m pip install --no-deps --ignore-installed . skip: True # [py27] From cd3f794216a4579860814a5dff5509ceb96422b5 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:52:01 -0600 Subject: [PATCH 007/546] Update xyalign to 1.1.5 (#11680) --- recipes/xyalign/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/xyalign/meta.yaml b/recipes/xyalign/meta.yaml index e4381ea0df374..0de8484c8eb61 100644 --- a/recipes/xyalign/meta.yaml +++ b/recipes/xyalign/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.4" %} -{% set sha256 = "719eb9331efade6d487f750b131d404121e1b6a0cb5e7382ade7105eaf26c12d" %} +{% set version = "1.1.5" %} +{% set sha256 = "6cc607b4c6b45fcc4d95ad7051920aefe74ff33dcd2bc74a358c68d8543fffe3" %} package: name: xyalign From 07c815d8fe81d4c7173aee4f2444660f6208f4f1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:52:15 -0600 Subject: [PATCH 008/546] Update illumina-utils to 2.5 (#11677) --- recipes/illumina-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-utils/meta.yaml b/recipes/illumina-utils/meta.yaml index be046139a2b1c..e2ec2b9965f0e 100644 --- a/recipes/illumina-utils/meta.yaml +++ b/recipes/illumina-utils/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.4.1" %} +{% set version = "2.5" %} package: name: 'illumina-utils' @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/i/illumina-utils/illumina-utils-{{ version }}.tar.gz - sha256: 'a006cb66279f526b1627954022f032a43fc6500904894c40a0c814ffafa2e5b4' + sha256: '664f2c6a003afe4d424b5b16a14344e320dce3e226d6f8970b5abc65297aed44' build: number: 0 From 14ca7f6a4fac395136cd7f1812f8484c4f075ec0 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 10:52:29 -0600 Subject: [PATCH 009/546] Update toulligqc to 1.0 (#11675) --- recipes/toulligqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index 3f40a6f774cfd..d56a0761fa72f 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.10" %} -{% set sha256 = "4442bb5ee655487d643f86a5115d88bc2dd0ab457b746573ff482d505091cd3a" %} +{% set version = "1.0" %} +{% set sha256 = "285b50996f67961acf3ee1a9d6ce9aeb8200ff9adaa22f4ffadb5836b5ca276a" %} package: name: toulligqc From cc94fdba4a96b27172aeb0701c64cc71abe83333 Mon Sep 17 00:00:00 2001 From: Philippe Bordron Date: Wed, 31 Oct 2018 19:13:53 +0100 Subject: [PATCH 010/546] Fix some dependencies (#11725) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit With phyloseq 1.20: ̀``` Quitting from lines 74-113 (r_beta_diversity.Rmd) Error in .C(ape:::node_depth_edgelength, PACKAGE = "ape", as.integer(Ntip), : Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Calls: ... UniFrac -> fastUniFrac -> ape_node_depth_edge_length -> .C Execution halted ``` With vegan 2.5: ̀``` Quitting from lines 74-113 (r_beta_diversity.Rmd) Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N * : "veg_distance" not available for .C() for package "vegan" Calls: ... distance -> do.call -> do.call -> vegdist -> vegdist -> .C Execution halted ``` --- recipes/frogs/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/frogs/meta.yaml b/recipes/frogs/meta.yaml index c4165917a839e..a12f11b547a3d 100644 --- a/recipes/frogs/meta.yaml +++ b/recipes/frogs/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 skip: true # [py3k] source: @@ -36,9 +36,10 @@ requirements: - r-phangorn >=2.2.0 - pandoc <2.0 - r-rmarkdown >=1.5 - - bioconductor-phyloseq >=1.20.0 + - bioconductor-phyloseq >=1.22.0 - r-plotly >=4.7.1 - r-gridextra >=2.2.1 + - r-vegan <2.5 test: commands: From dc9b9a786853cfee6d12a894809c9676cdbdc799 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 12:20:11 -0600 Subject: [PATCH 011/546] Update card_trick to 0.1.2 (#11650) --- recipes/card_trick/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/card_trick/meta.yaml b/recipes/card_trick/meta.yaml index 363bab40a6631..cad7bff77858f 100644 --- a/recipes/card_trick/meta.yaml +++ b/recipes/card_trick/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.0" %} +{% set version = "0.1.2" %} package: name: card_trick @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/c/card-trick/card-trick-{{ version }}.tar.gz - sha256: ce42bde3570e19b459972b19f9c6a62d8714fd2f8cbb485d9e3e6d6af9260029 + sha256: 50929e592fe4f38fe10f3feca85692ed68e1000b11f1c7e10a58c4fe4d2c15cb build: noarch: python From 6f36caa7d13f78d1cbcf66c4501eccef0f5b2df9 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 31 Oct 2018 12:23:14 -0600 Subject: [PATCH 012/546] Update sbpipe to 4.21.0 (#11653) * Update sbpipe to 4.21.0 * fix maintainer --- recipes/sbpipe/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/sbpipe/meta.yaml b/recipes/sbpipe/meta.yaml index 8310730a3e788..bcbdbf017b12d 100644 --- a/recipes/sbpipe/meta.yaml +++ b/recipes/sbpipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sbpipe" %} -{% set version = "4.20.0" %} +{% set version = "4.21.0" %} {% set file_ext = "tar.gz" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} - sha256: c417db041e8990f41bc56101b7a4be7a861136bac67207dec47b83546ca26d50 + sha256: 5bd144975ac27697b59326e6d767505b28d5a1dbfa8db346f43d1ae2a8bdf205 build: noarch: python @@ -42,6 +42,6 @@ about: summary: SBpipe is a collection of pipelines for systems modelling of biological networks. It allows mathematical modellers to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. SBpipe can run models implemented in COPASI, Python or coded in any other programming language using Python as a wrapper module. Pipelines can run on multicore computers, Sun Grid Engine (SGE), Load Sharing Facility (LSF) clusters, or via Snakemake. extra: - recipe-maintainers: 'Piero Dalle Pezze' + recipe-maintainers: pdp10 identifiers: - doi:10.1186/s12918-017-0423-3 From f8e39cf22fbd989c8ff96a6017082811d5f4224f Mon Sep 17 00:00:00 2001 From: Federico Marini Date: Thu, 1 Nov 2018 01:15:58 +0100 Subject: [PATCH 013/546] adding iSEE (and one of its dependencies, scRNAseq) from R/Bioconductor (#8803) * added skeletons for both iSEE and scRNAseq, used in the examples and vignette * updated with new build system * specify r base version in recipe yaml * correct specification of version * linting the recipes by removing fn: field * removing version number of R, seem to be malformed? * specifying R version to build against * specifying R version to build against, both places --- recipes/bioconductor-isee/build.sh | 4 ++ recipes/bioconductor-isee/meta.yaml | 74 +++++++++++++++++++++ recipes/bioconductor-scrnaseq/meta.yaml | 33 +++++++++ recipes/bioconductor-scrnaseq/post-link.sh | 46 +++++++++++++ recipes/bioconductor-scrnaseq/pre-unlink.sh | 1 + 5 files changed, 158 insertions(+) create mode 100644 recipes/bioconductor-isee/build.sh create mode 100644 recipes/bioconductor-isee/meta.yaml create mode 100644 recipes/bioconductor-scrnaseq/meta.yaml create mode 100644 recipes/bioconductor-scrnaseq/post-link.sh create mode 100644 recipes/bioconductor-scrnaseq/pre-unlink.sh diff --git a/recipes/bioconductor-isee/build.sh b/recipes/bioconductor-isee/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-isee/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isee/meta.yaml b/recipes/bioconductor-isee/meta.yaml new file mode 100644 index 0000000000000..12eda85eab1db --- /dev/null +++ b/recipes/bioconductor-isee/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.0.1" %} +{% set name = "iSEE" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2b50c65a41fbb62f95f98375903af933504b0cab09ce785c5537259da3ee0fd7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-base >=3.5.1 + - r-colourpicker + - r-cowplot + - r-dplyr + - r-dt + - r-ggplot2 + - r-igraph + - r-mgcv + - r-rentrez + - r-reshape2 + - r-rintrojs + - r-scales + - r-shiny + - r-shinyace + - r-shinydashboard + - r-shinyjs + - r-vipor + - r-viridislite + run: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-base >=3.5.1 + - r-colourpicker + - r-cowplot + - r-dplyr + - r-dt + - r-ggplot2 + - r-igraph + - r-mgcv + - r-rentrez + - r-reshape2 + - r-rintrojs + - r-scales + - r-shiny + - r-shinyace + - r-shinydashboard + - r-shinyjs + - r-vipor + - r-viridislite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.' diff --git a/recipes/bioconductor-scrnaseq/meta.yaml b/recipes/bioconductor-scrnaseq/meta.yaml new file mode 100644 index 0000000000000..4379c1c1ccf31 --- /dev/null +++ b/recipes/bioconductor-scrnaseq/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.6.0" %} +{% set name = "scRNAseq" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c2272f78750ac96df37276483d3d11380d54354dbdcf0aa223b9e7d62ed04b54 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-summarizedexperiment + - r-base + run: + - bioconductor-summarizedexperiment + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: CC0 + summary: 'Gene-level read counts of three public scRNA-seq datasets. See vignette for details.' diff --git a/recipes/bioconductor-scrnaseq/post-link.sh b/recipes/bioconductor-scrnaseq/post-link.sh new file mode 100644 index 0000000000000..39176aa32189f --- /dev/null +++ b/recipes/bioconductor-scrnaseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="scRNAseq_1.6.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/scRNAseq_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/scRNAseq_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_1.6.0_src_all.tar.gz" +) +MD5="16591406c49256c925cbb666e25d19b5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-scrnaseq/pre-unlink.sh b/recipes/bioconductor-scrnaseq/pre-unlink.sh new file mode 100644 index 0000000000000..6285b7c9b4e81 --- /dev/null +++ b/recipes/bioconductor-scrnaseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ scRNAseq From 4fbd1385554428f331735215b1ddfeed4030e2e2 Mon Sep 17 00:00:00 2001 From: Huidong Chen Date: Wed, 31 Oct 2018 20:20:06 -0400 Subject: [PATCH 014/546] update stream to 0.3.0 (#11732) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * add bioconductor-chromvar recipe * update bioconductor-chromvar recipe * add r-nabor recipe * update r-nabor recipe * update bioconductor-chromvar recipe * update r-nabor recipe * update stream to 0.3.0 * update stream to 0.3.0 --- recipes/stream/meta.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/stream/meta.yaml b/recipes/stream/meta.yaml index 0957f2327e890..c2cb5ed00691e 100644 --- a/recipes/stream/meta.yaml +++ b/recipes/stream/meta.yaml @@ -1,20 +1,15 @@ package: name: stream - version: 0.2.6 + version: 0.3.0 source: url: https://github.com/pinellolab/STREAM/archive/stream_python3.zip - sha256: cbc8333f6d6bb6580abeae7717391d877bc374fcf11c8ad20a8bb2749b79c8d2 + sha256: 782e50c9f884fd4f88771a2b33b18a3c03500f51cdb1cadec2350c8141707f3d build: number: 0 skip: True # [py27] -about: - home: 'https://github.com/pinellolab/stream' - license: Affero - summary: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data - requirements: build: - python @@ -47,6 +42,7 @@ requirements: - shapely - networkx>=2.0 - gunicorn + - bioconductor-chromvar run: - r-base - r-xml @@ -75,8 +71,14 @@ requirements: - python-slugify - shapely - networkx>=2.0 - - gunicorn + - gunicorn + - bioconductor-chromvar test: imports: - stream + +about: + home: https://github.com/pinellolab/STREAM + license: Affero + summary: STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http://stream.pinellolab.org From 25e88dc4fd243957c801de1afed6379fc5c0e3cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Pedro=20Camargo?= Date: Wed, 31 Oct 2018 22:21:24 -0300 Subject: [PATCH 015/546] Add r-goeveg (#11734) * r-goeveg * Remove "fn" --- recipes/r-goeveg/build.sh | 1 + recipes/r-goeveg/meta.yaml | 41 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 recipes/r-goeveg/build.sh create mode 100644 recipes/r-goeveg/meta.yaml diff --git a/recipes/r-goeveg/build.sh b/recipes/r-goeveg/build.sh new file mode 100644 index 0000000000000..5bf492ab9fc06 --- /dev/null +++ b/recipes/r-goeveg/build.sh @@ -0,0 +1 @@ +$R CMD INSTALL --build . diff --git a/recipes/r-goeveg/meta.yaml b/recipes/r-goeveg/meta.yaml new file mode 100644 index 0000000000000..3ec4d5a786da1 --- /dev/null +++ b/recipes/r-goeveg/meta.yaml @@ -0,0 +1,41 @@ +{% set version = '0.3.3' %} + +package: + name: r-goeveg + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/goeveg_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/goeveg/goeveg_{{ version }}.tar.gz + sha256: 8620c9532b66bd77c72b8cedb81106b637ca845f680504c3ed3f81bc0373c6dc + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-fields + - r-mgcv + - r-vegan + run: + - r-base + - r-fields + - r-mgcv + - r-vegan + +test: + commands: + - $R -e "library('goeveg')" + +about: + home: http://github.com/fgoral/goeveg + license: GPL (>= 2) + summary: A collection of functions useful in (vegetation) community analyses and ordinations, + mainly to facilitate plotting and interpretation. Includes automatic species selection + for ordination diagrams, species response curves and rank-abundance curves. + license_family: GPL3 From 2cbea8072dbea1c2e4c4bb4bef33123d877b4a82 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Wed, 31 Oct 2018 22:46:24 -0400 Subject: [PATCH 016/546] Bump ksw version to 0.2.1 (#11731) --- recipes/ksw/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ksw/meta.yaml b/recipes/ksw/meta.yaml index 931d86d12b4d0..9df4e8f2da7bc 100644 --- a/recipes/ksw/meta.yaml +++ b/recipes/ksw/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ksw" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -10,7 +10,7 @@ build: source: url: https://github.com/nh13/ksw/releases/download/{{ version }}/{{ version }}.tar.gz - sha256: 1dca0be5f47558287ab9a397af02478fb48d359a910d29b6a457a582eea3825c + sha256: cf6dc8ce453a2670ae546a5ac270ec0d97092a5a8b29ab53d5846ea7aaf597ca requirements: build: From 3a1f34ee1fcf05280dfb4db8ead27470757614c1 Mon Sep 17 00:00:00 2001 From: Michael Knudsen Date: Thu, 1 Nov 2018 06:58:33 +0100 Subject: [PATCH 017/546] Bumped gatk4 version (#11738) --- recipes/gatk4/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml index f2481c48de308..9b146a0517f68 100644 --- a/recipes/gatk4/meta.yaml +++ b/recipes/gatk4/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "4.0.10.0" %} -{% set sha256 = "6a149750dfcdb250e07198cf1726d2f0958d2b8f257618b3b585194c4c392283" %} +{% set version = "4.0.11.0" %} +{% set sha256 = "5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536" %} package: name: gatk4 From 8ad5f8a743dce362a3229eb753f7aac7149aadc2 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Thu, 1 Nov 2018 05:57:09 -0400 Subject: [PATCH 018/546] Update: PureCN (1.13.1) with additional segmentation options (#11740) --- recipes/bioconductor-purecn/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index 6e01406e1ef97..e41c001e6f894 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,14 +1,14 @@ -{% set version = "1.11.20" %} +{% set version = "1.13.1" %} {% set name = "PureCN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: https://github.com/lima1/PureCN/archive/cdd2df3.tar.gz + url: https://github.com/lima1/PureCN/archive/de563d2.tar.gz #url: https://depot.galaxyproject.org/software/bioconductor-purecn/bioconductor-purecn_{{ version }}_src_all.tar.gz - sha256: 711861830f36d74f3db8d43aad7dd6e9c3aaaceaec28677cf29ad72643730863 + sha256: fd38af3a8b7e62e3280d5178040ece0ad4deb5e385ea9ff3126b088b95770308 build: number: 2 rpaths: @@ -18,6 +18,7 @@ requirements: host: - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-copynumber>=1.20.0,<1.22.0' - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' @@ -43,6 +44,7 @@ requirements: run: - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-copynumber>=1.20.0,<1.22.0' - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' From 7bc0b009e6581e681d193f7fda41a5b39fbef7a4 Mon Sep 17 00:00:00 2001 From: nh3 Date: Thu, 1 Nov 2018 12:20:29 +0000 Subject: [PATCH 019/546] Update scanpy-scripts to v0.0.3 (#11743) * Update to scanpy-scripts to v0.0.3 --- recipes/scanpy-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 985f849167008..939d849976c70 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.0.2' %} +{% set version = '0.0.3' %} package: name: scanpy-scripts @@ -6,7 +6,7 @@ package: source: url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/v{{ version }}.tar.gz - sha256: 4d9d3193857e5f801540236db547aa91db6c1db47c43943915f130c4fa8a31b2 + sha256: 5d00666986d933d0bcddfdbef24cba86decf1ae5bf46df71fe53e87fc701ac71 build: number: 0 From d369e5c6b0c8bdb26f27b87f5c0253c5f10bb4d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C5=BDiga=20Avsec?= Date: Thu, 1 Nov 2018 14:46:42 +0100 Subject: [PATCH 020/546] update kipoi to 0.5.7 (#11744) * update kipoi * using the old hack of first installing the deps --- recipes/kipoi/meta.yaml | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/recipes/kipoi/meta.yaml b/recipes/kipoi/meta.yaml index 7f251f73ba822..3b2cfc966ab8e 100644 --- a/recipes/kipoi/meta.yaml +++ b/recipes/kipoi/meta.yaml @@ -1,29 +1,27 @@ {% set name = "kipoi" %} -{% set version = "0.3.6" %} +{% set version = "0.5.7" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "6a2482e91c4fd168411bfb5c8c5ad7833669f6c02ad2af8f3ec21cac06541302" %} +{% set hash_value = "8471eaaf0cafa6b5cd62b6831f4a1d0bf0ef49440510237b07fca7d4233631cb" %} package: name: '{{ name|lower }}' version: '{{ version }}' source: - fn: '{{ name }}-{{ version }}.{{ file_ext }}' url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} '{{ hash_type }}': '{{ hash_value }}' build: - number: 1 + number: 0 entry_points: - kipoi = kipoi.__main__:main script: pip install 'related>=0.6.0' enum34 epc && python setup.py install --single-version-externally-managed --record=record.txt + noarch: python requirements: build: - git-lfs - - gcc # [not osx] - - llvm # [osx] - python - pip - setuptools @@ -32,13 +30,13 @@ requirements: - numpy - pandas - tqdm -# - related >=0.6.0 -# - enum34 + # - related >=0.6.0 + # - enum34 - colorlog - cookiecutter - h5py + - urllib3 >=1.21.1,<1.23 run: - - libgcc # [not osx] - git-lfs - python - pyyaml @@ -46,11 +44,12 @@ requirements: - numpy - pandas - tqdm -# - related >=0.6.0 -# - enum34 + # - related >=0.6.0 + # - enum34 - colorlog - cookiecutter - h5py + - urllib3 >=1.21.1,<1.23 test: imports: @@ -59,9 +58,6 @@ test: - kipoi.external - kipoi.external.related - kipoi.external.torch - - kipoi.postprocessing - - kipoi.postprocessing.variant_effects - - kipoi.postprocessing.variant_effects.utils commands: - "kipoi --help" requires: From beaecb93922e592834d63e16d132df577b42158e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C5=BDiga=20Avsec?= Date: Thu, 1 Nov 2018 15:25:54 +0100 Subject: [PATCH 021/546] Add kipoi_veff (#11745) * update kipoi * using the old hack of first installing the deps * added kipoi_veff * add kipoi_veff * add noarch: python * remove kipoiseq --- recipes/kipoi_veff/meta.yaml | 103 +++++++++++++++++++++++++++++++++++ 1 file changed, 103 insertions(+) create mode 100644 recipes/kipoi_veff/meta.yaml diff --git a/recipes/kipoi_veff/meta.yaml b/recipes/kipoi_veff/meta.yaml new file mode 100644 index 0000000000000..98af99c1e2f83 --- /dev/null +++ b/recipes/kipoi_veff/meta.yaml @@ -0,0 +1,103 @@ +{% set name = "kipoi_veff" %} +{% set version = "0.1.2" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "385a11320fc4db43d61f0462aa79045baebe03f68821ead5002f6b47fcd2a861" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' + +build: + number: 0 + script: python setup.py install --single-version-externally-managed --record=record.txt + noarch: python + +requirements: + build: + - python + - setuptools + - kipoi >=0.5.5 + - pyvcf + - cyvcf2 + - pybedtools + - pysam + - intervaltree + - deepdish + - matplotlib + - seaborn + - shapely + - descartes + - future + - numpy + - pandas + - tqdm + # Provided by kipoi + # - related >=0.6.0 + # - enum34 + - colorlog + - cookiecutter + - h5py + - urllib3 >=1.21.1,<1.23 + run: + - python + - kipoi >=0.5.5 + - pyvcf + - cyvcf2 + - pybedtools + - pysam + - intervaltree + - deepdish + - matplotlib + - seaborn + - shapely + - descartes + - future + - numpy + - pandas + - tqdm + # - related >=0.6.0 + # - enum34 + - colorlog + - cookiecutter + - h5py + - urllib3 >=1.21.1,<1.23 + +test: + imports: + - kipoi_veff + - kipoi_veff.external + - kipoi_veff.external.concise + - kipoi_veff.utils + commands: + - "kipoi veff --help" + requires: + # - bumpversion + # - coveralls + # - cython + # - epc + # - jedi + # - keras + # - pytest >=3.3.1 + # - pytest-cov + # - pytest-pep8 + # - pytest-xdist + # - scikit-learn + # - tensorflow + # - wheel + +about: + home: https://github.com/kipoi/kipoi-veff + license: MIT license + license_family: MIT + summary: 'kipoi_veff: variant effect prediction plugin for Kipoi' + description: 'kipoi_veff: variant effect prediction plugin for Kipoi' + doc_url: 'https://kipoi.org/veff-docs/' + +extra: + recipe-maintainers: + - Avsecz From b7ad649b1157a5c4f7efc0c1f624d6f6ffda3e56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C5=BDiga=20Avsec?= Date: Thu, 1 Nov 2018 17:10:42 +0100 Subject: [PATCH 022/546] Add kipoiseq (#11746) * update kipoi * using the old hack of first installing the deps * added kipoi_veff * add kipoi_veff * add noarch: python * remove kipoiseq * Add kipoiseq --- recipes/kipoiseq/meta.yaml | 80 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 recipes/kipoiseq/meta.yaml diff --git a/recipes/kipoiseq/meta.yaml b/recipes/kipoiseq/meta.yaml new file mode 100644 index 0000000000000..8f369783d9329 --- /dev/null +++ b/recipes/kipoiseq/meta.yaml @@ -0,0 +1,80 @@ +{% set name = "kipoiseq" %} +{% set version = "0.2.2" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "c6e62520a46c010fcfb0a7b807e7c84fbe880e61a9a2665ace397f9fb421ec75" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' + + +build: + number: 0 + script: python setup.py install --single-version-externally-managed --record=record.txt + noarch: python + +requirements: + build: + - python + - setuptools + - kipoi >=0.5.5 + - pybedtools + - pyfaidx + - genomelake + - numpy + - pandas + - tqdm + - gffutils + run: + - python + - kipoi >=0.5.5 + - pybedtools + - pyfaidx + - genomelake + - numpy + - pandas + - tqdm + - gffutils + +test: + imports: + - kipoiseq + - kipoiseq.dataloaders + - kipoiseq.transforms + requires: + # - bumpversion + # - coveralls + # - cython + # - epc + # - jedi + # - keras + # - pybedtools + # - pytest >=3.3.1 + # - pytest-cov + # - pytest-pep8 + # - pytest-xdist + # - scikit-learn + # - tensorflow + # - wheel + +about: + home: https://github.com/kipoi/kipoiseq + license: MIT license + license_family: MIT + summary: 'kipoiseq: sequence-based data-laoders for Kipoi' + description: 'kipoiseq: sequence-based data-laoders for Kipoi' + doc_url: 'https://kipoi.org/kipoiseq/' + +extra: + recipe-maintainers: + - Avsecz + + + + + From 127f66575fc7d9af259f6facf45319777b9758d0 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Thu, 1 Nov 2018 12:48:33 -0400 Subject: [PATCH 023/546] Add bcftools affy2vcf version 1.9 plugin (#11382) --- .../1.9/affy2vcf.c.patch | 119 +++++ recipes/bcftools-gtc2vcf-plugin/1.9/build.sh | 35 ++ .../1.9/fixref.c.patch | 107 +++++ .../1.9/gtc2vcf.c.patch | 410 ++++++++++++++++++ recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml | 55 +++ 5 files changed, 726 insertions(+) create mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch create mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/build.sh create mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch create mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch create mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch b/recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch new file mode 100644 index 0000000000000..ec89a7b984274 --- /dev/null +++ b/recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch @@ -0,0 +1,119 @@ +--- gtc2vcf-b890909/affy2vcf.c.orig 2018-10-11 10:20:20.163766095 -0400 ++++ gtc2vcf-b890909/affy2vcf.c 2018-10-11 10:22:47.924639141 -0400 +@@ -192,7 +192,8 @@ + + int moff = 0, *off = NULL; + int ncols = ksplit_core(str.s, ',', &moff, &off); +- for (int i=0; iprobeset_id); +- for (int i=0; in_records; i++) ++ int i; ++ for (i=0; in_records; i++) + { + free(annot->records[i].probe_set); + free(annot->records[i].dbsnp); +@@ -297,7 +299,8 @@ + + static void report_destroy(report_t *report) + { +- for (int i=0; in_samples; i++) free(report->cel_files[i]); ++ int i; ++ for (i=0; in_samples; i++) free(report->cel_files[i]); + free(report->genders); + } + +@@ -309,7 +312,8 @@ + { + bcf_hdr_t *hdr = bcf_hdr_init("w"); + int n = faidx_nseq(fai); +- for (int i=0; iab_delta ) + { +@@ -393,7 +398,8 @@ + ncols = ksplit_core(str.s, '\t', &moff, &off); + if ( strcmp(&str.s[off[0]], "probeset_id") ) error("Malformed first line from summary file: %s\n%s\n", summary_fn, str.s); + +- for (int i=1; in_samples; i++) fprintf(sex_fh, "%s\t%d\n", report->cel_files[i], report->genders[i]); ++ int i; ++ for (i=0; in_samples; i++) fprintf(sex_fh, "%s\t%d\n", report->cel_files[i], report->genders[i]); + fclose(sex_fh); + report_destroy(report); + } +@@ -650,4 +658,4 @@ + bcf_hdr_destroy(hdr); + hts_close(out_fh); + return 0; +-} +\ No newline at end of file ++} diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh b/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh new file mode 100644 index 0000000000000..4b4b793ce661c --- /dev/null +++ b/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh @@ -0,0 +1,35 @@ +#!/bin/sh + +export VERSION=1.9 +export C_INCLUDE_PATH=${PREFIX}/include +export CPP_INCLUDE_PATH=${PREFIX}/include +export CXX_INCLUDE_PATH=${PREFIX}/include +export CPLUS_INCLUDE_PATH=${PREFIX}/include +export LIBRARY_PATH=${PREFIX}/lib +export CPPFLAGS="$CPPFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export CFLAGS="$CFLAGS -I$PREFIX/include" + +mkdir -p $PREFIX/bin +mkdir -p $PREFIX/libexec/bcftools + +# Copy plugin source to the bcftools plugin directory. +cp gtc2vcf-b890909/affy2vcf.c bcftools-$VERSION/plugins/ +cp gtc2vcf-b890909/gtc2vcf.c bcftools-$VERSION/plugins/ + +# Compile htslib and bcftools with affy2vcf and gtc2vcf plugins. +pushd htslib-$VERSION +autoheader +(autoconf || autoconf) +./configure --disable-bz2 --disable-lzma --prefix=$PREFIX +make +popd + +pushd bcftools-$VERSION +make +popd + +# Move custom bcftools plugins to the ~/libexec/bcftools directory. +mv bcftools-$VERSION/plugins/affy2vcf.so $PREFIX/libexec/bcftools/ +mv bcftools-$VERSION/plugins/fixref.so $PREFIX/libexec/bcftools/ +mv bcftools-$VERSION/plugins/gtc2vcf.so $PREFIX/libexec/bcftools/ diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch b/recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch new file mode 100644 index 0000000000000..473e19023a8c0 --- /dev/null +++ b/recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch @@ -0,0 +1,107 @@ +--- bcftools-1.9/plugins/fixref.c.orig 2018-06-30 03:48:02.000000000 -0400 ++++ bcftools-1.9/plugins/fixref.c 2018-10-03 09:03:07.270160080 -0400 +@@ -90,6 +90,7 @@ + #define MODE_TOP2FWD 2 + #define MODE_FLIP2FWD 3 + #define MODE_USE_ID 4 ++#define MODE_SWAP 6 + + typedef struct + { +@@ -104,12 +105,14 @@ + typedef struct + { + char *dbsnp_fname; +- int mode, discard; ++ int mode, discard, flip_baf; + bcf_hdr_t *hdr; + faidx_t *fai; + int rid, skip_rid; + i2m_t *i2m; + int32_t *gts, ngts, pos; ++ float *bafs; ++ int32_t nbafs; + uint32_t nsite,nok,nflip,nunresolved,nswap,nflip_swap,nonSNP,nonACGT,nonbiallelic; + uint32_t count[4][4], npos_err, unsorted; + } +@@ -130,6 +133,7 @@ + " Currently the following modes are recognised:\n" + " flip .. flips non-ambiguous SNPs and ignores the rest\n" + " id .. swap REF/ALT and GTs using the ID column to determine the REF allele\n" ++ " swap .. swap REF/ALT columns and GTs and ignore the rest\n" + " stats .. collect and print stats\n" + " top .. converts from Illumina TOP strand to fwd\n" + "\n" +@@ -148,7 +152,8 @@ + " -i, --use-id Swap REF/ALT using the ID column to determine the REF allele, implies -m id.\n" + " Download the dbSNP file from\n" + " https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf\n" +- " -m, --mode Collect stats (\"stats\") or convert (\"flip\", \"id\", \"top\") [stats]\n" ++ " -m, --mode Collect stats (\"stats\") or convert (\"flip\", \"id\", \"swap\", \"top\") [stats]\n" ++ " -b --flip-baf Flip BAF when swapping genotypes\n" + "\n" + "Examples:\n" + " # run stats\n" +@@ -178,10 +183,11 @@ + {"discard",no_argument,NULL,'d'}, + {"fasta-ref",required_argument,NULL,'f'}, + {"use-id",required_argument,NULL,'i'}, ++ {"flip-baf",no_argument,NULL,'b'}, + {NULL,0,NULL,0} + }; + int c; +- while ((c = getopt_long(argc, argv, "?hf:m:di:",loptions,NULL)) >= 0) ++ while ((c = getopt_long(argc, argv, "?hf:m:di:b:",loptions,NULL)) >= 0) + { + switch (c) + { +@@ -190,11 +196,13 @@ + else if ( !strcasecmp(optarg,"flip") ) args.mode = MODE_FLIP2FWD; + else if ( !strcasecmp(optarg,"id") ) args.mode = MODE_USE_ID; + else if ( !strcasecmp(optarg,"stats") ) args.mode = MODE_STATS; ++ else if ( !strcasecmp(optarg,"swap") ) args.mode = MODE_SWAP; + else error("The source strand convention not recognised: %s\n", optarg); + break; + case 'i': args.dbsnp_fname = optarg; args.mode = MODE_USE_ID; break; + case 'd': args.discard = 1; break; + case 'f': ref_fname = optarg; break; ++ case 'b': args.flip_baf = 1; break; + case 'h': + case '?': + default: error("%s", usage()); break; +@@ -231,6 +239,13 @@ + } + } + bcf_update_genotypes(args->hdr,rec,args->gts,args->ngts); ++ ++ if (args->flip_baf && bcf_get_format_float(args->hdr, rec, "BAF", &args->bafs, &args->nbafs) >= 0) ++ { ++ float *ptr = args->bafs; ++ for (i=0; inbafs; i++, ptr++) *ptr = 1 - *ptr; ++ bcf_update_format_float(args->hdr, rec, "BAF", args->bafs, args->nbafs); ++ } + + return rec; + } +@@ -430,6 +445,13 @@ + if ( ir==revint(ib) ) { args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),1); } + error("FIXME: this should not happen %s:%d\n", bcf_seqname(args.hdr,rec),rec->pos+1); + } ++ else if ( args.mode==MODE_SWAP ) ++ { ++ if ( ir==ia ) return ret; ++ if ( ir==ib ) { args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),1); } ++ args.nunresolved++; ++ return args.discard ? NULL : ret; ++ } + else if ( args.mode==MODE_TOP2FWD ) + { + int pair = 1 << ia | 1 << ib; +@@ -567,6 +589,7 @@ + fprintf(stderr,"NS\tnon-biallelic\t%u\n", args.nonbiallelic); + + free(args.gts); ++ free(args.bafs); + if ( args.fai ) fai_destroy(args.fai); + if ( args.i2m ) kh_destroy(i2m, args.i2m); + } diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch b/recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch new file mode 100644 index 0000000000000..fd43df0fc62b6 --- /dev/null +++ b/recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch @@ -0,0 +1,410 @@ +--- gtc2vcf-b890909/gtc2vcf.c.orig 2018-10-11 10:31:54.875895471 -0400 ++++ gtc2vcf-b890909/gtc2vcf.c 2018-10-11 10:55:39.935944745 -0400 +@@ -66,7 +66,8 @@ + else + { + int c = 0; +- for (int i=0; ifp, (void *)&idat->m_run_infos, sizeof(int32_t)); + idat->run_infos = (RunInfo *)malloc(idat->m_run_infos * sizeof(RunInfo)); +- for (int i=0; im_run_infos; i++) ++ for (i=0; im_run_infos; i++) + { + read_pfx_string(idat->fp, &idat->run_infos[i].run_time, NULL); + read_pfx_string(idat->fp, &idat->run_infos[i].block_type, NULL); +@@ -329,13 +331,14 @@ + read_bytes(idat->fp, (void *)&idat->number_toc_entries, sizeof(int32_t)); + idat->id = (uint16_t *)malloc(idat->number_toc_entries * sizeof(uint16_t)); + idat->toc = (int64_t *)malloc(idat->number_toc_entries * sizeof(int64_t)); +- for (int i=0; inumber_toc_entries; i++) ++ int i; ++ for (i=0; inumber_toc_entries; i++) + { + read_bytes(idat->fp, (void *)&idat->id[i], sizeof(uint16_t)); + read_bytes(idat->fp, (void *)&idat->toc[i], sizeof(int64_t)); + } + +- for (int i=0; inumber_toc_entries; i++) idat_read(idat, idat->id[i]); ++ for (i=0; inumber_toc_entries; i++) idat_read(idat, idat->id[i]); + + return idat; + } +@@ -358,7 +361,8 @@ + free(idat->unknown5); + free(idat->unknown6); + free(idat->unknown7); +- for (int i=0; im_run_infos; i++) ++ int i; ++ for (i=0; im_run_infos; i++) + { + free(idat->run_infos[i].run_time); + free(idat->run_infos[i].block_type); +@@ -402,7 +406,8 @@ + fprintf(stream, "Mid Blocks Count ,%d\n", idat->mid_block->item_num); + fprintf(stream, "[Assay]\n"); + fprintf(stream, "IlmnID,Sd,Mean,Nbeads\n"); +- for (int i=0; inum_snps; i++) ++ int i; ++ for (i=0; inum_snps; i++) + { + int32_t ilmn_id; + get_element(idat->ilmn_id, (void *)&ilmn_id, i); +@@ -415,14 +420,14 @@ + fprintf(stream, "%d,%d,%d,%d\n", ilmn_id, sd, mean, nbeads); + } + fprintf(stream, "[Mid Blocks]\n"); +- for (int i=0; imid_block->item_num; i++) ++ for (i=0; imid_block->item_num; i++) + { + int8_t mid_block; + get_element(idat->mid_block, (void *)&mid_block, i); + fprintf(stream, "%d\n", mid_block); + } + fprintf(stream, "[Run Infos]\n"); +- for (int i=0; im_run_infos; i++) ++ for (i=0; im_run_infos; i++) + { + fprintf(stream, "%s\t%s\t%s\t%s\t%s\n", idat->run_infos[i].run_time, idat->run_infos[i].block_type, + idat->run_infos[i].block_pars, idat->run_infos[i].block_code, idat->run_infos[i].code_version); +@@ -546,17 +551,18 @@ + static uint8_t *bpm_norm_lookups(bpm_t *bpm) + { + uint8_t sorted_norm_ids[256]; +- for (int i=0; i<256; i++) sorted_norm_ids[i] = 0xFF; +- for (int i=0; inum_loci; i++) ++ int i; ++ for (i=0; i<256; i++) sorted_norm_ids[i] = 0xFF; ++ for (i=0; inum_loci; i++) + { + int norm_id = bpm->locus_entries[i].norm_id; + sorted_norm_ids[norm_id] = norm_id; + } + int j=0; +- for (int i=0; i<256; i++) if ( sorted_norm_ids[i] != 0xFF ) sorted_norm_ids[j++] = sorted_norm_ids[i]; ++ for (i=0; i<256; i++) if ( sorted_norm_ids[i] != 0xFF ) sorted_norm_ids[j++] = sorted_norm_ids[i]; + uint8_t *norm_lookups = (uint8_t *)malloc(256 * sizeof(uint8_t *)); + memset((void *)norm_lookups, 0xFF, 256 * sizeof(uint8_t *)); +- for (int i=0; ifp, (void *)&bpm->num_loci, sizeof(int32_t)); + read_array(bpm->fp, (void **)&bpm->indexes, NULL, bpm->num_loci, sizeof(int32_t), 0); + bpm->names = (char **)malloc(bpm->num_loci * sizeof(char *)); +- for (int i=0; inum_loci; i++) read_pfx_string(bpm->fp, &bpm->names[i], NULL); ++ int i; ++ for (i=0; inum_loci; i++) read_pfx_string(bpm->fp, &bpm->names[i], NULL); + read_array(bpm->fp, (void **)&bpm->norm_ids, NULL, bpm->num_loci, sizeof(uint8_t), 0); + + bpm->locus_entries = (LocusEntry *)malloc(bpm->num_loci * sizeof(LocusEntry)); + LocusEntry locus_entry; +- for (int i=0; inum_loci; i++) ++ for (i=0; inum_loci; i++) + { + memset(&locus_entry, 0, sizeof(LocusEntry)); + locusentry_read(&locus_entry, bpm->fp); +@@ -599,14 +606,14 @@ + memcpy(&bpm->locus_entries[ idx ], &locus_entry, sizeof(LocusEntry)); + } + bpm->norm_lookups = bpm_norm_lookups(bpm); +- for (int i=0; inum_loci; i++) ++ for (i=0; inum_loci; i++) + { + if ( i != bpm->locus_entries[i].index - 1 ) error("Manifest format error: read invalid number of assay entries\n"); + } + + read_bytes(bpm->fp, (void *)&bpm->m_header, sizeof(int32_t)); + bpm->header = (char **)malloc(bpm->m_header * sizeof(char *)); +- for (int i=0; im_header; i++) read_pfx_string(bpm->fp, &bpm->header[i], NULL); ++ for (i=0; im_header; i++) read_pfx_string(bpm->fp, &bpm->header[i], NULL); + + if ( !heof(bpm->fp) ) error("BPM reader did not reach the end of file %s at position %ld\n", bpm->fn, htell(bpm->fp)); + +@@ -621,13 +628,14 @@ + free(bpm->manifest_name); + free(bpm->control_config); + free(bpm->indexes); ++ int i; + if ( bpm->names ) + { +- for (int i=0; inum_loci; i++) free(bpm->names[i]); ++ for (i=0; inum_loci; i++) free(bpm->names[i]); + free(bpm->names); + } + free(bpm->norm_ids); +- for (int i=0; inum_loci; i++) ++ for (i=0; inum_loci; i++) + { + free(bpm->locus_entries[i].ilmn_id); + free(bpm->locus_entries[i].name); +@@ -650,7 +658,7 @@ + } + free(bpm->locus_entries); + free(bpm->norm_lookups); +- for (int i=0; im_header; i++) free(bpm->header[i]); ++ for (i=0; im_header; i++) free(bpm->header[i]); + free(bpm->header); + free(bpm); + } +@@ -664,9 +672,10 @@ + + static void bpm_to_csv(const bpm_t *bpm, FILE *stream) + { +- for (int i=0; im_header; i++) fprintf(stream, "%s\n", bpm->header[i]); ++ int i; ++ for (i=0; im_header; i++) fprintf(stream, "%s\n", bpm->header[i]); + fprintf(stream, "Index,NormID,IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID,Exp_Clusters,Intensity_Only,Assay_Type,Frac A,Frac C,Frac G,Frac T,RefStrand\n"); +- for (int i=0; inum_loci; i++) ++ for (i=0; inum_loci; i++) + { + LocusEntry *locus_entry = &bpm->locus_entries[i]; + fprintf(stream, "%d,%d,%s,%s,%s,%s,%010d,,%010d,,%s,%s,%s,%s,%s,%s,,%s,,,,%d,%d,%d,%f,%f,%f,%f,%s\n", +@@ -813,7 +822,8 @@ + int moff = 0, *off = NULL; + bpm->m_header = ksplit_core(str.s, '\n', &moff, &off); + bpm->header = (char **)malloc(bpm->m_header * sizeof(char *)); +- for (int i=0; im_header; i++) bpm->header[i] = strdup(&str.s[off[i]]); ++ int i; ++ for (i=0; im_header; i++) bpm->header[i] = strdup(&str.s[off[i]]); + free(off); + + str.l = 0; +@@ -851,7 +861,7 @@ + tsv_register(tsv, "RefStrand", tsv_read_string, &locus_entry.ref_strand); + + bpm->locus_entries = (LocusEntry *)malloc(bpm->num_loci * sizeof(LocusEntry)); +- for (int i=0; inum_loci; i++) ++ for (i=0; inum_loci; i++) + { + memset(&locus_entry, 0, sizeof(LocusEntry)); + locus_entry.norm_id = 0xFF; +@@ -959,6 +969,7 @@ + egt_t *egt = (egt_t *)calloc(1, sizeof(egt_t)); + egt->fn = strdup(fn); + egt->fp = hopen(egt->fn, "rb"); ++ int i; + if ( egt->fp == NULL ) error("Could not open %s\n", egt->fn); + if ( is_gzip(egt->fp) ) error("File %s is gzip compressed and currently cannot be seeked\n", egt->fn); + +@@ -982,21 +993,21 @@ + + read_bytes(egt->fp, (void *)&egt->num_records, sizeof(int32_t)); + egt->cluster_records = (ClusterRecord *)malloc(egt->num_records * sizeof(ClusterRecord)); +- for (int i=0; inum_records; i++) clusterrecord_read(&egt->cluster_records[i], egt->fp); +- for (int i=0; inum_records; i++) clusterscore_read(&egt->cluster_records[i].cluster_score, egt->fp); ++ for (i=0; inum_records; i++) clusterrecord_read(&egt->cluster_records[i], egt->fp); ++ for (i=0; inum_records; i++) clusterscore_read(&egt->cluster_records[i].cluster_score, egt->fp); + + // toss useless strings such as aa_ab_bb/aa_ab/aa_bb/ab_bb +- for (int i=0; inum_records; i++) read_pfx_string(egt->fp, NULL, NULL); ++ for (i=0; inum_records; i++) read_pfx_string(egt->fp, NULL, NULL); + + egt->loci_names = (char **)malloc(egt->num_records * sizeof(char *)); +- for (int i=0; inum_records; i++) ++ for (i=0; inum_records; i++) + { + read_pfx_string(egt->fp, &egt->loci_names[i], NULL); + } +- for (int i=0; inum_records; i++) read_bytes(egt->fp, (void *)&egt->cluster_records[i].address, sizeof(int32_t)); ++ for (i=0; inum_records; i++) read_bytes(egt->fp, (void *)&egt->cluster_records[i].address, sizeof(int32_t)); + + int32_t aa_n, ab_n, bb_n; +- for (int i=0; inum_records; i++) ++ for (i=0; inum_records; i++) + { + read_bytes(egt->fp, (void *)&aa_n, sizeof(int32_t)); + read_bytes(egt->fp, (void *)&ab_n, sizeof(int32_t)); +@@ -1025,7 +1036,8 @@ + free(egt->date_created); + free(egt->manifest_name); + free(egt->cluster_records); +- for (int i=0; inum_records; i++) free(egt->loci_names[i]); ++ int i; ++ for (i=0; inum_records; i++) free(egt->loci_names[i]); + free(egt->loci_names); + free(egt); + } +@@ -1056,7 +1068,8 @@ + fprintf(stream, "Records Count ,%d\n", egt->num_records); + fprintf(stream, "[Assay]\n"); + fprintf(stream, "Name,AA.N,AA.R_dev,AA.R_mean,AA.Theta_dev,AA.Theta_mean,AB.N,AB.R_dev,AB.R_mean,AB.Theta_dev,AB.Theta_mean,BB.N,BB.R_dev,BB.R_mean,BB.Theta_dev,BB.Theta_mean,Intensity Threshold,Cluster Separation,GenTrain Score,Original Score,Edited,Address\n"); +- for (int i=0; inum_records; i++) ++ int i; ++ for (i=0; inum_records; i++) + { + ClusterRecord *cluster_record = &egt->cluster_records[i]; + fprintf(stream, "%s,%d,%f,%f,%f,%f,%d,%f,%f,%f,%f,%d,%f,%f,%f,%f,%f,%f,%f,%f,%d,%d\n", +@@ -1341,17 +1354,18 @@ + read_bytes(gtc->fp, (void *)>c->number_toc_entries, sizeof(int32_t)); + gtc->id = (uint16_t *)malloc(gtc->number_toc_entries * sizeof(uint16_t)); + gtc->toc = (int32_t *)malloc(gtc->number_toc_entries * sizeof(int32_t)); +- for (int i=0; inumber_toc_entries; i++) ++ int i; ++ for (i=0; inumber_toc_entries; i++) + { + read_bytes(gtc->fp, (void *)>c->id[i], sizeof(uint16_t)); + read_bytes(gtc->fp, (void *)>c->toc[i], sizeof(int32_t)); + } + +- for (int i=0; inumber_toc_entries; i++) gtc_read(gtc, gtc->id[i]); ++ for (i=0; inumber_toc_entries; i++) gtc_read(gtc, gtc->id[i]); + + gtc->sin_theta = (float *)malloc(gtc->m_normalization_transforms * sizeof(float)); + gtc->cos_theta = (float *)malloc(gtc->m_normalization_transforms * sizeof(float)); +- for (int i=0; im_normalization_transforms; i++) ++ for (i=0; im_normalization_transforms; i++) + { + gtc->sin_theta[i] = sinf(gtc->normalization_transforms[i].theta); + gtc->cos_theta[i] = cosf(gtc->normalization_transforms[i].theta); +@@ -1450,7 +1464,8 @@ + fprintf(stream, "SNP Count ,%d\n", gtc->num_snps); + fprintf(stream, "[Assay]\n"); + fprintf(stream, "Raw X,Raw Y,GType,Top Alleles,Score,B Allele Freq,Log R Ratio\n"); +- for (int i=0; inum_snps; i++) ++ int i; ++ for (i=0; inum_snps; i++) + { + uint16_t raw_x = 0, raw_y = 0; + get_element(gtc->raw_x, (void *)&raw_x, i); +@@ -1468,7 +1483,7 @@ + } + fprintf(stream, "[Normalization Transforms]\n"); + fprintf(stream, "Version,Offset X,Offset Y,Scale X,Scale Y,Shear,Theta\n"); +- for (int i=0; im_normalization_transforms; i++) ++ for (i=0; im_normalization_transforms; i++) + { + fprintf(stream, "%d,%f,%f,%f,%f,%f,%f\n", + gtc->normalization_transforms[i].version, +@@ -1595,11 +1610,13 @@ + { + // print header + fprintf(stream, "Index\tName\tAddress\tChr\tPosition\tGenTrain Score\tFrac A\tFrac C\tFrac G\tFrac T"); +- for (int i=0; isample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name); ++ int i; ++ for (i=0; isample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name); + fprintf(stream, "\n"); + + // print loci +- for (int j=0; jnum_loci; j++) ++ int j; ++ for (j=0; jnum_loci; j++) + { + fprintf(stream, "%d\t%s\t%d\t%s\t%s\t%f\t%f\t%f\t%f\t%f", bpm->indexes[j], + bpm->names[j], +@@ -1611,7 +1628,7 @@ + bpm->locus_entries[j].frac_c, + bpm->locus_entries[j].frac_g, + bpm->locus_entries[j].frac_t); +- for (int i=0; igenotypes, (void *)&genotype, j); +@@ -1663,7 +1680,8 @@ + { + bcf_hdr_t *hdr = bcf_hdr_init("w"); + int n = faidx_nseq(fai); +- for (int i=0; inum_loci; j++) ++ int j; ++ for (j=0; jnum_loci; j++) + { + bcf_clear(rec); + rec->rid = bcf_hdr_name2id_flexible(hdr, bpm->locus_entries[j].chrom); +@@ -1721,7 +1740,8 @@ + b_top[0] = revnt(b_top[0]); + } + bcf_update_alleles(hdr, rec, alleles, 2); +- for (int i=0; igenotypes, (void *)&genotype, j); +@@ -1927,7 +1947,8 @@ + int moff = 0, *off = NULL, ncols = ksplit_core(line.s, '\t', &moff, &off); + kstring_t str = {0, 0, NULL}; + int *col2sample = (int *) malloc(sizeof(int)*ncols); +- for (int i=0; i0 ) ksprintf(&str, ","); +@@ -2144,7 +2165,8 @@ + { + int flags = 0, n; + char **tags = hts_readlist(str, 0, &n); +- for (int i=0; ifn, '/'); + char *str = ptr ? ptr+1 : gtc[i]->fn; +@@ -2376,10 +2399,10 @@ + bpm_destroy(bpm); + if ( gtc_list ) + { +- for (int i=0; i Date: Thu, 1 Nov 2018 17:49:51 +0100 Subject: [PATCH 024/546] Removing dependencies (#11742) --- recipes/biobb_common/meta.yaml | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/recipes/biobb_common/meta.yaml b/recipes/biobb_common/meta.yaml index 1aaefd912b4c2..a4c465035658e 100644 --- a/recipes/biobb_common/meta.yaml +++ b/recipes/biobb_common/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_common" %} -{% set version = "0.0.5" %} +{% set version = "0.0.6" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "c0cd2d39d120d2fa3047a90b6f54fa6990c02988ece128cc9b4ccc1f1ed89b83" %} +{% set hash_value = "1a19c73f337cd9880483e8bfd1eadb6e6e9b9eef14635152fd8a99308a61be26" %} package: name: '{{ name|lower }}' @@ -18,22 +18,16 @@ build: requirements: host: - - python >=3.5 + - python >=3 - setuptools - pyyaml - - nose - - jupyter - requests - biopython - - cwltool run: - - python >=3.5 + - python >=3 - pyyaml - - nose - - jupyter - requests - biopython - - cwltool test: imports: From c756d0b17f778600e8a20c55b709bca003e97094 Mon Sep 17 00:00:00 2001 From: Michael Knudsen Date: Thu, 1 Nov 2018 18:41:36 +0100 Subject: [PATCH 025/546] Bumped fastq-screen version (#11739) --- recipes/fastq-screen/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/fastq-screen/meta.yaml b/recipes/fastq-screen/meta.yaml index 47183430908da..bd3000674bdba 100644 --- a/recipes/fastq-screen/meta.yaml +++ b/recipes/fastq-screen/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.3" %} -{% set sha256 = "220696f7366eb64cd6ff26355b89ac0c959887b17b5ad9f88903f58a4a71cec6" %} +{% set version = "0.13.0" %} +{% set sha256 = "972e4dd99a9bedd3023e5ae9cbf98594c1608e43f6c10e44a6ab63fed4fdecbc" %} package: name: fastq-screen @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 requirements: build: @@ -33,4 +33,3 @@ about: home: 'http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/' license: GPLv3 summary: 'FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect' - From d3808ce010272bbc56bea9b34faf55390f365d60 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Thu, 1 Nov 2018 14:39:24 -0400 Subject: [PATCH 026/546] Add RNFtools 0.3.1.3 (#11747) * Add RNFtools 0.3.1.3 * Fix build * Remove argparse from dependencies * Skip py35 --- recipes/rnftools/0.3.0.2/meta.yaml | 45 -------------------------- recipes/rnftools/0.3.1.0/meta.yaml | 51 ------------------------------ recipes/rnftools/0.3.1.1/meta.yaml | 50 ----------------------------- recipes/rnftools/build.sh | 6 ++++ recipes/rnftools/meta.yaml | 50 ++++++++++++++++++----------- 5 files changed, 37 insertions(+), 165 deletions(-) delete mode 100644 recipes/rnftools/0.3.0.2/meta.yaml delete mode 100644 recipes/rnftools/0.3.1.0/meta.yaml delete mode 100644 recipes/rnftools/0.3.1.1/meta.yaml create mode 100755 recipes/rnftools/build.sh diff --git a/recipes/rnftools/0.3.0.2/meta.yaml b/recipes/rnftools/0.3.0.2/meta.yaml deleted file mode 100644 index 9a09882290d71..0000000000000 --- a/recipes/rnftools/0.3.0.2/meta.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{% set version = "0.3.0.2" %} -{% set sha256 = "881f44c30b133912561c8346e69294491a5a7e40d865937bcc0fc0727e29da2c" %} - -package: - name: rnftools - version: {{ version }} - -source: - url: https://github.com/karel-brinda/rnftools/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 2 - skip: True # [py27] - script: pip install . - -requirements: - host: - - python - - pysam - - snakemake - - argparse - run: - - python - - samtools - - pysam - - wgsim - - dwgsim - - art - - mason - - curesim - - snakemake - - argparse - -test: - commands: - - rnftools -h - imports: - - rnftools - -about: - home: http://karel-brinda.github.io/rnftools - license: MIT - summary: 'RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.' - diff --git a/recipes/rnftools/0.3.1.0/meta.yaml b/recipes/rnftools/0.3.1.0/meta.yaml deleted file mode 100644 index e5cc40066acba..0000000000000 --- a/recipes/rnftools/0.3.1.0/meta.yaml +++ /dev/null @@ -1,51 +0,0 @@ -{% set version = "0.3.1.0" %} -{% set sha256 = "6dcd036ca52f5f84a8caa8d21543bd00c467ea3584e42125bcf2ef4d99f57cd5" %} - -package: - name: rnftools - version: {{ version }} - -source: - url: https://github.com/karel-brinda/rnftools/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 2 - skip: True # [py27] - script: pip install . - -requirements: - host: - - python - - pysam - - snakemake - - argparse - - reportlab - run: - - python - - samtools - - pysam - - wgsim - - dwgsim - - art - - mason - - curesim - - snakemake - - argparse - - pyfaidx - - bwa - - gnuplot >=5.0 - - beautifulsoup4 - - reportlab - -test: - commands: - - rnftools -h - imports: - - rnftools - -about: - home: http://karel-brinda.github.io/rnftools - license: MIT - summary: 'RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.' - diff --git a/recipes/rnftools/0.3.1.1/meta.yaml b/recipes/rnftools/0.3.1.1/meta.yaml deleted file mode 100644 index 8741967bcd1fc..0000000000000 --- a/recipes/rnftools/0.3.1.1/meta.yaml +++ /dev/null @@ -1,50 +0,0 @@ -{% set version = "0.3.1.1" %} -{% set sha256 = "267025de6f075d19bda5cc2c78188b1ad7b6bc6d24aae77d8554c6a7274f3ec1" %} - -package: - name: rnftools - version: {{ version }} - -source: - url: https://github.com/karel-brinda/rnftools/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 2 - skip: True # [py27] - script: pip install . - -requirements: - host: - - python - - pysam - - snakemake - - argparse - run: - - python - - samtools - - pysam - - wgsim - - dwgsim - - art - - mason - - curesim - - snakemake - - argparse - - pyfaidx - - bwa - - gnuplot >=5.0 - - beautifulsoup4 - - reportlab ==3.3.0 - -test: - commands: - - rnftools -h - imports: - - rnftools - -about: - home: http://karel-brinda.github.io/rnftools - license: MIT - summary: 'RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.' - diff --git a/recipes/rnftools/build.sh b/recipes/rnftools/build.sh new file mode 100755 index 0000000000000..247c23fb3d260 --- /dev/null +++ b/recipes/rnftools/build.sh @@ -0,0 +1,6 @@ +#! /usr/bin/env bash + +set -e +set -o pipefail + +$PYTHON setup.py install -vvv --single-version-externally-managed --record=record.txt diff --git a/recipes/rnftools/meta.yaml b/recipes/rnftools/meta.yaml index 0a6c4787115a0..0801c42261258 100644 --- a/recipes/rnftools/meta.yaml +++ b/recipes/rnftools/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.1.2" %} -{% set sha256 = "566d69cd8484fca041d6f5d4cf71864ca6caa8521a2902b1a30a91ce4a68dfb1" %} +{% set version = "0.3.1.3" %} +{% set sha256 = "74b382d24c1262968f26ac622ce04e20642bb12a57fd2448075de542880bb13c" %} package: name: rnftools @@ -10,41 +10,53 @@ source: sha256: {{ sha256 }} build: - number: 2 - skip: True # [py27] - script: pip install . + number: 0 + entry_points: + - rnftools = rnftools.scripts:rnftools_script + skip: True # [py27 or py35]¬ requirements: host: - - python + - beautifulsoup4 + - pip + - pyfaidx - pysam - - snakemake - - argparse - run: - python - - samtools - - pysam - - wgsim - - dwgsim + - snakemake-minimal + - svg42pdf >=0.2.2 + run: - art - - mason - - curesim - - snakemake - - argparse - - pyfaidx + - beautifulsoup4 - bwa + - curesim + - dwgsim - gnuplot >=5.0 - - beautifulsoup4 + - mason + - pyfaidx + - pysam + - python - reportlab ==3.3.0 + - samtools + - snakemake-minimal + - svg42pdf >=0.2.2 + - wgsim test: commands: - rnftools -h imports: - rnftools + - rnftools.lavender + - rnftools.mishmash + - rnftools.rnfformat + - rnftools.utils about: home: http://karel-brinda.github.io/rnftools license: MIT summary: 'RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.' +extra: + recipe-maintainers: + - karel-brinda + From f32d218ae20df58751387baabe7b0cca0df85936 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 1 Nov 2018 21:18:07 +0100 Subject: [PATCH 027/546] Removing dependencies (#11749) * Removing dependencies * Removing pycompss dependency --- recipes/biobb_io/meta.yaml | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/recipes/biobb_io/meta.yaml b/recipes/biobb_io/meta.yaml index a975a570f3261..9d333997d22fd 100644 --- a/recipes/biobb_io/meta.yaml +++ b/recipes/biobb_io/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_io" %} -{% set version = "0.0.8" %} +{% set version = "0.1.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "fad79ebf5b5caac1478627c43ecc8dcfc1761b1378422e1d0ddbe35bed896713" %} +{% set hash_value = "c4f306882e06abd3dee1e36f659dd78c6b13050787a02709f9de6856ab21ad38" %} package: name: '{{ name|lower }}' @@ -18,16 +18,12 @@ build: requirements: host: - - python >=3.5 + - python >=3 - setuptools - - mistune ==0.7.4 - - jsonschema ==2.6.0 - biobb_common - requests run: - - python >=3.5 - - mistune ==0.7.4 - - jsonschema ==2.6.0 + - python >=3 - biobb_common - requests @@ -35,9 +31,6 @@ test: imports: - biobb_io - biobb_io.mmb_api - - biobb_io.pycompss - - biobb_io.pycompss.mmb_api - - biobb_io.test about: home: https://github.com/bioexcel/biobb_io From 15d4978d75281359c60ab2f1dcaff71ba8fc724f Mon Sep 17 00:00:00 2001 From: Florian Eggenhofer Date: Thu, 1 Nov 2018 18:42:12 -0300 Subject: [PATCH 028/546] Updated to version 1.0.5 (#11750) * Updated to version 1.0.5 * Update meta.yaml --- recipes/selectsequencesfrommsa/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/selectsequencesfrommsa/meta.yaml b/recipes/selectsequencesfrommsa/meta.yaml index eec39a9b3cf1a..e4355de66c52c 100644 --- a/recipes/selectsequencesfrommsa/meta.yaml +++ b/recipes/selectsequencesfrommsa/meta.yaml @@ -1,6 +1,6 @@ {% set name = "selectsequencesfrommsa" %} -{% set version = "1.0.2" %} -{% set md5 = "48ccf1a818f6784c93b1ce1e536697d0" %} +{% set version = "1.0.5" %} +{% set md5 = "8795132f23b7b6b7b4d3696ea704a766" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: md5: {{ md5 }} build: - number: 3 + number: 0 skip: True # [osx] requirements: host: - - stack >=1.3.2 + - stack >=1.7.1 - gmp - zlib - perl From eaf2741dc9c8d9e808af2be307473d126c355f3b Mon Sep 17 00:00:00 2001 From: Alan McCulloch Date: Fri, 2 Nov 2018 14:17:12 +1300 Subject: [PATCH 029/546] tardis patch for issue 27 (sampling paired fastq) (#11755) * New recipe for GBSX. * Added build noarch: generic to keep CircleCI happy. * Added identifier for gbsx. * tardis update to 1.0.19 (fix paired fastq sampling) * tardis update to 1.0.19 (fix paired fastq sampling) --- recipes/tardis/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/tardis/meta.yaml b/recipes/tardis/meta.yaml index 4276b0ff5863a..15a85bf81e2bb 100644 --- a/recipes/tardis/meta.yaml +++ b/recipes/tardis/meta.yaml @@ -1,13 +1,13 @@ {% set name = "tardis" %} -{% set version = "0.5.17" %} -{% set sha256 = "3442823498cfa3d5106a9f37188240777c9b00a550191b16796e290be36b8ef6" %} +{% set version = "1.0.19" %} +{% set sha256 = "d77e88b89db7ea66eaca1de606aca7cf5497e26714f5d446159d5287cf67bf8f" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/AgResearch/{{ name }}/archive/v{{ version }}.tar.gz + url: https://github.com/AgResearch/{{ name }}/archive/{{ version }}.tar.gz sha256: {{ sha256 }} build: From c02c8a8f32b319516d1e099f82d8f29ddff75973 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Thu, 1 Nov 2018 20:58:07 -0500 Subject: [PATCH 030/546] Update recipe for Circos (#11756) * Add libwebp as dependency --- recipes/circos/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/circos/meta.yaml b/recipes/circos/meta.yaml index 7f67593735dae..fa5811e401d4c 100644 --- a/recipes/circos/meta.yaml +++ b/recipes/circos/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 52d29bfd294992199f738a8d546a49754b0125319a1685a28daca71348291566 build: - number: 2 + number: 3 requirements: run: @@ -32,6 +32,7 @@ requirements: - perl-statistics-basic - perl-text-format - perl-time-hires + - libwebp <1.0.0 test: commands: From 6e152413d54aca8c0bb952d674974a0f8a9bc960 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Fri, 2 Nov 2018 01:44:31 -0400 Subject: [PATCH 031/546] Ctat mut (#11759) * locking picard * picard version --- recipes/ctat-mutations/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index 48f04ee5c5187..e949146af048b 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "0" %} +{% set build = "1" %} package: name: {{ name }} @@ -19,12 +19,12 @@ requirements: build: - python - gatk4 - - picard >=2.0.1 + - picard =2.18.14 run: - python - gatk4 - star - - picard >=2.0.1 + - picard =2.18.14 - bcftools - samtools - tabix From 0c1ae7990247abfee34bb2c0dfb8ce567f4fd986 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Fri, 2 Nov 2018 02:01:32 -0400 Subject: [PATCH 032/546] Revert "Ctat mut (#11759)" (#11760) This reverts commit 6e152413d54aca8c0bb952d674974a0f8a9bc960. --- recipes/ctat-mutations/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index e949146af048b..48f04ee5c5187 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "1" %} +{% set build = "0" %} package: name: {{ name }} @@ -19,12 +19,12 @@ requirements: build: - python - gatk4 - - picard =2.18.14 + - picard >=2.0.1 run: - python - gatk4 - star - - picard =2.18.14 + - picard >=2.0.1 - bcftools - samtools - tabix From 87fcc9f07949d1f5e552d01eb510d894d8f5cb28 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Fri, 2 Nov 2018 02:55:10 -0400 Subject: [PATCH 033/546] picard version locked (#11761) --- recipes/ctat-mutations/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index 48f04ee5c5187..e949146af048b 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "0" %} +{% set build = "1" %} package: name: {{ name }} @@ -19,12 +19,12 @@ requirements: build: - python - gatk4 - - picard >=2.0.1 + - picard =2.18.14 run: - python - gatk4 - star - - picard >=2.0.1 + - picard =2.18.14 - bcftools - samtools - tabix From 3029cf2687b08a2551205a9e78d2c75f00000e02 Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Fri, 2 Nov 2018 12:05:47 +0000 Subject: [PATCH 034/546] Add pymzml v0.7.10 (#11763) --- recipes/pymzml/0.7.10/meta.yaml | 35 +++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/pymzml/0.7.10/meta.yaml diff --git a/recipes/pymzml/0.7.10/meta.yaml b/recipes/pymzml/0.7.10/meta.yaml new file mode 100644 index 0000000000000..7423370a9c78b --- /dev/null +++ b/recipes/pymzml/0.7.10/meta.yaml @@ -0,0 +1,35 @@ +package: + name: pymzml + version: "0.7.10" + +source: + url: https://files.pythonhosted.org/packages/77/68/1d7e1fd39f7f6b4b638caaa1b11ef6e78f74916e7e78d66ee01f9dd0c5d4/pymzml-0.7.10.zip + md5: b55980a664eaf168c558a247c611b2a1 + +build: + noarch: python + number: 0 + script: python -m pip install --no-deps --ignore-installed . + +requirements: + host: + - python + - pip + - plotly + run: + - python + - plotly + +test: + imports: + - pymzml + +about: + home: http://pymzml.github.com + license: GNU General Public License (GPL) + summary: 'high-throughput mzML parsing' + license_family: LGPL + +extra: + identifiers: + - biotools:pymzml From 3f459ca17346a0e3fa1c880c74b62ed7d5207554 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Fri, 2 Nov 2018 14:10:12 -0700 Subject: [PATCH 035/546] MentaLiST: Remove old versions and pin dependencies in current versions (#10720) * Remove old versions and pin julia in current versions * Pin hdf5 * Pin hdf5=1.8.17 * Pin mpfr=3.1.* * Add build.sh for 0.1.9 * Use global pinning for hdf5 * Pin hdf5 again --- recipes/mentalist/0.1.3/meta.yaml | 36 ------------------ recipes/mentalist/0.1.4/meta.yaml | 36 ------------------ recipes/mentalist/0.1.5/meta.yaml | 40 -------------------- recipes/mentalist/0.1.6/meta.yaml | 40 -------------------- recipes/mentalist/0.1.7/meta.yaml | 41 --------------------- recipes/mentalist/0.1.8/meta.yaml | 41 --------------------- recipes/mentalist/{0.2.2 => 0.1.9}/build.sh | 9 +---- recipes/mentalist/0.1.9/meta.yaml | 14 +++---- recipes/mentalist/0.2.1/meta.yaml | 35 ------------------ recipes/mentalist/0.2.2/meta.yaml | 36 ------------------ recipes/mentalist/meta.yaml | 6 +-- 11 files changed, 11 insertions(+), 323 deletions(-) delete mode 100644 recipes/mentalist/0.1.3/meta.yaml delete mode 100644 recipes/mentalist/0.1.4/meta.yaml delete mode 100644 recipes/mentalist/0.1.5/meta.yaml delete mode 100644 recipes/mentalist/0.1.6/meta.yaml delete mode 100644 recipes/mentalist/0.1.7/meta.yaml delete mode 100644 recipes/mentalist/0.1.8/meta.yaml rename recipes/mentalist/{0.2.2 => 0.1.9}/build.sh (57%) delete mode 100644 recipes/mentalist/0.2.1/meta.yaml delete mode 100644 recipes/mentalist/0.2.2/meta.yaml diff --git a/recipes/mentalist/0.1.3/meta.yaml b/recipes/mentalist/0.1.3/meta.yaml deleted file mode 100644 index e6f4c56af1c67..0000000000000 --- a/recipes/mentalist/0.1.3/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.3" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 57874e2168b48c165fc68c2bab41819259ec828e298bc54cbc3da8f3c904c63e - -build: - number: 3 - skip: True # [osx] - -requirements: - host: - - julia >=0.6.1 - - hdf5 - - mpfr - - libxml2 - run: - - julia >=0.6.1 - - hdf5 - - mpfr - - libxml2 - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.4/meta.yaml b/recipes/mentalist/0.1.4/meta.yaml deleted file mode 100644 index 747d473d8eb2f..0000000000000 --- a/recipes/mentalist/0.1.4/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.4" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 7dc6bd983156a28d59ad480bea1d7761ebdcd25087db73ef9ce3fb0e59cd224b - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.5/meta.yaml b/recipes/mentalist/0.1.5/meta.yaml deleted file mode 100644 index ebf49838c33af..0000000000000 --- a/recipes/mentalist/0.1.5/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.5" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 7152813c3f8934ffb29413d670c5662098111203305962534a1ffcd7734a8144 - -build: - number: 3 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.6/meta.yaml b/recipes/mentalist/0.1.6/meta.yaml deleted file mode 100644 index 3ebebd1934c1d..0000000000000 --- a/recipes/mentalist/0.1.6/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.6" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 32518624f81378aae8ba5b7a8a6da077b2489609da00394bad1fca8d3fef2814 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.7/meta.yaml b/recipes/mentalist/0.1.7/meta.yaml deleted file mode 100644 index 0d109254345b8..0000000000000 --- a/recipes/mentalist/0.1.7/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.7" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: ba419318f9f8a1184de2d7711966f8debfe99c601f94c231bf3935b0adcd2984 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE - diff --git a/recipes/mentalist/0.1.8/meta.yaml b/recipes/mentalist/0.1.8/meta.yaml deleted file mode 100644 index 3d6b888dc9a31..0000000000000 --- a/recipes/mentalist/0.1.8/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.8" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 15a56b979f31aafbbb3c9512983568d62f9d8dada60dda15b6ff53a91f652ba7 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE - diff --git a/recipes/mentalist/0.2.2/build.sh b/recipes/mentalist/0.1.9/build.sh similarity index 57% rename from recipes/mentalist/0.2.2/build.sh rename to recipes/mentalist/0.1.9/build.sh index b35fa88516929..3a44013cd6f91 100644 --- a/recipes/mentalist/0.2.2/build.sh +++ b/recipes/mentalist/0.1.9/build.sh @@ -1,24 +1,17 @@ #!/bin/sh -# circumvent a bug in conda-build >=2.1.18,<3.0.10 -# https://github.com/conda/conda-build/issues/2255 -[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE -[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE - cp -r $SRC_DIR/src/*.jl $PREFIX/bin cp -r $SRC_DIR/scripts $PREFIX ln -s $PREFIX/bin/MentaLiST.jl $PREFIX/bin/mentalist chmod +x $PREFIX/bin/mentalist julia -e 'Pkg.init()' +julia -e 'Pkg.add("Suppressor")' julia -e 'Pkg.add("ArgParse")' julia -e 'Pkg.add("Bio")' julia -e 'Pkg.add("OpenGene")' julia -e 'Pkg.add("Logging")' julia -e 'Pkg.add("Lumberjack")' -julia -e 'Pkg.add("FastaIO")' -julia -e 'Pkg.add("JLD")' -julia -e 'Pkg.add("DataStructures")' rm -f "$PREFIX"/share/julia/site/lib/v*/*.ji rm -rf "$PREFIX"/share/julia/site/v*/METADATA diff --git a/recipes/mentalist/0.1.9/meta.yaml b/recipes/mentalist/0.1.9/meta.yaml index 1af4b75b7623c..5e5e513cc83b4 100644 --- a/recipes/mentalist/0.1.9/meta.yaml +++ b/recipes/mentalist/0.1.9/meta.yaml @@ -10,19 +10,19 @@ source: sha256: 44f6718c7d64d952e439fbddba6a413558c95b00de6f3daf0c0807b850914c3e build: - number: 2 + number: 3 skip: True # [osx] requirements: host: - - julia - - hdf5 - - mpfr + - julia 0.5.2 + - hdf5 1.8.17 + - mpfr 3.1.* - libxml2 run: - - julia - - hdf5 - - mpfr + - julia 0.5.2 + - hdf5 1.8.17 + - mpfr 3.1.* - libxml2 - unzip diff --git a/recipes/mentalist/0.2.1/meta.yaml b/recipes/mentalist/0.2.1/meta.yaml deleted file mode 100644 index 051a0ec50666d..0000000000000 --- a/recipes/mentalist/0.2.1/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.2.1" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: a148fcd552c9ce4964dd7cc88d7771fc5bde7d94ed46e8145ba61c8a88804c92 - -build: - number: 3 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - run: - - julia - - hdf5 - - mpfr - - libxml2 - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.2.2/meta.yaml b/recipes/mentalist/0.2.2/meta.yaml deleted file mode 100644 index a74ff17a72073..0000000000000 --- a/recipes/mentalist/0.2.2/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.2.2" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 1bf9cd79b3c2fee652bcef2d7e6b867fc4be172a59bcdf4258c4aeed8a929322 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml index 702b8d63bc337..227c65c883b5c 100644 --- a/recipes/mentalist/meta.yaml +++ b/recipes/mentalist/meta.yaml @@ -10,16 +10,16 @@ source: sha256: d456615fb9228737aff735d58b272d5bcefd241db6593ece218f2c26c27f165a build: - number: 0 + number: 1 skip: True # [osx] requirements: host: - - julia + - julia 0.6.1 - hdf5 - mpfr run: - - julia + - julia 0.6.1 - hdf5 - mpfr - libxml2 From 60acc69c7592a2caffee5b03ec4a7bbe63b7445f Mon Sep 17 00:00:00 2001 From: Joerg Fallmann Date: Fri, 2 Nov 2018 23:49:14 +0100 Subject: [PATCH 036/546] Updated segemehl 0.2 added segemehl 0.3 (#11753) * Updated segemehl 0.2 added segemehl 0.3 * Update meta.yaml * skipping osx for now --- recipes/segemehl/0.2.0/build.sh | 13 +++++++++++ recipes/segemehl/0.2.0/meta.yaml | 40 ++++++++++++++++++++++++++++++++ recipes/segemehl/build.sh | 6 ++--- recipes/segemehl/meta.yaml | 26 +++++++++++++++------ 4 files changed, 75 insertions(+), 10 deletions(-) create mode 100644 recipes/segemehl/0.2.0/build.sh create mode 100644 recipes/segemehl/0.2.0/meta.yaml diff --git a/recipes/segemehl/0.2.0/build.sh b/recipes/segemehl/0.2.0/build.sh new file mode 100644 index 0000000000000..6901dfb4b2577 --- /dev/null +++ b/recipes/segemehl/0.2.0/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +export C_INCLUDE_PATH=${PREFIX}/include:${PREFIX}/include/ncurses +export LIBRARY_PATH=${PREFIX}/lib + +cd segemehl +make segemehl.x -j${CPU_COUNT} +make testrealign.x -j${CPU_COUNT} +make lack.x -j${CPU_COUNT} + +for i in *.x ; do + install ${i} ${PREFIX}/bin +done diff --git a/recipes/segemehl/0.2.0/meta.yaml b/recipes/segemehl/0.2.0/meta.yaml new file mode 100644 index 0000000000000..335c906221a8a --- /dev/null +++ b/recipes/segemehl/0.2.0/meta.yaml @@ -0,0 +1,40 @@ +package: + name: segemehl + version: 0.2.0 + +about: + home: http://www.bioinf.uni-leipzig.de/Software/segemehl/ + summary: Short read mapping with gaps +build: + number: 5 + skip: True # [osx] + +source: + url: "http://www.bioinf.uni-leipzig.de/Software/segemehl/old/segemehl_0_2_0.tar.gz" + sha256: 2575139d2f2ba7bd534afcbe485c0570c177d1faaeb267c4cd873e65b8e72afb + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - zlib + - ncurses + run: + - ncurses + +test: + commands: + - segemehl.x --help 2>&1 | grep -A1 VERSION + - lack.x --help 2>&1 | grep -A1 VERSION + - testrealign.x --help 2>&1 | grep -A1 VERSION + +extra: + identifiers: + - biotools:segemehl + +about: + home: http://www.bioinf.uni-leipzig.de/Software/segemehl/ + license: GPL3 +# license_file: licence.txt + summary: Short read mapping with gaps diff --git a/recipes/segemehl/build.sh b/recipes/segemehl/build.sh index 6bec800869269..fcd8ffe389b33 100644 --- a/recipes/segemehl/build.sh +++ b/recipes/segemehl/build.sh @@ -1,10 +1,10 @@ -#!/bin/sh -cd segemehl +#!/bin/bash export C_INCLUDE_PATH=${PREFIX}/include:${PREFIX}/include/ncurses export LIBRARY_PATH=${PREFIX}/lib +export PKG_CONFIG_PATH=${PREFIX}/lib/pkgconfig -make -j 1 ## do not use >1 make threads! +make all -j${CPU_COUNT} ## do not use >1 make threads! for i in *.x ; do install ${i} ${PREFIX}/bin diff --git a/recipes/segemehl/meta.yaml b/recipes/segemehl/meta.yaml index 9373bb6d9955e..b3dc824fdede0 100644 --- a/recipes/segemehl/meta.yaml +++ b/recipes/segemehl/meta.yaml @@ -1,33 +1,45 @@ +{% set version = "0.3.1" %} +{% set sha256 = "04b6d92a118b897c8c7d1157c60b2671975cd21da17fe2b7e0200b83f8534c2b" %} + package: name: segemehl - version: 0.2.0 + version: {{ version }} about: home: http://www.bioinf.uni-leipzig.de/Software/segemehl/ summary: Short read mapping with gaps build: - number: 4 + number: 0 + skip: True # [osx] source: - url: "http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_0_2_0.tar.gz" - sha256: 2575139d2f2ba7bd534afcbe485c0570c177d1faaeb267c4cd873e65b8e72afb + url: "http://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/segemehl.tar.gz" + sha256: {{ sha256 }} requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} + - pkg-config host: - zlib - ncurses + - htslib run: - - zlib - ncurses + - htslib test: commands: - segemehl.x --help 2>&1 | grep -A1 VERSION - - lack.x --help 2>&1 | grep -A1 VERSION - - testrealign.x --help 2>&1 | grep -A1 VERSION + - haarz.x --help 2>&1 | grep -A1 VERSION extra: identifiers: - biotools:segemehl + +about: + home: http://www.bioinf.uni-leipzig.de/Software/segemehl/ + license: GPL3 + license_file: licence.txt + summary: Short read mapping with gaps From 824bad737077b9d062cae1c5574b48dc1743c1b7 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Sat, 3 Nov 2018 08:40:01 -0700 Subject: [PATCH 037/546] Update prince to v1.1 (#11765) --- recipes/prince/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/prince/meta.yaml b/recipes/prince/meta.yaml index 73b7de066df9a..2c00d3b950d9e 100644 --- a/recipes/prince/meta.yaml +++ b/recipes/prince/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PRINCE" %} -{% set version = "1.0" %} -{% set sha256 = "b5478d9c77f8a8beb31ab3d6ed1ffd1e00c756ac9685658b16b69f04178e4b7b" %} +{% set version = "1.1" %} +{% set sha256 = "51402ad195b8460435ddf3d0ad5f0b84802b233d0bc08b1c7dda04be6c6de736" %} package: name: {{ name|lower }} From 8b2757f05fb7ce404c3889fed42c5bf89aba3edb Mon Sep 17 00:00:00 2001 From: Andreas Heger Date: Sat, 3 Nov 2018 22:45:16 +0000 Subject: [PATCH 038/546] update ruffus to version 2.8.0 (#11766) * update ruffus to version 2.8.0 * {AH} add licence file to about section --- recipes/ruffus/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/ruffus/meta.yaml b/recipes/ruffus/meta.yaml index 2b5fd37482dae..794d5d51f719d 100644 --- a/recipes/ruffus/meta.yaml +++ b/recipes/ruffus/meta.yaml @@ -1,10 +1,10 @@ package: name: ruffus - version: 2.7 + version: 2.8 source: - url: https://files.pythonhosted.org/packages/ea/32/5048607dd7a9104406789b15fb4078e774121b23190c9e464d4dd1f7ed89/ruffus-2.7.0.tar.gz - sha256: 4bd46461d31aa532357019a33d8045f4e57e52f4ee41643b5b3a7372e380cae0 + url: https://files.pythonhosted.org/packages/ac/c7/5652e44a3644dfdf8cdfa17c2bb7933896dddec99888f57bf2adbbcca226/ruffus-2.8.0.tar.gz + sha256: 609e76e88de2d11362ed2a312917508f14daf56413fd1b3c7d5a96aaa14bb5e9 build: noarch: python @@ -27,3 +27,4 @@ about: home: http://www.ruffus.org.uk/ license: MIT summary: "Light-weight Python Computational Pipeline Management" + license_file: LICENSE.TXT From eabf52887749a840b05ae5e3da7fd59a762ba967 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sun, 4 Nov 2018 10:38:51 +0100 Subject: [PATCH 039/546] Fix docs (#11769) * Docs are currently broken, start fixing them * try again --- recipes/r-genometricorr/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/r-genometricorr/meta.yaml b/recipes/r-genometricorr/meta.yaml index 787b8851399c6..2feb50f47970a 100644 --- a/recipes/r-genometricorr/meta.yaml +++ b/recipes/r-genometricorr/meta.yaml @@ -54,7 +54,7 @@ about: extra: identifiers: - - doi: doi.org/10.1371/journal.pcbi.1002529 + - doi:10.1371/journal.pcbi.1002529 recipe-maintainers: - MathiasHaudgaard - FrodePedersen From 49e4aa2a41e39f56307536a8707136b80e2cdcb1 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Sun, 4 Nov 2018 05:29:51 -0500 Subject: [PATCH 040/546] Update: CNVkit (0.9.6dev) with GATK4 fixes (#11770) --- recipes/cnvkit/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml index 7bf2dbce10cba..f8dd94278da7f 100644 --- a/recipes/cnvkit/meta.yaml +++ b/recipes/cnvkit/meta.yaml @@ -1,14 +1,15 @@ -{% set version="0.9.5" %} +{% set version="0.9.6a0" %} package: name: cnvkit version: {{ version }} source: - url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz - sha256: 6dbbb311eb255ed229567005a5380574442d724306f17e8d0b70341781061bfd + #url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz + url: https://github.com/etal/cnvkit/archive/ea3ce56.tar.gz + sha256: 4de92b95a4bd05b9745e71c301452aedc2358717032599440f92a7447ad06612 build: - number: 1 + number: 0 requirements: host: From 84f1bcca3f28eef633cb551b1b4acc55d1afc68d Mon Sep 17 00:00:00 2001 From: Winni Kretzschmar Date: Sun, 4 Nov 2018 11:51:00 +0100 Subject: [PATCH 041/546] Fix missing cortexpy dependency upgrade (#11768) * Fix missing cortexpy dependency upgrade * Bump build number --- recipes/abeona/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index c8378700b77ca..f13f265198798 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [not py36] - number: 0 + number: 1 entry_points: - abeona=abeona.__main__:main script: '$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv ' @@ -23,7 +23,7 @@ requirements: run: - mccortex ==1.0 - nextflow ==0.32.0 - - cortexpy ==0.44.0 + - cortexpy ==0.45.6 - kallisto ==0.44.0 - bwa - pandas From 381256c973aec60c6e9f99f32282cc9b2a54758e Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Sun, 4 Nov 2018 15:57:42 +0100 Subject: [PATCH 042/546] Biobb model (#11722) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adding biobb_model recipe * Adding MANIFEST.in to include data files * Exposing checkStruc * Adding helpdocs files * Ssp (#11724) * Update md5sum and delete old version. * Update build number. * Revert "Update build number." This reverts commit 4497a36000e188291a6fe70a9365234ed1c0ba80. * Add host requirement. * Do not restrict snakemake version. * Add DECIPHER (#11688) * Add DECIPHER * Change biostrings version * Change R version * r-facets (#11717) * r-facets * r-facets - fix * r-facets - fix macos * r-facets - skip macos * r-facets - unskip macos add fortran * merge bulk into master (#11728) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1  (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN packages lacking license file * Add missing libnetcdf requirement to bioconductor-mzr * Remove r-alakazam (moved to conda-forge) Fix linting issue: ``` recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating ``` * [BULK] Many R 3.5 only packages (#11410) * [BULK] Bulk update 191018b (#11419) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1  (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN packages lacking license file * Add missing libnetcdf requirement to bioconductor-mzr * Remove r-alakazam (moved to conda-forge) Fix linting issue: ``` recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating ``` * [BULK] Many R 3.5 only packages (#11410) * Update pinning to R>=3.5 and a few runtime dependencies. * CSAW is R 3.5 only * Packages using beachmat are 3.5 only * Packages using bioconductor-singlecellexperiment are R 3.5 only * [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452) * Don't use r-base >=3.5, use a conda_build_config.yaml instead * blacklist r-phangorn * Update variancepartition * R 3.5 for packages requiring singlecellexperiment * Update a few packages * Update a number of recipes (#11482) * Update ensemblVEP and derfinder (#11504) * Bulk update 251018 (#11577) * [BULK] various package updates * blacklist bioconductor-mzr * A couple tweaks * [BULK] Update 261018 (#11611) * Apparently the r-rgeos bit works properly now. * Add tissueenrich and try to fix scpipe on Linux * A meaningless change just to trigger an update in bulk. (#11618) * [BULK] update 271018 (#11628) * Bump bioconductor-esetvis * Fix yaqcaffy * Fix more * Another R 3.5 recipe * [BULK] update 281018 (#11689) * Add some files * Fix arrayexpress * Fix another 2 * Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697) * Update blacklist (#11706) * [BULK] fix bioconductor-tissueenrich (#11720) * taxonkit 0.2.5 (#11318) * Update csvtk (#11319) * taxonkit 0.2.5 * csvtk 0.15.0 * bumping GROOT to 0.8.1 (#11323) * HiCMatrix version 3 (#11322) * Correcting dependencies * Version 3 of HiCMatrix, the October release * Update confindr to 0.4.3 (#11330) * Drop-seq_tools: Version 2.0.0 (#11326) * Update meta.yaml * Update build.sh some tool names changed to fit Camel case * Update motus to build only for python3 (#11331) * Update fpa to 0.2 version (#11333) * update taxonkit to 0.3.0 (#11339) * ntcard 1.1.0 (#11338) * Update rgi (#11335) * first commit * update dependencies list * change source to github * change build number * testing circleci * update meta and build * fix build * move build script into meta * remove older recipes * line fix in bootstrap.py * change python & matplotlib versions; add build.sh file * add preprocessing selector to skip python 2.7 * move build script into meta.yaml * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046. * Update gmap to version 2018-07-04. (#11332) MAX_READLENGTH environment variable has been disused since 2016-08-16. * Upgrade r-biodb to 1.2.0a. (#11341) * Upgrade r-biodb to 1.2.0a. * Update meta.yaml * Updated ont-tombo to version 1.5. (#11329) * Updated ont-tombo to version 1.5. * Updated with actual github release version hash. * remove graphicsmagick (#11342) * Build kraken2 for osx (#11343) * First try for a bcalm recipes (#11344) * New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347) - cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig generation and manipulation command line tools including bam to bigwig conversion. - bcbio: fixes for QC on variants and peddy for CWL runs * Try avoid some dependancy (#11349) * Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348) * Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 Also add about:home . * Workaround https://github.com/conda-forge/bison-feedstock/issues/7 * Better bcalm recipes (#11350) * Try avoid some dependancy * Correct mess in build number, sorry * R biodb (#11351) * rebuild r-biodb * trigger build * Add recipe for pypairs (#11356) * Update smoove to 0.2.1. (#11360) * Update duphold to 0.0.9. (#11359) * Update goleft to 0.2.0 (#11361) * Bump slicedimage to 1.0.0 (#11362) * Bump slicedimage to 1.0.1 (#11365) * Added new versions for biopet-sampleconfig (#11268) * perl-velvetoptimiser: update to 2.2.6 (#11369) * update to 2.2.6 * remove unneeded patch * Scanpy upgrade (#11371) * Bump version * Upgrade Scanpy * Bump starfish to 0.0.25 (#11370) * bumping groot to 0.8.2 (#11374) * vep: bump subversion (#11367) * Updated Krocus 1.0.1 (#11355) * Add tiptoft * Fix meta.yaml for tiptoft * Add build script * Updated krocus 1.0.1 * Add tiptoft 0.1.4 (#11352) * Add tiptoft * Fix meta.yaml for tiptoft * Add build script * Kodoja v0.0.9 (#11373) * Add recipe for seer (#11263) * Add recipe for seer * lets try this * Add newer compiler * Using boost-cpp * messed up version string * Attempt building boost * Use c++11 in boost * Use python for boost install * Correct python version spec * try with different python version * Fix b2 command * Fix popd command * build and link boost program options statically * Fix tests * Match dependency order * Link openblas instead of blas * Forcing rebuild with openblas * Don't use armadillo wrapper * Making review changes. Also trying original tests * Previous tests were correct * Add recipe for the translate-gard npm package version 1.0.3 (#11364) * Fix umi tools (#11376) umi_tools: clean up dependencies * add support tools to PATH (#11379) * Bump to v2.2.1 (#11380) * Bump starfish to 0.0.26 (#11378) * Update fpa to 0.3 (#11375) * Update fpa to 0.3 * Correct error in sha256 * Reset build number * Update trial to 2.5.5 (#11386) * Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388) * Update: bioconductor-titancna; 1.19.1 with hg38 support * Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled * Add r-polysat version 1.7-3 (#11384) * Update biomart version so that compatible with r351 (#11366) * Update biomart version so that compatible with r351 * Update meta.yaml reset build number as per https://bioconda.github.io/guidelines.html#buildnum * Update entrez-direct to 10.0.20180927. (#11387) * Added recipe for SonicParanoid 1.0.13 (#11271) * Added recipe for SonicParanoid 1.0.13 * removed 'x.x' for numpy, added basic test * fixed linter related errors * compiler set to cxx and added host section (same build error!) * removed host section * moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md * removed build: noarch * added build and extra sections * set build number to 0; removed skip build; added python3 minimum version; added test for all executables. * restored sh python module as requirement * added Make to run; updated release to latest commit * remove c compiler from meta.yaml * modified build.sh to compile source codel added make in build section * updated to latest commit * updated to latest version with make included in setup.py * reverted build.sh to the simplest version (python setup.py install) * Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389) * Bump IgBLAST to 1.9.0 (#11393) Bump IgBLAST to 1.9.0 Re-package the binary version this time. There are problems building the source version when the configure script reaches this step: "trying to build the NCBI SRA/VDB Toolkit from GitHub" The previous problem about the binaries linking against libbz2.so, for which we had no conda package, is now solved. Also, this saves about 45 minutes compilation time. * Add consan (#11395) * Add consan * Skip osx * Update: vardict, vardict-java 1.5.7 (#11394) * Update: vardict, vardict-java 1.5.7 Latest vardict-java release and corresponding vardict with bug fixes after testing with 1.5.6 * Reduce test output to try and fix build problems * Experiment 2 for build problems: remove r-base from run * Experiment 3 for build problems: add r-base in host * update recipe for 3.9.1 (#11397) * evofold2 (#11396) * evofold2 * wrapper * Update meta.yaml * minor * Update rnastructure to 6.1. (#11400) * Ctat mut (#11401) * updating version number * correct URL * proper hash * Revert "Ctat mut (#11401)" (#11402) This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0. * update version (#11403) * any2fasta 0.4.2 (new formula) (#11407) * W4mclassfilter v0.98.9 (#11385) * Added files to build version 0.98.9 * Update meta.yaml * Update meta.yaml * updated SonicParanoid recipe to version 1.0.14 (#11409) * updated SonicParanoid recipe to version 1.0.14 * Update to version 1.0.2 of PopDel (#11398) * Update to version 1.0.2 of PopDel Update to version 1.0.2. * Reset build number to 0 * PacBio: require Meson 0.48.1 for all recipes (#11090) * Meson 0.47 inserted duplicate RPATHs in macOS binaries, causing `install_name_tool` failures when installing the package. Requiring 0.48.1 ensures we do not run into these issues anymore in the future. * rebuild with latest openmpi (#11411) * Remove kfoots from the blacklist (#11416) * Update gseapy to 0.9.7 (#11417) * Update gseapy to 0.9.7 * remove noarch * Add SC3 as dependency (#11427) * Add recipe for r-poppr (#11418) * Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412) * Update IQ-TREE to 1.6.7.1 (#11429) * Update IQ-TREE to 1.6.7.1 * Change build number * Update: r-deconstructsigs with fixes for hg38 (#11431) The 1.8.0 release, from 2016, has some issues with hg38 and other custom genomes that are fixed in development (raerose01/deconstructSigs#27). There hasn't been a new release pushed so this rolls these into a new sub-version and makes them available. * Update entrez-direct to 10.2.20181018. (#11432) * Add assembly-scan recipe (#11425) * remove python 2.7 skip (#11424) Preparation for rnaQUAST * Add fastq-scan recipe (#11415) * Add patch to fix racon/rampler path in racon_wrapper. (#11434) Fixes #11405. * meme rebuild (#11433) * Update nanocomp to 0.23.1 (#11436) * Update nanocomp to 0.23.1 * remove noarch * Update abricate to 0.8.10 (#11446) * Update angsd to 0.923 (#11445) * Update alfred to 0.1.13 (#11444) * Update alfred to 0.1.13 * Try w/o patch * Update antarna to 2.0.6 (#11442) * Update admixtools to 5.1 (#11443) * Update admixtools to 5.1 * Let makefile choose which bins to install * Update alignstats to 0.5 (#11441) * Update xatlas to 0.2.1 (#11437) * r-gpca (#11428) * r-gpca * r-gpca recipe * Update meta.yaml * Removed All Comments * gseapy bump version 0.9.8 (#11440) * gseapy bump version 0.9.8 * version * titancna: fix for hg38, remove conda build hacks (#11447) * titancna: fix for hg38, remove conda build hacks * Re-add r-base 3.4 pin to avoid 3.5 errors * Hmmlearn older version (#11450) * Adding pygtftk * removed pygtftk from master * add older version of hmmlearn * Add card_trick (#11451) * Add card_trick * Restrict to py3 * Update checkm-genome to 1.0.12 (#11455) * Bump drep (#11457) * Update squid to 1.5 (#11466) * Update ncbi-ngs-sdk to 2.9.3 (#11467) * elprep: bumped major version (#11414) * elprep: bumped major version * fixed hash * fix download link, fixed licence * fixed tests * skip osx build * FRED2 as a conda package (#11469) * Attempt to get FRED2 as a conda package * SHA update * 99 little bugs in the code * Fix things Björn mentioned * add rnaQUAST recipe (#11470) * Update bioconda-utils to 0.14.9 (#11454) * Rapidup (#11474) * Update to v0.7 * Update Buildnumber * rapid: update to v0.6 * rapid: update to v0.6 * update grid (#11478) * Adding biobb_model recipe (#11472) * Updated wtdbg to v2.1 (#11486) * update stream to 0.2.6 (#11483) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * Update meta.yaml (#11487) * Update connectome-workbench to 1.3.2 (#11468) Now needs QT 5.7 * Update deblur to 1.1.0 (#11500) * Update domclust to 1.2.8 (#11498) * WisecondorX: bump version (#11501) * Bump as GitHub wasn't working yesterday (#11502) * Added recipe for Sequenza (#10367) * Added recipe for Sequenza * Removed fn entry in source section * Trying with only one URL * copynumber is a bioconductor package * Added missing requirements section * Removed mailing list address * Added doi * Added license_file * Trying with different license_file path * Fred2 bump (#11503) * Bump as GitHub wasn't working yesterday * Fix licence etc * Scanpy scripts (#11413) Doing squash and merge as requested by @nh3 * Bump version * First implementation of scanpy-scripts bioconda recipe. * fix path in build.sh * Remove "noarch" flag as requested by bioconda recipe checklist * Add a post install notice that post install test needs bats-core. * Add more dependencies * Skip building for python versions other than 3.6 * Target v0.0.2 which has non-ascii characters removed * Lower version requirement for pandas and matplotlib to be the same as scanpy * Requirement matplotlib>=3.0.0, declare noarch * New: hmftools-cobalt; Update: hmftools-purple (#11507) - hmftools-cobalt: Add latest version of PURPLE associated read counter, COBALT, with support for hg38. - hmftools-purple: PURPLE release with hg38 support. * Update Picard to 2.18.15. (#11505) * Genenotebook (#11476) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * dependency versions * v0.1.5 * Update pinning (#11514) * Bump build number for updated dependency (#11510) * Bump build number for updated dependency * Try adding r-base to host requirements * Try adding other requirements to host * Pin to R version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Tweak dependency version syntax * Pin R and package versions correctly * PacBio: Update pbcore to 1.6.5 (#11513) * Bump r seurat scripts version (#11292) * Bump version * Remove noarch * Could wrongly quoted version be causing an issue? * Tweak pinning to try and fix CI error * seqcluster:fix UMI detection. (#11511) * seqcluster:fix UMI detection. * Fix dependency * quast 5.0.1 (#11479) * quast 5.0.1 * quast 5.0.1: remove third-party site packages from the distibution pack * quast 5.0.1: skip Glimmer in test * quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build) * quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build) * quast 5.0.1: Python 2 and 3 compatible code in build.sh * wcX bugfixes (#11508) * wcX bugfixes * fixed shasum * Update fastspar to 0.0.7 (#11515) * Update iqtree to 1.6.7.2 (#11525) * Update illumina-interop to 1.1.6 (#11523) * Update hapbin to 1.3.0 (#11522) * Update hlama to 3.0.1 (#11520) * Update gb_taxonomy_tools to 1.0.1 (#11519) * Update gffcompare to 0.10.5 (#11517) * Update fast5seek to 0.1.1 (#11516) * Update deepbinner to 0.2.0 (#11499) * Update deepbinner to 0.2.0 * Update meta.yaml Try same fix as in #11240 * Update ncbi-vdb to 2.9.3 (#11550) * Update mikado to 1.2.4 (#11549) * Update perl-pcap to 3.5.2 (#11543) * Update python-hyphy-python to 0.1.9 (#11545) * Update mlst to 2.15.2 (#11547) * Update perl-sanger-cgp-vcf to 2.2.1 (#11542) * Update merfishtools to 1.5.0 (#11537) * Update perl-sanger-cgp-vagrent to 3.3.3 (#11536) * Update nonpareil to 3.3.3 (#11535) * Update prophex to 0.1.1 (#11532) * Update krakenuniq to 0.5.3 (#11527) * Update novoplasty to 2.7.2 (#11530) * Update minced to 0.3.2 (#11529) * Update mapdamage2 to 2.0.8 (#11528) * Update perl-sanger-cgp-allelecount to 4.0.0 (#11538) * Update pyvolve to 0.9.0 (#11531) * Genenotebook (#11512) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * add plek (#11554) * Update pyimzml to 1.2.4 (#11534) * Bump shovill (#11555) * PacBio: Update minimum pbcore version (#11556) * We want all users of PacBio tools to be able to use our utilities with pbmm2 alignments. * Add recipe for translate-gard v1.0.4 (#11557) * bioconductor-rnaseqsamplesizedata (#11475) * Adding Recipe for bioconductor-rnaseqsamplesizedata * Updated metadata for RnaSeqSampleSizeData * nextflow 18.10.1 (#11558) * Update raxml to 8.2.12 (#11567) * Update r-fgwas to 0.3.6 (#11566) * Update rapid to 0.7 (#11565) * Update r-spieceasi to 1.0.2 (#11564) * Update rcorrector to 1.0.3.1 (#11562) * Update quicktree to 2.4 (#11560) * Update paladin to 1.4.4 (#11541) * Update paladin to 1.4.4 * delete md5 * Update build.sh * Update build.sh * Fix and unblacklist Tadarida-D (#11568) * Add recipe for rgt * Fix and un-blacklist tadarida-d * Remove RGT * bumping groot (#11575) * update pymzml (#11573) * Add bioconductor-rnaseqsamplesize (#11559) * Add bioconductor-rnaseqsamplesize * Update recipe * Fixing some URLs * Update dependencies missing * Update trumicount to 0.9.11 (#11576) * Update ConFindr to 0.4.4 (#11578) * Added new versions for biopet-scatterregions (#11572) * Added new versions for biopet-bamstats (#11571) * R ggbiplot (#11584) * add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)' * add r-ggbiplot * update meta.yaml * update meta.yaml * update * update * update * update * update * update * update * update * update * fix errors * fix errors number 1 * Update rebaler to 0.1.2 (#11563) * Update rebaler to 0.1.2 * Remove fn * bump graphclust (#11585) * Update seqyclean to 1.10.09 (#11589) * Update stringmlst to 0.5.1 (#11590) * Update snp-dists to 0.6.2 (#11592) * Update snippy to 4.3.3 (#11596) * Update canu to 1.8 (#11600) * Update starfish to 0.0.27 (#11599) * Update womtool to 36 (#11594) * Update telseq to 0.0.2 (#11598) * Update snp-sites to 2.4.1 (#11588) * Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471) * Added recipe for pydemult * Bumped version in favor of py3.5 * bump vcf2db to latest commit (#11601) * bump vcf2db to latest commit * fix shasum * Fixing source url * Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604) * megan (#11046) * megan6: initial commit * megan6: intermediate commit * megan: made tests work * megan: doc improvement * megan: added osx dmg file * megan: add java to build requirements * megan: removed new line * megan: removed osx sources * Update meta.yaml * bumping hulk (#11607) * Update hotspot3d to 1.8.2 (#11521) * Update hotspot3d to 1.8.2 * Add perl-json as dependency * Add perl-archive-extract as dependency * Fqzcomp (#11606) * Added recipe for fqzcomp * There is no configure script * Maybe this works * Added gcc as build requirement * Removed gcc again (lint issue) * Maybe these exports will do the trick * Nope! * Added cxx as host requirement * Compilers are only allowed in build section * There is no need for make install * Copy-paste error... * Add vcf-annotator recipe (#11481) * Add vcf-annotator recipe * added pyvcf dependency * Update meta.yaml * stacks: fix for @ in exe_path (#11580) * stacks: fix for @ in exe_path * stacks: fixed path * New version with bugfix and different progressiveMauve version. (#11613) * Sspupdate (#11614) * New version with bugfix and different progressiveMauve version. * Keeping old version as folder. * Push build number. * Update SVDB to version 1.3.0 (#11506) * new file: recipes/svdb/1.1.2/meta.yaml renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch modified: recipes/svdb/meta.yaml * deleted: 1.1.2/meta.yaml deleted: 1.1.2/svdb.patch * Bump nanosim (#11608) * Bump nanosim * Add scipy as dep * Add recipe for perl-number-range (#11621) * New build for grid (#11620) * update grid * update build num * Recipe for das_tool 1.1.1 (#10528) * recipe for das_tool 1.1.1 * Add recipe for sompy (#11624) * cmake modified to build with NDEBUG (#11328) * cmake modified to build with NDEBUG * Update meta.yaml * new build with fasta test * new build with fasta test * Fix and unblacklist TwoPaCo (#11622) * Add recipe for TwoPaCo * Unblacklist twopaco * Modify and unblacklist recipe for ESTmapper (#11623) * Modify and unblacklist recipe for ESTmapper * Add patch * Modify and unblacklist recipe for Metaseq (#11625) * Fix recipe for metaseq and remove from blacklist * Remove build.sh * nextflow 18.10.1 build 2 (#11630) * Add Clust (#11619) * Add clust * Clean recipe * Add "noarch" * Add DOI * Add build file * Python 2.7 * Fix scikit-learn dependency * Trigger new build * Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631) - PureCN: adds support for specifying cores on command line - PURPLE: adds X library dependencies required for creating plots * scripts/travis-run.sh: added a cleaner method to check for env vars (#11612) * Increase the number of k value usable in bcalm (request by @Malfoy) (#11610) * Increase the number of k value usable in bcalm (request by @Malfoy) * Change compilation parameter to reduce memory impact of compilation * Update anndata to 0.6.11 (#11637) * Update nglview to 1.1.7 (#11643) * Update binsanity to 0.2.7.1 (#11644) * Update cgat-core to 0.5.4 (#11645) * Update nanosv to 1.2.2 (#11673) * Update abeona to 0.36.0 (#11670) * Update pyfaidx to 0.5.5.2 (#11659) * Update agfusion to 1.23 (#11668) * Update iqtree to 1.6.8 (#11686) * update iqtree to 1.6.8 * Trigger rebuild * Update validators to 0.12.2 (#11672) * Update python-edlib to 1.2.3.post1 (#11664) * update for Purge Haplotigs (#11690) * Update loompy to 2.0.16 (#11667) * Update loompy to 2.0.16 * Update meta.yaml * IgBLAST 1.10.0 (#11693) * Update wtforms-alchemy to 0.16.7 (#11679) * Update sickle to 0.6.4 (#11663) * Update sickle to 0.6.4 * Remove fn and libgcc runtime dep * Update confindr to 0.4.5 (#11696) * Batvi (#11695) * batvi initial * Guideline compatibility.. * Dummy test section.. * Missing java dependency.. * use openjdk instead of java-jdk .. * source specified in github .. * trigger build (package did not have batindel directory) .. * update SHA256 .. * update SHA256 .. * Update pythonpy to 0.4.11 (#11661) * Update cortexpy to 0.45.6 (#11660) * Update sevenbridges-python to 0.16.0 (#11674) * Update solvebio to 2.7.0 (#11657) * Update mathstats to 0.2.6.5 (#11656) * Update goatools to 0.8.9 (#11641) * Add gnies (#11627) * Add gnies * noarch python * Update meta.yaml * Add recipe for SKA v1.0 (#11581) * Add recipe for SKA v1.0 * Add lib path for zlib * Older gcc * Correct install dir * Try static linking * Dynamic linking on OS X * ldd command test * correct program * Remove ldd command * Add recipe for transit version 2.3.1 (#11701) * Add recipe for transit version 2.3.1 * Use skip, add spaces. * Update meta.yaml (#11699) * remove pyqi (#11704) * Update python-chado to 2.2.0 (#11714) * update python-chado * 2.2.1 * Update vcfanno to 0.3.1 (#11710) * FGMP-1.0.1 (#11278) * FGMP-1.0.1 recipe * remove unncessary build info * add r-nabor (#11716) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * add r-nabor recipe * update r-nabor recipe * update r-nabor recipe * r-pctgcdata (#11715) * r-pctgcdata * r-pctgcdata - fix * r-pctgcdata - fix * Update meta.yaml * Fix plek by a new branch (#11605) * Modify the PLEK recipe * Start fixing PLEK, though it requires compilation * update build.sh * update yaml * fix build.sh * update build.sh * Update recipe for plek * add bioconductor-chromvar recipe (#11718) * add bioconductor-chromvar recipe * fix bioconductor-tissueenrich * Apparently the popdel recipe didn't get correctly merged * Final merge conflicts * Update Moff to 2.0 (#11726) * ver. 2.0 * ver. 2.0 * fixing pymzml * moff2.0 recipe * Update meta.yaml * Update meta.yaml * Update pyensembl to 1.7.2 (#11685) * Update arvados-python-client to 1.2.0.20180905185317 (#11684) * Update fitter to 1.0.8 (#11683) * Update atropos to 1.1.19 (#11681) * Update xyalign to 1.1.5 (#11680) * Update illumina-utils to 2.5 (#11677) * Update toulligqc to 1.0 (#11675) * Fix some dependencies (#11725) With phyloseq 1.20: ̀``` Quitting from lines 74-113 (r_beta_diversity.Rmd) Error in .C(ape:::node_depth_edgelength, PACKAGE = "ape", as.integer(Ntip), : Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Calls: ... UniFrac -> fastUniFrac -> ape_node_depth_edge_length -> .C Execution halted ``` With vegan 2.5: ̀``` Quitting from lines 74-113 (r_beta_diversity.Rmd) Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N * : "veg_distance" not available for .C() for package "vegan" Calls: ... distance -> do.call -> do.call -> vegdist -> vegdist -> .C Execution halted ``` * Update card_trick to 0.1.2 (#11650) * Update sbpipe to 4.21.0 (#11653) * Update sbpipe to 4.21.0 * fix maintainer * adding iSEE (and one of its dependencies, scRNAseq) from R/Bioconductor (#8803) * added skeletons for both iSEE and scRNAseq, used in the examples and vignette * updated with new build system * specify r base version in recipe yaml * correct specification of version * linting the recipes by removing fn: field * removing version number of R, seem to be malformed? * specifying R version to build against * specifying R version to build against, both places * update stream to 0.3.0 (#11732) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * add bioconductor-chromvar recipe * update bioconductor-chromvar recipe * add r-nabor recipe * update r-nabor recipe * update bioconductor-chromvar recipe * update r-nabor recipe * update stream to 0.3.0 * update stream to 0.3.0 * Add r-goeveg (#11734) * r-goeveg * Remove "fn" * Bump ksw version to 0.2.1 (#11731) * Bumped gatk4 version (#11738) * Update: PureCN (1.13.1) with additional segmentation options (#11740) * Update scanpy-scripts to v0.0.3 (#11743) * Update to scanpy-scripts to v0.0.3 * update kipoi to 0.5.7 (#11744) * update kipoi * using the old hack of first installing the deps * Add kipoi_veff (#11745) * update kipoi * using the old hack of first installing the deps * added kipoi_veff * add kipoi_veff * add noarch: python * remove kipoiseq * Add kipoiseq (#11746) * update kipoi * using the old hack of first installing the deps * added kipoi_veff * add kipoi_veff * add noarch: python * remove kipoiseq * Add kipoiseq * Add bcftools affy2vcf version 1.9 plugin (#11382) * Removing dependencies (#11742) * Bumped fastq-screen version (#11739) * Add RNFtools 0.3.1.3 (#11747) * Add RNFtools 0.3.1.3 * Fix build * Remove argparse from dependencies * Skip py35 * Removing dependencies (#11749) * Removing dependencies * Removing pycompss dependency * Updated to version 1.0.5 (#11750) * Updated to version 1.0.5 * Update meta.yaml * tardis patch for issue 27 (sampling paired fastq) (#11755) * New recipe for GBSX. * Added build noarch: generic to keep CircleCI happy. * Added identifier for gbsx. * tardis update to 1.0.19 (fix paired fastq sampling) * tardis update to 1.0.19 (fix paired fastq sampling) * Update recipe for Circos (#11756) * Add libwebp as dependency * Ctat mut (#11759) * locking picard * picard version * Revert "Ctat mut (#11759)" (#11760) This reverts commit 6e152413d54aca8c0bb952d674974a0f8a9bc960. * picard version locked (#11761) * Add pymzml v0.7.10 (#11763) * MentaLiST: Remove old versions and pin dependencies in current versions (#10720) * Remove old versions and pin julia in current versions * Pin hdf5 * Pin hdf5=1.8.17 * Pin mpfr=3.1.* * Add build.sh for 0.1.9 * Use global pinning for hdf5 * Pin hdf5 again * Updated segemehl 0.2 added segemehl 0.3 (#11753) * Updated segemehl 0.2 added segemehl 0.3 * Update meta.yaml * skipping osx for now * Update prince to v1.1 (#11765) * update ruffus to version 2.8.0 (#11766) * update ruffus to version 2.8.0 * {AH} add licence file to about section * Fix docs (#11769) * Docs are currently broken, start fixing them * try again * Update: CNVkit (0.9.6dev) with GATK4 fixes (#11770) * Fix missing cortexpy dependency upgrade (#11768) * Fix missing cortexpy dependency upgrade * Bump build number * Removing dependencies --- recipes/biobb_model/build.sh | 3 +++ recipes/biobb_model/meta.yaml | 17 +++++------------ 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/recipes/biobb_model/build.sh b/recipes/biobb_model/build.sh index 4b2f81a4b0d0e..864d47dd4df73 100644 --- a/recipes/biobb_model/build.sh +++ b/recipes/biobb_model/build.sh @@ -9,3 +9,6 @@ cp $SP_DIR/biobb_model/model/mutate.py $PREFIX/bin/mutate chmod u+x $SP_DIR/biobb_model/model/fix_side_chain.py cp $SP_DIR/biobb_model/model/fix_side_chain.py $PREFIX/bin/fix_side_chain + +chmod u+x $SP_DIR/biobb_model/structure_checking/checkStruc.py +cp $SP_DIR/biobb_model/structure_checking/checkStruc.py $PREFIX/bin/checkStruc diff --git a/recipes/biobb_model/meta.yaml b/recipes/biobb_model/meta.yaml index 783ac3cc1ad98..005b30ac14e36 100644 --- a/recipes/biobb_model/meta.yaml +++ b/recipes/biobb_model/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_model" %} -{% set version = "0.0.6" %} +{% set version = "0.1.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "08a65063de45b6fafe1ccbc85197688c1571aacf1250c9f3a288a3885a2840f0" %} +{% set hash_value = "07a201ec93b9f5798afe3dfb22e90022880c43227db7f9587acb1ca48aa64122" %} package: name: '{{ name|lower }}' @@ -18,16 +18,12 @@ build: requirements: host: - - python >=3.5 + - python >=3 - setuptools - - mistune ==0.7.4 - - jsonschema ==2.6.0 - biobb_common - biopython run: - - python >=3.5 - - mistune ==0.7.4 - - jsonschema ==2.6.0 + - python >=3 - biobb_common - biopython @@ -35,18 +31,15 @@ test: imports: - biobb_model - biobb_model.model - - biobb_model.pycompss - - biobb_model.pycompss.model - biobb_model.structure_checking - biobb_model.structure_manager - - biobb_model.test about: home: https://github.com/bioexcel/biobb_model license: Apache Software License license_family: APACHE license_file: '' - summary: biobb_model is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. + summary: Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms. description: "[![Documentation Status](https://readthedocs.org/projects/biobb-model/badge/?version=latest)](https://biobb-model.readthedocs.io/en/latest/?badge=latest)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f98ed1286f244616bf39352e1877d310)](https://www.codacy.com/app/andriopau/biobb_model?utm_source=github.com&utm_medium=referral&utm_content=bioexcel/biobb_model&utm_campaign=Badge_Grade)\n\ \n# biobb_model\n\n### Introduction\nBiobb_model is the Biobb module collection to check and model 3d structures,\ncreate mutations or reconstruct missing atoms.\nBiobb (BioExcel building blocks) packages\ \ are Python building blocks that\ncreate new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs\ From a5431f8099c7818587001789eee1bfde538cd1e9 Mon Sep 17 00:00:00 2001 From: Winni Kretzschmar Date: Sun, 4 Nov 2018 21:16:00 +0100 Subject: [PATCH 043/546] Bump cortexpy to next patch version (#11771) --- recipes/cortexpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cortexpy/meta.yaml b/recipes/cortexpy/meta.yaml index 4713a4e341f14..d3ec6101a3bae 100644 --- a/recipes/cortexpy/meta.yaml +++ b/recipes/cortexpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cortexpy" %} -{% set version = "0.45.6" %} +{% set version = "0.45.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e70810bd10d8aad9c7f3ffc9bd1e6bd4af004aa9893da7ce0cc93a9c565e4f5e + sha256: '8a8abca578dbf1e637cfc8af67c9dc09bd0887e5a0c4055fe21937503577dfb5' build: skip: True # [not py36] From 1c94b38c871e23739d956ac3f3903a87e7b71709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Sun, 4 Nov 2018 22:44:08 +0100 Subject: [PATCH 044/546] Bump phylopandas to 0.7.1 (#11773) * Bump phylopandas * small fix --- recipes/phylopandas/build.sh | 3 --- recipes/phylopandas/meta.yaml | 27 ++++++++++++++------------- 2 files changed, 14 insertions(+), 16 deletions(-) delete mode 100644 recipes/phylopandas/build.sh diff --git a/recipes/phylopandas/build.sh b/recipes/phylopandas/build.sh deleted file mode 100644 index 5227f51eca79f..0000000000000 --- a/recipes/phylopandas/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record record.txt diff --git a/recipes/phylopandas/meta.yaml b/recipes/phylopandas/meta.yaml index 55ec9ba0180b5..9a83efa56b163 100644 --- a/recipes/phylopandas/meta.yaml +++ b/recipes/phylopandas/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "0.1.4" %} - +{% set version = "0.7.1" %} package: name: phylopandas - version: {{ version }} + version: "{{ version }}" source: url: https://pypi.io/packages/source/p/phylopandas/phylopandas-{{ version }}.tar.gz - sha256: a6e34e4b98a7b687fc24367b54042ae976b17565f2059bc549b6337247f14cad + sha256: 71567c4eefd4b807b18a26a79aa09ce2e88e05e08f719869d326aa2f90adfc0b build: noarch: python - number: 1 + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " requirements: host: - - python - - setuptools - - pandas - - biopython - + - pip + - python >3 run: - - python + - python >3 - pandas + - pandas-flavor - biopython + - dendropy test: imports: - phylopandas + - phylopandas.seqio + - phylopandas.treeio about: home: https://github.com/Zsailer/phylopandas - license: MIT License - summary: 'Pandas for phylogenetics' + license: MIT license_family: MIT + summary: Pandas for phylogenetics From 01556ac1df6a56535fd21ad268eaa96501eef43e Mon Sep 17 00:00:00 2001 From: Winni Kretzschmar Date: Mon, 5 Nov 2018 10:12:35 +0100 Subject: [PATCH 045/546] Bump abeonas cortexpy dependency patch version (#11774) --- recipes/abeona/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index f13f265198798..5703af8cd462d 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [not py36] - number: 1 + number: 2 entry_points: - abeona=abeona.__main__:main script: '$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv ' @@ -23,7 +23,7 @@ requirements: run: - mccortex ==1.0 - nextflow ==0.32.0 - - cortexpy ==0.45.6 + - cortexpy ==0.45.7 - kallisto ==0.44.0 - bwa - pandas From 124b13c520e3a3fd8d2399367e2700512d91016c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= Date: Mon, 5 Nov 2018 10:25:21 +0100 Subject: [PATCH 046/546] Macs2 update (#11741) * Updated macs2 and switch to cb3 * Added noarch and py2.7 only * Added static URL because of unusual filename * Refactored tests * Cleaned recipe, removed noarch * Final cleanup of meta.yaml * Added license file and r-base dependency * Re-added numpy requirement on host * Added r-base to host section --- recipes/macs2/build.sh | 18 ------------------ recipes/macs2/meta.yaml | 36 +++++++++++++++++++++++------------- 2 files changed, 23 insertions(+), 31 deletions(-) delete mode 100644 recipes/macs2/build.sh diff --git a/recipes/macs2/build.sh b/recipes/macs2/build.sh deleted file mode 100644 index c6e584384568c..0000000000000 --- a/recipes/macs2/build.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash - -if [[ `uname` == 'Darwin' ]]; then - export MACOSX_DEPLOYMENT_TARGET=10.9 -fi - -# From setup.py: User must check GCC, if >= 4.6, use -Ofast, otherwise -O3. -GCCVERSION=$( gcc -dumpversion ) -GCCVERSION_MAJOR=$(echo $GCCVERSION | awk 'BEGIN {FS="."}; {print $1}') -GCCVERSION_MINOR=$(echo $GCCVERSION | awk 'BEGIN {FS="."}; {print $2}') - -if [ $GCCVERSION_MAJOR -le 4 ]; then - if [ $GCCVERSION_MINOR -le 5 ]; then - sed -i'' -e 's/"-Ofast"/"-O3"/g' setup.py - fi -fi - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/macs2/meta.yaml b/recipes/macs2/meta.yaml index efab938e3a704..262b6c1040dee 100644 --- a/recipes/macs2/meta.yaml +++ b/recipes/macs2/meta.yaml @@ -1,31 +1,41 @@ +{% set name = "macs2" %} +{% set version = "2.1.2" %} + package: - name: macs2 - version: 2.1.1.20160309 + name: "{{ name|lower }}" + version: "{{ version }}" source: - url: https://pypi.python.org/packages/9f/99/a8ac96b357f6b0a6f559fe0f5a81bcae12b98579551620ce07c5183aee2c/MACS2-2.1.1.20160309.tar.gz - md5: 1cc2fab44b232992060c7ab592bf43fa + url: https://files.pythonhosted.org/packages/5e/32/0108a85d9a91c18413e8492bea631725cdbc20b45970ef63e8d0020ef2da/MACS2-2.1.2.1.tar.gz + sha256: 6ee9381bda61bacf65e2e31bde267cbcd61a1304457f8a00a0eb7632dd12419b build: - number: 3 + number: 0 skip: True # [py3k] + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " requirements: - build: - - {{ compiler('c') }} host: - python - - numpy + - pip + - numpy >=1.6 + - r-base run: + - numpy >=1.6 - python - - numpy - r-base test: commands: - - macs2 --version 2>&1 > /dev/null + - macs2 -h about: - home: https://github.com/taoliu/MACS/ - license: BSD New - summary: MACS -- Model-based Analysis of ChIP-Seq + home: http://github.com/taoliu/MACS/ + license: BSD + license_family: BSD + license_file: COPYING + summary: Model Based Analysis for ChIP-Seq data + +extra: + recipe-maintainers: + - jenzopr From 4cdd170a90df035d266004a5ececb6fbe0e045ae Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Mon, 5 Nov 2018 11:58:53 +0100 Subject: [PATCH 047/546] update to 2.2.2 (#11775) --- recipes/python-chado/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/python-chado/meta.yaml b/recipes/python-chado/meta.yaml index f2a3ff46723b7..7210f702b5db5 100644 --- a/recipes/python-chado/meta.yaml +++ b/recipes/python-chado/meta.yaml @@ -1,10 +1,10 @@ package: name: python-chado - version: "2.2.1" + version: "2.2.2" source: - url: https://files.pythonhosted.org/packages/56/d4/d2fc5dfa0ef39e01680033ca40c59934a409abe9320b8eb3f5830d42c86b/chado-2.2.1.tar.gz - sha256: b2f11fac0f950ddf6bfc1170a68c4c8a7dbb588d5046d42ae6191acc1f0bf547 + url: https://files.pythonhosted.org/packages/c6/25/f3f8e1a7434d844158e6ec206567e7046efb8ad73b89ae4a721a75bbfa2c/chado-2.2.2.tar.gz + sha256: 811275dbee9966b131a8f20017a942fe03d90b426ba62c0bec9eb98e81fae15c build: noarch: python From 47a73d1367244b929e314fb55c2e9a3abdb4f9cf Mon Sep 17 00:00:00 2001 From: Winni Kretzschmar Date: Mon, 5 Nov 2018 14:08:30 +0100 Subject: [PATCH 048/546] Bump abeona to 0.37.2 (#11777) --- recipes/abeona/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index 5703af8cd462d..c378ee5b181e9 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.36.0" %} -{% set sha256 = "1f48f6b83e66393da24e9774f17edc03703994c7f721bc09b17db8d089277f91" %} +{% set version = "0.37.2" %} +{% set sha256 = "567e48db7da42e51046098cd989d59c8ed597a0381cf94193dad755e994847b5" %} package: name: abeona @@ -11,7 +11,7 @@ source: build: skip: true # [not py36] - number: 2 + number: 0 entry_points: - abeona=abeona.__main__:main script: '$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv ' From cc57a0ff19849fce4151540f21a891e9f6514ec3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Pedro=20Camargo?= Date: Mon, 5 Nov 2018 13:20:42 -0200 Subject: [PATCH 049/546] Bump Clust to 1.8.7 (#11780) --- recipes/clust/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clust/meta.yaml b/recipes/clust/meta.yaml index 1f74aa6081db8..b1e264ee100ab 100644 --- a/recipes/clust/meta.yaml +++ b/recipes/clust/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clust" %} -{% set version = "1.8.4" %} +{% set version = "1.8.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1855b333fc18f7d788c640c678800bf032c466e565fe953bd7057f794a04adba + sha256: b65f2805788a0c197b1cf7dfadd247bd579e309bed068c48da234456fb327701 build: number: 0 From 64b12a4a89e3382f14429c2a52a5615ff9e8b37e Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Mon, 5 Nov 2018 14:27:59 -0800 Subject: [PATCH 050/546] Bracken: Only build py27 (#11700) * Only build py27 * Change installation location of two scripts * quote bash variables * Just added some whitespace to re-trigger build * Fix symlinks in build process --- recipes/bracken/build.sh | 8 +++++--- recipes/bracken/meta.yaml | 4 ++-- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/bracken/build.sh b/recipes/bracken/build.sh index bbc60ed73277c..4a4d3d5043039 100644 --- a/recipes/bracken/build.sh +++ b/recipes/bracken/build.sh @@ -1,11 +1,13 @@ #!/bin/bash -mkdir -p "${PREFIX}"/bin +mkdir -p "${PREFIX}"/bin/src sh install_bracken.sh cp bracken "${PREFIX}"/bin cp bracken-build "${PREFIX}"/bin -cp src/est_abundance.py "${PREFIX}"/bin && chmod +x "${PREFIX}"/bin/est_abundance.py -cp src/generate_kmer_distribution.py "${PREFIX}"/bin && chmod +x "${PREFIX}"/bin/generate_kmer_distribution.py +cp src/est_abundance.py "${PREFIX}"/bin/src && chmod +x "${PREFIX}"/bin/src/est_abundance.py +ln -s "${PREFIX}"/bin/src/est_abundance.py "${PREFIX}"/bin/est_abundance.py +cp src/generate_kmer_distribution.py "${PREFIX}"/bin/src && chmod +x "${PREFIX}"/bin/src/generate_kmer_distribution.py +ln -s "${PREFIX}"/bin/src/generate_kmer_distribution.py "${PREFIX}"/bin/generate_kmer_distribution.py cp src/kreport2mpa.py "${PREFIX}"/bin && chmod +x "${PREFIX}"/bin/kreport2mpa.py cp src/kmer2read_distr "${PREFIX}"/bin cp analysis_scripts/combine_bracken_outputs.py "${PREFIX}"/bin && chmod +x "${PREFIX}"/bin/combine_bracken_outputs.py diff --git a/recipes/bracken/meta.yaml b/recipes/bracken/meta.yaml index f4b53fea6095e..368eafa36f3d2 100644 --- a/recipes/bracken/meta.yaml +++ b/recipes/bracken/meta.yaml @@ -10,8 +10,8 @@ source: sha256: {{ sha256 }} build: - skip: True # [osx] - number: 0 + skip: True # [osx or not py27] + number: 1 requirements: build: From affca613ed3e6239dd1f8120ef5bdb45d3d020c3 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 6 Nov 2018 00:51:29 -0500 Subject: [PATCH 051/546] Update minimap2 to v2.14 (#11787) --- recipes/mappy/meta.yaml | 4 ++-- recipes/minimap2/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index 080dc7563f308..a27108593596a 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.13" %} +{% set version = "2.14" %} package: name: mappy @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/m/mappy/mappy-{{ version }}.tar.gz - sha256: 6a5008d53a44b157f39c5578fa6dce33ef3989270156f5e0a8fa08a19cfed21e + sha256: 3015c03141d3c7378329910f920d43739e569302245d602c60c31a9c5e864525 build: number: 0 diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 5e31ced962d0d..f545a377306de 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.13" %} +{% set version = "2.14" %} package: name: minimap2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/lh3/minimap2/archive/v{{ version }}.tar.gz - sha256: b6e4a3502eb4b7f9566f936d741a4749e5539b292ffd7bdbe84f600c77d2fa72 + sha256: 88abb9603ba244dae345932ae609faca7e62bb44ebaa9873aeec35c883e07a9e build: number: 0 From 6dd10e0732a0c97e012925ead62436a6ec7efb1b Mon Sep 17 00:00:00 2001 From: Adam Taranto Date: Mon, 5 Nov 2018 22:49:34 -0800 Subject: [PATCH 052/546] Update tirmite to v 1.1.1 (#11784) * Update tirmite to v 1.1.1 * Delete build.sh * skip py27 --- recipes/tirmite/build.sh | 3 --- recipes/tirmite/meta.yaml | 30 ++++++++++++++++++++---------- 2 files changed, 20 insertions(+), 13 deletions(-) delete mode 100644 recipes/tirmite/build.sh diff --git a/recipes/tirmite/build.sh b/recipes/tirmite/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/tirmite/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml index c28e37bab2061..90bedbb9990af 100644 --- a/recipes/tirmite/meta.yaml +++ b/recipes/tirmite/meta.yaml @@ -1,18 +1,25 @@ +{% set name = "tirmite" %} +{% set version = "1.1.1" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "b56ff33626253e95edc27af9503febc1ac5becaf00921acb2477b0d010790412" %} + package: - name: tirmite - version: "1.1.0" + name: '{{ name|lower }}' + version: '{{ version }}' source: - url: https://pypi.python.org/packages/10/66/4636b9a8a700dd417c5f4d7f1ef7e81f2aa3492372a22868f9c54b23e2dd/tirmite-1.1.0.tar.gz - md5: 1439e917c4d8449566f60cf5036ae1b1 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' build: - number: 1 skip: True # [py27] + number: 0 entry_points: - tirmite=tirmite.cmd_tirmite:main - tsplit-LTR=tirmite.cmd_LTR:main - tsplit-TIR=tirmite.cmd_TIR:main + script: python setup.py install --single-version-externally-managed --record=record.txt requirements: host: @@ -21,8 +28,6 @@ requirements: - pandas >=0.20.3 - biopython >=1.70 - pymummer >=0.10.3 - - run: - python - pandas >=0.20.3 @@ -32,7 +37,6 @@ requirements: test: imports: - tirmite - commands: - tirmite --help - tsplit-LTR --help @@ -41,6 +45,12 @@ test: about: home: https://github.com/Adamtaranto/TIRmite license: MIT License - summary: 'Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.' license_family: MIT - + license_file: '' + summary: Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons. + description: "Build profile Hidden Markov Models for Terminal Inverted repeat families (TIR-pHMMs) and map to genomic sequences for annotation of MITES and complete DNA-Transposons with variable internal sequence composition." + doc_url: '' + dev_url: '' + +extra: + recipe-maintainers: 'Adam Taranto' \ No newline at end of file From 203a9efff25130dce84946367a8b115dc2b4819f Mon Sep 17 00:00:00 2001 From: Joachim Wolff Date: Tue, 6 Nov 2018 10:33:50 +0100 Subject: [PATCH 053/546] Update to version 4 (#11788) --- recipes/hicmatrix/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hicmatrix/meta.yaml b/recipes/hicmatrix/meta.yaml index 6c3c3f4402498..037cd550a5e6e 100644 --- a/recipes/hicmatrix/meta.yaml +++ b/recipes/hicmatrix/meta.yaml @@ -1,10 +1,10 @@ package: name: hicmatrix - version: '3' + version: '4' source: - url: https://github.com/deeptools/HiCMatrix/archive/3.tar.gz - sha256: aa63dfda78779063b50af65a08d0bb8cba2d473a1caf10c28823ab868c838e48 + url: https://github.com/deeptools/HiCMatrix/archive/4.tar.gz + sha256: 6bcb5c72d4f3a310acda829b3c5a98573ed69d016f8185297ebd72a4430c2bcc build: number: 0 From 86be995e3da6d650fe45480c456f04967b57b022 Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Tue, 6 Nov 2018 11:43:07 +0100 Subject: [PATCH 054/546] Genenotebook (#11712) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number --- recipes/genenotebook/build.sh | 2 ++ recipes/genenotebook/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/build.sh b/recipes/genenotebook/build.sh index 360efc995f30e..9409c9c24712b 100644 --- a/recipes/genenotebook/build.sh +++ b/recipes/genenotebook/build.sh @@ -5,8 +5,10 @@ set -exo pipefail outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} mkdir -p $outdir $PREFIX/bin ls -l . + npm install --unsafe-perm METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle cp -R genenotebook_v${PKG_VERSION}/* $outdir + ln -s ${outdir}/genenotebook ${PREFIX}/bin/genenotebook diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index 31494fe13b885..34d3968ab72ea 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.5' %} -{% set sha256 = '6196e6c8ad3aebbd356f291f641f5a698f13f36578497f6534e70aee900dde05' %} +{% set version = '0.1.6' %} +{% set sha256 = '999e179d0d441b984ae661f134030893a3aab11048084794f38f1adcd48f089c' %} package: name: {{ name|lower }} From f5c1bc8209e907403cb79b20627e2bbe7287b762 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Tue, 6 Nov 2018 14:58:39 +0100 Subject: [PATCH 055/546] python-chado 2.2.3 (#11791) --- recipes/python-chado/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/python-chado/meta.yaml b/recipes/python-chado/meta.yaml index 7210f702b5db5..1260e341d88c4 100644 --- a/recipes/python-chado/meta.yaml +++ b/recipes/python-chado/meta.yaml @@ -1,10 +1,10 @@ package: name: python-chado - version: "2.2.2" + version: "2.2.3" source: - url: https://files.pythonhosted.org/packages/c6/25/f3f8e1a7434d844158e6ec206567e7046efb8ad73b89ae4a721a75bbfa2c/chado-2.2.2.tar.gz - sha256: 811275dbee9966b131a8f20017a942fe03d90b426ba62c0bec9eb98e81fae15c + url: https://files.pythonhosted.org/packages/b8/3c/88961886e414e1eb5f43c283e02ce2d598abebd63bcf61391851b7cf34fe/chado-2.2.3.tar.gz + sha256: 8b8aec89c4b14cd16793fa58c9634df9690ee0066d79a8ea6ff73d8e974b1a5d build: noarch: python From e195d56de55029563d8716707434993bfbcd101e Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Tue, 6 Nov 2018 09:56:49 -0500 Subject: [PATCH 056/546] Update: bcbio (1.1.1); TitanCNA (plot fix) (#11789) * Update: bcbio (1.1.1); TitanCNA (plot fix) * biocondcutor: ensure r-base in host * TitanCNA: add missing run dependencies --- recipes/bcbio-nextgen/meta.yaml | 10 +++++----- recipes/bioconductor-titancna/meta.yaml | 13 ++++++++++--- 2 files changed, 15 insertions(+), 8 deletions(-) diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 00548de786e81..3347ffc47a442 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -1,15 +1,15 @@ package: name: bcbio-nextgen - version: '1.1.1a' + version: '1.1.1' build: - number: 12 + number: 0 skip: true # [not py27] source: - #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.0.tar.gz - url: https://github.com/bcbio/bcbio-nextgen/archive/b84fc4e.tar.gz - sha256: 5ae203bbbdc7181397fff34a4de9c9f42aaa3aafb32fa7b3048c06576ad01024 + url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz + #url: https://github.com/bcbio/bcbio-nextgen/archive/b84fc4e.tar.gz + sha256: 756334f29c31d5bbf99014827b0bef8d9d3776dcfba8a7a780e8436adcde2fd5 requirements: host: diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 53161790bf015..54c5b6158c281 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -6,18 +6,19 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: https://github.com/gavinha/TitanCNA/archive/eb288ea.tar.gz + url: https://github.com/gavinha/TitanCNA/archive/8fb529d.tar.gz # - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' # - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' # - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6cb5349fedb9d6ab70b2c13b46eb9d83b12604f2b7d0ae0d8d91e62e6543897d + sha256: 81c071a64caa2c2384a9e25170ac9844183e2f2bf03d2a5c808e44d594cd4400 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: host: + - r-base 3.4.1 - perl # for adding in correct path references to scripts - 'bioconductor-genomeinfodb >=1.8.7' - 'bioconductor-genomicranges >=1.24.3' @@ -39,6 +40,12 @@ requirements: - 'bioconductor-rsamtools >=1.24.0' - 'bioconductor-variantannotation >=1.18.7' - 'r-foreach >=1.4.3' + - r-data.table + - r-dplyr + - r-optparse + - r-domc + - bioconductor-snpchip + - r-stringr build: - {{ compiler('c') }} - make From f0ac632c81a05e8215934d0d901137db31388aca Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Tue, 6 Nov 2018 09:24:05 -0600 Subject: [PATCH 057/546] Update recipe for Octopus (#11786) --- recipes/octopus/build.sh | 10 +++++++++- recipes/octopus/conda_build_config.yaml | 10 +++++----- recipes/octopus/meta.yaml | 26 +++++++++++++++++-------- 3 files changed, 32 insertions(+), 14 deletions(-) diff --git a/recipes/octopus/build.sh b/recipes/octopus/build.sh index 54fcff90de72f..66327ad0f861a 100755 --- a/recipes/octopus/build.sh +++ b/recipes/octopus/build.sh @@ -1,6 +1,14 @@ #!/bin/bash + set -eu -o pipefail +export CPATH=${PREFIX}/include +export CMAKE_LDFLAGS="-L${PREFIX}/lib" +export LIBRARY_PATH=${PREFIX}/lib + +# https://github.com/luntergroup/octopus/issues/38 +export HTSLIB_ROOT=${PREFIX}/lib + cd build -cmake -DINSTALL_PREFIX=ON -DCMAKE_INSTALL_PREFIX=$PREFIX -DINSTALL_ROOT=ON -DCMAKE_BUILD_TYPE=Release -DBOOST_ROOT=$PREFIX -DBoost_NO_SYSTEM_PATHS=ON .. +cmake -DINSTALL_PREFIX=ON -DCMAKE_INSTALL_PREFIX=${PREFIX}/bin -DINSTALL_ROOT=ON -DCMAKE_BUILD_TYPE=Release -DBOOST_ROOT=${PREFIX} -DBoost_NO_SYSTEM_PATHS=ON .. make install diff --git a/recipes/octopus/conda_build_config.yaml b/recipes/octopus/conda_build_config.yaml index a864705eed8d4..bb25bc7de033b 100644 --- a/recipes/octopus/conda_build_config.yaml +++ b/recipes/octopus/conda_build_config.yaml @@ -1,6 +1,6 @@ -c_compiler: - - gcc # [linux] - - clang # [osx] -cxx_compiler: - - gxx # [linux] +c_compiler: + - gcc # [linux] + - clang # [osx] +cxx_compiler: + - gxx # [linux] - clangxx # [osx] diff --git a/recipes/octopus/meta.yaml b/recipes/octopus/meta.yaml index f4edbf9356e0e..36a6a4f081dd3 100644 --- a/recipes/octopus/meta.yaml +++ b/recipes/octopus/meta.yaml @@ -1,19 +1,21 @@ -{% set version="0.5.1b" %} -about: - home: https://github.com/luntergroup/octopus - license: MIT - summary: Bayesian haplotype-based mutation calling +{% set name = "octopus" %} +{% set version = "0.5.2b" %} +{% set sha256 = "080e8946a3171769567c0b541b1c964b19148d4545f1c6767838b856a2804a05" %} + package: - name: octopus + name: {{ name }} version: {{ version }} + build: number: 0 # Not building on osx CircleCI and unsure how to fix; does not pick # up 7.2 compilers skip: true # [osx] + source: - url: https://github.com/luntergroup/octopus/archive/v0.5.1-beta.tar.gz - sha256: 51724a7d88df13cb213e6406b5693e236bcc68fbc1fedd39783ae175875558e1 + url: https://github.com/luntergroup/{{ name }}/archive/v0.5.2-beta.tar.gz + sha256: {{ sha256 }} + requirements: build: - {{ compiler('c') }} @@ -34,6 +36,14 @@ requirements: - bzip2 - xz - zlib + test: commands: - octopus -h + +about: + home: https://github.com/luntergroup/octopus + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework." From a7527429b3b1127a580f18e8846cb99bfffdc19e Mon Sep 17 00:00:00 2001 From: Shaun Jackman Date: Tue, 6 Nov 2018 07:56:44 -0800 Subject: [PATCH 058/546] abyss 2.1.3 (#11783) See https://github.com/bcgsc/abyss/releases/tag/2.1.3 --- recipes/abyss/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index 61df152743411..b2562fe774a61 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -1,5 +1,5 @@ {% set name = "abyss" %} -{% set version = "2.1.1" %} +{% set version = "2.1.3" %} package: name: {{ name|lower }} @@ -10,7 +10,7 @@ build: source: url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz - sha256: aca9e5ad984282ced81038dfc20205ba0bb59ff4edf427419451b632aa567e9f + sha256: 23a3e6562b2fa6f0e970d2c452ef98a799ac9892c86a7207f42c7a6ae6df09ab requirements: build: From 659916bed35ecf7ca24717086c5a03ffc5aa3228 Mon Sep 17 00:00:00 2001 From: lowandrew Date: Tue, 6 Nov 2018 11:14:31 -0500 Subject: [PATCH 059/546] Update ConFindr to 0.4.6 (#11797) --- recipes/confindr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/confindr/meta.yaml b/recipes/confindr/meta.yaml index 51fef3a1d4c09..24e6ff35ce578 100644 --- a/recipes/confindr/meta.yaml +++ b/recipes/confindr/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.5" %} -{% set sha256 = "9207a3c2ffb50af78e5284584eacd151a5173e356cb02c5ef4d7a4ade3223ee0" %} +{% set version = "0.4.6" %} +{% set sha256 = "8a387955ae904883c3cbcee26d9e1b5f1203c24fbdd3daa1400530a60bff87e6" %} package: name: confindr From 5393ac28c2793fae527a4cf535347894de4104a2 Mon Sep 17 00:00:00 2001 From: "Kevin R. Thornton" Date: Tue, 6 Nov 2018 08:18:44 -0800 Subject: [PATCH 060/546] bump libsequence to 1.9.6 (#11796) --- recipes/libsequence/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/libsequence/meta.yaml b/recipes/libsequence/meta.yaml index 76aa41fa61e3c..e0c0dc477bf88 100644 --- a/recipes/libsequence/meta.yaml +++ b/recipes/libsequence/meta.yaml @@ -1,11 +1,11 @@ package: name: libsequence - version: '1.9.5' + version: '1.9.6' source: - url: http://github.com/molpopgen/libsequence/archive/1.9.5.tar.gz - md5: 8750c44e5939f9d06dcc8acc676e95ba + url: http://github.com/molpopgen/libsequence/archive/1.9.6.tar.gz + md5: b497ca4ebf04019a9b9a814d7cb9f3f9 build: skip: True # [osx] @@ -18,7 +18,7 @@ requirements: test: commands: - - libsequenceConfig --version | grep 1.9.5 > /dev/null + - libsequenceConfig --version | grep 1.9.6 > /dev/null about: home: http://http://molpopgen.github.io/libsequence/ From 51df0844438fa8c391170912a916a91aac8c25d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 6 Nov 2018 18:23:50 +0100 Subject: [PATCH 061/546] Revert "Update to version 4 of HiCMatrix" (#11800) * Revert "bump libsequence to 1.9.6 (#11796)" This reverts commit 5393ac28c2793fae527a4cf535347894de4104a2. * Revert "Update ConFindr to 0.4.6 (#11797)" This reverts commit 659916bed35ecf7ca24717086c5a03ffc5aa3228. * Revert "abyss 2.1.3 (#11783)" This reverts commit a7527429b3b1127a580f18e8846cb99bfffdc19e. * Revert "Update recipe for Octopus (#11786)" This reverts commit f0ac632c81a05e8215934d0d901137db31388aca. * Revert "Update: bcbio (1.1.1); TitanCNA (plot fix) (#11789)" This reverts commit e195d56de55029563d8716707434993bfbcd101e. * Revert "python-chado 2.2.3 (#11791)" This reverts commit f5c1bc8209e907403cb79b20627e2bbe7287b762. * Revert "Genenotebook (#11712)" This reverts commit 86be995e3da6d650fe45480c456f04967b57b022. * Revert "Update to version 4 (#11788)" This reverts commit 203a9efff25130dce84946367a8b115dc2b4819f. --- recipes/hicmatrix/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hicmatrix/meta.yaml b/recipes/hicmatrix/meta.yaml index 037cd550a5e6e..6c3c3f4402498 100644 --- a/recipes/hicmatrix/meta.yaml +++ b/recipes/hicmatrix/meta.yaml @@ -1,10 +1,10 @@ package: name: hicmatrix - version: '4' + version: '3' source: - url: https://github.com/deeptools/HiCMatrix/archive/4.tar.gz - sha256: 6bcb5c72d4f3a310acda829b3c5a98573ed69d016f8185297ebd72a4430c2bcc + url: https://github.com/deeptools/HiCMatrix/archive/3.tar.gz + sha256: aa63dfda78779063b50af65a08d0bb8cba2d473a1caf10c28823ab868c838e48 build: number: 0 From 3ca5419f5504875fcbee65f8d752c0924ef4f4fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Tue, 6 Nov 2018 18:24:26 +0100 Subject: [PATCH 062/546] r-bedr (#11795) --- recipes/r-bedr/build.sh | 38 ++++++++++++++++++++++++++++++++ recipes/r-bedr/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 recipes/r-bedr/build.sh create mode 100644 recipes/r-bedr/meta.yaml diff --git a/recipes/r-bedr/build.sh b/recipes/r-bedr/build.sh new file mode 100644 index 0000000000000..0d4c7b256e696 --- /dev/null +++ b/recipes/r-bedr/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/bedr + mv * $PREFIX/lib/R/library/bedr + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-bedr/meta.yaml b/recipes/r-bedr/meta.yaml new file mode 100644 index 0000000000000..176019126776f --- /dev/null +++ b/recipes/r-bedr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = '1.0.4' %} + +package: + name: r-bedr + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/bedr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/bedr/bedr_{{ version }}.tar.gz + sha256: 435d5839e4b1f976832fa92f2c27c042ec6b0c65fb37eb9f846464f940b25a14 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-r.utils >=2.0.2 + - r-venndiagram >=1.6.4 + - r-data.table >=1.8.11 + - r-testthat >=0.7.1 + - r-yaml >=2.1.10 + + run: + - r-base + - r-r.utils >=2.0.2 + - r-venndiagram >=1.6.4 + - r-data.table >=1.8.11 + - r-testthat >=0.7.1 + - r-yaml >=2.1.10 + +test: + commands: + - $R -e "library('bedr')" + +about: + home: https://CRAN.R-project.org/package=bedr + license: GPL-2 + summary: Genomic regions processing using open-source command line tools such as 'BEDTools', + 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform + genome arithmetic e.g indexing, formatting and merging. bedr API enhances access + to these tools as well as offers additional utilities for genomic regions processing. + license_family: GPL2 From df4beb72c4e52c9408d86159ac1fd1823e6c58e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Pedro=20Camargo?= Date: Tue, 6 Nov 2018 18:14:21 -0200 Subject: [PATCH 063/546] Bump Clust to 1.8.9 (#11804) --- recipes/clust/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clust/meta.yaml b/recipes/clust/meta.yaml index b1e264ee100ab..12a12a163c0bd 100644 --- a/recipes/clust/meta.yaml +++ b/recipes/clust/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clust" %} -{% set version = "1.8.7" %} +{% set version = "1.8.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b65f2805788a0c197b1cf7dfadd247bd579e309bed068c48da234456fb327701 + sha256: 68a74dc267662e245facde8192ffbfc341626a089553a7f58c1954e7deb7ba1e build: number: 0 From e7433f805244c62a8b31e9299a0bd9cd44a2d1dc Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Wed, 7 Nov 2018 16:09:43 +0800 Subject: [PATCH 064/546] R shinyBS v0.25.0 (#11806) * add shinyBS 0.25 * update * update --- recipes/r-shinybs/build.sh | 2 ++ recipes/r-shinybs/meta.yaml | 29 +++++++++++++++++++++++++++++ 2 files changed, 31 insertions(+) create mode 100644 recipes/r-shinybs/build.sh create mode 100644 recipes/r-shinybs/meta.yaml diff --git a/recipes/r-shinybs/build.sh b/recipes/r-shinybs/build.sh new file mode 100644 index 0000000000000..e3921285a046d --- /dev/null +++ b/recipes/r-shinybs/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +R CMD INSTALL --build . diff --git a/recipes/r-shinybs/meta.yaml b/recipes/r-shinybs/meta.yaml new file mode 100644 index 0000000000000..ff2a2a7f87e99 --- /dev/null +++ b/recipes/r-shinybs/meta.yaml @@ -0,0 +1,29 @@ +package: + name: 'r-shinybs' + version: '0.25.0' +source: + url: + - 'https://github.com/likelet/shinyBS/archive/v0.25.0.tar.gz' + sha256: 5ec863bbbca3831094c81e552262730544e9efb0426c01b5caa4b51b539b005e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - {{ compiler('c') }} + host: + - r-base + - 'r-shiny >=0.8.0' + run: + - r-base + - 'r-shiny >=0.8.0' +test: + commands: + - '$R -e "library(shinyBS)"' +about: + date: '2014-03-13' + summary: 'Twitter Bootstrap Components for Shiny' + home: 'https://github.com/ebailey78/shinyBS' + license: 'GPL-3' From a89f819021f2a8caab1c481eb6937b87d45ccd12 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 7 Nov 2018 10:19:10 +0100 Subject: [PATCH 065/546] Revert "R shinyBS v0.25.0 (#11806)" (#11807) This reverts commit e7433f805244c62a8b31e9299a0bd9cd44a2d1dc. --- recipes/r-shinybs/build.sh | 2 -- recipes/r-shinybs/meta.yaml | 29 ----------------------------- 2 files changed, 31 deletions(-) delete mode 100644 recipes/r-shinybs/build.sh delete mode 100644 recipes/r-shinybs/meta.yaml diff --git a/recipes/r-shinybs/build.sh b/recipes/r-shinybs/build.sh deleted file mode 100644 index e3921285a046d..0000000000000 --- a/recipes/r-shinybs/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -R CMD INSTALL --build . diff --git a/recipes/r-shinybs/meta.yaml b/recipes/r-shinybs/meta.yaml deleted file mode 100644 index ff2a2a7f87e99..0000000000000 --- a/recipes/r-shinybs/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: 'r-shinybs' - version: '0.25.0' -source: - url: - - 'https://github.com/likelet/shinyBS/archive/v0.25.0.tar.gz' - sha256: 5ec863bbbca3831094c81e552262730544e9efb0426c01b5caa4b51b539b005e -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - {{ compiler('c') }} - host: - - r-base - - 'r-shiny >=0.8.0' - run: - - r-base - - 'r-shiny >=0.8.0' -test: - commands: - - '$R -e "library(shinyBS)"' -about: - date: '2014-03-13' - summary: 'Twitter Bootstrap Components for Shiny' - home: 'https://github.com/ebailey78/shinyBS' - license: 'GPL-3' From 0edd502e5a84776edaa20bff18dba5f7fc6f1c56 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Wed, 7 Nov 2018 04:40:02 -0500 Subject: [PATCH 066/546] Update meta.yaml (#11805) * Update meta.yaml * Update meta.yaml --- recipes/fgbio/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml index b692b06a089ae..6a2e69a8f447c 100644 --- a/recipes/fgbio/meta.yaml +++ b/recipes/fgbio/meta.yaml @@ -1,5 +1,5 @@ -{% set version="0.6.1" %} -{% set tag="ca68d7e" %} +{% set version="0.7.0" %} +{% set tag="0.7.0" %} about: home: https://github.com/fulcrumgenomics/fgbio @@ -12,11 +12,11 @@ package: build: noarch: python - number: 1 + number: 0 source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: c35286ccf82158ffcc8944a063461b9aa8636499bb99f9df92a592adba95c854 + sha256: 4369101434d0f46ac3063456403d9e1e1bc463ca983302eb52a6a68d93e57be1 requirements: host: From 37fe929fe829851c682f409c8d31f465f4d7e6de Mon Sep 17 00:00:00 2001 From: Eric Roberts Date: Wed, 7 Nov 2018 04:40:53 -0500 Subject: [PATCH 067/546] Update genomedata 1.4.1 to require older dependencies (#11799) --- recipes/genomedata/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml index 0957377086487..eac59d5e52315 100644 --- a/recipes/genomedata/meta.yaml +++ b/recipes/genomedata/meta.yaml @@ -24,7 +24,7 @@ build: - genomedata-close-data=genomedata._close_data:main - genomedata-report=genomedata._report:main - genomedata-erase-data=genomedata._erase_data:main - number: 2 + number: 3 requirements: build: @@ -34,14 +34,14 @@ requirements: - setuptools - forked-path - pytables >=3.4.3 - - textinput + - textinput <=0.1.1 - hgtools run: - python - forked-path - pytables >=3.4.3 - - textinput + - textinput <=0.1.1 - hgtools - bedtools - ucsc-bigwigtobedgraph From 3ae3898d245424c0263157683212449b38b784e1 Mon Sep 17 00:00:00 2001 From: Tom Smith Date: Wed, 7 Nov 2018 09:41:19 +0000 Subject: [PATCH 068/546] updates umi_tools dedpendencies (#11801) * updates umi_tools dedpendencies * Update meta.yaml --- recipes/umi_tools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/umi_tools/meta.yaml b/recipes/umi_tools/meta.yaml index 02d4ccbb8332b..a1170710e8034 100644 --- a/recipes/umi_tools/meta.yaml +++ b/recipes/umi_tools/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256hash }} build: - number: 2 + number: 3 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" entry_points: - umi_tools = umi_tools.umi_tools:main @@ -28,7 +28,7 @@ requirements: - setuptools >=1.1 - numpy >=1.7 - pandas >=0.12.0 - - pysam >=0.8.4 + - pysam >=0.9 - future run: - python @@ -37,7 +37,7 @@ requirements: - regex - numpy >=1.7 - pandas >=0.12.0 - - pysam >=0.8.4 + - pysam >=0.9 - future test: From d89628e28cb3cfdd23b5b668400c4a6c63c34a49 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Wed, 7 Nov 2018 12:11:46 +0100 Subject: [PATCH 069/546] Add comet-ms 2018012 (#11793) --- recipes/comet/build.sh | 6 ++++++ recipes/comet/meta.yaml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/comet/build.sh create mode 100644 recipes/comet/meta.yaml diff --git a/recipes/comet/build.sh b/recipes/comet/build.sh new file mode 100644 index 0000000000000..5679dcd163755 --- /dev/null +++ b/recipes/comet/build.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +chmod 755 comet.2018012.linux.exe +cp comet.2018012.linux.exe ${PREFIX}/bin/comet +cd ${PREFIX}/bin/ +ln -s comet comet.exe diff --git a/recipes/comet/meta.yaml b/recipes/comet/meta.yaml new file mode 100644 index 0000000000000..f26d43da19f95 --- /dev/null +++ b/recipes/comet/meta.yaml @@ -0,0 +1,30 @@ +{% set name = "comet-ms" %} +{% set version = "2018012" %} +{% set sha256_linux = "5ca42762884b74a62b21e6013e302cd291663361788a3a23ab195254976dbb99" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://sourceforge.net/projects/{{ name }}/files/comet_{{ version }}.zip + sha256: {{ sha256_linux }} + +build: + number: 0 + skip: True # [osx] + +test: + commands: + - comet.exe -p && rm comet.params.new + - comet -p && rm comet.params.new + +about: + home: http://comet-ms.sourceforge.net/ + license: Apache License 2.0 + summary: 'Comet is a command line tool that does MS/MS database search.' + +extra: + identifiers: + - doi:10.1007/s13361-015-1179-x + - doi:10.1002/pmic.201200439 From cd921daaef287ffc1b5897e466b9d3868febdbba Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Wed, 7 Nov 2018 06:11:54 -0500 Subject: [PATCH 070/546] Update: DeepVariant (0.7.1); bcbio (latest development) (#11810) --- recipes/bcbio-nextgen/meta.yaml | 10 +++++----- recipes/deepvariant/meta.yaml | 8 ++++---- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 3347ffc47a442..db0b44b865e75 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -1,15 +1,15 @@ package: name: bcbio-nextgen - version: '1.1.1' + version: '1.1.2a' build: number: 0 skip: true # [not py27] source: - url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz - #url: https://github.com/bcbio/bcbio-nextgen/archive/b84fc4e.tar.gz - sha256: 756334f29c31d5bbf99014827b0bef8d9d3776dcfba8a7a780e8436adcde2fd5 + #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz + url: https://github.com/bcbio/bcbio-nextgen/archive/8d40ce7.tar.gz + sha256: 138f2ce9d5ceb4183e066cb3af1e46208a15968fade11b7162ede8c3085e3295 requirements: host: @@ -34,7 +34,7 @@ requirements: - htslib - ipyparallel >=6.0.2 - ipython-cluster-helper >=0.6.1 - - joblib + - joblib >=0.12 - logbook - matplotlib - mock diff --git a/recipes/deepvariant/meta.yaml b/recipes/deepvariant/meta.yaml index cb518ff28a14e..f36676fbd6de8 100644 --- a/recipes/deepvariant/meta.yaml +++ b/recipes/deepvariant/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.0" %} -{% set sha256 = "d57b05385d9c371239b04a2b33bbcea14e998daf3a570df09f51267d2935fa97" %} +{% set version = "0.7.1" %} +{% set sha256 = "03228109600f944357b3536930f73553ae7714939f10a693394fe725811d5688" %} # When updating, also need to update model reference in post-link.sh package: @@ -40,8 +40,8 @@ requirements: - htslib - numpy - curl - - tensorflow 1.9.* - - protobuf 3.4.* + - tensorflow 1.11.* + - protobuf - contextlib2 - enum34 - intervaltree From 114dd390b6b48d2ed851d52370eb306f36ebb360 Mon Sep 17 00:00:00 2001 From: James Chuang Date: Wed, 7 Nov 2018 15:55:02 -0500 Subject: [PATCH 071/546] Fix detection of python 3 in when building MEME 5.0.2 (#11816) * Fix detection of python 3 in MEME build script. Add additional commands for tests. * Revert MEME test command to avoid MPI errors. * Make sed statement in meme-chip python 3 detection portable to BSD sed for macOS compatibility. Also add perl-file-which to requirements list, as it's listed as a missing requirement upon meme install. --- recipes/meme/build.sh | 6 +++--- recipes/meme/meta.yaml | 15 +++++++++++++-- 2 files changed, 16 insertions(+), 5 deletions(-) diff --git a/recipes/meme/build.sh b/recipes/meme/build.sh index 5e40faf7d09f8..0e1a9596b0ca4 100644 --- a/recipes/meme/build.sh +++ b/recipes/meme/build.sh @@ -22,8 +22,8 @@ ln -s $PREFIX/libexec/meme*/* $PREFIX/bin/ # if building with python3, # modify meme-chip script to use python3 version of DREME -if [[ $PGK_BUILDNUM == *"py3"* ]] -then - sed -i '994s/dreme/dreme-py3/' $PREFIX/bin/meme-chip +if [ $PY3K==1 ]; then + sed -i.bak '994s/dreme/dreme-py3/' $PREFIX/bin/meme-chip + rm $PREFIX/bin/meme-chip.bak fi diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml index 9a73d102910ed..53d86c3a1f8d1 100644 --- a/recipes/meme/meta.yaml +++ b/recipes/meme/meta.yaml @@ -11,7 +11,7 @@ source: - mast.patch build: - number: 4 + number: 5 detect_binary_files_with_prefix: True requirements: @@ -39,6 +39,7 @@ requirements: - perl-math-cdf - perl-log-log4perl - perl-json + - perl-file-which - openmpi run: - yaml @@ -60,14 +61,24 @@ requirements: - perl-math-cdf - perl-log-log4perl - perl-json + - perl-file-which - openmpi test: commands: - meme -version - - mast -version - meme-chip -version + - glam2 -version + - tomtom -version - centrimo -version + - ame -version + - spamo -version + - gomo -version + - fimo -version + - mast -version + - mcast -version + - glam2scan -version + - momo simple -version about: home: http://alternate.meme-suite.org/ From 7b11788ab996b3ec9943e9038248378a94ac4750 Mon Sep 17 00:00:00 2001 From: Carlos Date: Wed, 7 Nov 2018 22:03:00 +0100 Subject: [PATCH 072/546] PeptideShaker updated to v1.16.32 (#11812) SearchGUI updated to v3.3.6 --- recipes/peptide-shaker/meta.yaml | 4 ++-- recipes/peptide-shaker/peptide-shaker.py | 2 +- recipes/searchgui/meta.yaml | 4 ++-- recipes/searchgui/searchgui.py | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index a16d2a1b79a23..4ad480af43673 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PeptideShaker" %} -{% set version = "1.16.31" %} +{% set version = "1.16.32" %} # Do not forget to update the version string in the peptide-shaker.py file about: @@ -22,7 +22,7 @@ build: source: url: http://genesis.ugent.be/maven2/eu/isas/peptideshaker/{{ name }}/{{ version }}/{{ name }}-{{ version }}.zip - sha256: 7086bf35b9f0ac0ad52d940f782373cd05f0b5cac638d3e696311939de980602 + sha256: 4db6d3d4c23d0bf5679fe7514e5e8be39775c2cb7ff541ee7cd0d5fceac6b0ef requirements: host: diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index 4a1c38ebdd156..b2719b60397a0 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -13,7 +13,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'PeptideShaker-1.16.31.jar' +jar_file = 'PeptideShaker-1.16.32.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index a1a7e2b2f9e46..9d7e2003e0cbd 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SearchGUI" %} -{% set version = "3.3.5" %} +{% set version = "3.3.6" %} # Do not forget to update the version string in the searchgui.py file about: @@ -17,7 +17,7 @@ build: source: url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz - sha256: 331a109f63b1dc9a8f5b7b8c47fd59c04671b072e153bfd2e0a46b2fb4205443 + sha256: 6e22b4c2d37ef8e3e9edc2a07194b25aad69c0b38746651d64b795111e6c13c9 requirements: host: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index 1550fabf12cd5..c99de69aa287a 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -13,7 +13,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'SearchGUI-3.3.5.jar' +jar_file = 'SearchGUI-3.3.6.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] From 5eeef5c7ebaa4645387ed2d03e7050127a178c7a Mon Sep 17 00:00:00 2001 From: aemiol <38737287+aemiol@users.noreply.github.com> Date: Wed, 7 Nov 2018 19:24:42 -0500 Subject: [PATCH 073/546] update grid to use mosdepth (#11818) * update grid * update build num * edit grid to use mosdepth for depth coverage * Update meta.yaml --- recipes/grid/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/grid/meta.yaml b/recipes/grid/meta.yaml index edfa1b22ec8cb..0fb46766cf4b3 100644 --- a/recipes/grid/meta.yaml +++ b/recipes/grid/meta.yaml @@ -3,12 +3,12 @@ package: version: "1.1" build: - number: 1 - noarch: generic - + skip: True # [osx] + number: 2 + source: url: https://github.com/ohlab/GRiD/archive/1.1.tar.gz - sha256: cb2781d4b2d54da138042de9c4486d273f45282ad5f85c520a6e2087122784fd + sha256: d0cf0fc2407d4678e38c3bf9f895771d73a67505b9f27b065692785186b88b3f requirements: run: @@ -25,6 +25,7 @@ requirements: - seqtk - bedtools - blast + - mosdepth - readline>=6.2 test: From e680d9376dd82accb4b69669539f0f204992b1b9 Mon Sep 17 00:00:00 2001 From: Erik Kastman Date: Wed, 7 Nov 2018 18:48:34 -0600 Subject: [PATCH 074/546] CodingQuarry OSX Testing (#11815) * add CodingQuarry v2.0 recipe * re-try codingquarry with updated makefile and ananconda compilers * update build to make folders if doesnt exist * add biopython for accessory scripts and fix shebang * fix shebang for cufflinks python script * remove comma from cxxflags for mac * try adding llvm-openmp for build? * Try explicitly removing makefile CC and LDFLAG definitions * Build looks ok but test fails; try adding llvm-openmp to run requirements * Simplify CXXFLAGS assignment --- recipes/codingquarry/build.sh | 35 ++++++++++++++++++ recipes/codingquarry/conda_build_config.yaml | 6 +++ recipes/codingquarry/meta.yaml | 39 ++++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100755 recipes/codingquarry/build.sh create mode 100644 recipes/codingquarry/conda_build_config.yaml create mode 100644 recipes/codingquarry/meta.yaml diff --git a/recipes/codingquarry/build.sh b/recipes/codingquarry/build.sh new file mode 100755 index 0000000000000..8e561ee8d9c6a --- /dev/null +++ b/recipes/codingquarry/build.sh @@ -0,0 +1,35 @@ +#!/bin/sh + +#modify makefile to use correct compiler c++ +sed -i.bak -e 's/\${CC}/${CXX}/g' -e 's/\${CFLAGS}/${CXXFLAGS}/g' makefile + +#remove explicit CC, CXX, and LDFLAGS definitions to use conda ones +sed -i.bak '1,4d' makefile + +CXXFLAGS="$CXXFLAGS -fopenmp -g -O3" + +#now build +make + +#link +mkdir -p $PREFIX/bin +mv CodingQuarry $PREFIX/bin +sed -i.bak 's|/usr/bin/python|/usr/bin/env python|' CufflinksGTF_to_CodingQuarryGFF3.py +mv CufflinksGTF_to_CodingQuarryGFF3.py $PREFIX/bin +mv run_CQ-PM_mine.sh $PREFIX/bin +mv run_CQ-PM_stranded.sh $PREFIX/bin +mv run_CQ-PM_unstranded.sh $PREFIX/bin + +#fix scripts in QuarryFiles directory +if [ "$PY3K" == 1 ]; then + 2to3 -w $SRC_DIR/QuarryFiles/scripts/fastaTranslate.py +fi +sed -i.bak 's|/usr/bin/python|/usr/bin/env python|' $SRC_DIR/QuarryFiles/scripts/fastaTranslate.py +sed -i.bak 's|/usr/bin/python|/usr/bin/env python|' $SRC_DIR/QuarryFiles/scripts/gene_errors_Xs.py +sed -i.bak 's|/usr/bin/python|/usr/bin/env python|' $SRC_DIR/QuarryFiles/scripts/split_fasta.py +mkdir -p ${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION}/QuarryFiles +cp -R $SRC_DIR/QuarryFiles ${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION}/QuarryFiles + +#required ENV variable +mkdir -p ${PREFIX}/etc/conda/activate.d/ +echo "export QUARRYFILES=${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION}/QuarryFiles" > ${PREFIX}/etc/conda/activate.d/${PKG_NAME}-${PKG_VERSION}.sh diff --git a/recipes/codingquarry/conda_build_config.yaml b/recipes/codingquarry/conda_build_config.yaml new file mode 100644 index 0000000000000..a864705eed8d4 --- /dev/null +++ b/recipes/codingquarry/conda_build_config.yaml @@ -0,0 +1,6 @@ +c_compiler: + - gcc # [linux] + - clang # [osx] +cxx_compiler: + - gxx # [linux] + - clangxx # [osx] diff --git a/recipes/codingquarry/meta.yaml b/recipes/codingquarry/meta.yaml new file mode 100644 index 0000000000000..a4e78c8dee677 --- /dev/null +++ b/recipes/codingquarry/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "CodingQuarry" %} +{% set version = "2.0" %} +{% set sha256 = "1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://sourceforge.net/projects/codingquarry/files/{{ name }}_v{{ version}}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('cxx') }} + - llvm-openmp # [osx] + host: + - python + run: + - python + - biopython + - llvm-openmp # [osx] + +test: + commands: + - CodingQuarry 2>&1 | grep "CodingQuarry v. 2.0" + +about: + home: https://sourceforge.net/p/codingquarry/ + license: GPL-3 + license_family: GPL + summary: 'CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.' + +extra: + identifiers: + - doi:10.1186/s12864-015-1344-4 From 66d63ba671b0c35377e3712626fc3cf1a67ad496 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Wed, 7 Nov 2018 20:51:47 -0500 Subject: [PATCH 075/546] Update: vardict-java (1.5.8) (#11817) --- recipes/vardict-java/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vardict-java/meta.yaml b/recipes/vardict-java/meta.yaml index 730ab1c3042c0..fd39ee6fd0388 100644 --- a/recipes/vardict-java/meta.yaml +++ b/recipes/vardict-java/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.7" %} +{% set version = "1.5.8" %} package: name: vardict-java @@ -6,7 +6,7 @@ package: source: url: https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v{{ version }}/VarDict-{{ version }}.zip - sha256: 597fa238f6812123b715c0d324a2827910ff68e7a16e6c9e045d4e192e199fe6 + sha256: 36a177b06114ea939d24f7037b6e339b58e572763736a589232f0ced3731735b build: number: 0 From 6c6af5b31d1deca7483ed17b4efaa1843b59b1fc Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 8 Nov 2018 03:12:56 +0100 Subject: [PATCH 076/546] update openms recipe to 2.4.0 (#11779) * update openms recipe to 2.4.0 * reset build number * Update meta.yaml * Update meta.yaml --- recipes/openms/2.2.0/build.sh | 22 --------- recipes/openms/2.2.0/meta.yaml | 62 ------------------------ recipes/openms/{2.3.0 => }/activate.sh | 0 recipes/openms/{2.3.0 => }/build.sh | 0 recipes/openms/{2.3.0 => }/deactivate.sh | 0 recipes/openms/{2.3.0 => }/meta.yaml | 15 +++--- 6 files changed, 6 insertions(+), 93 deletions(-) delete mode 100644 recipes/openms/2.2.0/build.sh delete mode 100644 recipes/openms/2.2.0/meta.yaml rename recipes/openms/{2.3.0 => }/activate.sh (100%) rename recipes/openms/{2.3.0 => }/build.sh (100%) rename recipes/openms/{2.3.0 => }/deactivate.sh (100%) rename recipes/openms/{2.3.0 => }/meta.yaml (83%) diff --git a/recipes/openms/2.2.0/build.sh b/recipes/openms/2.2.0/build.sh deleted file mode 100644 index 96f523c71f792..0000000000000 --- a/recipes/openms/2.2.0/build.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/sh - -export C_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib -export LD_LIBRARY_PATH=${PREFIX}/lib - -mkdir contrib-build -cd contrib-build -cmake -DBUILD_TYPE=WILDMAGIC ../contrib - -cd .. -mkdir build -cd build - -ORIGIN='$ORIGIN' -export ORIGIN -LDFLAGS='-Wl,-rpath,$${ORIGIN}/../lib' - -cmake .. -DOPENMS_CONTRIB_LIBS='../../contrib-build' -DCMAKE_INSTALL_PREFIX=$PREFIX -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF -DBoost_LIB_VERSION=1.64.0 -DBoost_INCLUDE_DIR=$PREFIX/include -DBoost_LIBRARY_DIRS=$PREFIX/lib -DBoost_LIBRARIES=$PREFIX/lib -DBoost_DEBUG=ON -DBOOST_LIBRARYDIR=$PREFIX/lib/ -DBOOST_USE_STATIC=OFF - -make -j2 TOPP UTILS OpenMS -make install diff --git a/recipes/openms/2.2.0/meta.yaml b/recipes/openms/2.2.0/meta.yaml deleted file mode 100644 index 017e1efe2495e..0000000000000 --- a/recipes/openms/2.2.0/meta.yaml +++ /dev/null @@ -1,62 +0,0 @@ -{% set name = "OpenMS" %} -{% set version = "2.2.0" %} -{% set boost = "1.64" %} -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/OpenMS/OpenMS/releases/download/Release2.2.0/OpenMS-{{ version }}-src.tar.gz - sha256: 61e7d24890abb6f462e2f026efb0dc88b84639b228d96e919c8074d3b11d286e - -build: - number: 2 - skip: True # [py3k] - -requirements: - build: - - {{ compiler('cxx') }} - - cmake - host: - - glib - - autoconf - - automake - - python - - zlib - - libtool - - xerces-c - - gsl - - boost - - eigen - - glpk >=4.60 - - bzip2 - - qt <5 - - libsvm >=3.21 - - seqan-library ==1.4.2 - - coinmp - run: - - python - - glib - - zlib - - xerces-c - - gsl - - boost - - eigen - - glpk >=4.60 - - bzip2 - - qt <5 - - libsvm >=3.21 - - coinmp -test: - commands: - - FileMerger --help - -about: - home: https://github.com/OpenMS/OpenMS - license: BSD - summary: OpenMS is an open-source software C++ library for LC-MS data management and analyses - -extra: - identifiers: - - biotools:openms - - doi:10.1007/978-1-60761-987-1_23 diff --git a/recipes/openms/2.3.0/activate.sh b/recipes/openms/activate.sh similarity index 100% rename from recipes/openms/2.3.0/activate.sh rename to recipes/openms/activate.sh diff --git a/recipes/openms/2.3.0/build.sh b/recipes/openms/build.sh similarity index 100% rename from recipes/openms/2.3.0/build.sh rename to recipes/openms/build.sh diff --git a/recipes/openms/2.3.0/deactivate.sh b/recipes/openms/deactivate.sh similarity index 100% rename from recipes/openms/2.3.0/deactivate.sh rename to recipes/openms/deactivate.sh diff --git a/recipes/openms/2.3.0/meta.yaml b/recipes/openms/meta.yaml similarity index 83% rename from recipes/openms/2.3.0/meta.yaml rename to recipes/openms/meta.yaml index 009df279545b7..80ea2758e6ac5 100644 --- a/recipes/openms/2.3.0/meta.yaml +++ b/recipes/openms/meta.yaml @@ -1,16 +1,15 @@ {% set name = "OpenMS" %} -{% set version = "2.3.0" %} -{% set boost = "1.64" %} +{% set version = "2.4.0" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/OpenMS/OpenMS/releases/download/Release{{ version }}/OpenMS-{{ version }}-src.tar.gz - sha256: 574c3ea73ec3e57f87446a86563d2c954baa290b3cf72aff8fa149c2a086bba4 + sha256: 86e8176b0f89cc86a10f5c3e60c34140d591e9e6c85f129ccbfa13ecb16a9af2 build: - number: 3 + number: 0 # osx times out on travis skip: True # [py3k or osx] @@ -21,23 +20,21 @@ requirements: - autoconf - automake host: - - glib - python - zlib - libtool - xerces-c - gsl - - boost + - boost =1.64 - eigen - glpk >=4.60 - bzip2 - - qt <5 + - qt >=5.5 - libsvm >=3.21 - seqan-library ==1.4.2 - coinmp run: - python - - glib - zlib - xerces-c - gsl @@ -45,7 +42,7 @@ requirements: - eigen - glpk >=4.60 - bzip2 - - qt <5 + - qt >=5.5 - libsvm >=3.21 - coinmp test: From 84d45d035a42bbbd05f961d92fb927e3d141c9d6 Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Thu, 8 Nov 2018 10:40:00 +0300 Subject: [PATCH 077/546] Feature/pheniqs (#11819) --- recipes/pheniqs/build.sh | 3 +-- recipes/pheniqs/meta.yaml | 10 +++++----- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/recipes/pheniqs/build.sh b/recipes/pheniqs/build.sh index f4e3bde884cf0..f1a33b27da973 100644 --- a/recipes/pheniqs/build.sh +++ b/recipes/pheniqs/build.sh @@ -5,6 +5,5 @@ set -x -e export LD_LIBRARY_PATH="${PREFIX}/lib" make all PREFIX=${PREFIX} make install PREFIX=${PREFIX} +make test -#This is really a test -pheniqs demux --config test/000000000-BDGGG/demultiplex.json -VD diff --git a/recipes/pheniqs/meta.yaml b/recipes/pheniqs/meta.yaml index 9e9784ab43dc3..69b993adf18aa 100644 --- a/recipes/pheniqs/meta.yaml +++ b/recipes/pheniqs/meta.yaml @@ -1,16 +1,16 @@ {% set name = "pheniqs" %} -{% set version = "2.0.3" %} -{% set sha256 = "c8d031ce93cadeb66ab6eb59aca77f101b48cbfbaeae17e7f59f849bd7c36c9d" %} +{% set version = "2.0.6" %} +{% set sha256 = "ecfbe45a1eb5436bbfe2139b29c05d3c6339cf51012ebcab30732f0d178619e0" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 source: - url: https://github.com/biosails/{{ name }}/archive/{{ version }}-beta.tar.gz + url: https://github.com/biosails/{{name}}/archive/{{version}}.tar.gz sha256: {{ sha256 }} requirements: @@ -27,13 +27,13 @@ requirements: - rapidjson - samtools - htslib + - python - zlib test: commands: - pheniqs --version - pheniqs --help - - pheniqs demux --help about: home: http://biosails.github.io/pheniqs From 13839782fbc945b6222c565ddb2c8efa4180bd6c Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Thu, 8 Nov 2018 11:15:17 +0100 Subject: [PATCH 078/546] Update Picard to 2.18.16 (#11820) --- recipes/picard/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index 5ef728bd5b34f..6a98ff39cd676 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.18.15" %} -{% set sha256 = "f4f521f57a199b1884982a34938af0e70939bbbe7b818795288810529558f480" %} +{% set version = "2.18.16" %} +{% set sha256 = "0aae8886ab29b9eeb40118994ad944fed2e1d043b5a5dc497884b5795a42e975" %} package: name: picard From 8ee8981270bcece66bf5aac7d1c8ae6ad5934404 Mon Sep 17 00:00:00 2001 From: Matthias De Smet Date: Thu, 8 Nov 2018 12:13:34 +0100 Subject: [PATCH 079/546] VEP: bump subversion (#11821) --- recipes/ensembl-vep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml index aeb3f7f4830d7..88544b483519e 100644 --- a/recipes/ensembl-vep/meta.yaml +++ b/recipes/ensembl-vep/meta.yaml @@ -1,4 +1,4 @@ -{% set version="94.4" %} +{% set version="94.5" %} package: name: ensembl-vep @@ -6,7 +6,7 @@ package: source: url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz - sha256: 6bc9550190299e04435e99538292502fe385627687181cd6b7728aeea51582e6 + sha256: 2ca9675b0775e21725ee0d0f1058a8f31fc2fdd9520e7bf11c70f3f19cb4ba94 build: number: 0 From 28a4e562d7491482c18d410154c6985864bbbc93 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Thu, 8 Nov 2018 14:55:35 +0100 Subject: [PATCH 080/546] prosolo recipe update to version 0.5.0 (#11814) * prosolo: update version number, sha256 and repo URL * prosolo: bump rust requirement to current version * prosolo: remove version specific dependency comments * prosolo: remove patch from build.sh, hoping conda build is beyond 3.0.10 * prosolo: remove OSX skipping, hoping it will work with current rust * prosolo: update cargo build command * prosolo: manually set HOME for OSX, which is not set properly and needed by cargo * prosolo: add git config for cargo on OSX to function properly, thanks to @natir for the solution provided in: * remove /usr/lib64 from LIBRARY_PATH, as this troubles OSX * prosolo: put back clangdev dependencies * prosolo: try OSX fix with pkg-config build dep --- recipes/prosolo/build.sh | 17 +++++++++++------ recipes/prosolo/meta.yaml | 18 +++++++----------- 2 files changed, 18 insertions(+), 17 deletions(-) diff --git a/recipes/prosolo/build.sh b/recipes/prosolo/build.sh index 7dfbd2f05df46..f6c2c64f42392 100644 --- a/recipes/prosolo/build.sh +++ b/recipes/prosolo/build.sh @@ -1,10 +1,15 @@ #!/bin/bash -euo -# circumvent a bug in conda-build >=2.1.18,<3.0.10 -# https://github.com/conda/conda-build/issues/2255 -# TODO: remove once CI uses conda-build >=3.0.10 -[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE -[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE +# taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh +if [ "$(uname)" == "Darwin" ]; then + + # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory + export HOME="/Users/distiller" + + # according to https://github.com/rust-lang/cargo/issues/2422#issuecomment-198458960 removing circle ci default configuration solves cargo trouble downloading crates + git config --global --unset url.ssh://git@github.com.insteadOf + +fi # build statically linked binary with Rust -C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib:/usr/lib64 cargo install --root $PREFIX --verbose --debug +C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib cargo install --path . --root $PREFIX --verbose --debug diff --git a/recipes/prosolo/meta.yaml b/recipes/prosolo/meta.yaml index 4dd0019fdf931..282916fc2819e 100644 --- a/recipes/prosolo/meta.yaml +++ b/recipes/prosolo/meta.yaml @@ -1,28 +1,25 @@ -{% set version = "0.4.0" %} +{% set version = "0.5.0" %} package: name: prosolo version: {{ version }} build: - # only on OSX, `cargo install` fails with: `thread 'main' panicked at 'assertion failed: src_path.is_absolute()', src/tools/cargo/src/cargo/core/manifest.rs:311` - # looks like a `cargo` bug, that may go away with newer `rust` versions; check osx with rust>1.21 when available - skip: True # [not linux64] - number: 4 + number: 0 source: - url: https://github.com/PROSIC/prosolo/archive/v{{ version }}.tar.gz - md5: 6b91b9a3dfb915891fb9df702249ff99 + url: https://github.com/prosolo/prosolo/archive/v{{ version }}.tar.gz + sha256: a778c5cab84b38842b7a80772c85e8bc590e25caca0f405711af7f60e8762ba6 requirements: build: - {{ compiler('c') }} + - rust >=1.30 + - pkg-config #[osx] host: - - rust >=1.21 - gsl - openblas - zlib - # new cram dependencies for rust-htslib 0.16.0 - bzip2 - xz - clangdev @@ -30,7 +27,6 @@ requirements: - gsl - openblas - zlib - # new cram dependencies for rust-htslib 0.16.0 - bzip2 - xz - clangdev @@ -40,6 +36,6 @@ test: - prosolo single-cell-bulk --help about: - home: https://github.com/PROSIC/prosolo/tree/v{{ version }} + home: https://github.com/prosolo/prosolo/tree/v{{ version }} license: GPLv3 summary: A highly sensitive and accurate Bayesian caller for variants in single cell sequencing data. From cc49407c832689a5b12b8f059a7f5488520957a0 Mon Sep 17 00:00:00 2001 From: Sebastian Roskosch Date: Thu, 8 Nov 2018 18:26:21 +0100 Subject: [PATCH 081/546] Update PopDel to version 1.0.3 (#11811) --- recipes/popdel/Makefile.patch | 16 ++++++++-------- recipes/popdel/meta.yaml | 6 +++--- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/recipes/popdel/Makefile.patch b/recipes/popdel/Makefile.patch index a69bce3dff8ef..c2e3da1675e7a 100644 --- a/recipes/popdel/Makefile.patch +++ b/recipes/popdel/Makefile.patch @@ -9,21 +9,21 @@ - -CXX=g++ CC=$(CXX) - + # Set this to include SeqAn libraries, either system wide @@ -14,14 +7,13 @@ CXXFLAGS+=-I$(SEQAN_LIB) -DSEQAN_HAS_ZLIB=1 -std=c++14 -DSEQAN_DISABLE_VERSION_CHECK LDLIBS=-lz -lpthread - + -DATE=on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1) --VERSION=1.0.2-$(shell git log --pretty=format:"%h" --date=iso | head -n 1) -+DATE=on 2018-10-18 -+VERSION=1.0.2 +-VERSION=1.0.3-$(shell git log --pretty=format:"%h" --date=iso | head -n 1) ++DATE=on 2018-11-07 ++VERSION=1.0.3 CXXFLAGS+=-DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\" - + # Enable warnings CXXFLAGS+=-W -Wall -Wno-long-long -pedantic -Wno-variadic-macros -Wno-unused-result - + - HEADERS=parse_popdel.h insert_histogram_popdel.h workflow_popdel.h utils_popdel.h popdel_view_parameter_parsing.h HEADERS+=popdel_profile/*.h @@ -31,7 +31,7 @@ @@ -30,14 +22,6 @@ all: CXXFLAGS+=-O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 all: popdel - + -.PHONY: profiling -profiling: CXXFLAGS+=-g -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=1 -profiling: popdel diff --git a/recipes/popdel/meta.yaml b/recipes/popdel/meta.yaml index 906833101c19a..406e3bd7d5566 100644 --- a/recipes/popdel/meta.yaml +++ b/recipes/popdel/meta.yaml @@ -1,10 +1,10 @@ package: name: popdel - version: "1.0.2" + version: "1.0.3" source: - url: https://github.com/kehrlab/PopDel/archive/v1.0.2.tar.gz - sha256: 606d18e87dc0cd83265b1cc976a1a153637e948fff1af2f9929f043fac991e01 + url: https://github.com/kehrlab/PopDel/archive/v1.0.3.tar.gz + sha256: ec25d48354a20869095c5b5658de3b6b6ca2acf05670d4bf3e67d9a66a72368d patches: - Makefile.patch From e73133839ff074e7efda82be64db7c021ea044c9 Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Thu, 8 Nov 2018 14:10:15 -0500 Subject: [PATCH 082/546] Bioconductor BiocOncoTK (#11826) * Recipe contributes bioconcotk, It is a "test" recipe, to see how bioconductor-skeleton creates the conda recipe. It is also used to test the python code in bioconductor-skeleton, within the bioconda-utils package. * Change R version so that it builds latest release * Update meta.yaml * Create conda_build_config.yaml --- recipes/bioconductor-bioconcotk/build.sh | 4 ++ .../conda_build_config.yaml | 2 + recipes/bioconductor-bioconcotk/meta.yaml | 48 +++++++++++++++++++ 3 files changed, 54 insertions(+) create mode 100644 recipes/bioconductor-bioconcotk/build.sh create mode 100644 recipes/bioconductor-bioconcotk/conda_build_config.yaml create mode 100644 recipes/bioconductor-bioconcotk/meta.yaml diff --git a/recipes/bioconductor-bioconcotk/build.sh b/recipes/bioconductor-bioconcotk/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-bioconcotk/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioconcotk/conda_build_config.yaml b/recipes/bioconductor-bioconcotk/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-bioconcotk/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-bioconcotk/meta.yaml b/recipes/bioconductor-bioconcotk/meta.yaml new file mode 100644 index 0000000000000..cf72e0a081743 --- /dev/null +++ b/recipes/bioconductor-bioconcotk/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.3" %} +{% set name = "BiocOncoTK" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 76b8e4f16e37ce7f2426d14af6a86b8735e74d20ecff86651b0f6e93c0dcc714 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - bioconductor-complexheatmap + - bioconductor-s4vectors + - r-base + - r-bigrquery + - r-dplyr + - r-dt + - r-httr + - r-magrittr + - r-rjson + - r-shiny + run: + - bioconductor-complexheatmap + - bioconductor-s4vectors + - r-base + - r-bigrquery + - r-dplyr + - r-dt + - r-httr + - r-magrittr + - r-rjson + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provide a central interface to various tools for genome-scale analysis of cancer studies.' From 9c5f438ef2847a88c54319064b3a33252efbc1cd Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Thu, 8 Nov 2018 14:35:32 -0500 Subject: [PATCH 083/546] Revert "Bioconductor BiocOncoTK (#11826)" (#11828) This reverts commit e73133839ff074e7efda82be64db7c021ea044c9. --- recipes/bioconductor-bioconcotk/build.sh | 4 -- .../conda_build_config.yaml | 2 - recipes/bioconductor-bioconcotk/meta.yaml | 48 ------------------- 3 files changed, 54 deletions(-) delete mode 100644 recipes/bioconductor-bioconcotk/build.sh delete mode 100644 recipes/bioconductor-bioconcotk/conda_build_config.yaml delete mode 100644 recipes/bioconductor-bioconcotk/meta.yaml diff --git a/recipes/bioconductor-bioconcotk/build.sh b/recipes/bioconductor-bioconcotk/build.sh deleted file mode 100644 index da43ce2168312..0000000000000 --- a/recipes/bioconductor-bioconcotk/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioconcotk/conda_build_config.yaml b/recipes/bioconductor-bioconcotk/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-bioconcotk/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-bioconcotk/meta.yaml b/recipes/bioconductor-bioconcotk/meta.yaml deleted file mode 100644 index cf72e0a081743..0000000000000 --- a/recipes/bioconductor-bioconcotk/meta.yaml +++ /dev/null @@ -1,48 +0,0 @@ -{% set version = "1.0.3" %} -{% set name = "BiocOncoTK" %} -{% set bioc = "3.7" %} - -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 76b8e4f16e37ce7f2426d14af6a86b8735e74d20ecff86651b0f6e93c0dcc714 -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - host: - - bioconductor-complexheatmap - - bioconductor-s4vectors - - r-base - - r-bigrquery - - r-dplyr - - r-dt - - r-httr - - r-magrittr - - r-rjson - - r-shiny - run: - - bioconductor-complexheatmap - - bioconductor-s4vectors - - r-base - - r-bigrquery - - r-dplyr - - r-dt - - r-httr - - r-magrittr - - r-rjson - - r-shiny -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provide a central interface to various tools for genome-scale analysis of cancer studies.' From c1a8ba786d7442c58f0a9a87f516ee6ddabae89e Mon Sep 17 00:00:00 2001 From: Len Trigg Date: Fri, 9 Nov 2018 09:49:17 +1300 Subject: [PATCH 084/546] rtg-tools: update to 3.10 (#11829) --- recipes/rtg-tools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/rtg-tools/meta.yaml b/recipes/rtg-tools/meta.yaml index d6128bf196e15..cec61dc3245df 100644 --- a/recipes/rtg-tools/meta.yaml +++ b/recipes/rtg-tools/meta.yaml @@ -1,14 +1,14 @@ -{% set version="3.9.1" %} +{% set version="3.10" %} package: name: rtg-tools version: {{ version }} source: url: https://github.com/RealTimeGenomics/rtg-tools/releases/download/{{ version }}/rtg-tools-{{ version }}-nojre.zip - md5: e56e9737db69f49ba71575c5450ab5c1 + md5: 9bce7766a5b7e5b6852e585519a01f4e build: - number: 1 + number: 0 noarch: generic requirements: From 3189b0bce4a6e2aac2dbd4dbcff4e7ea7089589c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 18:30:30 -0700 Subject: [PATCH 085/546] Update alfred to 0.1.15 (#11831) --- recipes/alfred/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index 430d3bbc993c2..d029f68ee0eb1 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.13" %} -{% set sha256 = "5ef66a11f74c97c4dc9e20f1c9982d3881d64e50b8d2ece2fc240c3429940120" %} +{% set version = "0.1.15" %} +{% set sha256 = "a5a18129019821fac8b346166820d70604190ba36f5a8051f11433de8e9f8478" %} package: name: alfred From b056de4dfe628f3ac200ee90aad59952e1013c31 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 19:07:55 -0700 Subject: [PATCH 086/546] Update anndata to 0.6.13 (#11833) --- recipes/anndata/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/anndata/meta.yaml b/recipes/anndata/meta.yaml index cf3a50899a2a5..16249d12d134e 100644 --- a/recipes/anndata/meta.yaml +++ b/recipes/anndata/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.11" %} -{% set sha256 = "21bc16ea08c0f46e9c7139ba9762cd26329fe7f30a4c5159f85389c9a3626407" %} +{% set version = "0.6.13" %} +{% set sha256 = "0b5109e27b8f83ff57b22c97941c0a1782afa0b927a9fae9be2618fbd056409a" %} package: name: anndata From 9402d4ae048f27f6bf6d16ba860610c9b776da4f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 19:08:11 -0700 Subject: [PATCH 087/546] Update bioconductor-compass to 1.18.1 (#11832) --- recipes/bioconductor-compass/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index 658e44863a54b..ec454ae0f7efa 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.18.0" %} +{% set version = "1.18.1" %} {% set name = "COMPASS" %} {% set bioc = "3.7" %} @@ -10,7 +10,7 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a25c213a31ea4c63c54793cc448cb841d2dfda9e45e4db70b6c8a131cdd0b114 + sha256: be92660b167bf8c89d6091e3e5b5cdc25a4d9e6d4881a7799a986504543a4da0 build: number: 0 rpaths: From 57b0e3b0558677b2a63f752dd1dfd0e2f7ba366d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 19:44:01 -0700 Subject: [PATCH 088/546] Update arvados-python-client to 1.2.0.20181108215719 (#11836) --- recipes/arvados-python-client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index 44e74758c3246..f7eb174af3e95 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.2.0.20180905185317" %} +{% set version="1.2.0.20181108215719" %} package: name: arvados-python-client @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - sha256: 87d79e15cbeb1659d4a44c3d844455c697a191d6fb9e3cef6c5eaf9a3af6ccc3 + sha256: 19343aa6051c11192f54e4c06e74a65b0f7d27bc0256f4fe2c379a964f9eeed3 build: number: 0 From ea4da3ecd0d1a0ca483de4ca4216c265bae1dd23 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 19:54:50 -0700 Subject: [PATCH 089/546] Update abeona to 0.39.3 (#11834) --- recipes/abeona/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index c378ee5b181e9..73ed9ec00de34 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.37.2" %} -{% set sha256 = "567e48db7da42e51046098cd989d59c8ed597a0381cf94193dad755e994847b5" %} +{% set version = "0.39.3" %} +{% set sha256 = "2acf5851b025a29f8f97d96377349ffa5bb04ac2e5ad4cc1ef375b79fa55f724" %} package: name: abeona From 7f29b4633618060e437afe3ce920e6e067c5fa46 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 20:10:54 -0700 Subject: [PATCH 090/546] Update sccaller to 1.21 (#11597) * Update sccaller to 1.21 * hard-code `v1.2` in file name, see source repo --- recipes/sccaller/build.sh | 8 ++++++-- recipes/sccaller/meta.yaml | 6 +++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/sccaller/build.sh b/recipes/sccaller/build.sh index bc327a48345ff..192d7b9b33a12 100644 --- a/recipes/sccaller/build.sh +++ b/recipes/sccaller/build.sh @@ -4,7 +4,11 @@ set -eu -o pipefail SHARE=share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $PREFIX/$SHARE mkdir -p $PREFIX/bin -cp $SRC_DIR/${PKG_NAME}_v$PKG_VERSION.py $PREFIX/$SHARE/${PKG_NAME}_v$PKG_VERSION.py + +# TODO: substitute `v1.2` with variable or remove, depending on upstream decision at +cp $SRC_DIR/${PKG_NAME}_v1.2.py $PREFIX/$SHARE/${PKG_NAME}_v1.2.py + echo "#!/usr/bin/env bash" >$PREFIX/bin/sccaller -echo "python2.7 $PREFIX/$SHARE/${PKG_NAME}_v$PKG_VERSION.py \$@" >>$PREFIX/bin/sccaller +# TODO: substitute `v1.2` with variable or remove, depending on upstream decision at +echo "python2.7 $PREFIX/$SHARE/${PKG_NAME}_v1.2.py \$@" >>$PREFIX/bin/sccaller chmod 0755 "${PREFIX}/bin/sccaller" diff --git a/recipes/sccaller/meta.yaml b/recipes/sccaller/meta.yaml index 5b74ad4beb475..1a485ad03da56 100644 --- a/recipes/sccaller/meta.yaml +++ b/recipes/sccaller/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SCcaller" %} -{% set version = "1.2" %} +{% set version = "1.21" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/biosinodx/{{ name }}/archive/v{{ version }}.tar.gz - md5: 757efa2a758004136d79faa65bdd4d71 + sha256: d7895e6319390641715054af7abed940ba20a99f4b1079334ce7a94a5e365f75 build: - number: 1 + number: 0 skip: True # [not py27] requirements: From 3374fd02bf5edf76c73968400c611e081306e624 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 8 Nov 2018 20:50:10 -0700 Subject: [PATCH 091/546] Update fastp to 0.19.5 (#11839) --- recipes/fastp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fastp/meta.yaml b/recipes/fastp/meta.yaml index 9e4d773a31706..507688f50109d 100644 --- a/recipes/fastp/meta.yaml +++ b/recipes/fastp/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.19.4" %} +{% set version="0.19.5" %} package: name: fastp @@ -6,7 +6,7 @@ package: source: url: https://github.com/OpenGene/fastp/archive/v{{ version }}.tar.gz - sha256: f20f1f3b1d1afa9ac347c9aaacc41782cac1665eda730e84523db6a1f0227c5f + sha256: 7a3f508ddc19466c2523884a8abc869ef0deb96957cfdf44736546ac1a578ab1 build: number: 0 From 15ae877cbe0e843e706a888be5ae3804229d91ff Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 9 Nov 2018 13:12:17 +0100 Subject: [PATCH 092/546] rMATS-4.0.2 (#11809) --- recipes/rmats/LICENSE | 26 ++++++++++++++++++++++++++ recipes/rmats/build.sh | 19 ++++++++++++------- recipes/rmats/meta.yaml | 20 ++++++++++---------- 3 files changed, 48 insertions(+), 17 deletions(-) create mode 100644 recipes/rmats/LICENSE diff --git a/recipes/rmats/LICENSE b/recipes/rmats/LICENSE new file mode 100644 index 0000000000000..9934c2ce2e61b --- /dev/null +++ b/recipes/rmats/LICENSE @@ -0,0 +1,26 @@ +The Regents of the University of California +Software License +SURVIV: SURVIVAL ANALYSIS OF MRNA ISOFORM VARIATION USING LARGE SCALE RNA-SEQUENCE DATA (UCLA Case no. 2016-678) + +Commercial reservation +This License governs use of the accompanying Software, and your use of the Software constitutes acceptance of this license. + +You may use this Software for any non-commercial purpose, subject to the restrictions in this license. Some purposes which can be non-commercial are teaching, academic research, and personal experimentation. + +You may not use or distribute this Software or any derivative works in any form for any commercial purpose. Examples of commercial purposes would be running business operations, licensing, leasing, or selling the Software, or distributing the Software for use with commercial products. If you wish to obtain a commercial license to use this Software, please contact the authors. + +You may modify this Software and distribute the modified Software for non-commercial purposes; however, you may not grant rights to the Software or derivative works that are broader than those provided by this License. For example, you may not distribute modifications of the Software under terms that would permit commercial use, or under terms that purport to require the Software or derivative works to be sublicensed to others. + +You agree: +1. 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That if you sue anyone over patents that you think may apply to the Software or anyone's use of the Software, your license to the Software ends automatically. +7. That your rights under the License end automatically if you breach it in any way. +8. The Authors, UCLA and the Regents of the University of California reserves all rights not expressly granted to you in this license. +9. Nothing in this Agreement grants by implication, estoppel, or otherwise any rights to any intellectual property owned by the Regents of the University of California, except as explicitly set forth in this license. +10. You will hold the Regents of the harmless for all claims, suits, losses, liabilities, damages, costs, fees, and expenses resulting from their respective activities arising from this license. +11. You will not use any name, trade name, trademark, name of any campus, or other designation of the Regents of the University of California in advertising, publicity, or other promotional activity, except as permitted herein. +12. If you wish to obtain a commercial license to use this software, please contact the authors at yxing@ucla.edu. diff --git a/recipes/rmats/build.sh b/recipes/rmats/build.sh index 7d8e555b8319d..f774897df0b4f 100644 --- a/recipes/rmats/build.sh +++ b/recipes/rmats/build.sh @@ -1,12 +1,17 @@ #!/bin/bash mkdir $PREFIX/rMATS -cp -R ./* $PREFIX/rMATS -echo '#!/bin/bash' > $PREFIX/bin/RNASeq-MATS.py -echo 'RMATS_INSTALL_DIR=$(dirname $(dirname "$0"))/rMATS' >> $PREFIX/bin/RNASeq-MATS.py -echo 'python $RMATS_INSTALL_DIR/RNASeq-MATS.py "$@"' >> $PREFIX/bin/RNASeq-MATS.py -chmod +x $PREFIX/bin/RNASeq-MATS.py +if [[ "$(uname)" == "Darwin" ]]; then + SRCDIR="rMATS-turbo-Mac-UCS4" +else + SRCDIR="rMATS-turbo-Linux-UCS4" +fi -rm -rf $PREFIX/rMATS/testData $PREFIX/rMATS/gtf -rm $PREFIX/rMATS/testRun.sh +cp -R $SRCDIR/* $PREFIX/rMATS +chmod +x $PREFIX/rMATS/rmats.py +ln -s $PREFIX/rMATS/rmats.py $PREFIX/bin/rmats.py + +# for backwards compatibility with the previous recipe, create a symlink named +# for the previously-used executable +ln -s $PREFIX/rMATS/rmats.py $PREFIX/bin/RNASeq-MATS.py diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index aaf3be45822a5..40422af965e61 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -1,34 +1,34 @@ +{% set version = "4.0.2" %} + package: name: rmats - version: '3.2.5' + version: {{ version }} source: - sha256: 13e4fb9d97bad1fa0b53b9e8e358e42cfc9f7619c52e1999afb3b8249de67a28 - url: https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.3.2.5.tgz + sha256: afab002a9ae836d396909aede96318f6dab6e5818078246419dd563624bf26d1 + url: https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.{{ version }}.tgz build: - number: 2 - skip: True # [py3k] + number: 0 + skip: True # [py3k or osx] requirements: host: - python - numpy - scipy - - pysam ==0.9.0 run: - python - numpy - scipy - - pysam ==0.9.0 - - samtools ==1.3.1 - - star + - star >=2.5 test: commands: - - RNASeq-MATS.py + - rmats.py about: home: http://rnaseq-mats.sourceforge.net license: MIT summary: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. + license_file: LICENSE From 819f622f53f131a5145bc49f37d8a826fbaa6604 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:13:50 -0700 Subject: [PATCH 093/546] Update scanpy to 1.3.3 (#11867) --- recipes/scanpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scanpy/meta.yaml b/recipes/scanpy/meta.yaml index f83583a57261a..4f7b3b207ec23 100644 --- a/recipes/scanpy/meta.yaml +++ b/recipes/scanpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scanpy" %} -{% set version = "1.3.2" %} +{% set version = "1.3.3" %} package: name: {{ name|lower }} @@ -9,7 +9,7 @@ build: skip: True # [not py36] source: url: https://github.com/theislab/scanpy/archive/{{ version }}.tar.gz - sha256: 24266a2c7ef6673e8619ad132e91f55f3c15c005b4a7682395a1d36d1c7ff038 + sha256: a1ade2079498c2cc8df3da85e94330f64955f4a8f9266829aa0093b4f3aef2f5 requirements: host: From 0ff7828ebf3f705ce734aa650c8b4582ae305f04 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:14:06 -0700 Subject: [PATCH 094/546] Update starfish to 0.0.29 (#11865) --- recipes/starfish/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/starfish/meta.yaml b/recipes/starfish/meta.yaml index 806748b87dec9..954112757b991 100644 --- a/recipes/starfish/meta.yaml +++ b/recipes/starfish/meta.yaml @@ -1,4 +1,4 @@ -{% set STARFISH_VERSION = "0.0.27" %} +{% set STARFISH_VERSION = "0.0.29" %} package: name: starfish @@ -6,7 +6,7 @@ package: source: url: https://github.com/spacetx/starfish/archive/{{ STARFISH_VERSION }}.zip - sha256: 0502319556f699e82758fb7cf128f8ec7d2b3ca1356b9386e9e8ab55caf0e1da + sha256: 2c9dd59f5ee0dc0b5b0f3780a27770236682c79c1fea194532eba7253bef4ba6 build: noarch: python From 73dce73e3eb926329f8439b1f2f372ef8fc1aeaa Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:14:31 -0700 Subject: [PATCH 095/546] Update treemaker to 1.2 (#11856) --- recipes/treemaker/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/treemaker/meta.yaml b/recipes/treemaker/meta.yaml index c18a4401a9760..0d2e7823a3406 100644 --- a/recipes/treemaker/meta.yaml +++ b/recipes/treemaker/meta.yaml @@ -1,8 +1,8 @@ {% set name = "treemaker" %} -{% set version = "1.1" %} +{% set version = "1.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "f26b28a8effd759b4e187f7e10213b1c48b84c4bcd849f6acf5c96ff5c18ee80" %} +{% set hash_value = "a79d236632424c9fa92a352fd3253d839f4814011da1bec6c2bbaa0085023db5" %} package: name: '{{ name|lower }}' @@ -14,7 +14,7 @@ source: build: noarch: python - number: 1 + number: 0 entry_points: - treemaker = treemaker:main script: python -m pip install --no-deps --ignore-installed . From ad0196efff78d6d5a012d4d6edbf13aa45db420e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:14:42 -0700 Subject: [PATCH 096/546] Update snippy to 4.3.5 (#11858) --- recipes/snippy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml index a5137146fd51e..09e0b9c62865b 100644 --- a/recipes/snippy/meta.yaml +++ b/recipes/snippy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "snippy" %} -{% set version = "4.3.3" %} -{% set sha256 = "eaee16f915f67180b334c4d7aa3a8588081ec004036651621b1d579f853d0bcd" %} +{% set version = "4.3.5" %} +{% set sha256 = "eca58b15459739532c21bc1723efd668aab73e85c2671f6519de67b5d3acb0cf" %} package: name: '{{ name }}' From 013dd10eb5eee3b7050db881e4780022f26655c1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:14:51 -0700 Subject: [PATCH 097/546] Update planemo to 0.56.0 (#11859) --- recipes/planemo/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index c28e786f4d46d..9034e8987cea2 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "planemo" %} -{% set version = "0.55.0" %} +{% set version = "0.56.0" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: fa12d3694c64b3f76c5f0f5199b0dab325ca8c6af78b7026c8092464a0378701 + sha256: b790bd73eb6be68e57b986b5149427fba3328808e98ffb2a26e80f02df789736 build: - number: 1 + number: 0 noarch: python entry_points: - planemo=planemo.cli:planemo From 6d0160458c08c1c873137c9d1fd0b44ad183fd5b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:15:03 -0700 Subject: [PATCH 098/546] Update pypeflow to 2.1.1 (#11860) --- recipes/pypeflow/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/pypeflow/meta.yaml b/recipes/pypeflow/meta.yaml index 9fd611203f141..1a83df748b4bb 100644 --- a/recipes/pypeflow/meta.yaml +++ b/recipes/pypeflow/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.0.4" %} -{% set sha256 = "f39e227e44286b2a4ba2106eb7f4ec069b87c79f04118b9125c0a275764d6156" %} +{% set version = "2.1.1" %} +{% set sha256 = "5bcac740c6fb39b70f6d4b3dd08f572e19b141d32db696ba8cb9bfa912def7ca" %} package: name: pypeflow @@ -10,6 +10,7 @@ source: sha256: '{{ sha256 }}' build: + number: 0 noarch: true script: $PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . From 3409cb86650e5c39906c79809a278bd3a9c64472 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:15:15 -0700 Subject: [PATCH 099/546] Update nanoplot to 1.19.0 (#11851) --- recipes/nanoplot/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nanoplot/meta.yaml b/recipes/nanoplot/meta.yaml index 6445d466f5aa6..a4b2b574dcd1c 100644 --- a/recipes/nanoplot/meta.yaml +++ b/recipes/nanoplot/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.18.2" %} +{% set version = "1.19.0" %} package: name: nanoplot @@ -6,12 +6,12 @@ package: source: url: https://pypi.io/packages/source/n/nanoplot/NanoPlot-{{ version }}.tar.gz - sha256: 8d7a7fcc23887b72d9c1587ec89379436f433cc5dcbe1a5fad4359e3a7166e96 + sha256: cb16097f84ca05fb4d6f711504f4925d3b85169978703e9f2c691452476fe7cd build: entry_points: - NanoPlot=nanoplot.NanoPlot:main - number: 1 + number: 0 skip: True # [py27] requirements: From e184c1af3eb10e707eea4237e449af268a3890da Mon Sep 17 00:00:00 2001 From: Adam Rivers Date: Fri, 9 Nov 2018 09:16:47 -0500 Subject: [PATCH 100/546] Added build file for itsxpress 1.7.2 (#11823) * added build file for itsxpress 1.7.2 * Updates to license and maintainer info * Updates to license info * Updates to license info --- recipes/itsxpress/1.7.1/meta.yaml | 53 +++++++++++++++++++++++++++++++ recipes/itsxpress/meta.yaml | 11 ++++--- 2 files changed, 59 insertions(+), 5 deletions(-) create mode 100644 recipes/itsxpress/1.7.1/meta.yaml diff --git a/recipes/itsxpress/1.7.1/meta.yaml b/recipes/itsxpress/1.7.1/meta.yaml new file mode 100644 index 0000000000000..ecfbf7b35bfd9 --- /dev/null +++ b/recipes/itsxpress/1.7.1/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "itsxpress" %} +{% set version = "1.7.1" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "2e04503cb1c4261e75672dfb7c2999ce27fac539d8918ec5ebd53392216d2164" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://files.pythonhosted.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' + +build: + number: 0 + entry_points: + - itsxpress=itsxpress.main:main + script: python -m pip install --no-deps --ignore-installed . + skip: True # [py27] + +requirements: + host: + - pip + - python + run: + - pip + - python + - biopython >=1.60 + - hmmer >=3.1 + - bbmap + - vsearch + +test: + imports: + - itsxpress + commands: + - itsxpress --help + +about: + home: http://github.com/usda-ars-gbru/itsxpress + license: 'License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication' + license_family: 'PUBLIC-DOMAIN' + license_file: '' + summary: 'ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files' + + +extra: + recipe-maintainers: 'Adam R. Rivers' + identifiers: + - biotools:ITSxpress + - doi:10.5281/zenodo.1304349 + - doi:10.12688/f1000research.15704.1 diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml index ecfbf7b35bfd9..e8bb80c92463d 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -1,8 +1,8 @@ {% set name = "itsxpress" %} -{% set version = "1.7.1" %} +{% set version = "1.7.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "2e04503cb1c4261e75672dfb7c2999ce27fac539d8918ec5ebd53392216d2164" %} +{% set hash_value = "1f3359d416e1b840be5aead25915b152456b1201c2fc9a9665162d4442887665" %} package: name: '{{ name|lower }}' @@ -39,14 +39,15 @@ test: about: home: http://github.com/usda-ars-gbru/itsxpress - license: 'License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication' + license: 'CC0 1.0' license_family: 'PUBLIC-DOMAIN' - license_file: '' + # license_file: '' summary: 'ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files' extra: - recipe-maintainers: 'Adam R. Rivers' + recipe-maintainers: + - arivers identifiers: - biotools:ITSxpress - doi:10.5281/zenodo.1304349 From c44aa40f748f50d5f100390cf6eba7835c9fb8a6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 07:17:22 -0700 Subject: [PATCH 101/546] Update nanoplotter to 1.1.1 (#11848) --- recipes/nanoplotter/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nanoplotter/meta.yaml b/recipes/nanoplotter/meta.yaml index 999c368159010..f483bf3b84ea8 100644 --- a/recipes/nanoplotter/meta.yaml +++ b/recipes/nanoplotter/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.1.1" %} package: name: nanoplotter @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/n/nanoplotter/nanoplotter-{{ version }}.tar.gz - sha256: 9629c321e44af28b2062c813c5a7c127c6ef0b86084d0b96233b86859ae17773 + sha256: 5ed2fef3c0c798a71af54e81b10c3bb10fb21e84fc68850376d5102cf9220dd0 build: - number: 2 + number: 0 skip: True # [py27] requirements: From 38964c397dcf540d0edc4faee6841d9e21d5c0f6 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 9 Nov 2018 16:34:14 +0100 Subject: [PATCH 102/546] Changing image source (#11776) * Changing image source * Moving rms and clustering to analysis --- recipes/biobb_common/meta.yaml | 2 +- recipes/biobb_io/meta.yaml | 2 +- recipes/biobb_md/build.sh | 6 ------ recipes/biobb_md/meta.yaml | 14 +++++--------- recipes/biobb_model/meta.yaml | 2 +- 5 files changed, 8 insertions(+), 18 deletions(-) diff --git a/recipes/biobb_common/meta.yaml b/recipes/biobb_common/meta.yaml index a4c465035658e..cf29e4ffa2eb8 100644 --- a/recipes/biobb_common/meta.yaml +++ b/recipes/biobb_common/meta.yaml @@ -48,7 +48,7 @@ about: \n### Version 0.0.4\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/)\ \ & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2018\ \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\ - \ see the file\n[LICENSE](LICENSE) for details.\n\n![](docs/source/_static/bioexcel_logo.png \"Bioexcel\")\n\n\n" + \ see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" doc_url: '' dev_url: '' diff --git a/recipes/biobb_io/meta.yaml b/recipes/biobb_io/meta.yaml index 9d333997d22fd..880d8c25a8a3b 100644 --- a/recipes/biobb_io/meta.yaml +++ b/recipes/biobb_io/meta.yaml @@ -44,7 +44,7 @@ about: \ API documentation](http://biobb_io.readthedocs.io/en/latest/).\n\n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org)\ \ at the\nBSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\ \n* (c) 2015-2018 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License\ - \ 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file\n[LICENSE](LICENSE) for details.\n\n![](docs/source/_static/bioexcel_logo.png \"Bioexcel\")\n\n\n" + \ 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" doc_url: '' dev_url: '' diff --git a/recipes/biobb_md/build.sh b/recipes/biobb_md/build.sh index e45d548a81fee..e3475ba9a58a6 100644 --- a/recipes/biobb_md/build.sh +++ b/recipes/biobb_md/build.sh @@ -4,9 +4,6 @@ python3 setup.py install --single-version-externally-managed --record=record.txt mkdir -p $PREFIX/bin -chmod u+x $SP_DIR/biobb_md/gromacs/cluster.py -cp $SP_DIR/biobb_md/gromacs/cluster.py $PREFIX/bin/cluster - chmod u+x $SP_DIR/biobb_md/gromacs/editconf.py cp $SP_DIR/biobb_md/gromacs/editconf.py $PREFIX/bin/editconf @@ -28,9 +25,6 @@ cp $SP_DIR/biobb_md/gromacs/mdrun.py $PREFIX/bin/mdrun chmod u+x $SP_DIR/biobb_md/gromacs/pdb2gmx.py cp $SP_DIR/biobb_md/gromacs/pdb2gmx.py $PREFIX/bin/pdb2gmx -chmod u+x $SP_DIR/biobb_md/gromacs/rms.py -cp $SP_DIR/biobb_md/gromacs/rms.py $PREFIX/bin/rms - chmod u+x $SP_DIR/biobb_md/gromacs/solvate.py cp $SP_DIR/biobb_md/gromacs/solvate.py $PREFIX/bin/solvate diff --git a/recipes/biobb_md/meta.yaml b/recipes/biobb_md/meta.yaml index ef8965fa7d477..da611a155f7f9 100644 --- a/recipes/biobb_md/meta.yaml +++ b/recipes/biobb_md/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_md" %} -{% set version = "0.0.2" %} +{% set version = "0.1.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "1337b79f2761742338910dcf67230f68a4a4f84d2a4417afe80eb70c5454d57b" %} +{% set hash_value = "7d007aac538bee9a201d1fdf1523092c4ea8444f6851e2ee1562793208c390f9" %} package: name: '{{ name|lower }}' @@ -18,11 +18,11 @@ build: requirements: host: - - python >=3.5 + - python >=3 - setuptools - biobb_common run: - - python >=3.5 + - python >=3 - biobb_common test: @@ -30,10 +30,6 @@ test: - biobb_md - biobb_md.gromacs - biobb_md.gromacs_extra - - biobb_md.pycompss - - biobb_md.pycompss.gromacs - - biobb_md.pycompss.gromacs_extra - - biobb_md.test about: home: https://github.com/bioexcel/biobb_md @@ -47,7 +43,7 @@ about: \n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB\ \ (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2018\ \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\ - \ see the file\n[LICENSE](LICENSE) for details.\n\n![](docs/source/_static/bioexcel_logo.png \"Bioexcel\")\n\n\n" + \ see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" doc_url: '' dev_url: '' diff --git a/recipes/biobb_model/meta.yaml b/recipes/biobb_model/meta.yaml index 005b30ac14e36..9210a6dc2268b 100644 --- a/recipes/biobb_model/meta.yaml +++ b/recipes/biobb_model/meta.yaml @@ -46,7 +46,7 @@ about: \ site:\n[latest API documentation](http://biobb_model.readthedocs.io/en/latest/).\n\n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in\ \ the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n\ (EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2018 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ - \nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file\n[LICENSE](LICENSE) for details.\n\n![](docs/source/_static/bioexcel_logo.png \"Bioexcel\")\n\n\n" + \nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" doc_url: '' dev_url: '' From d292150ca73820388ce112294cd693661e42035b Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 9 Nov 2018 16:57:27 +0100 Subject: [PATCH 103/546] prosic: update build # and adjust to prosolo setup, incl. yacrd workarounds in build.sh (#11870) --- recipes/prosic/build.sh | 13 ++++++++++++- recipes/prosic/meta.yaml | 8 ++++++-- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/recipes/prosic/build.sh b/recipes/prosic/build.sh index abc7c53a33371..50a92a2357583 100644 --- a/recipes/prosic/build.sh +++ b/recipes/prosic/build.sh @@ -1,4 +1,15 @@ #!/bin/bash -euo +# taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh +if [ "$(uname)" == "Darwin" ]; then + + # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory + export HOME="/Users/distiller" + + # according to https://github.com/rust-lang/cargo/issues/2422#issuecomment-198458960 removing circle ci default configuration solves cargo trouble downloading crates + git config --global --unset url.ssh://git@github.com.insteadOf + +fi + # build statically linked binary with Rust -C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib cargo install --root $PREFIX +C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib cargo install --path . --root $PREFIX diff --git a/recipes/prosic/meta.yaml b/recipes/prosic/meta.yaml index 0bd7a91441f94..f152d4d54db55 100644 --- a/recipes/prosic/meta.yaml +++ b/recipes/prosic/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/PROSIC/prosic2/archive/v{{ version }}.tar.gz @@ -15,11 +15,15 @@ source: requirements: build: - {{ compiler('c') }} + - rust >=1.30 + - pkg-config #[osx] host: - - rust >=1.12 - gsl - openblas - zlib + - bzip2 + - xz + - clangdev run: - gsl - openblas From 34327c1d7688623e52c447facf14d07861faf9ff Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Fri, 9 Nov 2018 17:07:07 +0100 Subject: [PATCH 104/546] Add macOS build for comet-ms (#11825) --- recipes/comet/build.sh | 17 ++++++++++++++--- recipes/comet/meta.yaml | 11 +++++++---- 2 files changed, 21 insertions(+), 7 deletions(-) diff --git a/recipes/comet/build.sh b/recipes/comet/build.sh index 5679dcd163755..484438e23f510 100644 --- a/recipes/comet/build.sh +++ b/recipes/comet/build.sh @@ -1,6 +1,17 @@ #!/usr/bin/env bash +set -e +set -x -chmod 755 comet.2018012.linux.exe -cp comet.2018012.linux.exe ${PREFIX}/bin/comet -cd ${PREFIX}/bin/ +platform="$(uname)" +if [ "$platform" = "Darwin" ]; then + unzip comet_source_"$PKG_VERSION".zip + sed -i bak -e 's/ -static//' Makefile + make +elif [ "$platform" = "Linux" ]; then + mv comet.2018012.linux.exe comet.exe +fi +chmod 755 comet.exe +mkdir -p "$PREFIX"/bin +cp comet.exe "$PREFIX"/bin/comet +cd "$PREFIX"/bin/ ln -s comet comet.exe diff --git a/recipes/comet/meta.yaml b/recipes/comet/meta.yaml index f26d43da19f95..2310934c42ff5 100644 --- a/recipes/comet/meta.yaml +++ b/recipes/comet/meta.yaml @@ -1,6 +1,6 @@ {% set name = "comet-ms" %} {% set version = "2018012" %} -{% set sha256_linux = "5ca42762884b74a62b21e6013e302cd291663361788a3a23ab195254976dbb99" %} +{% set sha256_src_bin_bundle = "5ca42762884b74a62b21e6013e302cd291663361788a3a23ab195254976dbb99" %} package: name: {{ name }} @@ -8,11 +8,14 @@ package: source: url: https://sourceforge.net/projects/{{ name }}/files/comet_{{ version }}.zip - sha256: {{ sha256_linux }} + sha256: {{ sha256_src_bin_bundle }} build: - number: 0 - skip: True # [osx] + number: 1 + +requirements: + build: + - {{ compiler('cxx') }} test: commands: From e0dbf50f0f2d94954692081971b93881605827e3 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:37:37 -0700 Subject: [PATCH 105/546] Update sevenbridges-python to 0.17.0 (#11866) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index c2b33ed6b4b76..8443ea0c386ec 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.16.0" %} -{% set sha256 = "3f194f032dd76e30f8ffe3bec5110bbc853d45f90090419f2816e3df9710f9ec" %} +{% set version = "0.17.0" %} +{% set sha256 = "2fb224b48ac1dc2e3954344429031aafa190ae1021dd9ec55ad1f4ae0deec1c8" %} package: name: sevenbridges-python From cbddf7221784d3450b0131e1268a2d3508ead228 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:38:11 -0700 Subject: [PATCH 106/546] Update phylopandas to 0.7.2 (#11864) --- recipes/phylopandas/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phylopandas/meta.yaml b/recipes/phylopandas/meta.yaml index 9a83efa56b163..2c2f410ae4743 100644 --- a/recipes/phylopandas/meta.yaml +++ b/recipes/phylopandas/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} package: name: phylopandas @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/phylopandas/phylopandas-{{ version }}.tar.gz - sha256: 71567c4eefd4b807b18a26a79aa09ce2e88e05e08f719869d326aa2f90adfc0b + sha256: 8d3eefec6f744d89fc3f143964c93e76c80e73070df8abc68980e114c31a006f build: noarch: python From b9a09fa9b2862278e31f8c95eae3ad8d4552cbfe Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:38:24 -0700 Subject: [PATCH 107/546] Update solvebio to 2.8.0 (#11863) --- recipes/solvebio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/solvebio/meta.yaml b/recipes/solvebio/meta.yaml index 8ceb25933c2d7..9ad3eb6a53c24 100644 --- a/recipes/solvebio/meta.yaml +++ b/recipes/solvebio/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.7.0" %} -{% set sha256 = "b248098c107e4cda4c8c0f4ad0b900c7c058c4f48088623b144215a1c268a01e" %} +{% set version = "2.8.0" %} +{% set sha256 = "337d34398b9d46661d301d38fc6d3e3716bbbb287276a18d25f5531440716187" %} package: name: solvebio From 8dbb07fa774ccec8023307582a3517a220320438 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:38:42 -0700 Subject: [PATCH 108/546] Update pyensembl to 1.7.3 (#11862) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index c3d8cc76b3a9d..406565a040d1a 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "1.7.2" %} -{% set sha256 = "0e40b0963d0e2a2e54adf90e414d459edd4d5c623d5c0827d44a1365d2beb845" %} +{% set version = "1.7.3" %} +{% set sha256 = "2a225fb646bb8e7a5c96c30f51ada3fe354952798a6513c26cd7c9c38beb155c" %} package: name: {{ name|lower }} From 31afc4ca030ba6a98491e4ae607e9ef02a63e010 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:38:58 -0700 Subject: [PATCH 109/546] Update snp-dists to 0.6.3 (#11861) --- recipes/snp-dists/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snp-dists/meta.yaml b/recipes/snp-dists/meta.yaml index 2c9922437b51a..c08fcb6c445ab 100644 --- a/recipes/snp-dists/meta.yaml +++ b/recipes/snp-dists/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snp-dists" %} -{% set version = "0.6.2" %} +{% set version = "0.6.3" %} package: name: {{ name }} @@ -10,7 +10,7 @@ build: source: url: https://github.com/tseemann/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 4a012a1aa6e837cadadfdda15fa5ce824a299378212d0f8b0cb93a1f7693c43a + sha256: b7454fdb4ced2ed3f5245334b99c4717005e19495d7bc77fd893b291ba6ccc17 requirements: build: From dfd1398037d89a6a6a30a35a114bc11310ccc011 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:39:12 -0700 Subject: [PATCH 110/546] Update prince to 1.2 (#11857) --- recipes/prince/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/prince/meta.yaml b/recipes/prince/meta.yaml index 2c00d3b950d9e..304324e75bcfa 100644 --- a/recipes/prince/meta.yaml +++ b/recipes/prince/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PRINCE" %} -{% set version = "1.1" %} -{% set sha256 = "51402ad195b8460435ddf3d0ad5f0b84802b233d0bc08b1c7dda04be6c6de736" %} +{% set version = "1.2" %} +{% set sha256 = "bb599790bffce970bd4e37d8aff5318f49149199c544d1640cdff074d66518a9" %} package: name: {{ name|lower }} From fb7852489bc4aae239611f5089e39a2b6d20735a Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:39:42 -0700 Subject: [PATCH 111/546] Update scvi to 0.2.2 (#11854) --- recipes/scvi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scvi/meta.yaml b/recipes/scvi/meta.yaml index fe18ddaa4c32a..7ef2bcde0a91e 100644 --- a/recipes/scvi/meta.yaml +++ b/recipes/scvi/meta.yaml @@ -1,8 +1,8 @@ {% set name = "scvi" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "cf5800ba1ca415968756aaeec70c0468f8189a62054b647e56c8e471e9324a03" %} +{% set hash_value = "ff083ab9a348eba86f376c1eb2a40ca7d4babad03dffb55edd4e939972e84749" %} package: name: '{{ name|lower }}' From fb3036e569be5d3e144a464e4e7d78af57708d4d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:39:59 -0700 Subject: [PATCH 112/546] Update neurodocker to 0.4.2 (#11850) --- recipes/neurodocker/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/neurodocker/meta.yaml b/recipes/neurodocker/meta.yaml index a18e2e7f80acf..6911185015524 100644 --- a/recipes/neurodocker/meta.yaml +++ b/recipes/neurodocker/meta.yaml @@ -1,6 +1,6 @@ {% set name = "neurodocker" %} -{% set version = "0.4.1" %} -{% set sha256 = "af437fc937adfe359a51fd9b79d7f09936fc79c395643db8b9c43b43381a2e9a" %} +{% set version = "0.4.2" %} +{% set sha256 = "7fb8afe302244c18a96308c4a2c54f8dc756c457158daa7c0b33382db7726c0c" %} package: name: "{{ name|lower }}" From b199e418a66eb5ce639bc2dd45e5851ff018f72c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:40:21 -0700 Subject: [PATCH 113/546] Update lighter to 1.1.2 (#11849) --- recipes/lighter/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/lighter/meta.yaml b/recipes/lighter/meta.yaml index a9452e9ea869f..1efc1ec72b583 100644 --- a/recipes/lighter/meta.yaml +++ b/recipes/lighter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Lighter" %} -{% set version = "1.1.1" %} -{% set sha256 = "9b29b87cd87f6d57ef8c39d22fb8679977128a1bdf557d8c161eae2816e374b7" %} +{% set version = "1.1.2" %} +{% set sha256 = "89abc34137beffc43382fbe53deb25c3c2f5cee7e6ca2b7f669931d70065993a" %} package: name: '{{ name|lower }}' @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 0 requirements: build: From 5c01bdeb8ed41da934fc40dbe2996f8e028fc149 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:40:42 -0700 Subject: [PATCH 114/546] Update illumina-utils to 2.6 (#11847) --- recipes/illumina-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-utils/meta.yaml b/recipes/illumina-utils/meta.yaml index e2ec2b9965f0e..b1ad24d718667 100644 --- a/recipes/illumina-utils/meta.yaml +++ b/recipes/illumina-utils/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5" %} +{% set version = "2.6" %} package: name: 'illumina-utils' @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/i/illumina-utils/illumina-utils-{{ version }}.tar.gz - sha256: '664f2c6a003afe4d424b5b16a14344e320dce3e226d6f8970b5abc65297aed44' + sha256: '4ee7108d6ae67fc7d6c70bee4f775d38dfd921c10e4b020bd177838c649446ea' build: number: 0 From bd484e3f4e6b4c9d3e32f4acba0c35235f14135d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:40:57 -0700 Subject: [PATCH 115/546] Update kipoi to 0.6.0 (#11846) --- recipes/kipoi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kipoi/meta.yaml b/recipes/kipoi/meta.yaml index 3b2cfc966ab8e..ca44d38f95673 100644 --- a/recipes/kipoi/meta.yaml +++ b/recipes/kipoi/meta.yaml @@ -1,8 +1,8 @@ {% set name = "kipoi" %} -{% set version = "0.5.7" %} +{% set version = "0.6.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "8471eaaf0cafa6b5cd62b6831f4a1d0bf0ef49440510237b07fca7d4233631cb" %} +{% set hash_value = "dd44a074221042e3a891274333042b45d2202ab2fa207bac187462619051c976" %} package: name: '{{ name|lower }}' From 0fca75571ec24e9d7cf5e90225368ee0b607ae00 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:41:05 -0700 Subject: [PATCH 116/546] Update kipoi_veff to 0.2.0 (#11845) --- recipes/kipoi_veff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kipoi_veff/meta.yaml b/recipes/kipoi_veff/meta.yaml index 98af99c1e2f83..db0599c8dc175 100644 --- a/recipes/kipoi_veff/meta.yaml +++ b/recipes/kipoi_veff/meta.yaml @@ -1,8 +1,8 @@ {% set name = "kipoi_veff" %} -{% set version = "0.1.2" %} +{% set version = "0.2.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "385a11320fc4db43d61f0462aa79045baebe03f68821ead5002f6b47fcd2a861" %} +{% set hash_value = "5c13c1b44b5512325c87efcade325701c0fbeb348dc8b8652204781a2f1cfd59" %} package: name: '{{ name|lower }}' From 3e9502280e1c27dfb428f261f71aa7f5ea64cbc8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:41:16 -0700 Subject: [PATCH 117/546] Update hicmatrix to 4 (#11843) --- recipes/hicmatrix/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hicmatrix/meta.yaml b/recipes/hicmatrix/meta.yaml index 6c3c3f4402498..037cd550a5e6e 100644 --- a/recipes/hicmatrix/meta.yaml +++ b/recipes/hicmatrix/meta.yaml @@ -1,10 +1,10 @@ package: name: hicmatrix - version: '3' + version: '4' source: - url: https://github.com/deeptools/HiCMatrix/archive/3.tar.gz - sha256: aa63dfda78779063b50af65a08d0bb8cba2d473a1caf10c28823ab868c838e48 + url: https://github.com/deeptools/HiCMatrix/archive/4.tar.gz + sha256: 6bcb5c72d4f3a310acda829b3c5a98573ed69d016f8185297ebd72a4430c2bcc build: number: 0 From 9ae52bbda670ada5f8f874c0816c9dc02c36ad6d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 9 Nov 2018 10:42:03 -0700 Subject: [PATCH 118/546] Update chewbbaca to 2.0.15 (#11662) * Update chewbbaca to 2.0.13 * Update chewbbaca to 2.0.15 --- recipes/chewbbaca/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index fa9ed2db81249..cc04d2e1f1dec 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,6 +1,6 @@ {% set name='chewBBACA' %} -{% set version='2.0.12' %} -{% set sha256='8438819aa7d8304a45b62abf6d24aa933a76853cd6b56043c833ebb5aae0f61e' %} +{% set version='2.0.15' %} +{% set sha256='26333b802d69e91b43c1d78c9cc235e89d787b299d3624f29be344e52d2285b1' %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 skip: True # [ py27 ] entry_points: - chewBBACA.py = CHEWBBACA.chewBBACA:main From c3e791ed875816db54ecba06ecf6f8a522d24450 Mon Sep 17 00:00:00 2001 From: Sebastian Roskosch Date: Fri, 9 Nov 2018 18:42:43 +0100 Subject: [PATCH 119/546] Update PopDel to version 1.0.4 (#11869) --- recipes/popdel/Makefile.patch | 6 +++--- recipes/popdel/meta.yaml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/popdel/Makefile.patch b/recipes/popdel/Makefile.patch index c2e3da1675e7a..a31ec8c115409 100644 --- a/recipes/popdel/Makefile.patch +++ b/recipes/popdel/Makefile.patch @@ -16,9 +16,9 @@ LDLIBS=-lz -lpthread -DATE=on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1) --VERSION=1.0.3-$(shell git log --pretty=format:"%h" --date=iso | head -n 1) -+DATE=on 2018-11-07 -+VERSION=1.0.3 +-VERSION=1.0.4-$(shell git log --pretty=format:"%h" --date=iso | head -n 1) ++DATE=on 2018-11-09 ++VERSION=1.0.4 CXXFLAGS+=-DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\" # Enable warnings diff --git a/recipes/popdel/meta.yaml b/recipes/popdel/meta.yaml index 406e3bd7d5566..f015eadc03948 100644 --- a/recipes/popdel/meta.yaml +++ b/recipes/popdel/meta.yaml @@ -1,10 +1,10 @@ package: name: popdel - version: "1.0.3" + version: "1.0.4" source: - url: https://github.com/kehrlab/PopDel/archive/v1.0.3.tar.gz - sha256: ec25d48354a20869095c5b5658de3b6b6ca2acf05670d4bf3e67d9a66a72368d + url: https://github.com/kehrlab/PopDel/archive/v1.0.4.tar.gz + sha256: eb611363a5279b5d7db0dcc8de9b086f73fd34e1516c762425ea655917e55041 patches: - Makefile.patch From c3bc9082aa8fbf046ed691e9901af65e4674a460 Mon Sep 17 00:00:00 2001 From: Andreas Heger Date: Fri, 9 Nov 2018 22:57:48 +0000 Subject: [PATCH 120/546] New recipe: cgat-daisy - benchmarking system and combinatorial workflows (#11421) * recipe creation * {AH} add licence_text to about section * {AH} use 0.1.2 tar-ball with missing files --- recipes/cgat-daisy/build.sh | 6 ++++++ recipes/cgat-daisy/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/cgat-daisy/build.sh create mode 100644 recipes/cgat-daisy/meta.yaml diff --git a/recipes/cgat-daisy/build.sh b/recipes/cgat-daisy/build.sh new file mode 100644 index 0000000000000..db7d5ed90e471 --- /dev/null +++ b/recipes/cgat-daisy/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +sed -i'' -e 's/install_requires=install_requires,//g' setup.py + +$PYTHON setup.py install + diff --git a/recipes/cgat-daisy/meta.yaml b/recipes/cgat-daisy/meta.yaml new file mode 100644 index 0000000000000..4297c0f365491 --- /dev/null +++ b/recipes/cgat-daisy/meta.yaml @@ -0,0 +1,40 @@ + +package: + name: cgat-daisy + version: 0.1.2 + +source: + url: https://files.pythonhosted.org/packages/70/a7/2daf44080c0ba39fb983846e2f1622888a2a0ef9be3f0fba35d6e4229363/cgat-daisy-0.1.2.tar.gz + sha256: 261df47834b2180261cbefa1fd65b254a33bef1a9259703fa55ccc6f03ad9b91 + +build: + noarch: python + number: 0 + +requirements: + host: + - docutils + - future + - pytest + - six + - sphinx + - python + - pep8 + + run: + - cgatcore + - pandas + - sqlalchemy + - ruffus + - ruamel_yaml + - pysam + +test: + commands: + - daisy run --help + +about: + home: https://github.com/cgat-developers/cgat-daisy + license: MIT + license_file: LICENSE + summary: "A system to design and execute benchmarks" From 61043497574f90ec1d4da7870bf8e4c7a7ce2f3e Mon Sep 17 00:00:00 2001 From: Shaun Jackman Date: Sat, 10 Nov 2018 05:25:33 -0800 Subject: [PATCH 121/546] abyss 2.1.4 (#11875) See https://github.com/bcgsc/abyss/releases/tag/2.1.4 --- recipes/abyss/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index b2562fe774a61..3c21f0155c62a 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -1,5 +1,5 @@ {% set name = "abyss" %} -{% set version = "2.1.3" %} +{% set version = "2.1.4" %} package: name: {{ name|lower }} @@ -10,7 +10,7 @@ build: source: url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz - sha256: 23a3e6562b2fa6f0e970d2c452ef98a799ac9892c86a7207f42c7a6ae6df09ab + sha256: 2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc requirements: build: From 904ef7009f636b2f4cd646053848ac1831f590a4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 11:35:56 -0700 Subject: [PATCH 122/546] Update quasitools to 0.5.1 (#11879) --- recipes/quasitools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/quasitools/meta.yaml b/recipes/quasitools/meta.yaml index c69a655004c91..7025cce5f43d5 100644 --- a/recipes/quasitools/meta.yaml +++ b/recipes/quasitools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: quasitools @@ -6,7 +6,7 @@ package: source: url: https://github.com/phac-nml/quasitools/archive/v{{ version }}.tar.gz - sha256: ac20cd5364aebac7fa6d5f53e9b390ce6465782ded8593413202b79788b7b29e + sha256: 9c9acf068fb375677ea9b9eb6af0d0f5f72295966bfb0e4e4f99d244dc6ecba6 build: number: 0 From fbd326c8505976287ce9f23bc6f10a6d2036e4df Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 11:36:10 -0700 Subject: [PATCH 123/546] Update transit to 2.3.2 (#11878) --- recipes/transit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/transit/meta.yaml b/recipes/transit/meta.yaml index 72cb441034d2e..baede1c7501b8 100644 --- a/recipes/transit/meta.yaml +++ b/recipes/transit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "transit" %} -{% set version = "2.3.1" %} +{% set version = "2.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/mad-lab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: ca2dd3543789acf5f4f7327ddac0a27b7ddb2ff7966959a148a84382ccddb486 + sha256: f5c2d4f9f070ad6176e7bb79c62f2388f313864d14d9ef74c5c3ca21a49d19eb build: number: 0 From fac97be30c9e8c11099ad530865c54694c45926f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Pedro=20Camargo?= Date: Sat, 10 Nov 2018 17:09:53 -0200 Subject: [PATCH 124/546] Add bioconductor-metavizr (#11876) * Add bioconductor-metavizr * Change r-base version * Change r-base version again --- recipes/bioconductor-metavizr/build.sh | 4 ++ recipes/bioconductor-metavizr/meta.yaml | 54 +++++++++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 recipes/bioconductor-metavizr/build.sh create mode 100644 recipes/bioconductor-metavizr/meta.yaml diff --git a/recipes/bioconductor-metavizr/build.sh b/recipes/bioconductor-metavizr/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-metavizr/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metavizr/meta.yaml b/recipes/bioconductor-metavizr/meta.yaml new file mode 100644 index 0000000000000..ebb3f3f37f0dd --- /dev/null +++ b/recipes/bioconductor-metavizr/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.2.1" %} +{% set name = "metavizr" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2c2b4ad681d2fc0c326462021fc3246ed5b813546603fcd0c2d172b46cc89684 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - bioconductor-biobase + - bioconductor-epivizr + - bioconductor-epivizrdata + - bioconductor-epivizrserver + - bioconductor-epivizrstandalone + - bioconductor-genomeinfodb + - 'bioconductor-metagenomeseq >=1.17.1' + - bioconductor-phyloseq + - 'r-base <=3.4.1' + - r-data.table + - r-digest + - r-httr + - r-vegan + run: + - bioconductor-biobase + - bioconductor-epivizr + - bioconductor-epivizrdata + - bioconductor-epivizrserver + - bioconductor-epivizrstandalone + - bioconductor-genomeinfodb + - 'bioconductor-metagenomeseq >=1.17.1' + - bioconductor-phyloseq + - 'r-base <=3.4.1' + - r-data.table + - r-digest + - r-httr + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as well.' From 122ce83130df9b1748715c48c64e371c9c622ed0 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Sat, 10 Nov 2018 17:12:21 -0500 Subject: [PATCH 125/546] locking python version to 2.7 (#11880) --- recipes/ctat-mutations/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index e949146af048b..f8d9585c5a14a 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "1" %} +{% set build = "2" %} package: name: {{ name }} @@ -17,11 +17,11 @@ build: requirements: build: - - python + - python =2.7 - gatk4 - picard =2.18.14 run: - - python + - python =2.7 - gatk4 - star - picard =2.18.14 From bb9ac95750b74912ae3a6d6f58652bc2274e9418 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 16:06:54 -0700 Subject: [PATCH 126/546] Update arvados-python-client to 1.2.0.20181109162613 (#11881) --- recipes/arvados-python-client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index f7eb174af3e95..417aa1718be1f 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.2.0.20181108215719" %} +{% set version="1.2.0.20181109162613" %} package: name: arvados-python-client @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - sha256: 19343aa6051c11192f54e4c06e74a65b0f7d27bc0256f4fe2c379a964f9eeed3 + sha256: 09465ea4079c8e9eb72a37db8e3abb33546c43a8a662ba02b557734a952fa318 build: number: 0 From f2f8fe3912d3c6858e7e1d8b2ed6f2c6c030b30e Mon Sep 17 00:00:00 2001 From: Romain Lopez Date: Sat, 10 Nov 2018 15:23:35 -0800 Subject: [PATCH 127/546] version 0.2.2 (#11838) --- recipes/scvi/meta.yaml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/recipes/scvi/meta.yaml b/recipes/scvi/meta.yaml index 7ef2bcde0a91e..93fca5376e73f 100644 --- a/recipes/scvi/meta.yaml +++ b/recipes/scvi/meta.yaml @@ -26,26 +26,35 @@ requirements: - pytorch >=0.4.1 - matplotlib >=2.0 - scikit-learn >=0.18 - - scipy >=1.0 + - scipy >=1.1 - h5py >=2.8 - pandas >=0.2 - - loompy >=2.0 + - loompy ==2.0.9 - tqdm >=4 - anndata >=0.6 - xlrd >=1.0 + - jupyter>=1.0.0 + - nbconvert>=5.4.0 + - nbformat>=4.4.0 + - ipython>=7 + run: - python >=3.6 - numpy >=1.0 - pytorch >=0.4.1 - matplotlib >=2.0 - scikit-learn >=0.18 - - scipy >=1.0 + - scipy >=1.1 - h5py >=2.8 - pandas >=0.2 - - loompy >=2.0 + - loompy ==2.0.9 - tqdm >=4 - anndata >=0.6 - xlrd >=1.0 + - jupyter>=1.0.0 + - nbconvert>=5.4.0 + - nbformat>=4.4.0 + - ipython>=7 test: imports: From a70e69813bcd0fdf53d92df0bfe595553f3b4e44 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 16:51:28 -0700 Subject: [PATCH 128/546] Update scikits-datasmooth to 0.7.1 (#11887) --- recipes/scikits-datasmooth/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/scikits-datasmooth/meta.yaml b/recipes/scikits-datasmooth/meta.yaml index 755c4c9a970ed..37bfbb1b0892c 100644 --- a/recipes/scikits-datasmooth/meta.yaml +++ b/recipes/scikits-datasmooth/meta.yaml @@ -1,14 +1,14 @@ package: name: scikits-datasmooth - version: "0.7.0" + version: "0.7.1" source: - url: https://github.com/jjstickel/scikit-datasmooth/releases/download/v0.7.0/scikit-datasmooth-0.7.0.tar.gz - sha256: d25f60f5618f9ec3533da197fd6bdd30ea90aebc8400b30b0127d739ad241060 + url: https://github.com/jjstickel/scikit-datasmooth/releases/download/v0.7.1/scikit-datasmooth-0.7.1.tar.gz + sha256: 8af9c39a299bec5389126c6d1e8d01e708cb58877a5d80a10e02a7ec160fb937 build: noarch: python - number: 1 + number: 0 script: python -m pip install --no-deps --ignore-installed . requirements: From 84de05a385202bc07a94865bfeaffc1fe0176b9c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 17:51:00 -0700 Subject: [PATCH 129/546] Update elprep to 4.0.1 (#11892) --- recipes/elprep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/elprep/meta.yaml b/recipes/elprep/meta.yaml index 16676b3276158..0b75b06a404d2 100644 --- a/recipes/elprep/meta.yaml +++ b/recipes/elprep/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '4.0.0' %} +{% set version = '4.0.1' %} package: name: elprep @@ -6,7 +6,7 @@ package: source: url: https://github.com/ExaScience/elprep/releases/download/v{{ version }}/elprep-v{{ version }}.tar.gz - sha256: ffde4f75e35e8772764a6432bb81e765226b7a32dce4967fa520dd1b6fd3b11d + sha256: 5088294a5e497612ebed6fbec3aadf9ec8ed8fcc43692422220bc3f5d2200687 build: From 12dedf1ae95e0a842874dc2f8ba490c573440d1d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 17:51:12 -0700 Subject: [PATCH 130/546] Update bcftools-snvphyl-plugin to 1.9 (#11890) --- recipes/bcftools-snvphyl-plugin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bcftools-snvphyl-plugin/meta.yaml b/recipes/bcftools-snvphyl-plugin/meta.yaml index 80c44ae94e88f..bfe8738acc546 100644 --- a/recipes/bcftools-snvphyl-plugin/meta.yaml +++ b/recipes/bcftools-snvphyl-plugin/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.8" %} -{% set sha256 = "4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced" %} +{% set version = "1.9" %} +{% set sha256 = "6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8" %} about: home: https://github.com/phac-nml/snvphyl-tools license: Apache-2.0 @@ -9,7 +9,7 @@ about: genomes and constructing a phylogenetic tree. This package is the bcftools C plugin build: - number: 2 + number: 0 skip: true # [osx] package: From 78d10a2274740f67781cd1d00238dc6a12813b20 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 17:51:24 -0700 Subject: [PATCH 131/546] Update beast to 1.10.3 (#11889) --- recipes/beast/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/beast/meta.yaml b/recipes/beast/meta.yaml index ddb79df30e8de..081e2083d2640 100644 --- a/recipes/beast/meta.yaml +++ b/recipes/beast/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.2" %} -{% set sha256 = "110f16664be7d585fff6bbcf83db2a7d2ee7c882f94f80ffd0fb75cacc6d2113" %} +{% set version = "1.10.3" %} +{% set sha256 = "53afa45e815a191302b7ca501b69fe66d5bc61c381636dbfa10f9023b0411aca" %} package: name: beast From 840a14eb9bfc95bd8ec2881ac84dab2359432e61 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 17:51:36 -0700 Subject: [PATCH 132/546] Update masurca to 3.2.8 (#11885) --- recipes/masurca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index 013c70f0dabe7..b69b9bad8ed48 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "masurca" %} -{% set version = "3.2.7" %} +{% set version = "3.2.8" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/alekseyzimin/masurca/releases/download/{{ version }}/MaSuRCA-{{ version }}.tar.gz - sha256: 3d3df9276d221551fd190cad3d037d56ce70691592cb28198e7bffc7c07760b2 + sha256: b9ab27803d2a0bd8426b5c2e949874e9bc31c9cca8f7f0c8b487664d04cd0fe8 build: number: 0 From b4b9f5fab32136a0ba92cd5518f052a4d25324e9 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 17:51:47 -0700 Subject: [PATCH 133/546] Update pisces to 5.2.9.122 (#11883) --- recipes/pisces/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pisces/meta.yaml b/recipes/pisces/meta.yaml index fb19df966c4e4..ac573d33277c5 100644 --- a/recipes/pisces/meta.yaml +++ b/recipes/pisces/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "5.2.7.47" %} +{% set version = "5.2.9.122" %} package: name: pisces @@ -6,10 +6,10 @@ package: source: url: https://github.com/Illumina/Pisces/releases/download/v{{ version }}/Pisces_{{ version }}.tar.gz - sha256: 69f8e2c08c09b9d75a346474305e5cc4adc4713b11f788398a516fa2ab7e834f + sha256: 3edd036cb5906548f2698d8d22f59e9ddb0bca7c3d8415eb1aee01a5cc777d4a build: - number: 2 + number: 0 skip: False requirements: From 535f669764582f167ea9ba497ce2ad773c72fd50 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 17:52:00 -0700 Subject: [PATCH 134/546] Update strelka to 2.9.10 (#11884) --- recipes/strelka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/strelka/meta.yaml b/recipes/strelka/meta.yaml index 50c4bab84ed80..0a1392b8fa068 100644 --- a/recipes/strelka/meta.yaml +++ b/recipes/strelka/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.9.7" %} -{% set sha256 = "7ebad74fc469eb2cdf4a2fbd526dbb4087888e5d9bd95bccd4cf633317f3909e" %} +{% set version = "2.9.10" %} +{% set sha256 = "bde30e34e06548c876ff63658efd3d7e6a2e7b465909243ab7e2ed599f83312b" %} package: name: strelka From db76c0c5162e636bfdfcba516348270c7e5bdbd0 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 19:33:45 -0700 Subject: [PATCH 135/546] Update perl-xml-xpath to 1.44 (#11895) --- recipes/perl-xml-xpath/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-xml-xpath/meta.yaml b/recipes/perl-xml-xpath/meta.yaml index 9dd6ff3b4f12c..b29919122b290 100644 --- a/recipes/perl-xml-xpath/meta.yaml +++ b/recipes/perl-xml-xpath/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-xml-xpath - version: "1.33" + version: "1.44" source: - url: https://cpan.metacpan.org/authors/id/M/MA/MANWAR/XML-XPath-1.33.tar.gz - md5: dcbd03d687de06a402fed58197eb94f1 + url: https://cpan.metacpan.org/authors/id/M/MA/MANWAR/XML-XPath-1.44.tar.gz + sha256: 1cc9110705165dc09dd09974dd7c0b6709c9351d6b6b1cef5a711055f891dd0f build: - number: 1 + number: 0 requirements: host: From eec33e1b87620f743828a0142aa0e2095a4a827f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 19:34:11 -0700 Subject: [PATCH 136/546] Update perl-test-most to 0.35 (#11893) --- recipes/perl-test-most/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-most/meta.yaml b/recipes/perl-test-most/meta.yaml index b2602c8e05cee..248cd92622e22 100644 --- a/recipes/perl-test-most/meta.yaml +++ b/recipes/perl-test-most/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-test-most - version: "0.34" + version: "0.35" source: - url: http://cpan.metacpan.org/authors/id/O/OV/OVID/Test-Most-0.34.tar.gz - md5: 6fa1f097bedbc18f46b08ac9eb79bba9 + url: http://cpan.metacpan.org/authors/id/O/OV/OVID/Test-Most-0.35.tar.gz + sha256: 9897a6f4d751598d2ed1047e01c1554b01d0f8c96c45e7e845229782bf6f657f build: - number: 2 + number: 0 requirements: host: From bde3d0f453d9b30c15e1f385bd860494b359609e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 19:41:37 -0700 Subject: [PATCH 137/546] Update perl-mce-shared to 1.839 (#11896) --- recipes/perl-mce-shared/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-mce-shared/meta.yaml b/recipes/perl-mce-shared/meta.yaml index a694210dc48e8..a9398c3b44018 100644 --- a/recipes/perl-mce-shared/meta.yaml +++ b/recipes/perl-mce-shared/meta.yaml @@ -1,14 +1,14 @@ {% set name = "perl-mce-shared" %} -{% set version = "1.838" %} -{% set sha256 = "ee853fc83688d7e4d7dc032472ba88f80c161c9799fd98efb2d36bb6126a4f91" %} +{% set version = "1.839" %} +{% set sha256 = "f25dd3d67103adea1e1f862e67182cba1c7b64cf55b8dcded32752dd488321bc" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-Shared-1.838.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-Shared-1.839.tar.gz sha256: {{ sha256 }} build: From 575cd28bec93a3814d1d3f267b8e77c43fcfda14 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:31:02 -0700 Subject: [PATCH 138/546] Update perl-test-warnings to 0.026 (#11942) --- recipes/perl-test-warnings/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-warnings/meta.yaml b/recipes/perl-test-warnings/meta.yaml index 6c107d4c413d1..213a262f8fa6b 100644 --- a/recipes/perl-test-warnings/meta.yaml +++ b/recipes/perl-test-warnings/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-test-warnings - version: "0.021" + version: "0.026" source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-Warnings-0.021.tar.gz - md5: "fcbc42414de51392348c27420d3c14b0" + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-Warnings-0.026.tar.gz + sha256: "ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08" requirements: host: @@ -15,7 +15,7 @@ requirements: - perl build: - number: 3 + number: 0 test: imports: From c9a8e4855d2f59bc0c1b34af58e40239a5f79214 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:31:17 -0700 Subject: [PATCH 139/546] Update perl-authen-sasl-saslprep to 1.100 (#11939) --- recipes/perl-authen-sasl-saslprep/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-authen-sasl-saslprep/meta.yaml b/recipes/perl-authen-sasl-saslprep/meta.yaml index 8886a49ce20ae..3e08a354d5b80 100644 --- a/recipes/perl-authen-sasl-saslprep/meta.yaml +++ b/recipes/perl-authen-sasl-saslprep/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-authen-sasl-saslprep - version: "1.011" + version: "1.100" source: - url: https://cpan.metacpan.org/authors/id/C/CF/CFAERBER/Authen-SASL-SASLprep-1.011.tar.gz - md5: eb9cc1f59968047e23ac44c02a0ecc21 + url: https://cpan.metacpan.org/authors/id/C/CF/CFAERBER/Authen-SASL-SASLprep-1.100.tar.gz + sha256: a4cccc34bb3f53acf0ba78c9fc61af8d156d109d1c10487ba5988a55077d1f70 build: - number: 2 + number: 0 requirements: host: From 0f706c7add0fa3af914638552bc72b7562e44589 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:32:36 -0700 Subject: [PATCH 140/546] Update perl-dbd-pg to 3.7.4 (#11938) --- recipes/perl-dbd-pg/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-dbd-pg/meta.yaml b/recipes/perl-dbd-pg/meta.yaml index 82bc31b74ad92..bcf0841d53539 100644 --- a/recipes/perl-dbd-pg/meta.yaml +++ b/recipes/perl-dbd-pg/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-dbd-pg - version: 3.5.3 + version: 3.7.4 source: - url: http://search.cpan.org/CPAN/authors/id/T/TU/TURNSTEP/DBD-Pg-3.5.3.tar.gz - md5: 21cdf31a8d1f77466920375aa766c164 + url: http://search.cpan.org/CPAN/authors/id/T/TU/TURNSTEP/DBD-Pg-3.7.4.tar.gz + sha256: 9ffa9c4e9d1d6b1483ec3259114b95998fd7e4a4168931c903b5ad5fd7a6783e build: - number: 1 + number: 0 requirements: host: From 241167a2309c50f247a43fc1d28d34c74cbcd551 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:32:44 -0700 Subject: [PATCH 141/546] Update perl-class-method-modifiers to 2.12 (#11937) --- recipes/perl-class-method-modifiers/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-class-method-modifiers/meta.yaml b/recipes/perl-class-method-modifiers/meta.yaml index 561b465eaaec5..6c9b0b63b8ac2 100644 --- a/recipes/perl-class-method-modifiers/meta.yaml +++ b/recipes/perl-class-method-modifiers/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-class-method-modifiers - version: "2.11" + version: "2.12" source: - url: http://cpan.metacpan.org/authors/id/E/ET/ETHER/Class-Method-Modifiers-2.11.tar.gz - md5: c6982e9e89325713d5afaff82cfe1744 + url: http://cpan.metacpan.org/authors/id/E/ET/ETHER/Class-Method-Modifiers-2.12.tar.gz + sha256: e44c1073020bf55b8c97975ed77235fd7e2a6a56f29b5c702301721184e27ac8 build: - number: 2 + number: 0 requirements: host: From f9d857c16f8bda71c0578142bd0ed38c53644097 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:32:55 -0700 Subject: [PATCH 142/546] Update perl-tree-dag_node to 1.31 (#11936) --- recipes/perl-tree-dag_node/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-tree-dag_node/meta.yaml b/recipes/perl-tree-dag_node/meta.yaml index 0df5a2421af43..366a6c66355e8 100644 --- a/recipes/perl-tree-dag_node/meta.yaml +++ b/recipes/perl-tree-dag_node/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-tree-dag_node - version: "1.29" + version: "1.31" source: - url: https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/Tree-DAG_Node-1.29.tgz - md5: 0d2c2f7cb7f12afafd28bbab75e15442 + url: https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/Tree-DAG_Node-1.31.tgz + sha256: 1c8ba69772568b3758054247097512c550efe31517c329fb65eef7afccc9d304 build: - number: 2 + number: 0 requirements: host: From fb02fd010828dad7f196626473bf1d22e9f6c68d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:33:03 -0700 Subject: [PATCH 143/546] Update perl-image-exiftool to 11.11 (#11935) --- recipes/perl-image-exiftool/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-image-exiftool/meta.yaml b/recipes/perl-image-exiftool/meta.yaml index 852e69c364058..1d3df3e87eefe 100644 --- a/recipes/perl-image-exiftool/meta.yaml +++ b/recipes/perl-image-exiftool/meta.yaml @@ -1,17 +1,17 @@ {% set name = "perl-image-exiftool" %} -{% set version = "11.01" %} -{% set sha256 = "705fbf4a42d772c548afff4c64b3db3e95eb347e5b48acd66dd7d7712c19bc9c" %} +{% set version = "11.11" %} +{% set sha256 = "e64eee75cdbc0944ea598bade44a2c100e7c940ce7d163cbbd087d2bd00cefeb" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/EX/EXIFTOOL/Image-ExifTool-11.01.tar.gz + url: https://cpan.metacpan.org/authors/id/E/EX/EXIFTOOL/Image-ExifTool-11.11.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 requirements: host: From 9456c4088d285902e1686b5c338d1a68aa2aa4cf Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:33:26 -0700 Subject: [PATCH 144/546] Update perl-moosex-app to 1.3701 (#11934) --- recipes/perl-moosex-app/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-moosex-app/meta.yaml b/recipes/perl-moosex-app/meta.yaml index 7b297dce7a1bc..f1a7f7648b5e9 100644 --- a/recipes/perl-moosex-app/meta.yaml +++ b/recipes/perl-moosex-app/meta.yaml @@ -1,14 +1,14 @@ package: name: perl-moosex-app - version: "1.35" + version: "1.3701" source: - url: https://cpan.metacpan.org/authors/id/M/MA/MAROS/MooseX-App-1.35.tar.gz - md5: be0ef3961d5a394e2366f7fbc0b62282 + url: https://cpan.metacpan.org/authors/id/M/MA/MAROS/MooseX-App-1.3701.tar.gz + sha256: 57ef199b45fa26bc519a4cc4713783b76ebe5b572b19870ff5df3c56ac0dd77f build: skip: True # [osx] - number: 2 + number: 0 requirements: host: From 71224810557c89836a8b371412131f169f089e22 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:33:39 -0700 Subject: [PATCH 145/546] Update perl-parse-recdescent to 1.967015 (#11933) --- recipes/perl-parse-recdescent/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-parse-recdescent/meta.yaml b/recipes/perl-parse-recdescent/meta.yaml index e28628c8e201a..64dd40a9b24fb 100644 --- a/recipes/perl-parse-recdescent/meta.yaml +++ b/recipes/perl-parse-recdescent/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-parse-recdescent - version: "1.967013" + version: "1.967015" source: - url: https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN/Parse-RecDescent-1.967013.tar.gz - md5: 98f582240556a4a92e5d57e480f9d39d + url: https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN/Parse-RecDescent-1.967015.tar.gz + sha256: 1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37 build: - number: 1 + number: 0 requirements: host: From 92f5d76114dfa6a0f5ca4056f6e585aa7e5ee884 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:33:48 -0700 Subject: [PATCH 146/546] Update perl-mime-types to 2.17 (#11932) --- recipes/perl-mime-types/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-mime-types/meta.yaml b/recipes/perl-mime-types/meta.yaml index ab0acedf5421f..7f39f22aa98ee 100644 --- a/recipes/perl-mime-types/meta.yaml +++ b/recipes/perl-mime-types/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-mime-types - version: "2.12" + version: "2.17" source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARKOV/MIME-Types-2.12.tar.gz - md5: bbd17e44183d0e958edd27ebf4673272 + url: https://cpan.metacpan.org/authors/id/M/MA/MARKOV/MIME-Types-2.17.tar.gz + sha256: e04ed7d42f1ff3150a303805f2689c28f80b92c511784d4641cb7f040d3e8ff6 build: - number: 1 + number: 0 requirements: host: From 0045b7525c93556938b1c66e120df8b9189c4131 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:33:58 -0700 Subject: [PATCH 147/546] Update perl-yaml to 1.27 (#11931) --- recipes/perl-yaml/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-yaml/meta.yaml b/recipes/perl-yaml/meta.yaml index 6397e95a18240..97647585aa7d8 100644 --- a/recipes/perl-yaml/meta.yaml +++ b/recipes/perl-yaml/meta.yaml @@ -1,17 +1,17 @@ {% set name = "perl-yaml" %} -{% set version = "1.26" %} -{% set sha256 = "fa2f99d54c4afbc5af9da6322609d2b697d0200b6bce6fdf644aff4242957fbc" %} +{% set version = "1.27" %} +{% set sha256 = "c992a1e820de0721b62b22521de92cdbf49edc306ab804c485b4b1ec25f682f9" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/T/TI/TINITA/YAML-1.26.tar.gz + url: https://cpan.metacpan.org/authors/id/T/TI/TINITA/YAML-1.27.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 requirements: host: From 6f3ccbe3332a3573efe7ae7dff89107c56ba3609 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:34:07 -0700 Subject: [PATCH 148/546] Update perl-cgi to 4.40 (#11930) --- recipes/perl-cgi/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-cgi/meta.yaml b/recipes/perl-cgi/meta.yaml index 5edb16e7af507..00eb90307e42d 100644 --- a/recipes/perl-cgi/meta.yaml +++ b/recipes/perl-cgi/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-cgi - version: '4.22' + version: '4.40' source: - url: https://cpan.metacpan.org/authors/id/L/LE/LEEJO/CGI-4.22.tar.gz - sha256: 8cd695f032b630fc4b5cf6c0a39912ff30cae0f7da03d01965ca2ac28b4dcca8 + url: https://cpan.metacpan.org/authors/id/L/LE/LEEJO/CGI-4.40.tar.gz + sha256: 10efff3061b3c31a33b3cc59f955aef9c88d57d12dbac46389758cef92f24f56 build: - number: 4 + number: 0 requirements: build: From 249f08b9947a4cfe05c54c26f81c601fde8bf1f5 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:34:22 -0700 Subject: [PATCH 149/546] Update perl-sub-uplevel to 0.2800 (#11929) --- recipes/perl-sub-uplevel/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-sub-uplevel/meta.yaml b/recipes/perl-sub-uplevel/meta.yaml index 716977061686a..d423b7b7dca96 100644 --- a/recipes/perl-sub-uplevel/meta.yaml +++ b/recipes/perl-sub-uplevel/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-sub-uplevel - version: "0.25" + version: "0.2800" source: - url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.25.tar.gz - md5: 5d0752dbfa94d0c91b25a264f47f5675 + url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz + sha256: b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293 build: - number: 3 + number: 0 requirements: build: From ea3636c4c05dba656e7d5d2c05ce9f43dc7362ff Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:34:32 -0700 Subject: [PATCH 150/546] Update perl-capture-tiny to 0.48 (#11927) --- recipes/perl-capture-tiny/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-capture-tiny/meta.yaml b/recipes/perl-capture-tiny/meta.yaml index 15c939893bee6..de87f2ff7d569 100644 --- a/recipes/perl-capture-tiny/meta.yaml +++ b/recipes/perl-capture-tiny/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-capture-tiny - version: "0.36" + version: "0.48" source: - url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Capture-Tiny-0.36.tar.gz - md5: db6444111c30ac01a76a4c118241c7b6 + url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Capture-Tiny-0.48.tar.gz + sha256: 6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19 build: - number: 2 + number: 0 requirements: # NOTE: All other required build & run modules specified in the CPAN metadata From 6aaef1c6a6cf3d970775d6fe8bf94e05aa22c5a1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:34:42 -0700 Subject: [PATCH 151/546] Update perl-xml-parser-lite to 0.722 (#11926) --- recipes/perl-xml-parser-lite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-xml-parser-lite/meta.yaml b/recipes/perl-xml-parser-lite/meta.yaml index e349809d6e26b..a4a31352d1108 100644 --- a/recipes/perl-xml-parser-lite/meta.yaml +++ b/recipes/perl-xml-parser-lite/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-xml-parser-lite - version: "0.721" + version: "0.722" source: - url: https://cpan.metacpan.org/authors/id/P/PH/PHRED/XML-Parser-Lite-0.721.tar.gz - md5: ad8a87b9bf413aa540c7cb724d650808 + url: https://cpan.metacpan.org/authors/id/P/PH/PHRED/XML-Parser-Lite-0.722.tar.gz + sha256: 6f90a027e1531a0e5406cf1de13c709b5216966df8f73d0bab9ab919209763ee build: - number: 2 + number: 0 requirements: host: From 9e860437ead9e10b8893ac865e2bf0a3b191b5e6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:34:54 -0700 Subject: [PATCH 152/546] Update perl-text-diff to 1.45 (#11925) --- recipes/perl-text-diff/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-text-diff/meta.yaml b/recipes/perl-text-diff/meta.yaml index 785a8a71b4cf8..01448e0e3d694 100644 --- a/recipes/perl-text-diff/meta.yaml +++ b/recipes/perl-text-diff/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-text-diff - version: "1.44" + version: "1.45" source: - url: https://cpan.metacpan.org/authors/id/N/NE/NEILB/Text-Diff-1.44.tar.gz - md5: 1f0bcd24b64b50a29ad1cf997c2247e9 + url: https://cpan.metacpan.org/authors/id/N/NE/NEILB/Text-Diff-1.45.tar.gz + sha256: e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04 build: - number: 2 + number: 0 requirements: host: From 7cc1eb724fe8409adbcb174210f890b3c5ec5007 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:35:03 -0700 Subject: [PATCH 153/546] Update perl-yaml-tiny to 1.73 (#11924) --- recipes/perl-yaml-tiny/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-yaml-tiny/meta.yaml b/recipes/perl-yaml-tiny/meta.yaml index d57f362f8f5ab..71817a2e50501 100644 --- a/recipes/perl-yaml-tiny/meta.yaml +++ b/recipes/perl-yaml-tiny/meta.yaml @@ -1,14 +1,14 @@ package: name: perl-yaml-tiny - version: "1.70" + version: "1.73" source: - url: http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/YAML-Tiny-1.70.tar.gz - md5: a475714e8d512aafc410ca4d7a117aa2 + url: http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/YAML-Tiny-1.73.tar.gz + sha256: bc315fa12e8f1e3ee5e2f430d90b708a5dc7e47c867dba8dce3a6b8fbe257744 build: - number: 1 + number: 0 requirements: host: From 09421d36e94ee984b4c2c76b648502172ed0dd9b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:35:16 -0700 Subject: [PATCH 154/546] Update perl-type-tiny to 1.004002 (#11921) --- recipes/perl-type-tiny/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-type-tiny/meta.yaml b/recipes/perl-type-tiny/meta.yaml index 3815bed1bc432..d8e7d06ef03eb 100644 --- a/recipes/perl-type-tiny/meta.yaml +++ b/recipes/perl-type-tiny/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-type-tiny" %} -{% set version = "1.002002" %} -{% set sha256 = "a85b0c8f99b5c9b5558f0bcc8893b44299fcccf3c264ff924940d09d91d8882c" %} +{% set version = "1.004002" %} +{% set sha256 = "e52c7e9593052aed157a15d473b5c25a1dbb3454bf3cd6913df94cc9bb2be707" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/T/TO/TOBYINK/Type-Tiny-1.002002.tar.gz + url: https://cpan.metacpan.org/authors/id/T/TO/TOBYINK/Type-Tiny-1.004002.tar.gz sha256: {{ sha256 }} build: From b81852ca79d5a49b2b9603eabd758f28ff8f4dc6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:35:25 -0700 Subject: [PATCH 155/546] Update perl-db-file to 1.843 (#11919) --- recipes/perl-db-file/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-db-file/meta.yaml b/recipes/perl-db-file/meta.yaml index b9f67916f45a7..c911352aada32 100644 --- a/recipes/perl-db-file/meta.yaml +++ b/recipes/perl-db-file/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-db-file - version: 1.835 + version: 1.843 source: - url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/DB_File-1.835.tar.gz - sha256: 41206f39a1bac49db8c1595e300b04c70e1393b2d78ccb9ef15c5c0b81037cfc + url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/DB_File-1.843.tar.gz + sha256: de24e3d1e56b1b56c1f143590fb8ab8b812ebd9697e9c01349b0ba11c36f346a build: - number: 6 + number: 0 requirements: build: From 063c35112ebf771e71b2ff2ce427d677a8ccc013 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:35:36 -0700 Subject: [PATCH 156/546] Update perl-perlio-gzip to 0.20 (#11920) --- recipes/perl-perlio-gzip/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-perlio-gzip/meta.yaml b/recipes/perl-perlio-gzip/meta.yaml index 6d43b1240c614..0e2607e9064e6 100644 --- a/recipes/perl-perlio-gzip/meta.yaml +++ b/recipes/perl-perlio-gzip/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-perlio-gzip - version: "0.19" + version: "0.20" source: - url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/PerlIO-gzip-0.19.tar.gz - md5: "dbcfc1450f6b593b65048b8ced061c98" + url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/PerlIO-gzip-0.20.tar.gz + sha256: "4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5" build: - number: 3 + number: 0 requirements: host: From f1afc50965773be7c57b97e48daf6af1805c6152 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:35:46 -0700 Subject: [PATCH 157/546] Update perl-specio to 0.43 (#11918) --- recipes/perl-specio/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-specio/meta.yaml b/recipes/perl-specio/meta.yaml index 220c47eb42440..4f09b9e207dc9 100644 --- a/recipes/perl-specio/meta.yaml +++ b/recipes/perl-specio/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-specio" %} -{% set version = "0.42" %} -{% set sha256 = "23298b93a26d7ae3c1d58106f5898d84ddc71b626afdbf801bddb04d5e524ef6" %} +{% set version = "0.43" %} +{% set sha256 = "3cd0debf7b6404127d5e0bb7fb78cfef9df5e2519d3d6ad7113b59ad1da9fa1d" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Specio-0.42.tar.gz + url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Specio-0.43.tar.gz sha256: {{ sha256 }} build: From db6cddb10a4c7267eca2a3aca6127fa8c1147579 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:35:55 -0700 Subject: [PATCH 158/546] Update perl-gd to 2.69 (#11917) --- recipes/perl-gd/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-gd/meta.yaml b/recipes/perl-gd/meta.yaml index b49b9929aab07..d984deabb251f 100644 --- a/recipes/perl-gd/meta.yaml +++ b/recipes/perl-gd/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-gd" %} -{% set version = "2.68" %} -{% set sha256 = "6aa3de0d49c22011d412789be664c46520b8d4eb4920fe30dbac501b88515e5c" %} +{% set version = "2.69" %} +{% set sha256 = "ddb02d491cfd84d30448438c84239b0893d84e9576a90c3b5ed109420fae545d" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/R/RU/RURBAN/GD-2.68.tar.gz + url: https://cpan.metacpan.org/authors/id/R/RU/RURBAN/GD-2.69.tar.gz sha256: {{ sha256 }} build: From 0cc3480ed2f1f7b490b318874f07aab748d06fd5 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:37:24 -0700 Subject: [PATCH 159/546] Update perl-ipc-run to 20180523.0 (#11916) --- recipes/perl-ipc-run/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-ipc-run/meta.yaml b/recipes/perl-ipc-run/meta.yaml index 07ac7d9a862ac..540bd42e94272 100644 --- a/recipes/perl-ipc-run/meta.yaml +++ b/recipes/perl-ipc-run/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-ipc-run - version: "0.94" + version: "20180523.0" source: - url: https://cpan.metacpan.org/authors/id/T/TO/TODDR/IPC-Run-0.94.tar.gz - md5: c963902894d3796b16624b3b4aea94b4 + url: https://cpan.metacpan.org/authors/id/T/TO/TODDR/IPC-Run-20180523.0.tar.gz + sha256: 3850d7edf8a4671391c6e99bb770698e1c45da55b323b31c76310913349b6c2f build: - number: 1 + number: 0 requirements: host: From 2081855f22e108a175e023badee6d5949bd0def8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:37:36 -0700 Subject: [PATCH 160/546] Update perl-xml-dom to 1.46 (#11915) --- recipes/perl-xml-dom/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-xml-dom/meta.yaml b/recipes/perl-xml-dom/meta.yaml index a958f1103e420..1739887085f9d 100644 --- a/recipes/perl-xml-dom/meta.yaml +++ b/recipes/perl-xml-dom/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-xml-dom - version: "1.45" + version: "1.46" source: - url: https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/XML-DOM-1.45.tar.gz - md5: f95fd6929b43d140db1afc0282513e65 + url: https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/XML-DOM-1.46.tar.gz + sha256: 8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e build: - number: 1 + number: 0 requirements: host: From fa6effebc2ad57db2f60a1cc07ab633f8e0e9066 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:37:49 -0700 Subject: [PATCH 161/546] Update perl-try-tiny-retry to 0.004 (#11911) --- recipes/perl-try-tiny-retry/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-try-tiny-retry/meta.yaml b/recipes/perl-try-tiny-retry/meta.yaml index d9ac24648bea6..ae0116b7dbc9a 100644 --- a/recipes/perl-try-tiny-retry/meta.yaml +++ b/recipes/perl-try-tiny-retry/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-try-tiny-retry - version: "0.002" + version: "0.004" source: - url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Try-Tiny-Retry-0.002.tar.gz - sha256: 4f6dd3addcab7dd2726f450cecaaadb21b33da59bec5df58f07fd91a87d9c38a + url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Try-Tiny-Retry-0.004.tar.gz + sha256: 8af70c1bd46d749388738b7ea03c703cac898be939a5ff37117a01ed7eda8bbe build: - number: 1 + number: 0 requirements: host: From 876e2be4e893397a837bf20a7bd3498a1fc51901 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:37:59 -0700 Subject: [PATCH 162/546] Update perl-test-class-moose to 0.95 (#11909) --- recipes/perl-test-class-moose/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-test-class-moose/meta.yaml b/recipes/perl-test-class-moose/meta.yaml index f6ab825945def..9ef86cb017908 100644 --- a/recipes/perl-test-class-moose/meta.yaml +++ b/recipes/perl-test-class-moose/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-test-class-moose" %} -{% set version = "0.94" %} -{% set sha256 = "182eadddaf09aef4701fe048238e91ad9f255a28958245b8ae6d74cdab46f824" %} +{% set version = "0.95" %} +{% set sha256 = "069c64997067ec30b952ec8cf0221230d43e3acb50781753c4191e2702a135ef" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Test-Class-Moose-0.94.tar.gz + url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Test-Class-Moose-0.95.tar.gz sha256: {{ sha256 }} build: From 53555b46f6f2c5ffc3af5dfa0328b9fbafcd27ad Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:38:09 -0700 Subject: [PATCH 163/546] Update perl-try-tiny to 0.30 (#11908) --- recipes/perl-try-tiny/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-try-tiny/meta.yaml b/recipes/perl-try-tiny/meta.yaml index ae3e7ac4766eb..dc923b249c22e 100644 --- a/recipes/perl-try-tiny/meta.yaml +++ b/recipes/perl-try-tiny/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-try-tiny - version: "0.24" + version: "0.30" source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Try-Tiny-0.24.tar.gz - md5: 1a12a51cfeb7e2c301e4ae093c7ecdfb + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Try-Tiny-0.30.tar.gz + sha256: da5bd0d5c903519bbf10bb9ba0cb7bcac0563882bcfe4503aee3fb143eddef6b build: - number: 3 + number: 0 requirements: host: From 5d6df131bb4d37b0374974f2cfd13a6da2a2e2ac Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:38:20 -0700 Subject: [PATCH 164/546] Update perl-xml-sax-writer to 0.57 (#11906) --- recipes/perl-xml-sax-writer/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-xml-sax-writer/meta.yaml b/recipes/perl-xml-sax-writer/meta.yaml index bcccf3d2891b2..c8b6f0890a9a3 100644 --- a/recipes/perl-xml-sax-writer/meta.yaml +++ b/recipes/perl-xml-sax-writer/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-xml-sax-writer - version: "0.56" + version: "0.57" source: - url: https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-SAX-Writer-0.56.tar.gz - md5: e5fa5e2b2f6867b1aca9b5b43e1ce361 + url: https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-SAX-Writer-0.57.tar.gz + sha256: 3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0 build: - number: 2 + number: 0 requirements: host: From 68e4793a6fd1c4f95dc2f4b1cec83bdab92ed1e4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:38:30 -0700 Subject: [PATCH 165/546] Update perl-moosex-getopt to 0.74 (#11905) --- recipes/perl-moosex-getopt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-moosex-getopt/meta.yaml b/recipes/perl-moosex-getopt/meta.yaml index 884b1115b4126..a9e98842c7c5e 100644 --- a/recipes/perl-moosex-getopt/meta.yaml +++ b/recipes/perl-moosex-getopt/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-moosex-getopt" %} -{% set version = "0.72" %} -{% set sha256 = "a378411a061ed239554d2b7f86b2b82bf55f600901243a6ec3fd29557d171b2e" %} +{% set version = "0.74" %} +{% set sha256 = "1de0df3b431ebe9f3563bdf4569eacd7e07e865a8397f2a990d0cb57d4cb2c24" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/MooseX-Getopt-0.72.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/MooseX-Getopt-0.74.tar.gz sha256: {{ sha256 }} build: From cc468b85ba81862e5c63da9b692943d5a3a1ac12 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:38:43 -0700 Subject: [PATCH 166/546] Update perl-devel-globaldestruction to 0.14 (#11904) --- recipes/perl-devel-globaldestruction/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-devel-globaldestruction/meta.yaml b/recipes/perl-devel-globaldestruction/meta.yaml index 8f568c5b22585..64a29bbeb7be2 100644 --- a/recipes/perl-devel-globaldestruction/meta.yaml +++ b/recipes/perl-devel-globaldestruction/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-devel-globaldestruction - version: "0.13" + version: "0.14" source: - url: http://cpan.metacpan.org/authors/id/H/HA/HAARG/Devel-GlobalDestruction-0.13.tar.gz - md5: e7be00040827e204b2b6cba2f3166074 + url: http://cpan.metacpan.org/authors/id/H/HA/HAARG/Devel-GlobalDestruction-0.14.tar.gz + sha256: 34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab build: - number: 2 + number: 0 requirements: host: From 3b741ed45afb175975900cf61c974625c4f4d275 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:38:54 -0700 Subject: [PATCH 167/546] Update perl-dbd-sqlite to 1.58 (#11903) --- recipes/perl-dbd-sqlite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-dbd-sqlite/meta.yaml b/recipes/perl-dbd-sqlite/meta.yaml index e0f2f84799988..ffcb1fd963d5e 100644 --- a/recipes/perl-dbd-sqlite/meta.yaml +++ b/recipes/perl-dbd-sqlite/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-dbd-sqlite - version: '1.50' + version: '1.58' source: - url: http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/DBD-SQLite-1.50.tar.gz - sha256: 3ac513ab73944fd7d4b672e1fe885dc522b6369d38f46a68e67e0045bf159ce1 + url: http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/DBD-SQLite-1.58.tar.gz + sha256: 7120dd99d0338dea2802fda8bfe3fbf10077d5af559f6c67ae35e9270d1a1d3b build: - number: 3 + number: 0 requirements: build: From b732f857a410cb5a7009954efba9c66a326f2054 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:39:01 -0700 Subject: [PATCH 168/546] Update perl-mce to 1.837 (#11902) --- recipes/perl-mce/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-mce/meta.yaml b/recipes/perl-mce/meta.yaml index 09ce0955a2d06..6e85101e70016 100644 --- a/recipes/perl-mce/meta.yaml +++ b/recipes/perl-mce/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-mce" %} -{% set version = "1.836" %} -{% set sha256 = "9ec7c2db7207f3e273a565777141d0218d1199833790c2c3c09cde23f462d312" %} +{% set version = "1.837" %} +{% set sha256 = "ea7a069dcd05cfb86b533e44cab842a8657c95a86052c3bbb00c45013617216a" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.836.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.837.tar.gz sha256: {{ sha256 }} build: From 8e4386a48a5773f4784e9955afda0ed8ec16a620 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:39:13 -0700 Subject: [PATCH 169/546] Update perl-mime-tools to 5.508 (#11900) --- recipes/perl-mime-tools/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-mime-tools/meta.yaml b/recipes/perl-mime-tools/meta.yaml index 0548072ed60b7..64d49ab9c1f7f 100644 --- a/recipes/perl-mime-tools/meta.yaml +++ b/recipes/perl-mime-tools/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-mime-tools - version: "5.507" + version: "5.508" source: - url: https://cpan.metacpan.org/authors/id/D/DS/DSKOLL/MIME-tools-5.507.tar.gz - md5: 98e1997b6ddd973ced9b2f6feb9d6aaf + url: https://cpan.metacpan.org/authors/id/D/DS/DSKOLL/MIME-tools-5.508.tar.gz + sha256: adffe86cd0b045d5a1553f48e72e89b9834fbda4f334c98215995b98cb17c917 build: - number: 1 + number: 0 requirements: host: From 69c817706427f0c9a5c4c291daabf814097babe1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:39:22 -0700 Subject: [PATCH 170/546] Update perl-xml-simple to 2.25 (#11899) --- recipes/perl-xml-simple/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-xml-simple/meta.yaml b/recipes/perl-xml-simple/meta.yaml index 3e354a715b38b..8e9d8ea29ad65 100644 --- a/recipes/perl-xml-simple/meta.yaml +++ b/recipes/perl-xml-simple/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-xml-simple - version: "2.22" + version: "2.25" source: - url: https://cpan.metacpan.org/authors/id/G/GR/GRANTM/XML-Simple-2.22.tar.gz - md5: 0914abddfce749453ed89b54029f2643 + url: https://cpan.metacpan.org/authors/id/G/GR/GRANTM/XML-Simple-2.25.tar.gz + sha256: 531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8 build: - number: 3 + number: 0 requirements: host: From e8c6191ca291b6f61e8574b0a887c008b6fa7a4a Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:39:31 -0700 Subject: [PATCH 171/546] Update perl-clone to 0.41 (#11898) --- recipes/perl-clone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-clone/meta.yaml b/recipes/perl-clone/meta.yaml index c6510b79756bb..eec8839730b78 100644 --- a/recipes/perl-clone/meta.yaml +++ b/recipes/perl-clone/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-clone" %} -{% set version = "0.39" %} -{% set sha256 = "acb046683e49d650b113634ecf57df000816a49e611b0fff70bf3f93568bfa2d" %} +{% set version = "0.41" %} +{% set sha256 = "e8c056dcf4bc8889079a09412af70194a54a269689ba72edcd91291a46a51518" %} package: name: {{ name }} From 7343189c2485b1712519272d747fbeda99a72e2c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:39:47 -0700 Subject: [PATCH 172/546] Update sina to 1.4.0 (#11882) * Update sina to 1.4.0 * Add tbb-devel (tbb should be implicit) * Remove zlib from run deps (implicit from exported host deps) --- recipes/sina/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/sina/meta.yaml b/recipes/sina/meta.yaml index 57252141ad05f..50f3ef0cc5729 100644 --- a/recipes/sina/meta.yaml +++ b/recipes/sina/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SINA" %} -{% set version = "1.3.5" %} -{% set sha256 = "8bab9f1c040598056dfcef9498f0ddb2ea803deb9e90d7f5ce3ecd1a96cdf850" %} +{% set version = "1.4.0" %} +{% set sha256 = "7e41c6c53ceb0c646b682a4bf1a94bf50c3382d6a571e7e00c02d424e7b41d84" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: url: https://github.com/epruesse/SINA/releases/download/v{{version}}/sina-{{version}}.tar.gz build: - number: 2 + number: 0 requirements: build: @@ -21,10 +21,11 @@ requirements: - arb-bio-devel - boost - zlib + - tbb-devel run: - arb-bio-tools - boost - - zlib + test: commands: - sina --help From 45b510a623f7eb6b77a407425eec104d5c07e201 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 10 Nov 2018 22:40:03 -0700 Subject: [PATCH 173/546] Update mothur to 1.41.0 (#11877) * Update mothur to 1.41.0 * Remove patches * Add hdf5 --- recipes/mothur/meta.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/mothur/meta.yaml b/recipes/mothur/meta.yaml index 58eccfefd4c22..69723d45fb272 100644 --- a/recipes/mothur/meta.yaml +++ b/recipes/mothur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.40.5" %} +{% set version = "1.41.0" %} package: name: mothur @@ -6,10 +6,7 @@ package: source: url: https://github.com/mothur/mothur/archive/v{{ version }}.tar.gz - md5: d57847849fdb961c3f66c9b9fdf3057b - patches: - - patch - - patch2 + sha256: b54b71e46f96ff2604ba8e3b33f95c067e6921cbb212b603365e6483d05574f1 build: number: 0 @@ -24,12 +21,14 @@ requirements: - readline - boost - blast-legacy + - hdf5 run: - zlib - ncurses - readline - boost - blast-legacy + - hdf5 test: commands: - mothur "#help()" @@ -41,4 +40,4 @@ about: license_family: GPL license_file: LICENSE.md summary: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. - dev_url: https://github.com/mothur/mothur \ No newline at end of file + dev_url: https://github.com/mothur/mothur From cef84336b90d70a11484cd30bf6dd37dcfac97c3 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Sun, 11 Nov 2018 02:32:49 -0500 Subject: [PATCH 174/546] adding urllib3 (#11943) --- recipes/ctat-mutations/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index f8d9585c5a14a..13f5f92fbac3f 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "2" %} +{% set build = "3" %} package: name: {{ name }} @@ -22,6 +22,7 @@ requirements: - picard =2.18.14 run: - python =2.7 + - urllib3 - gatk4 - star - picard =2.18.14 From 78d72f95697a46684704f206647d61c0f8aa3a98 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Sun, 11 Nov 2018 10:48:03 +0100 Subject: [PATCH 175/546] Force biobb_common >=0.0.6 (#11974) --- recipes/biobb_md/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_md/meta.yaml b/recipes/biobb_md/meta.yaml index da611a155f7f9..bd73d447db383 100644 --- a/recipes/biobb_md/meta.yaml +++ b/recipes/biobb_md/meta.yaml @@ -20,10 +20,10 @@ requirements: host: - python >=3 - setuptools - - biobb_common + - biobb_common >=0.0.6 run: - python >=3 - - biobb_common + - biobb_common >=0.0.6 test: imports: From fd331fbb548f52ed750b571c530e527502944bc9 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Sun, 11 Nov 2018 07:03:39 -0500 Subject: [PATCH 176/546] adding requests as dep (#11975) --- recipes/ctat-mutations/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index 13f5f92fbac3f..fd807aa12662b 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "3" %} +{% set build = "4" %} package: name: {{ name }} @@ -22,7 +22,7 @@ requirements: - picard =2.18.14 run: - python =2.7 - - urllib3 + - requests =2.18.4 - gatk4 - star - picard =2.18.14 From d180422360483fcffc72317e1dee1dff719e0312 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Sun, 11 Nov 2018 20:03:27 +0100 Subject: [PATCH 177/546] Change version of package and forcing biobb_common 0.0.6 (#11977) --- recipes/biobb_md/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_md/meta.yaml b/recipes/biobb_md/meta.yaml index bd73d447db383..1baf058debdc7 100644 --- a/recipes/biobb_md/meta.yaml +++ b/recipes/biobb_md/meta.yaml @@ -1,8 +1,8 @@ {% set name = "biobb_md" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "7d007aac538bee9a201d1fdf1523092c4ea8444f6851e2ee1562793208c390f9" %} +{% set hash_value = "195d75f8495fdda22bab22b11177661699cecbe58412dfac3b14db0ac1b0e72b" %} package: name: '{{ name|lower }}' From 22f8a5f5d73f15f8d9f8123b0d92d44d4254074f Mon Sep 17 00:00:00 2001 From: pvanheus Date: Sun, 11 Nov 2018 21:38:12 +0200 Subject: [PATCH 178/546] Recipe for SalmID.py (#11868) * Recipe for SalmID.py * Fixed download URL * Fix install step * whitespace change for restart * Use SalmID.py 0.1.23 with poetry build system --- recipes/salmid/build.sh | 5 +++++ recipes/salmid/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 recipes/salmid/build.sh create mode 100644 recipes/salmid/meta.yaml diff --git a/recipes/salmid/build.sh b/recipes/salmid/build.sh new file mode 100644 index 0000000000000..e5c1fc03ff9a9 --- /dev/null +++ b/recipes/salmid/build.sh @@ -0,0 +1,5 @@ +#!/bin/sh + +poetry build --format wheel +pip install --no-deps dist/salmid*.whl + diff --git a/recipes/salmid/meta.yaml b/recipes/salmid/meta.yaml new file mode 100644 index 0000000000000..1578e300be72f --- /dev/null +++ b/recipes/salmid/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "SalmID" %} +{% set version = "0.1.23" %} +{% set sha256 = "aadcee6a7ba87ff4681129e86238d5edb7617dc4adf291e651b05ccb6d450cc9" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/hcdenbakker/{{ name }}/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + skip: True # [not py3k] + number: 0 + +requirements: + host: + - poetry + run: + - python + +test: + commands: + - SalmID.py -v |grep SalmID.py >/dev/null 2>&1 + +about: + home: https://github.com/hcdenbakker/SalmID + summary: 'Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).' + license: MIT +extra: + recipe-maintainers: + - pvanheus + identifiers: + - DOI:10.5281/zenodo.1409766 From fa119824faa48cc9fdddacb86c9ec10f4967b90f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:43:06 -0700 Subject: [PATCH 179/546] Update perl-error to 0.17027 (#11970) --- recipes/perl-error/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-error/meta.yaml b/recipes/perl-error/meta.yaml index cdea8e45c3161..47813adb980e0 100644 --- a/recipes/perl-error/meta.yaml +++ b/recipes/perl-error/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-error - version: "0.17024" + version: "0.17027" source: - url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Error-0.17024.tar.gz - md5: 7e3676a7fb14f65f568f12d4b40a2a72 + url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Error-0.17027.tar.gz + sha256: 07b2ac8275dfa04144745a6c1900a596280f862b97d22bab0c5ce02682ebd3be build: - number: 1 + number: 0 requirements: host: From 10e6714b232a7b196aba585b886b462e8e68652e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:43:31 -0700 Subject: [PATCH 180/546] Update beagle-lib to 3.1.0 (#11969) --- recipes/beagle-lib/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/beagle-lib/meta.yaml b/recipes/beagle-lib/meta.yaml index 7e2a473a32d44..f8f7543abb91f 100644 --- a/recipes/beagle-lib/meta.yaml +++ b/recipes/beagle-lib/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "3.0.2" %} -{% set sha256 = "59a7081b61ead0a5738e813c6fcfb614d2c5bb49c29b28609de8e2b51bea3ec0" %} +{% set version = "3.1.0" %} +{% set sha256 = "f680bdace45dffbb175688aa8bf679710e4e60d000bbf332860de757d4e1c411" %} package: name: beagle-lib version: '{{version}}' source: - url: https://github.com/beagle-dev/beagle-lib/archive/v3.0.2.tar.gz + url: https://github.com/beagle-dev/beagle-lib/archive/v3.1.0.tar.gz sha256: '{{sha256}}' #patches: # [osx] # - osx_jni.patch # [osx] From 7238c276861ebc755838381a03f1c49dbb1c740c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:43:42 -0700 Subject: [PATCH 181/546] Update perl-net-ssleay to 1.85 (#11968) --- recipes/perl-net-ssleay/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-net-ssleay/meta.yaml b/recipes/perl-net-ssleay/meta.yaml index 5cf665a8e5c5f..936e8a9e2e616 100644 --- a/recipes/perl-net-ssleay/meta.yaml +++ b/recipes/perl-net-ssleay/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.84" %} -{% set sha256 = "823ec3cbb428309d6a9e56f362a9300693ce3215b7fede109adb7be361fff177" %} +{% set version = "1.85" %} +{% set sha256 = "9d8188b9fb1cae3bd791979c20554925d5e94a138d00414f1a6814549927b0c8" %} package: name: perl-net-ssleay version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MI/MIKEM/Net-SSLeay-1.84.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MI/MIKEM/Net-SSLeay-1.85.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 requirements: host: From 7d5f96b8cbd1b3ecde08db8169ff038641b617d8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:43:56 -0700 Subject: [PATCH 182/546] Update perl-digest-md5 to 2.55 (#11967) --- recipes/perl-digest-md5/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-digest-md5/meta.yaml b/recipes/perl-digest-md5/meta.yaml index 67972cb9d9e7b..a604024cef10b 100644 --- a/recipes/perl-digest-md5/meta.yaml +++ b/recipes/perl-digest-md5/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-digest-md5 - version: "2.52" + version: "2.55" source: - url: http://cpan.metacpan.org/authors/id/G/GA/GAAS/Digest-MD5-2.52.tar.gz - sha256: 0a7caed9931af2123e64f110e284e33d88cdd5d9a7e0514ae5a8b7ae1b90e43e + url: http://cpan.metacpan.org/authors/id/G/GA/GAAS/Digest-MD5-2.55.tar.gz + sha256: 03b198a2d14425d951e5e50a885d3818c3162c8fe4c21e18d7798a9a179d0e3c build: - number: 3 + number: 0 requirements: host: From b126883f9b02287aae549f2369dc827a014bfffc Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:44:09 -0700 Subject: [PATCH 183/546] Update perl-test-deep to 1.128 (#11966) --- recipes/perl-test-deep/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-deep/meta.yaml b/recipes/perl-test-deep/meta.yaml index 892af36f3d985..72c71b4c61fd3 100644 --- a/recipes/perl-test-deep/meta.yaml +++ b/recipes/perl-test-deep/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-test-deep - version: "1.120" + version: "1.128" source: - url: https://cpan.metacpan.org/authors/id/R/RJ/RJBS/Test-Deep-1.120.tar.gz - md5: a90859f4f362578d1671e3b9aae0d8c1 + url: https://cpan.metacpan.org/authors/id/R/RJ/RJBS/Test-Deep-1.128.tar.gz + sha256: 852d7e836fba8269b0b755082051a24a1a309d015a8b76838790af9e3760092f requirements: host: @@ -14,7 +14,7 @@ requirements: - perl build: - number: 3 + number: 0 test: imports: From e171a21f288e5c693b4abb9a2977a056ff8d9e47 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:44:20 -0700 Subject: [PATCH 184/546] Update perl-path-tiny to 0.108 (#11964) --- recipes/perl-path-tiny/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-path-tiny/meta.yaml b/recipes/perl-path-tiny/meta.yaml index a023d30aa164c..f9f5668be9546 100644 --- a/recipes/perl-path-tiny/meta.yaml +++ b/recipes/perl-path-tiny/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-path-tiny - version: "0.082" + version: "0.108" source: - url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.082.tar.gz - md5: 0a1d918d0b84a3459355d63411a6c084 + url: https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.108.tar.gz + sha256: 3c49482be2b3eb7ddd7e73a5b90cff648393f5d5de334ff126ce7a3632723ff5 build: - number: 2 + number: 0 requirements: host: From 1d56a52c226aef41a8d926681560950c4c6fab06 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:44:37 -0700 Subject: [PATCH 185/546] Update perl-mailtools to 2.20 (#11965) --- recipes/perl-mailtools/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-mailtools/meta.yaml b/recipes/perl-mailtools/meta.yaml index baffae48e6aa9..2292e49f611b3 100644 --- a/recipes/perl-mailtools/meta.yaml +++ b/recipes/perl-mailtools/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-mailtools - version: "2.14" + version: "2.20" source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARKOV/MailTools-2.14.tar.gz - md5: 813ae849683367bb75e6be89e4e8cc46 + url: https://cpan.metacpan.org/authors/id/M/MA/MARKOV/MailTools-2.20.tar.gz + sha256: f55606f7a9cc342ee9d5f996e2b6a4c0047e2ee47cd88c3250ecf0d0c5fb3196 build: - number: 1 + number: 0 requirements: host: From 4cf75b6a83b295b4fb52527a60d19583ec01e4c7 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:44:57 -0700 Subject: [PATCH 186/546] Update perl-exception-class to 1.44 (#11961) --- recipes/perl-exception-class/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-exception-class/meta.yaml b/recipes/perl-exception-class/meta.yaml index 7bd0038493f53..20fb23334bb05 100644 --- a/recipes/perl-exception-class/meta.yaml +++ b/recipes/perl-exception-class/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-exception-class - version: "1.40" + version: "1.44" source: - url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Exception-Class-1.40.tar.gz - md5: 07cd7a38be5f8134955e943cf666d453 + url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Exception-Class-1.44.tar.gz + sha256: 33f3fbf8b138d3b04ea4ec0ba83fb0df6ba898806bcf4ef393d4cafc1a23ee0d build: - number: 2 + number: 0 requirements: host: From 2e8295e18b65eb6bbdbaa45b16fa1adebc33a103 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:45:21 -0700 Subject: [PATCH 187/546] Update perl-termreadkey to 2.37 (#11958) --- recipes/perl-termreadkey/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-termreadkey/meta.yaml b/recipes/perl-termreadkey/meta.yaml index e1cdbdb8c6fe0..cd6818b6da873 100644 --- a/recipes/perl-termreadkey/meta.yaml +++ b/recipes/perl-termreadkey/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-termreadkey - version: "2.32" + version: "2.37" source: - url: https://cpan.metacpan.org/authors/id/J/JS/JSTOWE/TermReadKey-2.32.tar.gz - md5: c55420c3456b8e470a01d6557b1045a8 + url: https://cpan.metacpan.org/authors/id/J/JS/JSTOWE/TermReadKey-2.37.tar.gz + sha256: 4a9383cf2e0e0194668fe2bd546e894ffad41d556b41d2f2f577c8db682db241 build: - number: 1 + number: 0 requirements: build: From 7cffdc45d315fc4fbb2ad3e0511846c56809c434 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:45:34 -0700 Subject: [PATCH 188/546] Update perl-sub-exporter-progressive to 0.001013 (#11955) --- recipes/perl-sub-exporter-progressive/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-sub-exporter-progressive/meta.yaml b/recipes/perl-sub-exporter-progressive/meta.yaml index 8e31b2dd8e919..d8f2b50687cf7 100644 --- a/recipes/perl-sub-exporter-progressive/meta.yaml +++ b/recipes/perl-sub-exporter-progressive/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-sub-exporter-progressive - version: "0.001011" + version: "0.001013" source: - url: http://cpan.metacpan.org/authors/id/F/FR/FREW/Sub-Exporter-Progressive-0.001011.tar.gz - md5: bb50b3ba1538902b197c04818a84230a + url: http://cpan.metacpan.org/authors/id/F/FR/FREW/Sub-Exporter-Progressive-0.001013.tar.gz + sha256: d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056 build: - number: 3 + number: 0 requirements: host: From 82350c8e003bac09b8a4b0a85f5fe8b744786f0d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:46:01 -0700 Subject: [PATCH 189/546] Update perl-devel-size to 0.82 (#11954) --- recipes/perl-devel-size/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-devel-size/meta.yaml b/recipes/perl-devel-size/meta.yaml index e0d9097be2b11..8659e65e75af3 100644 --- a/recipes/perl-devel-size/meta.yaml +++ b/recipes/perl-devel-size/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-devel-size - version: "0.80" + version: "0.82" source: - url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.80.tar.gz - md5: 49d5060edaf076bc757a028614c60f41 + url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.82.tar.gz + sha256: 8f04fd67b538c7665ddf8a6cba4ed7b3427c35ea2740e9c6e977dc68c18c7489 build: - number: 1 + number: 0 requirements: host: From 555a3c3819dc1432dc42e6c0c4b7e9d30a5ec220 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:46:14 -0700 Subject: [PATCH 190/546] Update perl-archive-tar to 2.32 (#11953) --- recipes/perl-archive-tar/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-archive-tar/meta.yaml b/recipes/perl-archive-tar/meta.yaml index 98033d78f9adf..6d5e9d0429a3c 100644 --- a/recipes/perl-archive-tar/meta.yaml +++ b/recipes/perl-archive-tar/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-archive-tar - version: 2.18 + version: 2.32 source: - url: http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/Archive-Tar-2.18.tar.gz - md5: ed4d4ca0124adece439f5d97b05d3987 + url: http://search.cpan.org/CPAN/authors/id/B/BI/BINGOS/Archive-Tar-2.32.tar.gz + sha256: 92783780731ab0c9247adf43e70f4801e8317e3915ea87e38b85c8f734e8fca2 build: - number: 3 + number: 0 requirements: host: From 531606bbba9e83d34fc74a8bc3e1619b4a199074 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:46:25 -0700 Subject: [PATCH 191/546] Update perl-file-copy-recursive to 0.44 (#11950) --- recipes/perl-file-copy-recursive/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-file-copy-recursive/meta.yaml b/recipes/perl-file-copy-recursive/meta.yaml index 39b02c36ab558..1647b0e99ace0 100644 --- a/recipes/perl-file-copy-recursive/meta.yaml +++ b/recipes/perl-file-copy-recursive/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-file-copy-recursive - version: '0.38' + version: '0.44' source: - url: https://cpan.metacpan.org/authors/id/D/DM/DMUEY/File-Copy-Recursive-0.38.tar.gz - sha256: 84ccbddf3894a88a2c2b6be68ff6ef8960037803bb36aa228b31944cfdf6deeb + url: https://cpan.metacpan.org/authors/id/D/DM/DMUEY/File-Copy-Recursive-0.44.tar.gz + sha256: ae19a0b58dc1b3cded9ba9cfb109288d8973d474c0b4bfd28b27cf60e8ca6ee4 build: - number: 3 + number: 0 requirements: build: From 68ebf68793bfa31d98062ca8e5dc28ab367cc44f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:46:36 -0700 Subject: [PATCH 192/546] Update perl-date-manip to 6.73 (#11952) --- recipes/perl-date-manip/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-date-manip/meta.yaml b/recipes/perl-date-manip/meta.yaml index a453b5e5c4a3a..c89330647b032 100644 --- a/recipes/perl-date-manip/meta.yaml +++ b/recipes/perl-date-manip/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-date-manip" %} -{% set version = "6.72" %} -{% set sha256 = "38f4dd9d94b41092ca7b9da2ef72c3bb8b8c8bff6da14d785c612f3cc7a94da6" %} +{% set version = "6.73" %} +{% set sha256 = "d39295c7c3f19b43470d1203dded8cb649b41a1098e51b5b7c7cf17b662ca255" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/S/SB/SBECK/Date-Manip-6.72.tar.gz + url: https://cpan.metacpan.org/authors/id/S/SB/SBECK/Date-Manip-6.73.tar.gz sha256: {{ sha256 }} build: From 319971dead6558a7ddce8a9998c5c145ddc1b025 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:46:47 -0700 Subject: [PATCH 193/546] Update perl-statistics-descriptive to 3.0702 (#11949) --- recipes/perl-statistics-descriptive/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-statistics-descriptive/meta.yaml b/recipes/perl-statistics-descriptive/meta.yaml index bdc20c945a378..009f4087eed47 100644 --- a/recipes/perl-statistics-descriptive/meta.yaml +++ b/recipes/perl-statistics-descriptive/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-statistics-descriptive - version: "3.0612" + version: "3.0702" source: - url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0612.tar.gz - md5: e38cfbc1e3962d099b62a14a57a175f1 + url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0702.tar.gz + sha256: f98a10c625640170cdda408cccc72bdd7f66f8ebe5f59dec1b96185171ef11d0 build: - number: 2 + number: 0 requirements: host: From 4367adf2b9865107d49a113532cd5759ad12415e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:46:58 -0700 Subject: [PATCH 194/546] Update perl-test-pod to 1.52 (#11947) --- recipes/perl-test-pod/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-pod/meta.yaml b/recipes/perl-test-pod/meta.yaml index 017fedba650a5..b11360fb9217f 100644 --- a/recipes/perl-test-pod/meta.yaml +++ b/recipes/perl-test-pod/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-test-pod - version: "1.51" + version: "1.52" source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-Pod-1.51.tar.gz - md5: f806aa84de2f0c0fba48b3a5a8a4aecf + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-Pod-1.52.tar.gz + sha256: 60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc build: - number: 1 + number: 0 requirements: host: From 5351beb3895447f190238781f728e405e62384fc Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:47:11 -0700 Subject: [PATCH 195/546] Update perl-dbi to 1.642 (#11948) --- recipes/perl-dbi/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-dbi/meta.yaml b/recipes/perl-dbi/meta.yaml index 9a67160a2d7e1..395c9b3e9d8fc 100644 --- a/recipes/perl-dbi/meta.yaml +++ b/recipes/perl-dbi/meta.yaml @@ -1,14 +1,14 @@ {% set name = "perl-dbi" %} -{% set version = "1.641" %} -{% set sha256 = "5509e532cdd0e3d91eda550578deaac29e2f008a12b64576e8c261bb92e8c2c1" %} +{% set version = "1.642" %} +{% set sha256 = "3f2025023a56286cebd15cb495e36ccd9b456c3cc229bf2ce1f69e9ebfc27f5d" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/T/TI/TIMB/DBI-1.641.tar.gz + url: https://cpan.metacpan.org/authors/id/T/TI/TIMB/DBI-1.642.tar.gz sha256: {{ sha256 }} build: - number: 2 + number: 0 requirements: host: - perl From 08aeb603350f46347ed1d7712bfea986ad4706c1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:47:22 -0700 Subject: [PATCH 196/546] Update perl-socket6 to 0.29 (#11946) --- recipes/perl-socket6/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-socket6/meta.yaml b/recipes/perl-socket6/meta.yaml index 8e7e966a640a0..da45375d1d8ea 100644 --- a/recipes/perl-socket6/meta.yaml +++ b/recipes/perl-socket6/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-socket6 - version: "0.25" + version: "0.29" source: - url: http://cpan.metacpan.org/authors/id/U/UM/UMEMOTO/Socket6-0.25.tar.gz - md5: e6c40d662b1fc5ffd436b7f50daa1f04 + url: http://cpan.metacpan.org/authors/id/U/UM/UMEMOTO/Socket6-0.29.tar.gz + sha256: 468915fa3a04dcf6574fc957eff495915e24569434970c91ee8e4e1459fc9114 build: - number: 1 + number: 0 requirements: host: From cece781358c21a9a8facd416a5311fd7013513dc Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:47:39 -0700 Subject: [PATCH 197/546] Update perl-algorithm-cluster to 1.56 (#11945) --- recipes/perl-algorithm-cluster/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-algorithm-cluster/meta.yaml b/recipes/perl-algorithm-cluster/meta.yaml index 54ef8db95e1d3..015253af53c92 100644 --- a/recipes/perl-algorithm-cluster/meta.yaml +++ b/recipes/perl-algorithm-cluster/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-algorithm-cluster - version: "1.52" + version: "1.56" source: - url: http://cpan.metacpan.org/authors/id/M/MD/MDEHOON/Algorithm-Cluster-1.52.tar.gz - md5: 8a80e644e705c829e02a9339025c4225 + url: http://cpan.metacpan.org/authors/id/M/MD/MDEHOON/Algorithm-Cluster-1.56.tar.gz + sha256: 604f72d44ebf76d2bff08a07d7ec0121ea4eb8442215de99e9d1bc1658b8bf6b build: - number: 1 + number: 0 requirements: host: From 32964d99c01f1e8a698a834fa8bcf1983988497c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 13:48:20 -0700 Subject: [PATCH 198/546] Update perl-compress-raw-bzip2 to 2.081 (#11944) --- recipes/perl-compress-raw-bzip2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-compress-raw-bzip2/meta.yaml b/recipes/perl-compress-raw-bzip2/meta.yaml index 5bbb920decb1f..72640b75d3637 100644 --- a/recipes/perl-compress-raw-bzip2/meta.yaml +++ b/recipes/perl-compress-raw-bzip2/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-compress-raw-bzip2 - version: 2.074 + version: 2.081 source: - url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/Compress-Raw-Bzip2-2.074.tar.gz - md5: 6609c7cbadeedbb60fa4b057b7dc0ede + url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/Compress-Raw-Bzip2-2.081.tar.gz + sha256: 8692b5c9db91954408e24e805fbfda222879da80d89d9410791421e3e5bc3520 build: number: 0 From 58f89fbd6577fdb10bc1467ee021a70917c708f4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 14:44:07 -0700 Subject: [PATCH 199/546] Update beast to 1.10.4 (#11978) --- recipes/beast/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/beast/meta.yaml b/recipes/beast/meta.yaml index 081e2083d2640..8620d4db56fed 100644 --- a/recipes/beast/meta.yaml +++ b/recipes/beast/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.3" %} -{% set sha256 = "53afa45e815a191302b7ca501b69fe66d5bc61c381636dbfa10f9023b0411aca" %} +{% set version = "1.10.4" %} +{% set sha256 = "722d85457e7faa082862147630f2ec8aa500e2461fd31e41e339c92f8c9b7f8a" %} package: name: beast From f33db97dd8f423445d5dcf73dab4b4b81aa34dd6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Sun, 11 Nov 2018 22:53:24 +0100 Subject: [PATCH 200/546] Bump perl-io-interactive (#11979) --- recipes/perl-io-interactive/build.sh | 13 +++---------- recipes/perl-io-interactive/meta.yaml | 28 ++++----------------------- 2 files changed, 7 insertions(+), 34 deletions(-) diff --git a/recipes/perl-io-interactive/build.sh b/recipes/perl-io-interactive/build.sh index 6de255d53eec6..67918fe672fe6 100644 --- a/recipes/perl-io-interactive/build.sh +++ b/recipes/perl-io-interactive/build.sh @@ -1,13 +1,12 @@ #!/bin/bash # If it has Build.PL use that, otherwise use Makefile.PL -cpanm --installdeps . if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test + perl ./Build + perl ./Build test # Make sure this goes in site - ./Build install --installdirs site + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site @@ -18,9 +17,3 @@ else echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' exit 1 fi - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-io-interactive/meta.yaml b/recipes/perl-io-interactive/meta.yaml index 85f5400c2eb38..46f4e9837f2b2 100644 --- a/recipes/perl-io-interactive/meta.yaml +++ b/recipes/perl-io-interactive/meta.yaml @@ -1,47 +1,27 @@ package: name: perl-io-interactive - version: "1.021" + version: "1.022" source: - url: https://cpan.metacpan.org/authors/id/B/BD/BDFOY/IO-Interactive-1.021.tar.gz - md5: 1636503b9e7b34d88450233e2504b73f -# patches: - # List any patch files here - # - fix.patch + url: https://cpan.metacpan.org/authors/id/B/BD/BDFOY/IO-Interactive-1.022.tar.gz + sha256: 0ed53b8ae93ae877e98e0d89b7b429e29ccd1ee4c28e952c4ea9aa73d01febdc build: - skip: True # [osx] - number: 2 + number: 0 requirements: - build: - - {{ compiler('c') }} host: - perl - - perl-app-cpanminus - - perl-pathtools - perl-extutils-makemaker run: - perl test: - # Perl 'use' tests imports: - IO::Interactive - # You can also put a file called run_test.pl (or run_test.py) in the recipe - # that will be run at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: https://github.com/briandfoy/io-interactive license: perl_5 summary: 'Utilities for interactive I/O' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From d13c80e286dedde36613e58b9b887bf2a458de7c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 14:53:48 -0700 Subject: [PATCH 201/546] Update perl-role-tiny to 2.000006 (#11956) * Update perl-role-tiny to 2.000006 * perl-exporter should be a requirement --- recipes/perl-role-tiny/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/perl-role-tiny/meta.yaml b/recipes/perl-role-tiny/meta.yaml index c5817c2141c95..5e8ca2bac80bc 100644 --- a/recipes/perl-role-tiny/meta.yaml +++ b/recipes/perl-role-tiny/meta.yaml @@ -1,22 +1,23 @@ package: name: perl-role-tiny - version: "2.000001" + version: "2.000006" source: - url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Role-Tiny-2.000001.tar.gz - md5: f350f1f8c13652bf85da172380b39ec8 + url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Role-Tiny-2.000006.tar.gz + sha256: cc73418c904a0286ecd8915eac11f5be2a8d1e17ea9cb54c9116b0340cd3e382 build: - number: 2 + number: 0 requirements: host: - perl - - perl-test-fatal + - perl-exporter run: - perl - + - perl-exporter + test: # Perl 'use' tests imports: From 8cbb69968a20fa1b7df0b6b10880c0586d19f1fe Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 20:43:31 -0700 Subject: [PATCH 202/546] Update svviz to 1.6.2 (#11981) --- recipes/svviz/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/svviz/meta.yaml b/recipes/svviz/meta.yaml index e68626d516445..0556d3a483b1a 100644 --- a/recipes/svviz/meta.yaml +++ b/recipes/svviz/meta.yaml @@ -1,16 +1,16 @@ package: name: svviz - version: "1.5.1" + version: "1.6.2" source: - url: https://pypi.python.org/packages/3b/b1/3571a9cbff54a60cf3a9222c5a7c7c05e3bcca8bb1fc350fed221b8337e9/svviz-1.5.1.tar.gz - md5: 27497e1db3ddd27b5cf94896b7e4596c + url: https://files.pythonhosted.org/packages/1a/41/f74b81fef6fd95cab460a1711cca90201cfc8cfdc1a87fa3fb81ae5761ed/svviz-1.6.2.tar.gz + sha256: 16a419b9be5f25a0d2393ed13eeccadcdbaf8047c244be108f891c897c5349ed build: skip: True # [not py27 or osx] entry_points: - svviz = svviz.app:main - number: 1 + number: 0 requirements: host: From 67badd8dbfd986a3b87a185073ae170299037ee1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 20:44:19 -0700 Subject: [PATCH 203/546] Update galaxy-parsec to 1.0.5 (#11982) --- recipes/galaxy-parsec/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/galaxy-parsec/meta.yaml b/recipes/galaxy-parsec/meta.yaml index 940186595b23a..95da46bba30bd 100644 --- a/recipes/galaxy-parsec/meta.yaml +++ b/recipes/galaxy-parsec/meta.yaml @@ -1,10 +1,10 @@ package: name: galaxy-parsec - version: "1.0.4" + version: "1.0.5" source: - url: https://pypi.python.org/packages/f7/aa/5bbd266698de39c9897d58e26bac2bff714be73ac10ed5f41b8ac45213bb/galaxy-parsec-1.0.4.tar.gz - md5: 066e3d35f3a374095d0d90bf76214494 + url: https://files.pythonhosted.org/packages/79/dc/0266640b7ac1220f71eca83f28f8207801db2655d40e98af1c082634c762/galaxy-parsec-1.0.5.tar.gz + sha256: 3c45dee3fbdd8f4c5552d2d042708eaabef2b4e96c513ed4a91e86be5082006c build: noarch: python @@ -12,7 +12,7 @@ build: preserve_egg_dir: True entry_points: - parsec=parsec.cli:parsec - number: 1 + number: 0 requirements: host: From c507a3b0f45e2d552381e27e095724e9df57af0e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 20:51:27 -0700 Subject: [PATCH 204/546] Update pronto to 0.11.0 (#11987) --- recipes/pronto/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pronto/meta.yaml b/recipes/pronto/meta.yaml index 87c818fe9864d..cda52ea258173 100644 --- a/recipes/pronto/meta.yaml +++ b/recipes/pronto/meta.yaml @@ -1,17 +1,17 @@ package: name: pronto - version: "0.10.2" + version: "0.11.0" source: - url: https://pypi.python.org/packages/84/84/f9d445f6639a8c1970dad02047cb42bbb01a66170fcd68be3ea93d01ce5f/pronto-0.10.2.zip - md5: 24b20a2153d8b4223b447af0ac1e084a + url: https://files.pythonhosted.org/packages/a1/f4/a6e7bc04ba94fffe82ec4b3e73c9c3b7eb7fabbd1189871376059ed241e4/pronto-0.11.0.zip + sha256: 78fb9f876e46e635e3e43232edecbcfcae2c5650e3cee506016ae99e1e9131eb # patches: # List any patch files here # - fix.patch build: noarch: python - number: 1 + number: 0 entry_points: - pronto = pronto:main From 140c44f63dc0b3df8a7c557d806035b50cd5ba2e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 20:51:38 -0700 Subject: [PATCH 205/546] Update perl-extutils-manifest to 1.71 (#11986) --- recipes/perl-extutils-manifest/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-extutils-manifest/meta.yaml b/recipes/perl-extutils-manifest/meta.yaml index 3f1cc8c74e1f5..cc3835a609c5d 100644 --- a/recipes/perl-extutils-manifest/meta.yaml +++ b/recipes/perl-extutils-manifest/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-extutils-manifest - version: "1.70" + version: "1.71" source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/ExtUtils-Manifest-1.70.tar.gz - md5: 8ccb9c1f3bca14c117a74bc7b43be095 + url: https://cpan.metacpan.org/authors/id/B/BI/BINGOS/ExtUtils-Manifest-1.71.tar.gz + sha256: 00671b88ece23de3633a554cf3432d4b8351a598c55a79bfdb7ea1e3219747e1 build: - number: 2 + number: 0 requirements: host: From 66f191a6b4e817d7bceff5314079f7e8515af5b7 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:31:38 -0700 Subject: [PATCH 206/546] Update nmrglue to 0.6 (#11984) --- recipes/nmrglue/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nmrglue/meta.yaml b/recipes/nmrglue/meta.yaml index 556cf05da4b60..1dbe3e505f52e 100644 --- a/recipes/nmrglue/meta.yaml +++ b/recipes/nmrglue/meta.yaml @@ -1,13 +1,13 @@ package: name: nmrglue - version: "0.5" + version: "0.6" source: - url: https://pypi.python.org/packages/48/1e/be85936901a3a82a1dc14a8b41017ca86dcb8b966717c786e361e752c898/nmrglue-0.5.tar.gz - md5: 4cf63caceae0b9f0a144f07b6663e670 + url: https://files.pythonhosted.org/packages/da/17/05fc5bc4da8ff8be34b65ad48834201be9f7fe12dd59b0365b3542d67770/nmrglue-0.6.tar.gz + sha256: 2392555a8d0e558c7d12eee6f0d1bd71c5571972517bb252bf803484cf3c1300 build: - number: 1 + number: 0 requirements: build: From e1d13f918738231d0c1c344aadbabb9c838c72db Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:31:53 -0700 Subject: [PATCH 207/546] Update minepy to 1.2.2 (#11990) --- recipes/minepy/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/minepy/meta.yaml b/recipes/minepy/meta.yaml index 1ad56ad8d5f43..a6fe6e2a0e0b4 100644 --- a/recipes/minepy/meta.yaml +++ b/recipes/minepy/meta.yaml @@ -1,13 +1,13 @@ package: name: minepy - version: "1.2.0" + version: "1.2.2" source: - url: https://pypi.python.org/packages/e0/d1/b871d4779776aa3be524a892d085a964392a057476765dd07b1fd78687ae/minepy-1.2.0.tar.gz - md5: b22db1dfb5e96d909a46bacc072a77e6 + url: https://files.pythonhosted.org/packages/42/2e/1b805f156189cecae491d5794195a297d179bdde4f272e0d6acd13d88940/minepy-1.2.2.tar.gz + sha256: 82aee00c39db84b44e65b733f31e50c4b024832c8666cabfc3cf6aaec5ec7463 build: - number: 1 + number: 0 requirements: build: From 0e85cdfa9c63ed91a88906fd221dc7a7c500ff53 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:32:07 -0700 Subject: [PATCH 208/546] Update zeroc-ice to 3.7.1 (#11989) --- recipes/zeroc-ice/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/zeroc-ice/meta.yaml b/recipes/zeroc-ice/meta.yaml index 1e14d443cea3a..9a37fe725ff7b 100644 --- a/recipes/zeroc-ice/meta.yaml +++ b/recipes/zeroc-ice/meta.yaml @@ -1,13 +1,13 @@ package: name: zeroc-ice - version: '3.6.3' + version: '3.7.1' source: - url: https://pypi.python.org/packages/d4/13/090854b3a35ce66aeba13f6722868dc1f3b113175b4d7cd1a73e29718051/zeroc-ice-3.6.3.tar.gz - md5: 518402167fbb7788619fac3ca641b745 + url: https://files.pythonhosted.org/packages/67/77/44e30fbfaa920e4bffb38ed2216c75f1b0769d83cc53344987313b32526e/zeroc-ice-3.7.1.tar.gz + sha256: 4436a40e91eb6d12e6a8f3a3ea248786ea41a3f23e2e5e7f719fc84efd0c3c8d build: - number: 1 + number: 0 # segmentation fault with Python 3.6 skip: True # [not py2k and not py35] From cc0f5028ebc2c6889814a8f0799e479284000be1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:32:30 -0700 Subject: [PATCH 209/546] Update pdfkit to 0.6.1 (#11988) --- recipes/pdfkit/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pdfkit/meta.yaml b/recipes/pdfkit/meta.yaml index aa81e44fedfb2..35bab79d98476 100644 --- a/recipes/pdfkit/meta.yaml +++ b/recipes/pdfkit/meta.yaml @@ -1,13 +1,13 @@ build: - number: 1 + number: 0 skip: True # [osx] package: name: pdfkit - version: "0.5.0" + version: "0.6.1" source: - url: https://pypi.python.org/packages/source/p/pdfkit/pdfkit-0.5.0.zip - md5: 5cbe42c43d463f0794272a01e37a553f + url: https://files.pythonhosted.org/packages/a1/98/6988328f72fe3be4cbfcb6cbfc3066a00bf111ca7821a83dd0ce56e2cf57/pdfkit-0.6.1.tar.gz + sha256: ef1da35b78d534197e7ce4a604a4a190e9aa769e56634957535f3479a50d8cd1 requirements: host: - wkhtmltopdf From e3917d3d7a7ffaa9033e823d0de998e06f554a8e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:37:10 -0700 Subject: [PATCH 210/546] Update perl-json to 2.97001 (#11997) --- recipes/perl-json/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-json/meta.yaml b/recipes/perl-json/meta.yaml index 6ce037148bd06..08dcd90fa539d 100644 --- a/recipes/perl-json/meta.yaml +++ b/recipes/perl-json/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-json - version: "2.90" + version: "2.97001" source: - url: https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/JSON-2.90.tar.gz - md5: e1512169a623e790a3f69b599cc1d3b9 + url: https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/JSON-2.97001.tar.gz + sha256: e277d9385633574923f48c297e1b8acad3170c69fa590e31fa466040fc6f8f5a build: - number: 3 + number: 0 requirements: host: From 877fa36d61bba17b0d3e61be2fd82fdd5a3e7a91 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:37:22 -0700 Subject: [PATCH 211/546] Update nose-capturestderr to 1.2 (#11992) --- recipes/nose-capturestderr/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nose-capturestderr/meta.yaml b/recipes/nose-capturestderr/meta.yaml index 79e1790fa0f99..f9adee762bec5 100644 --- a/recipes/nose-capturestderr/meta.yaml +++ b/recipes/nose-capturestderr/meta.yaml @@ -1,14 +1,14 @@ package: name: nose-capturestderr - version: "1.0" + version: "1.2" source: - url: https://pypi.python.org/packages/92/a2/2798b7596040b90217bde9d578085ff652523f69e4de1f2622e8716f9649/nose-capturestderr-1.0.tar.gz - md5: 498707ee990533b77e3ffb0265e6802b + url: https://files.pythonhosted.org/packages/26/a1/08c85a5c5a77a3644e4269b23963f05aa92778494681b9cd0b183c6f1181/nose-capturestderr-1.2.tar.gz + sha256: 3a9d3986f44490a1286d9eacd66879dbb059b575f6660a228b2051a8617a89ab build: preserve_egg_dir: True - number: 1 + number: 0 skip: True # [not py27] requirements: From b0bf48b0399019fcddfc4b062e5ba7eacde5b33d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:50:25 -0700 Subject: [PATCH 212/546] Update snp-pipeline to 2.0.2 (#11996) --- recipes/snp-pipeline/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/snp-pipeline/meta.yaml b/recipes/snp-pipeline/meta.yaml index 3f8f2d2a5ef94..fa7a5dfe8da0c 100644 --- a/recipes/snp-pipeline/meta.yaml +++ b/recipes/snp-pipeline/meta.yaml @@ -1,13 +1,13 @@ package: name: snp-pipeline - version: "1.0.1" + version: "2.0.2" source: - url: https://pypi.python.org/packages/9c/86/e2a212735e229b5dd65c7f58f53822e820507bb4f95f870687f50046f99c/snp-pipeline-1.0.1.tar.gz - md5: d42bfefd2ccccdb5f880f3a74f4ff165 + url: https://files.pythonhosted.org/packages/fc/71/f753000d73317415ff1862d1ae3051064e75e5f2e7b95402f2f63a980f7b/snp-pipeline-2.0.2.tar.gz + sha256: 601fe984d64c021dfd9165229dd66e3e1a61f5702bd3e0a44f43b573e74f66f7 build: - number: 2 + number: 0 noarch: python entry_points: - cfsan_snp_pipeline = snppipeline.cfsan_snp_pipeline:main From 692fd4fb7d6420e47d400e45e5688f2a9c4af981 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 21:50:41 -0700 Subject: [PATCH 213/546] Update segtools to 1.2.1 (#11991) --- recipes/segtools/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/segtools/meta.yaml b/recipes/segtools/meta.yaml index 8158ecc8c1b7f..8ce692ba9f048 100644 --- a/recipes/segtools/meta.yaml +++ b/recipes/segtools/meta.yaml @@ -1,13 +1,13 @@ package: name: segtools - version: "1.1.14" + version: "1.2.1" source: - url: https://pypi.python.org/packages/79/51/95ffd8d01b29aa6a3546c7138f0afc24b683f356b112015b32a539ee4a08/segtools-1.1.14.tar.gz - md5: 55e42e724b32f6914122164127aa5b23 + url: https://files.pythonhosted.org/packages/1e/c0/f83633350a855e7fd2385f3b824bd5cfdd5bc1cda87b4bfba2eef5a969ac/segtools-1.2.1.tar.gz + sha256: 741f409020f91cee422949ccfbbcdf30dae7722083d83f1f1f27340e39d3d7d9 build: - number: 2 + number: 0 preserve_egg_dir: True skip: True # [not py27] entry_points: From b959fbafa6e965cbb25b20794c2f7a3efc06f9ff Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 22:19:57 -0700 Subject: [PATCH 214/546] Update hgtools to 8.1.1 (#12000) --- recipes/hgtools/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/hgtools/meta.yaml b/recipes/hgtools/meta.yaml index 6f6b62a42456a..7ce8aa6b61a46 100644 --- a/recipes/hgtools/meta.yaml +++ b/recipes/hgtools/meta.yaml @@ -1,13 +1,13 @@ package: name: hgtools - version: "6.5.1" + version: "8.1.1" source: - url: https://files.pythonhosted.org/packages/26/15/a902b096c5c4cb33269d7b69e779101e00cf77a9081250a947f2b2db41e5/hgtools-6.5.1.tar.gz - md5: ce8413687e43d5626cdcfee5024a9bc0 + url: https://files.pythonhosted.org/packages/cd/85/36b6b57837ad469adb2cf6be1bd429ad216550a6ccddadfb1ab849fc5c84/hgtools-8.1.1.tar.gz + sha256: 2f6646dd15572692c6dcf821b806b24c6f753b954bb46307b6acdefc69e5eedf build: - number: 2 + number: 0 noarch: python preserve_egg_dir: True From 8c2220ffdbfd0abd158b4f343cd34420f1dfb949 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 22:20:09 -0700 Subject: [PATCH 215/546] Update xopen to 0.3.5 (#11999) --- recipes/xopen/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/xopen/meta.yaml b/recipes/xopen/meta.yaml index be7866ed8e4d0..cb98f3ec23323 100644 --- a/recipes/xopen/meta.yaml +++ b/recipes/xopen/meta.yaml @@ -1,15 +1,15 @@ package: name: xopen - version: "0.3.2" + version: "0.3.5" source: - url: https://pypi.python.org/packages/63/7f/f18c758714d7f5714da95ef08eeacb04b6f9ef2e5853492c516cb979e4dc/xopen-0.3.2.tar.gz - md5: 1e8c7ec1ca903bd41483630280e6c2af + url: https://files.pythonhosted.org/packages/e6/7d/15cfc41aa384e6a1dc60852d4df863524c647d852d62190fa638ba9abb58/xopen-0.3.5.tar.gz + sha256: 3a418d5d3eacc6645d8f002635308651bb6e47b9cabb19ae3abad600aa117ce3 build: noarch: python - number: 1 + number: 0 script: python -m pip install --no-deps --ignore-installed . requirements: From 72e8d5d7827b7ad61646dff34da8540939838df6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 22:48:16 -0700 Subject: [PATCH 216/546] Update cgat-report to 0.8.1 (#12002) --- recipes/cgat-report/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/cgat-report/meta.yaml b/recipes/cgat-report/meta.yaml index 4ae02ba48e416..01db13ea29a38 100644 --- a/recipes/cgat-report/meta.yaml +++ b/recipes/cgat-report/meta.yaml @@ -1,15 +1,15 @@ package: name: cgat-report - version: 0.8.0 + version: 0.8.1 source: - url: https://files.pythonhosted.org/packages/09/e4/7e963dd2f22d489b233906a19c2bfc36c6eeff5aaea20d462b61ae19aceb/CGATReport-0.8.0.tar.gz - sha256: a798aabe24cc22fe94279c3d3df11fdd54ece985221cb8b5b10ccf519cee76ae + url: https://files.pythonhosted.org/packages/3e/d8/3ea3ff94face46d295370392091aae784e5afce5d4ffad9297a3181b8149/CGATReport-0.8.1.tar.gz + sha256: 9b195e937732ff81c521fd66c75797f5d59fddfffaa368270a056d80d9337dea build: noarch: python - number: 1 + number: 0 requirements: host: From 6f6a2022ab0c62c6fd410163e33331103e8c0b6f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 22:48:25 -0700 Subject: [PATCH 217/546] Update perl-svg to 2.84 (#12001) --- recipes/perl-svg/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-svg/meta.yaml b/recipes/perl-svg/meta.yaml index 84df567ffb4cd..0c35982fad8a7 100644 --- a/recipes/perl-svg/meta.yaml +++ b/recipes/perl-svg/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-svg - version: "2.64" + version: "2.84" source: - url: https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB/SVG-2.64.tar.gz - md5: ba4445ee72e2f3c29da332cb0119a2ad + url: https://cpan.metacpan.org/authors/id/M/MA/MANWAR/SVG-2.84.tar.gz + sha256: ec3d6ddde7a46fa507eaa616b94d217296fdc0d8fbf88741367a9821206f28af build: - number: 2 + number: 0 requirements: host: From eaa9ace63a79a8fd1812db3758985d4a5f5d17bd Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 22:48:37 -0700 Subject: [PATCH 218/546] Update perl-class-inspector to 1.32 (#12013) --- recipes/perl-class-inspector/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-class-inspector/meta.yaml b/recipes/perl-class-inspector/meta.yaml index 370e65eb7600f..8e98703b2e1b5 100644 --- a/recipes/perl-class-inspector/meta.yaml +++ b/recipes/perl-class-inspector/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-class-inspector - version: "1.28" + version: "1.32" source: - url: http://cpan.metacpan.org/authors/id/A/AD/ADAMK/Class-Inspector-1.28.tar.gz - md5: 7ab3ca22d3147236dddfb58f2366ad22 + url: https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Class-Inspector-1.32.tar.gz + sha256: cefadc8b5338e43e570bc43f583e7c98d535c17b196bcf9084bb41d561cc0535 build: - number: 2 + number: 0 requirements: host: From a319e3aed71ddf7eef8e8032f9971746772a0860 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 11 Nov 2018 23:16:05 -0700 Subject: [PATCH 219/546] Update rapmap to 0.5.0 (#12014) --- recipes/rapmap/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/rapmap/meta.yaml b/recipes/rapmap/meta.yaml index 04679b65b1659..3acbc5e97b949 100644 --- a/recipes/rapmap/meta.yaml +++ b/recipes/rapmap/meta.yaml @@ -1,10 +1,10 @@ package: name: rapmap - version: "v0.2.1" + version: "0.5.0" source: - url: https://github.com/COMBINE-lab/RapMap/archive/v0.2.1.tar.gz - sha256: bc2d62e5f278fb1b0f6a8591e5ddb5d505dee7152e659d04ee5630d2a5546830 + url: https://github.com/COMBINE-lab/RapMap/archive/v0.5.0.tar.gz + sha256: d047d5ae622d2282252eab4b7831ac60af24ec2c65ebb7774efc08605d2df807 requirements: build: @@ -15,7 +15,7 @@ requirements: run: build: - number: 2 + number: 0 skip: True # [osx] about: From fbf3d9edb9a7ccb8614f17312bf310b063f18af8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:19:14 -0700 Subject: [PATCH 220/546] Update inheritance to 0.1.3 (#12056) --- recipes/inheritance/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/inheritance/meta.yaml b/recipes/inheritance/meta.yaml index 95f66ebeaaade..8ec20181895e8 100644 --- a/recipes/inheritance/meta.yaml +++ b/recipes/inheritance/meta.yaml @@ -1,14 +1,14 @@ package: name: inheritance - version: 0.1.2 + version: 0.1.3 source: - url: https://pypi.python.org/packages/12/28/c51a03e8e186f6cc5004fa066ff1ad873cf41ab60052ca40bf542ed5dd59/inheritance-0.1.2.tar.gz - md5: 887a67cb749c7d082d676cdb5597f1fc + url: https://files.pythonhosted.org/packages/91/38/7c777a2d16250f8093c793acc6410ad237cdf487d836925feca4574b3ad6/inheritance-0.1.3.tar.gz + sha256: 5c682f39ff14354f40cb79981cbf41d3d3ca8576c062419f568a4bd0605c42b5 build: noarch: python - number: 1 + number: 0 skip: False requirements: From 3749bb860885334665789fb7fb468bec16b763cb Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:19:41 -0700 Subject: [PATCH 221/546] Update perl-test-notabs to 2.02 (#12055) --- recipes/perl-test-notabs/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-notabs/meta.yaml b/recipes/perl-test-notabs/meta.yaml index 12fe628e71c39..0c01b344c7c25 100644 --- a/recipes/perl-test-notabs/meta.yaml +++ b/recipes/perl-test-notabs/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-test-notabs - version: "1.4" + version: "2.02" source: - url: https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/Test-NoTabs-1.4.tar.gz - md5: 1b135805eebb93ca502df585655f34ca + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-NoTabs-2.02.tar.gz + sha256: fb75c6a38721f0169e11c1e7dbe5329ed7216885a0b01123f342dd86d3356030 build: - number: 2 + number: 0 requirements: host: From 9fabf54d3366e016126f46cccaef0794681ef7b1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:19:55 -0700 Subject: [PATCH 222/546] Update myriad to 0.1.4 (#12054) --- recipes/myriad/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/myriad/meta.yaml b/recipes/myriad/meta.yaml index d2328bad2e433..d09df3670b5e8 100644 --- a/recipes/myriad/meta.yaml +++ b/recipes/myriad/meta.yaml @@ -1,13 +1,13 @@ package: name: myriad - version: "0.1.3" + version: "0.1.4" source: - url: https://pypi.python.org/packages/fc/10/280fdc6b6989d7ee559bc79d7060e911af7d7f7b99cbc6c01d6a10f8dc49/myriad-0.1.3.tar.gz - md5: d1114c7bb9fce8eff89364e4def99036 + url: https://files.pythonhosted.org/packages/93/6a/89cc3d04157c38625786956d22e39f2fcd322754d4812abefa3997306bfd/myriad-0.1.4.zip + sha256: ae1d836f0e9c37b90b94c185555e485e2c7e36458a4709e39e4aefc3945fdfd5 build: - number: 2 + number: 0 skip: True # [not py27] entry_points: - myriad = myriad.components:main From a6ee1dcbee91fd9b6c1b1d0e7543ae01b39e9f1b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:20:09 -0700 Subject: [PATCH 223/546] Update perl-test-leaktrace to 0.16 (#12053) --- recipes/perl-test-leaktrace/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-leaktrace/meta.yaml b/recipes/perl-test-leaktrace/meta.yaml index 09cab43676beb..56bb27b21c676 100644 --- a/recipes/perl-test-leaktrace/meta.yaml +++ b/recipes/perl-test-leaktrace/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-test-leaktrace - version: "0.15" + version: "0.16" source: - url: https://cpan.metacpan.org/authors/id/G/GF/GFUJI/Test-LeakTrace-0.15.tar.gz - md5: 5eac99e7882970f41886c3e0cec185d8 + url: https://cpan.metacpan.org/authors/id/L/LE/LEEJO/Test-LeakTrace-0.16.tar.gz + sha256: 5f089eed915f1ec8c743f6d2777c3ecd0ca01df2f7b9e10038d316952583e403 build: - number: 1 + number: 0 requirements: host: From 7d2186609055b725f542e4559a746358de0561e9 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:20:36 -0700 Subject: [PATCH 224/546] Update presto to 0.5.10 (#12052) --- recipes/presto/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/presto/meta.yaml b/recipes/presto/meta.yaml index c39886a85d24d..001078a69841b 100644 --- a/recipes/presto/meta.yaml +++ b/recipes/presto/meta.yaml @@ -1,13 +1,13 @@ package: name: presto - version: "0.5.4" + version: "0.5.10" source: - url: https://pypi.python.org/packages/ea/89/b2695b05f0e106f700227c742dd7bbebc0e42879c8748741f52919adffd1/presto-0.5.4.tar.gz - md5: c58d69852a42fe01058fbbbf142bb4e6 + url: https://files.pythonhosted.org/packages/2a/0c/a00fcf38abd59d64678f90052624cd93dad6326009cb2f24c672cad64f43/presto-0.5.10.tar.gz + sha256: 893a6e92f3e1d49a063da74087868e385777f7d9cafb68f9e48131f89c5ca668 build: - number: 1 + number: 0 # Presto only supports python3 skip: True # [not py3k] From 95f367ddfb7de757351e87f480f11f0ede4dfef6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:20:50 -0700 Subject: [PATCH 225/546] Update tabview to 1.4.3 (#12051) --- recipes/tabview/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/tabview/meta.yaml b/recipes/tabview/meta.yaml index 9324d77b0c973..97c94ed35e034 100644 --- a/recipes/tabview/meta.yaml +++ b/recipes/tabview/meta.yaml @@ -1,14 +1,14 @@ package: name: tabview - version: "1.4.2" + version: "1.4.3" source: - url: https://pypi.python.org/packages/f5/6c/75a807e740dcddbade3194cfaf05db72e378a714d2c16341b60d7044fe0f/tabview-1.4.2.tar.gz - md5: bcc8bc045051f4529d3cad43b56b61d2 + url: https://files.pythonhosted.org/packages/84/10/3ba8c474cfda857cb01b1e28b38de86dec2f35fa434cc0315727fb290f79/tabview-1.4.3.tar.gz + sha256: 48a5dd0c2658cd34c2aa6a89e50eea32754bebc45b38cacba762b212a13cce98 build: noarch: python - number: 2 + number: 0 skip: False requirements: From 0632ba39cd6224421261f3016bee1d05643d788e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:21:16 -0700 Subject: [PATCH 226/546] Update swalign to 0.3.4 (#12050) --- recipes/swalign/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/swalign/meta.yaml b/recipes/swalign/meta.yaml index 3a738e60c8a55..45878d39ff755 100644 --- a/recipes/swalign/meta.yaml +++ b/recipes/swalign/meta.yaml @@ -1,13 +1,13 @@ package: name: swalign - version: "0.3.3" + version: "0.3.4" source: - url: https://pypi.python.org/packages/72/97/cb26a99ee2e1796b0ab28a955e3568607826a44999654f6880d4e00174ac/swalign-0.3.3.tar.gz - md5: 64c55d09775d4875bc419a08a43dc6fa + url: https://files.pythonhosted.org/packages/f4/90/081f97995f17b59959effe8592eea11cd07287872bbee4ae1380206527aa/swalign-0.3.4.tar.gz + sha256: bc383f9a2c410e5933fd9a217c41c7607e04ad7cda4c3de8ee99ee22103756d3 build: - number: 2 + number: 0 skip: True # [py3k] requirements: From f7cebfb9d0e9aba5fbda8175016cec8fad02a585 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:21:34 -0700 Subject: [PATCH 227/546] Update cityhash to 0.2.3.post9 (#12049) --- recipes/cityhash/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/cityhash/meta.yaml b/recipes/cityhash/meta.yaml index 29fc528f92ca8..e8853de2a4597 100644 --- a/recipes/cityhash/meta.yaml +++ b/recipes/cityhash/meta.yaml @@ -1,14 +1,14 @@ package: name: cityhash - version: "0.1.7" + version: "0.2.3.post9" build: - number: 1 + number: 0 skip: True # [not py27] source: - url: https://pypi.python.org/packages/c8/7b/9ae60cb970412362f654fe1469b5b8fb230f6089ea0956fff2469d844be5/cityhash-0.1.7.tar.gz - md5: ecddde03ae5f62eec8551b3c20632c2a + url: https://files.pythonhosted.org/packages/25/67/65ad3755997c066766750525fdf3045609f5ee892fa5b037e7fc066505a4/cityhash-0.2.3.post9.tar.gz + sha256: aa8919c00e8d8699df42dd788eda4f24ad13086ea9d83407fd7da4a0206d9d18 requirements: host: From dbd1d03b7467a50bfd8383065d9180c43af512e4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:22:01 -0700 Subject: [PATCH 228/546] Update ont-fast5-api to 1.0.1 (#12047) --- recipes/ont-fast5-api/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ont-fast5-api/meta.yaml b/recipes/ont-fast5-api/meta.yaml index ded356ab4f2e1..806d7d6b8fa08 100644 --- a/recipes/ont-fast5-api/meta.yaml +++ b/recipes/ont-fast5-api/meta.yaml @@ -1,14 +1,14 @@ package: name: ont-fast5-api - version: "0.4.1" + version: "1.0.1" source: - url: https://pypi.python.org/packages/a1/89/ce95c0f39ce47dac75ff21be8a8194f0be70e1d9e5ddda8e3a4fc98359b5/ont-fast5-api-0.4.1.tar.gz - md5: b5674b9fabfa3d42e18c53108de8dd47 + url: https://files.pythonhosted.org/packages/e0/06/e824a888777a4cba9feb83f37fd7e9aa8a1f78e5ff9e1700e6e48fd05974/ont-fast5-api-1.0.1.tar.gz + sha256: f8bf15a4870c843dbedaacb2bb801005518d2c7c9942fef72cbda43dd078ddf9 build: noarch: python - number: 1 + number: 0 requirements: host: From 88d168ca710681caa7611872fc2d96e0a9b5c571 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:22:20 -0700 Subject: [PATCH 229/546] Update perl-test-warn to 0.36 (#12044) --- recipes/perl-test-warn/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-warn/meta.yaml b/recipes/perl-test-warn/meta.yaml index 3e10b1006c840..37b9c85bc1958 100644 --- a/recipes/perl-test-warn/meta.yaml +++ b/recipes/perl-test-warn/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-test-warn - version: "0.30" + version: "0.36" source: - url: http://cpan.metacpan.org/authors/id/C/CH/CHORNY/Test-Warn-0.30.tar.gz - md5: 8306b998a96d2cc69266b5248d550472 + url: https://cpan.metacpan.org/authors/id/B/BI/BIGJ/Test-Warn-0.36.tar.gz + sha256: ecbca346d379cef8d3c0e4ac0c8eb3b2613d737ffaaeae52271c38d7bf3c6cda build: - number: 3 + number: 0 requirements: host: From 0a0f0eb90a8288e30f7e8207b5ef89c2d866908d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:32:32 -0700 Subject: [PATCH 230/546] Update cogent to 1.9 (#12042) --- recipes/cogent/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/cogent/meta.yaml b/recipes/cogent/meta.yaml index 6da0e7c223f27..0d46e02e5203a 100644 --- a/recipes/cogent/meta.yaml +++ b/recipes/cogent/meta.yaml @@ -1,13 +1,13 @@ package: name: cogent - version: !!str 1.5.3 + version: !!str 1.9 source: - url: https://pypi.python.org/packages/source/c/cogent/cogent-1.5.3.tgz - md5: ecdfa0bc89e0c04c9d4d39cac9984498 + url: https://files.pythonhosted.org/packages/03/9e/a7156965da5edc34c3c07661c3b4bc4259caa3d9dcecaa5f7f3ff51eecd7/cogent-1.9.tar.gz + sha256: 57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14 build: - number: 2 + number: 0 skip: True [py3k or osx] requirements: From 4b60c9df3afac40d2cdb3916c4ef6ff2e0018b11 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:33:39 -0700 Subject: [PATCH 231/546] Update logbook to 1.4.1 (#12037) --- recipes/logbook/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/logbook/meta.yaml b/recipes/logbook/meta.yaml index 359848e5efb6e..d77de661b2376 100644 --- a/recipes/logbook/meta.yaml +++ b/recipes/logbook/meta.yaml @@ -2,14 +2,14 @@ package: name: logbook - version: "1.0.0" + version: "1.4.1" source: - url: https://pypi.python.org/packages/34/e8/6419c217bbf464fe8a902418120cccaf476201bd03b50958db24d6e90f65/Logbook-1.0.0.tar.gz - md5: 22fea705e067c118925898f0c30b0508 + url: https://files.pythonhosted.org/packages/74/fc/3e7557ed1ef1bd4e3ee189fc670416abfc7192b550e8d3c1d858a63f41ab/Logbook-1.4.1.tar.gz + sha256: 32375ce706d04a46886f9818bb953e53e0eda636552d7c0a2e482dd670fa56db build: - number: 1 + number: 0 skip: False requirements: From 3970912aaead3d0e55129fd76b34d386f6bcfc6f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:34:03 -0700 Subject: [PATCH 232/546] Update perl-test-eol to 2.00 (#12036) --- recipes/perl-test-eol/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-test-eol/meta.yaml b/recipes/perl-test-eol/meta.yaml index 72f09846c16b0..80bb6dd19b567 100644 --- a/recipes/perl-test-eol/meta.yaml +++ b/recipes/perl-test-eol/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-test-eol - version: "1.6" + version: "2.00" source: - url: https://cpan.metacpan.org/authors/id/F/FR/FREW/Test-EOL-1.6.tar.gz - md5: 1255e6ef49c417845aa70441c4b40c90 + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-EOL-2.00.tar.gz + sha256: 8e7f7e5d07d3be0f1d7d51bcda8af0962767eb2897fd48994df274c0f5ed6b50 build: - number: 2 + number: 0 requirements: host: From 9cad331055adf59f9711f93c645242b45422567a Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:34:18 -0700 Subject: [PATCH 233/546] Update perl-task-weaken to 1.06 (#12035) --- recipes/perl-task-weaken/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-task-weaken/meta.yaml b/recipes/perl-task-weaken/meta.yaml index dc7060650d8f9..4afff5dc75134 100644 --- a/recipes/perl-task-weaken/meta.yaml +++ b/recipes/perl-task-weaken/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-task-weaken - version: "1.04" + version: "1.06" source: - url: http://cpan.metacpan.org/authors/id/A/AD/ADAMK/Task-Weaken-1.04.tar.gz - md5: affd0c395515bb95d29968404d7fe6de + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Task-Weaken-1.06.tar.gz + sha256: 2383fedb9dbaef646468ea824afbf7c801076720cfba0df2a7a074726dcd66be build: - number: 1 + number: 0 requirements: host: From cf41c279f962f8af238f099baae5097ff48a1a49 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:39:41 -0700 Subject: [PATCH 234/546] Update pymzml to 2.0.6 (#12026) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index 26fee7fde6e41..1177ea1eb6d89 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.0.5" + version: "2.0.6" source: - url: https://files.pythonhosted.org/packages/09/1f/c353d3fb7318e848fc7a827c370af7efedf807620f3951d257bd26f1ac90/pymzml-2.0.5.zip - sha256: 75ddd7d22cbe54f9aab5cbf537718e4b85639334d165a672ea841e6602d0dfd5 + url: https://files.pythonhosted.org/packages/90/9e/0ae961f03ecca93312bbb0724e6891483863b0052485d36c3166243706b8/pymzml-2.0.6.zip + sha256: 415cddbcd96bbfb2c85bcfe185ed7a02f4667c5f6f01e405420726aeb517f412 build: noarch: python From e38bcb54ecc8bdaf31f794298d5eb5f149c2143e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:40:00 -0700 Subject: [PATCH 235/546] Update gxformat2 to 0.8.0 (#12021) --- recipes/gxformat2/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/gxformat2/meta.yaml b/recipes/gxformat2/meta.yaml index 71d1457a338ff..e49c805db9f52 100644 --- a/recipes/gxformat2/meta.yaml +++ b/recipes/gxformat2/meta.yaml @@ -1,13 +1,13 @@ package: name: gxformat2 - version: "0.2.0" + version: "0.8.0" source: - url: https://pypi.python.org/packages/cb/9e/996296fb03124406d78e51bb161c2ce1e09ebb20cdb7ca83d830dd598eb4/gxformat2-0.2.0.tar.gz - md5: d13123b54de67d8bb941399b54b728ee + url: https://files.pythonhosted.org/packages/e7/e4/484de6cb6980a91c8c1cb6b2908b355996e9f6b07043f1a7eeda9765cbbe/gxformat2-0.8.0.tar.gz + sha256: ee859a8bec6570be8b0be90ca53ecf8005126bb9edca537c0386fe807f247e63 build: - number: 2 + number: 0 noarch: python preserve_egg_dir: True script: python -m pip install --no-deps --ignore-installed . From 59183f66659513448eb7a45d1cce2fec97a7a132 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:40:19 -0700 Subject: [PATCH 236/546] Update graftm to 0.11.1 (#12017) --- recipes/graftm/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/graftm/meta.yaml b/recipes/graftm/meta.yaml index 95b2869792a21..648a2746ca876 100644 --- a/recipes/graftm/meta.yaml +++ b/recipes/graftm/meta.yaml @@ -1,13 +1,13 @@ package: name: graftm - version: "0.10.1" + version: "0.11.1" source: - url: https://pypi.python.org/packages/d3/45/fb464bff4ea40aae267c7f3f877b7d7fda506691d158aa7f60ed1ccc6bd2/graftm-0.10.1.tar.gz - md5: bcafb5ca4654617856162065ee1ecd27 + url: https://files.pythonhosted.org/packages/05/d4/2e5f7283cbd155ba82a443dde25617b769ca50f476877a63891242979fbd/graftm-0.11.1.tar.gz + sha256: b3b83d7dff5f3de573745ceda53b148fd2e58cc674e841e5802316d0b471744b build: - number: 1 + number: 0 skip: True # [not py27] requirements: From 8cc2c160b94d4404998ba249003be1ecc85b83ea Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:40:34 -0700 Subject: [PATCH 237/546] Update query_phenomizer to 1.2 (#12022) --- recipes/query_phenomizer/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index f3e11bf028da3..a0d364e9a2741 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -1,13 +1,13 @@ package: name: query_phenomizer - version: "0.5" + version: "1.2" source: - url: https://pypi.python.org/packages/e3/b2/d8f106d7f59aba6f198a6b2dc14237076517977c4208ca299ea8995fd43e/query_phenomizer-0.5.tar.gz - md5: 6141bd9f5743d9f828ee200eb62f8fbc + url: https://files.pythonhosted.org/packages/f8/a7/af989c9a672e267ef38009c32206f53c752cc7bac13b29b586c0b93a3da8/query_phenomizer-1.2.tar.gz + sha256: ae6f85331bfa7947fd0edf245780559581a7c728e563093d4b4dc44415517cc7 build: - number: 2 + number: 0 noarch: python entry_points: - query_phenomizer = query_phenomizer.__main__:cli From e600fb06f8e5cab1a2d57c9d518a820783c07664 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:40:48 -0700 Subject: [PATCH 238/546] Update perl-config-any to 0.32 (#12025) --- recipes/perl-config-any/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-config-any/meta.yaml b/recipes/perl-config-any/meta.yaml index 9e13f6fb6b1d0..a9afddb4ed6d0 100644 --- a/recipes/perl-config-any/meta.yaml +++ b/recipes/perl-config-any/meta.yaml @@ -1,14 +1,14 @@ package: name: perl-config-any - version: "0.27" + version: "0.32" source: - url: https://cpan.metacpan.org/authors/id/B/BR/BRICAS/Config-Any-0.27.tar.gz - md5: 0c8db36ebfeea250f554ebc50ee5b643 + url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Config-Any-0.32.tar.gz + sha256: 68da2a5cf25faedd4d24cf3d0d570995c199d5b950108a2de78d40deced36150 build: #skip: True # [osx] - number: 2 + number: 0 requirements: build: From d993b8400f741eeb6ac6451c72cb5951b73dbb6e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:41:05 -0700 Subject: [PATCH 239/546] Update schema to 0.6.8 (#12033) --- recipes/schema/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/schema/meta.yaml b/recipes/schema/meta.yaml index 30f13c121741c..4af6eb867ef2c 100644 --- a/recipes/schema/meta.yaml +++ b/recipes/schema/meta.yaml @@ -1,10 +1,10 @@ package: name: schema - version: "0.6.6" + version: "0.6.8" source: - url: https://pypi.python.org/packages/05/5c/25b7fccf722d579d1368415db031dbefedbbddac125363f7827af6aa5ece/schema-0.6.6.tar.gz - md5: 0da19403e5e2abd49e323b0c076dde18 + url: https://files.pythonhosted.org/packages/aa/2a/367594933a260273dea8cb38bbfe194681fdb66895e6bf41844049d3ff70/schema-0.6.8.tar.gz + sha256: fa1a53fe5f3b6929725a4e81688c250f46838e25d8c1885a10a590c8c01a7b74 requirements: host: @@ -16,7 +16,7 @@ requirements: build: noarch: python - number: 1 + number: 0 test: imports: From ddc2b37d3d0d8641deb6d00aa504e5fceb524877 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:41:20 -0700 Subject: [PATCH 240/546] Update fast5-research to 1.2.8 (#12032) --- recipes/fast5-research/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/fast5-research/meta.yaml b/recipes/fast5-research/meta.yaml index fd123d3a21196..a3c17966031b9 100644 --- a/recipes/fast5-research/meta.yaml +++ b/recipes/fast5-research/meta.yaml @@ -1,14 +1,14 @@ package: name: fast5-research - version: "1.0.9" + version: "1.2.8" source: - url: https://pypi.python.org/packages/0f/36/1ff39b4be2d7ae254c6ab7cae6acac3ae9b0ec637bd56a4ac5aa6396e378/fast5_research-1.0.9.tar.gz - md5: e841b8a334ac9eab0597945c94b69c42 + url: https://files.pythonhosted.org/packages/30/c4/b77e6dc14b2ebe7034ddbf1ced3035e78a26765e525e9dbfbd088edc4288/fast5_research-1.2.8.tar.gz + sha256: 42f0fd34c0d9514d2bdc6fb737fe5b657c5441142104b230cb245320bd0e1ae8 build: noarch: python - number: 1 + number: 0 requirements: host: From f80b603a06f62e6e9fc2132a5fb8a31c73ec5e25 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:41:47 -0700 Subject: [PATCH 241/546] Update python-sortedcontainers to 2.0.5 (#12046) --- recipes/python-sortedcontainers/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/python-sortedcontainers/meta.yaml b/recipes/python-sortedcontainers/meta.yaml index 607b604825935..5350a0f8c5b6a 100644 --- a/recipes/python-sortedcontainers/meta.yaml +++ b/recipes/python-sortedcontainers/meta.yaml @@ -1,11 +1,11 @@ -{% set version = "2.0.4" %} +{% set version = "2.0.5" %} package: name: "python-sortedcontainers" version: {{ version }} source: - url: https://files.pythonhosted.org/packages/94/17/39a70184c2dbdb844db6c58c51cb3c9bc572cc08642646e77f0f1bda143c/sortedcontainers-2.0.4.tar.gz - sha256: 607294c6e291a270948420f7ffa1fb3ed47384a4c08db6d1e9c92d08a6981982 + url: https://files.pythonhosted.org/packages/b9/30/accbf5c09c5fa25a3d5f762761e0d7ece6fdb12f2a9c43b840f73cef43ef/sortedcontainers-2.0.5.tar.gz + sha256: b74f2756fb5e23512572cc76f0fe0832fd86310f77dfee54335a35fb33f6b950 build: number: 0 noarch: python From e3cd6e4330405a23848c5162fbbb1fe2bf910565 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 01:42:16 -0700 Subject: [PATCH 242/546] Update tadtool to 0.77 (#12010) --- recipes/tadtool/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/tadtool/meta.yaml b/recipes/tadtool/meta.yaml index 4047b379d9eff..ab8dc313e03bf 100644 --- a/recipes/tadtool/meta.yaml +++ b/recipes/tadtool/meta.yaml @@ -1,14 +1,14 @@ package: name: tadtool - version: "0.75" + version: "0.77" source: - url: https://pypi.python.org/packages/44/30/60598da1708c9a5cf592b8ac5c73437de62adfcba3de28729489ca5b21c4/tadtool-0.75.tar.gz - md5: b3d459fce4af2e4a51150a5bf5db6995 + url: https://files.pythonhosted.org/packages/2a/2c/de2d88b171c7bb454c5edcf84154f098bd81db6f838046f80733bccec19d/tadtool-0.77.tar.gz + sha256: 18a6b2d158d2ef59b22c5e466bb578677cc597c847a11887bbeec12ca211c2cd build: noarch: python - number: 1 + number: 0 requirements: host: From 473d1d0f0f4a3db7093b968727ee3e7bc0040947 Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Mon, 12 Nov 2018 15:25:23 +0100 Subject: [PATCH 243/546] Genenotebook v0.1.7 (#12061) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 --- recipes/genenotebook/build.sh | 2 ++ recipes/genenotebook/meta.yaml | 7 ++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/genenotebook/build.sh b/recipes/genenotebook/build.sh index 9409c9c24712b..4e0c7dcb0d557 100644 --- a/recipes/genenotebook/build.sh +++ b/recipes/genenotebook/build.sh @@ -4,10 +4,12 @@ set -exo pipefail outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} mkdir -p $outdir $PREFIX/bin +pwd ls -l . npm install --unsafe-perm METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle + cp -R genenotebook_v${PKG_VERSION}/* $outdir ln -s ${outdir}/genenotebook ${PREFIX}/bin/genenotebook diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index 34d3968ab72ea..d4bc0b71b5c55 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.6' %} -{% set sha256 = '999e179d0d441b984ae661f134030893a3aab11048084794f38f1adcd48f089c' %} +{% set version = '0.1.7' %} +{% set sha256 = 'a9b0a987c25a18d1d009a9fbd58833843c2780418165db3f613cca09cb002364' %} package: name: {{ name|lower }} @@ -22,7 +22,7 @@ requirements: - mongodb>=3.4 build: - number: 1 + number: 0 test: commands: @@ -33,3 +33,4 @@ about: license: AGPL-3.0 license_file: LICENSE summary: A colleborative notebook for comparative genomics + From 2f1760d10daec60910807750c5ab7714626abd7a Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Mon, 12 Nov 2018 16:04:34 +0100 Subject: [PATCH 244/546] Add gitpython to snakemake dependencies (#11873) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit gitpython is listed as a dependency in Snakemake’s `setup.py`, but not as a run requirement in this recipe. --- recipes/snakemake-minimal/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/snakemake-minimal/meta.yaml b/recipes/snakemake-minimal/meta.yaml index 6424249f780e2..227d972de3694 100644 --- a/recipes/snakemake-minimal/meta.yaml +++ b/recipes/snakemake-minimal/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 612a16f2bba580c47183e4f752ed40b034852541ca3e96e480d01fb30ad9570c build: - number: 0 + number: 1 skip: True # [py27] script: python -m pip install --no-deps --ignore-installed . entry_points: @@ -41,6 +41,7 @@ requirements: - configargparse - appdirs - jsonschema + - gitpython test: imports: From 3b66907901125c07c511891525f6e3be182b1fcf Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Mon, 12 Nov 2018 09:35:50 -0600 Subject: [PATCH 245/546] Add recipe for RGT (#11830) --- recipes/rgt/build.sh | 51 +++++++ recipes/rgt/data.config | 80 +++++++++++ recipes/rgt/data.patch | 281 +++++++++++++++++++++++++++++++++++++ recipes/rgt/download-db.sh | 36 +++++ recipes/rgt/meta.yaml | 106 ++++++++++++++ recipes/rgt/post-link.sh | 7 + 6 files changed, 561 insertions(+) create mode 100644 recipes/rgt/build.sh create mode 100644 recipes/rgt/data.config create mode 100644 recipes/rgt/data.patch create mode 100755 recipes/rgt/download-db.sh create mode 100644 recipes/rgt/meta.yaml create mode 100644 recipes/rgt/post-link.sh diff --git a/recipes/rgt/build.sh b/recipes/rgt/build.sh new file mode 100644 index 0000000000000..38012fdbb9400 --- /dev/null +++ b/recipes/rgt/build.sh @@ -0,0 +1,51 @@ +#!/bin/bash + +$PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . + + +# copy additional scripts +chmod +x tools/*.py +cp tools/*.py ${PREFIX}/bin + + +# copy download scripts +chmod +x data/*.py +cp data/setupGenomicData.py ${PREFIX}/bin +cp data/setupLogoData.py ${PREFIX}/bin + + +# create folder for database download +target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} +mkdir -p ${target}/db/ + + +# copy config file where database is +cp ${RECIPE_DIR}/data.config ${target}/db/data.config +cp ${RECIPE_DIR}/data.config ${target}/db/data.config.user + + +# copy libraries, need to be in db folder +cp -r data/lib ${target}/db/ +if [ `uname` == Darwin ]; then + ln -s ${target}/db/lib/librgt_mac.so ${target}/db/lib/librgt.so +else + ln -s ${target}/db/lib/librgt_linux.so ${target}/db/lib/librgt.so +fi + + +# copy script to download database +chmod +x ${RECIPE_DIR}/download-db.sh +cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin + + +# set RGTDATA variable on env activation +mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d +cat <> ${PREFIX}/etc/conda/activate.d/rgt.sh +export RGTDATA=${target}/db/ +export DOWNLOAD_URL=https://github.com/CostaLab/reg-gen/archive/${PKG_VERSION}.tar.gz +EOF + +cat <> ${PREFIX}/etc/conda/deactivate.d/rgt.sh +unset RGTDATA +unset DOWNLOAD_URL +EOF diff --git a/recipes/rgt/data.config b/recipes/rgt/data.config new file mode 100644 index 0000000000000..642312d7bb1cb --- /dev/null +++ b/recipes/rgt/data.config @@ -0,0 +1,80 @@ +# Configuration file loaded at rgt startup. CAREFUL: any changes shall be overwritten +# whenever rgt is (re)installed. Use data.config.user for permanent changes. + +[mm9] +genome: mm9/genome_mm9.fa +chromosome_sizes: mm9/chrom.sizes.mm9 +genes_Gencode: mm9/genes_Gencode_mm9.bed +genes_RefSeq: mm9/genes_RefSeq_mm9.bed +annotation: mm9/gencode.vM1.annotation.gtf +gene_alias: mm9/alias_mouse.txt +repeat_maskers: mm9/repeat_maskers + +[mm10] +genome: mm10/genome_mm10.fa +chromosome_sizes: mm10/chrom.sizes.mm10 +genes_Gencode: mm10/genes_Gencode_mm10.bed +genes_RefSeq: mm10/genes_RefSeq_mm10.bed +annotation: mm10/gencode.vM11.annotation.gtf +gene_alias: mm10/alias_mouse.txt + +[hg19] +genome: hg19/genome_hg19.fa +chromosome_sizes: hg19/chrom.sizes.hg19 +genes_Gencode: hg19/genes_Gencode_hg19.bed +genes_RefSeq: hg19/genes_RefSeq_hg19.bed +annotation: hg19/gencode.v19.annotation.gtf +gene_alias: hg19/alias_human.txt +repeat_maskers: hg19/repeat_maskers + +[hg38] +genome: hg38/genome_hg38.fa +chromosome_sizes: hg38/chrom.sizes.hg38 +genes_Gencode: hg38/genes_Gencode_hg38.bed +genes_RefSeq: hg38/genes_RefSeq_hg38.bed +annotation: hg38/gencode.v24.annotation.gtf +gene_alias: hg38/alias_human.txt +repeat_maskers: hg38/repeat_maskers + +[zv9] +genome: zv9/genome_zv9_ensembl_release_79.fa +chromosome_sizes: zv9/chrom.sizes.zv9 +gene_regions: zv9/genes_zv9.bed +annotation: zv9/Danio_rerio.Zv9.79.gtf +gene_alias: zv9/alias_zebrafish.txt + +[zv10] +genome: zv10/genome_zv10_ensembl_release_84.fa +chromosome_sizes: zv10/chrom.sizes.zv10 +gene_regions: zv10/genes_zv10.bed +annotation: zv10/Danio_rerio.GRCz10.84.gtf +gene_alias: zv10/alias_zebrafish.txt + +[MotifData] +pwm_dataset: motifs +logo_dataset: logos +repositories: jaspar_vertebrates + +[HmmData] +default_hmm_dnase: fp_hmms/dnase.hmm +default_hmm_dnase_bc: fp_hmms/dnase_bc.hmm +default_hmm_atac_paired: fp_hmms/atac_paired.pkl +default_hmm_atac_single: fp_hmms/atac_single.pkl +default_hmm_histone: fp_hmms/histone.hmm +default_hmm_dnase_histone: fp_hmms/dnase_histone.hmm +default_hmm_dnase_histone_bc: fp_hmms/dnase_histone_bc.hmm +default_hmm_atac_histone: fp_hmms/atac_histone.hmm +default_hmm_atac_histone_bc: fp_hmms/atac_histone_bc.hmm +default_bias_table_F_SH: fp_hmms/single_hit_bias_table_F.txt +default_bias_table_R_SH: fp_hmms/single_hit_bias_table_R.txt +default_bias_table_F_DH: fp_hmms/double_hit_bias_table_F.txt +default_bias_table_R_DH: fp_hmms/double_hit_bias_table_R.txt +default_bias_table_F_ATAC: fp_hmms/atac_bias_table_F.txt +default_bias_table_R_ATAC: fp_hmms/atac_bias_table_R.txt +dependency_model: fp_hmms/LearnDependencyModel.jar +slim_dimont_predictor: fp_hmms/SlimDimontPredictor.jar +default_test_fa: fp_hmms/test.fa + +[Library] +path_triplexator: lib/libtriplexator.so +path_c_rgt: lib/librgt.so diff --git a/recipes/rgt/data.patch b/recipes/rgt/data.patch new file mode 100644 index 0000000000000..565859cc92549 --- /dev/null +++ b/recipes/rgt/data.patch @@ -0,0 +1,281 @@ +--- setup.py 2018-07-17 10:02:03.000000000 -0500 ++++ setup.py.new 2018-10-18 17:47:10.366333398 -0500 +@@ -76,6 +76,7 @@ + + common_deps = ["cython", + "numpy>=1.4.0", ++ "numpy<=1.10", + "scipy>=1.0.0", + "pysam>=0.12.0", + "pyBigWig", +@@ -142,7 +143,6 @@ + ) + } + +- + ################################################################################################### + # Auxiliary Functions/Classes + ################################################################################################### +@@ -165,21 +165,6 @@ + except (BadOptionError, AmbiguousOptionError) as err: + largs.append(err.opt_str) + +- +-# recursive_chown_chmod Function +-def recursive_chown_chmod(path_to_walk, uid, gid, file_permission, path_permission): +- """ +- Recursively applies chown from path. +- """ +- for root_dir, directory_list, file_list in walk(path_to_walk): +- chown(root_dir, uid, gid) +- chmod(root_dir, path_permission) +- for f in file_list: +- current_complete_file = path.join(root_dir, f) +- chown(current_complete_file, uid, gid) +- chmod(current_complete_file, file_permission) +- +- + ################################################################################################### + # Processing Input Arguments + ################################################################################################### +@@ -226,168 +211,6 @@ + current_install_requires += tools_dictionary[tool_option][2] + + ################################################################################################### +-# Creating Data Path +-################################################################################################### +- +-# if the environment variable is set, use it; otherwise use the home directory as a default +-rgt_data_location = path.expanduser(getenv("RGTDATA", path.join(getenv("HOME"), "rgtdata"))) +- +-# Creating Data Path +-if not path.exists(rgt_data_location): +- makedirs(rgt_data_location) +- +-# Creating data.config +-data_config_file_name = path.join(rgt_data_location, "data.config") +-# if not os.path.isfile(data_config_file_name): +-data_config_file = open(data_config_file_name, "w") +-data_config_file.write("# Configuration file loaded at rgt startup. CAREFUL: any changes shall be overwritten\n" +- "# whenever rgt is (re)installed. Use data.config.user for permanent changes.\n\n") +- +-genome = "mm9" +-data_config_file.write("[" + genome + "]\n") +-data_config_file.write("genome: " + path.join(genome, "genome_mm9.fa\n")) +-data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.mm9\n")) +-data_config_file.write("genes_Gencode: " + path.join(genome, "genes_Gencode_mm9.bed\n")) +-data_config_file.write("genes_RefSeq: " + path.join(genome, "genes_RefSeq_mm9.bed\n")) +-data_config_file.write("annotation: " + path.join(genome, "gencode.vM1.annotation.gtf\n")) +-data_config_file.write("gene_alias: " + path.join(genome, "alias_mouse.txt\n\n")) +-data_config_file.write("repeat_maskers: " + path.join(genome, "repeat_maskers\n\n")) +-genome = "mm10" +-data_config_file.write("[" + genome + "]\n") +-data_config_file.write("genome: " + path.join(genome, "genome_mm10.fa\n")) +-data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.mm10\n")) +-data_config_file.write("genes_Gencode: " + path.join(genome, "genes_Gencode_mm10.bed\n")) +-data_config_file.write("genes_RefSeq: " + path.join(genome, "genes_RefSeq_mm10.bed\n")) +-data_config_file.write("annotation: " + path.join(genome, "gencode.vM11.annotation.gtf\n")) +-data_config_file.write("gene_alias: " + path.join(genome, "alias_mouse.txt\n\n")) +-genome = "hg19" +-data_config_file.write("[" + genome + "]\n") +-data_config_file.write("genome: " + path.join(genome, "genome_hg19.fa\n")) +-data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.hg19\n")) +-data_config_file.write("genes_Gencode: " + path.join(genome, "genes_Gencode_hg19.bed\n")) +-data_config_file.write("genes_RefSeq: " + path.join(genome, "genes_RefSeq_hg19.bed\n")) +-data_config_file.write("annotation: " + path.join(genome, "gencode.v19.annotation.gtf\n")) +-data_config_file.write("gene_alias: " + path.join(genome, "alias_human.txt\n\n")) +-data_config_file.write("repeat_maskers: " + path.join(genome, "repeat_maskers\n\n")) +-genome = "hg38" +-data_config_file.write("[" + genome + "]\n") +-data_config_file.write("genome: " + path.join(genome, "genome_hg38.fa\n")) +-data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.hg38\n")) +-data_config_file.write("genes_Gencode: " + path.join(genome, "genes_Gencode_hg38.bed\n")) +-data_config_file.write("genes_RefSeq: " + path.join(genome, "genes_RefSeq_hg38.bed\n")) +-data_config_file.write("annotation: " + path.join(genome, "gencode.v24.annotation.gtf\n")) +-data_config_file.write("gene_alias: " + path.join(genome, "alias_human.txt\n\n")) +-data_config_file.write("repeat_maskers: " + path.join(genome, "repeat_maskers\n\n")) +-genome = "zv9" +-data_config_file.write("[" + genome + "]\n") +-data_config_file.write("genome: " + path.join(genome, "genome_zv9_ensembl_release_79.fa\n")) +-data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.zv9\n")) +-data_config_file.write("gene_regions: " + path.join(genome, "genes_zv9.bed\n")) +-data_config_file.write("annotation: " + path.join(genome, "Danio_rerio.Zv9.79.gtf\n")) +-data_config_file.write("gene_alias: " + path.join(genome, "alias_zebrafish.txt\n\n")) +-genome = "zv10" +-data_config_file.write("[" + genome + "]\n") +-data_config_file.write("genome: " + path.join(genome, "genome_zv10_ensembl_release_84.fa\n")) +-data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.zv10\n")) +-data_config_file.write("gene_regions: " + path.join(genome, "genes_zv10.bed\n")) +-data_config_file.write("annotation: " + path.join(genome, "Danio_rerio.GRCz10.84.gtf\n")) +-data_config_file.write("gene_alias: " + path.join(genome, "alias_zebrafish.txt\n\n")) +- +-data_config_file.write("[MotifData]\n") +-data_config_file.write("pwm_dataset: motifs\n") +-data_config_file.write("logo_dataset: logos\n") +-data_config_file.write("repositories: jaspar_vertebrates\n\n") +-data_config_file.write("[HmmData]\n") +-data_config_file.write("default_hmm_dnase: fp_hmms/dnase.hmm\n") +-data_config_file.write("default_hmm_dnase_bc: fp_hmms/dnase_bc.hmm\n") +-data_config_file.write("default_hmm_atac_paired: fp_hmms/atac_paired.pkl\n") +-data_config_file.write("default_hmm_atac_single: fp_hmms/atac_single.pkl\n") +-data_config_file.write("default_hmm_histone: fp_hmms/histone.hmm\n") +-data_config_file.write("default_hmm_dnase_histone: fp_hmms/dnase_histone.hmm\n") +-data_config_file.write("default_hmm_dnase_histone_bc: fp_hmms/dnase_histone_bc.hmm\n") +-data_config_file.write("default_hmm_atac_histone: fp_hmms/atac_histone.hmm\n") +-data_config_file.write("default_hmm_atac_histone_bc: fp_hmms/atac_histone_bc.hmm\n") +-data_config_file.write("default_bias_table_F_SH: fp_hmms/single_hit_bias_table_F.txt\n") +-data_config_file.write("default_bias_table_R_SH: fp_hmms/single_hit_bias_table_R.txt\n") +-data_config_file.write("default_bias_table_F_DH: fp_hmms/double_hit_bias_table_F.txt\n") +-data_config_file.write("default_bias_table_R_DH: fp_hmms/double_hit_bias_table_R.txt\n") +-data_config_file.write("default_bias_table_F_ATAC: fp_hmms/atac_bias_table_F.txt\n") +-data_config_file.write("default_bias_table_R_ATAC: fp_hmms/atac_bias_table_R.txt\n") +-data_config_file.write("dependency_model: fp_hmms/LearnDependencyModel.jar\n") +-data_config_file.write("slim_dimont_predictor: fp_hmms/SlimDimontPredictor.jar\n") +-data_config_file.write("default_test_fa: fp_hmms/test.fa\n\n") +-data_config_file.write("[Library]\n") +-data_config_file.write("path_triplexator: " + triplexes_file + "\n") +-data_config_file.write("path_c_rgt: " + path.join("lib", libRGT) + "\n") +- +-data_config_file.close() +- +-# Creating data.config.user, but only if not already present +-user_config_file_name = path.join(rgt_data_location, "data.config.user") +-if not os.path.isfile(user_config_file_name): +- user_config_file = open(user_config_file_name, "w") +- +- user_config_file.write("# Here you can overwrite any property set in the data.config file. It shall not be\n" +- "# be overwritten in any case, so if you are experiencing problems rename or remove this\n" +- "# file. See data.config for how the file should be formatted.\n\n") +- genome = "self_defined" +- user_config_file.write("# Template to add a genomic section.\n") +- user_config_file.write("#[" + genome + "]\n") +- user_config_file.write("#genome: undefined\n") +- user_config_file.write("#chromosome_sizes: undefined\n") +- user_config_file.write("#gene_regions: undefined\n") +- user_config_file.write("#annotation: undefined\n") +- user_config_file.write("#gene_alias: undefined\n\n") +- +-script_dir = path.dirname(path.abspath(__file__)) +- +-# Copying data from package folder to installation folder +-""" +-Copy Files Dictionary: +- * Insert in the dictionary below a key + list in the format X:[Y1,Y2,...Yn], representing: +- - X: A path in the data folder structure. +- - Y1,Y2,...Yn: files/folders inside the path X to be copied. +-""" +-copy_files_dictionary = { +- ".": ["setupGenomicData.py", "setupLogoData.py"], +- "lib": ["libtriplexator.so", "libtriplexator.dylib", libRGT], +- "hg19": ["genes_Gencode_hg19.bed", "chrom.sizes.hg19", "alias_human.txt", "genes_RefSeq_hg19.bed"], +- "hg38": ["genes_Gencode_hg38.bed", "chrom.sizes.hg38", "alias_human.txt", "genes_RefSeq_hg38.bed"], +- "mm9": ["genes_Gencode_mm9.bed", "chrom.sizes.mm9", "alias_mouse.txt", "genes_RefSeq_mm9.bed"], +- "mm10": ["genes_Gencode_mm10.bed", "chrom.sizes.mm10", "alias_mouse.txt", "genes_RefSeq_mm10.bed"], +- "zv9": ["genes_zv9.bed", "chrom.sizes.zv9", "alias_zebrafish.txt"], +- "zv10": ["genes_zv10.bed", "chrom.sizes.zv10", "alias_zebrafish.txt"], +- "fp_hmms": ["dnase.hmm", "dnase_bc.hmm", "histone.hmm", "dnase_histone.hmm", "dnase_histone_bc.hmm", +- "single_hit_bias_table_F.txt", "single_hit_bias_table_R.txt", "atac_paired.pkl", "atac_single.pkl", +- "atac_bias_table_F.txt", "atac_bias_table_R.txt", "atac_histone.hmm", "atac_histone_bc.hmm", +- "double_hit_bias_table_F.txt", "double_hit_bias_table_R.txt", "H3K4me3_proximal.hmm", +- "LearnDependencyModel.jar", "SlimDimontPredictor.jar", "test.fa"], +- "motifs": ["jaspar_vertebrates", "uniprobe_primary", "uniprobe_secondary", "hocomoco", +- "jaspar_vertebrates.fpr", "uniprobe_primary.fpr", "uniprobe_secondary.fpr", "hocomoco.fpr", +- "jaspar_vertebrates.mtf", "uniprobe_primary.mtf", "uniprobe_secondary.mtf", "hocomoco.mtf"], +- "fig": ["rgt_logo.gif", "style.css", "default_motif_logo.png", "jquery-1.11.1.js", "jquery.tablesorter.min.js", +- "tdf_logo.png", "viz_logo.png"], +-} +-for copy_folder in copy_files_dictionary.keys(): +- copy_dest_path = path.join(rgt_data_location, copy_folder) +- if not path.exists(copy_dest_path): makedirs(copy_dest_path) +- for copy_file in copy_files_dictionary[copy_folder]: +- copy_source_file = path.join(script_dir, "data", copy_folder, copy_file) +- copy_dest_file = path.join(copy_dest_path, copy_file) +- if os.path.isfile(copy_source_file): +- copy(copy_source_file, copy_dest_file) +- else: +- dir_util.copy_tree(copy_source_file, copy_dest_file) +- +- # if not path.exists(copy_dest_file): +- # try: dir_util.copy_tree(copy_source_file, copy_dest_file) +- # except OSError as exc: +- # if exc.errno == ENOTDIR: +- # copy(copy_source_file, copy_dest_file) +- # else: +- # raise +- +-################################################################################################### + # Setup Function + ################################################################################################### + +@@ -452,19 +275,3 @@ + url="http://www.regulatory-genomics.org", + download_url="https://github.com/CostaLab/reg-gen/archive/{0}.zip".format(current_version), + platforms=supported_platforms) +- +-################################################################################################### +-# Termination +-################################################################################################### +- +-# Modifying Permissions when Running Superuser/Admin +-# $SUDO_USER exists only if you are sudo, and returns the original user name +-current_user = getenv("SUDO_USER") +-default_file_permission = 0o644 +-default_path_permission = 0o755 +- +-if current_user: +- current_user_uid = getpwnam(current_user).pw_uid +- current_user_gid = getpwnam(current_user).pw_gid +- recursive_chown_chmod(rgt_data_location, current_user_uid, current_user_gid, default_file_permission, +- default_path_permission) +--- data/setupGenomicData.py 2018-07-17 10:02:03.000000000 -0500 ++++ data/setupGenomicData.py.new 2018-10-20 15:55:35.434593709 -0500 +@@ -1,3 +1,5 @@ ++#!/usr/bin/env python ++ + ################################################################################################### + # Setup Genomic Data Script + # This script will fetch the necessary genomic data for all tools. Be aware that it will download +@@ -9,7 +11,7 @@ + from __future__ import print_function + import gzip + from optparse import OptionParser +-from os import system, path, remove, mkdir ++from os import system, path, remove, mkdir, getenv + from sys import platform + import re + +@@ -82,7 +84,7 @@ + ################################################################################################### + + # Current rgt data path +-curr_dir = path.dirname(path.realpath(__file__)) ++curr_dir = path.dirname(getenv("RGTDATA")) + + # Platform + supported_platforms = ["linux", "linux2", "darwin"] +--- data/setupLogoData.py 2018-07-17 10:02:03.000000000 -0500 ++++ data/setupLogoData.py.new 2018-10-20 15:57:06.592071379 -0500 +@@ -1,3 +1,5 @@ ++#!/usr/bin/env python ++ + ################################################################################################### + # Setup Logo Data Script + # This script will create all motif logos. Be aware that this is a time consuming procedure +@@ -10,7 +12,7 @@ + from __future__ import print_function + + from optparse import OptionParser +-from os import path, walk, mkdir ++from os import path, walk, mkdir, getenv + from sys import platform + + from Bio import motifs +@@ -44,7 +46,7 @@ + ################################################################################################### + + # Current rgt data path +-curr_dir = path.dirname(path.realpath(__file__)) ++curr_dir = path.dirname(getenv("RGTDATA")) + + # Platform + supported_platforms = ["linux", "linux2", "darwin"] diff --git a/recipes/rgt/download-db.sh b/recipes/rgt/download-db.sh new file mode 100755 index 0000000000000..7fbd250a46daa --- /dev/null +++ b/recipes/rgt/download-db.sh @@ -0,0 +1,36 @@ +#!/usr/bin/env bash + +echo "Downloading RGT database to ${RGTDATA}..." + +# RGTDATA is defined in build.sh, store the db there + +# download data from release +wget ${DOWNLOAD_URL} -O RGT.tar.gz +mkdir RGT +tar xf RGT.tar.gz -C RGT --strip-components 1 +cp -r RGT/data/fig/ ${RGTDATA} +cp -r RGT/data/fp_hmms/ ${RGTDATA} +cp -r RGT/data/motifs/ ${RGTDATA} +cp -r RGT/data/hg19/ ${RGTDATA} +cp -r RGT/data/hg38/ ${RGTDATA} +cp -r RGT/data/mm9/ ${RGTDATA} +cp -r RGT/data/mm10/ ${RGTDATA} +cp -r RGT/data/zv9/ ${RGTDATA} +cp -r RGT/data/zv10 ${RGTDATA} +rm -rf RGT +rm RGT.tar.gz + +cd ${RGTDATA} + +# download Genomic Data +setupGenomicData.py --all +setupGenomicData.py --hg19-rm +setupGenomicData.py --hg38-rm +setupGenomicData.py --mm9-rm + +# download Logo Data +setupLogoData.py --all + +echo "RGT database is downloaded." + +exit 0 diff --git a/recipes/rgt/meta.yaml b/recipes/rgt/meta.yaml new file mode 100644 index 0000000000000..acd4fd22bf339 --- /dev/null +++ b/recipes/rgt/meta.yaml @@ -0,0 +1,106 @@ +{% set name = "RGT" %} +{% set version = "0.11.4" %} +{% set sha256 = "914f3c7933b4b4f54cc6e8e10e384712bff12bfbe6f345bac614a60d9c410db6" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/CostaLab/reg-gen/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - data.patch + +build: + number: 0 + skip: True # [py3k] + entry_points: + - rgt-motifanalysis = rgt.motifanalysis.Main:main + - rgt-hint = rgt.HINT.Main:main + - rgt-THOR = rgt.THOR.THOR:main + - rgt-filterVCF = rgt.filterVCF.filterVCF:main + - rgt-viz = rgt.viz.Main:main + - rgt-TDF = rgt.tdf.Main:main + +requirements: + host: + - biopython >=1.64 + - scipy >=1.0.0 + - numpy >=1.4.0,<=1.11 + - numpy-base + - cython + - fisher >=0.1.5 + - hmmlearn >=0.2 + - htseq + - matplotlib >=1.1.0 + - matplotlib-venn + - mpmath + - natsort + - pip + - pybigwig + - ucsc-wigtobigwig + - ucsc-bigwigmerge + - ucsc-bedtobigbed + - ucsc-bigbedtobed + - ucsc-bedgraphtobigwig + - pysam >=0.12.0 + - python + - pyvcf + - pyx + - scikit-learn >=0.19.0,<0.20.0 + - configparser + - zlib + run: + - biopython >=1.64 + - scipy >=1.0.0 + - numpy >=1.4.0,<=1.11 + - numpy-base + - cython + - fisher >=0.1.5 + - hmmlearn >=0.2 + - htseq + - matplotlib >=1.1.0 + - matplotlib-venn + - mpmath + - natsort + - pybigwig + - ucsc-wigtobigwig + - ucsc-bigwigmerge + - ucsc-bedtobigbed + - ucsc-bigbedtobed + - ucsc-bedgraphtobigwig + - pysam >=0.12.0 + - python + - pyvcf + - pyx + - scikit-learn >=0.19.0,<0.20.0 + - configparser + - moods + - zlib + +test: + imports: + - rgt + - rgt.HINT + - rgt.THOR + - rgt.filterVCF + - rgt.motifanalysis + - rgt.tdf + - rgt.viz + commands: + - rgt-motifanalysis --help 2>&1 > /dev/null + - rgt-hint --help 2>&1 > /dev/null + - rgt-THOR --help 2>&1 > /dev/null + - rgt-filterVCF --help 2>&1 > /dev/null + - rgt-viz --help 2>&1 > /dev/null + - rgt-TDF | grep "rgt-TDF" > /dev/null + +about: + home: http://www.regulatory-genomics.org + license: GPL + license_family: GPL + license_file: LICENSE + summary: Toolkit to perform regulatory genomics data analysis + doc_url: http://www.regulatory-genomics.org/rgt/tutorial/ + dev_url: https://github.com/CostaLab/reg-gen diff --git a/recipes/rgt/post-link.sh b/recipes/rgt/post-link.sh new file mode 100644 index 0000000000000..6eeee7991923f --- /dev/null +++ b/recipes/rgt/post-link.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +cat <> ${PREFIX}/.messages.txt + +Please run download-db.sh to download all required RGT database files to ${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}/db/ + +EOF From df30102d868fcf78a8e628dfbf05d1a6c6d9ca9d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 11:53:58 -0700 Subject: [PATCH 246/546] Update moca to 0.4.3 (#12007) --- recipes/moca/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/moca/meta.yaml b/recipes/moca/meta.yaml index 0ba955d1a64ad..10900dbb9ea2c 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -1,13 +1,13 @@ package: name: moca - version: "0.3.4" + version: "0.4.3" source: - url: https://pypi.python.org/packages/1c/d1/6f35a10eda0d458c4c921756c0e4cd3dc11bac664023784e82dc8c1d0fb7/moca-0.3.4.tar.gz - md5: 8fc7a56a695bc339cc6b306f52ff6339 + url: https://files.pythonhosted.org/packages/4e/d3/fb34a619ca59fdf8d19aee79f2666941113a83ce525c1b19f7c7898faffb/moca-0.4.3.tar.gz + sha256: ec7a858629fe5552205cd280e77ee993a38bb065d9e5d22080099bb9b1f81f05 build: - number: 2 + number: 0 skip: true #[not py27] preserve_egg_dir: true entry_points: From 546f501a8e0148ea835cb6a30258bdbb42f1edd1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 11:54:17 -0700 Subject: [PATCH 247/546] Update pyalveo to 1.0.5 (#12004) * Update pyalveo to 1.0.5 * add noarch --- recipes/pyalveo/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/pyalveo/meta.yaml b/recipes/pyalveo/meta.yaml index 4f45638aacdc6..aa3f288cfc731 100644 --- a/recipes/pyalveo/meta.yaml +++ b/recipes/pyalveo/meta.yaml @@ -1,13 +1,14 @@ package: name: pyalveo - version: "1.0.3" + version: "1.0.5" build: - number: 1 + number: 0 + noarch: python source: - url: https://pypi.python.org/packages/6e/5e/1c84eb6c633813c31576b44da09e89622cc80d24d02506301f18883b8312/pyalveo-1.0.3.tar.gz - md5: 9977a0dec7144aeb9eab1c183ea49d1e + url: https://files.pythonhosted.org/packages/a8/1f/1aae80f120eb4c53b4d666007c781dff2dcb2555bbe8c2dff96bc9c15c0c/pyalveo-1.0.5.tar.gz + sha256: 9087f7a16c47a7d4365c89333d90b4546b1e9c193c9da78c34d20960237579a7 requirements: host: From face55d95a91d92a8074e3d19ffa73b6b483396d Mon Sep 17 00:00:00 2001 From: Philipp Rescheneder Date: Mon, 12 Nov 2018 21:02:02 +0000 Subject: [PATCH 248/546] parasail-python (#12065) parasail-python added --- recipes/parasail-python/build.sh | 3 ++ recipes/parasail-python/meta.yaml | 64 +++++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 recipes/parasail-python/build.sh create mode 100644 recipes/parasail-python/meta.yaml diff --git a/recipes/parasail-python/build.sh b/recipes/parasail-python/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/parasail-python/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/parasail-python/meta.yaml b/recipes/parasail-python/meta.yaml new file mode 100644 index 0000000000000..e8fffa2383117 --- /dev/null +++ b/recipes/parasail-python/meta.yaml @@ -0,0 +1,64 @@ +{% set name = "parasail-python" %} +{% set version = "1.1.12" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/jeffdaily/parasail-python/archive/v{{ version }}.tar.gz + md5: 109fc497924030eebda60bde33f0976b + +build: + number: 1 +# noarch: python + #script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + +requirements: + host: + - python +# - numpy +# - pip +# - setuptools +# - zlib + build: + - python + - numpy + - pip + - setuptools + - {{ compiler('c') }} + #- {{ compiler('cxx') }} + #- gcc # [linux] + #- llvm # [osx] + - m4 + - autoconf + - automake + - libtool + - zlib +# - autoreconf +# host: +# - numpy +# - pip +# - python + run: + - numpy + - python + #- libgcc # [linux] + - zlib + +test: + imports: + - parasail + +about: + home: https://github.com/jeffdaily/parasail-python + license: BSD + license_family: BSD + license_file: + summary: pairwise sequence alignment library + doc_url: + dev_url: + +#extra: +# recipe-maintainers: +# - your-github-id-here From eb112c564a9be883a8846c8cd76891ff839c640c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 14:05:00 -0700 Subject: [PATCH 249/546] Update perl-bioperl-core to 1.007002 (#12040) --- recipes/perl-bioperl-core/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-bioperl-core/meta.yaml b/recipes/perl-bioperl-core/meta.yaml index 237c49e708d91..4e069d725d0c1 100644 --- a/recipes/perl-bioperl-core/meta.yaml +++ b/recipes/perl-bioperl-core/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-bioperl-core - version: "1.7.2" + version: "1.007002" source: - url: http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz - md5: a912c92b56d009198f1786b4cf560d5c + url: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz + sha256: 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1 build: - number: 3 + number: 0 requirements: host: From 4a97b4d4a7cdfcc1f4f46b5e30601be85f3f4f6b Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Mon, 12 Nov 2018 15:57:15 -0600 Subject: [PATCH 250/546] Set numpy to 1.11, warning otherwise (#12063) * Set numpy to 1.11, warning otherwise * Fix syntax --- recipes/rgt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/rgt/meta.yaml b/recipes/rgt/meta.yaml index acd4fd22bf339..b3f0762da5aa4 100644 --- a/recipes/rgt/meta.yaml +++ b/recipes/rgt/meta.yaml @@ -13,7 +13,7 @@ source: - data.patch build: - number: 0 + number: 1 skip: True # [py3k] entry_points: - rgt-motifanalysis = rgt.motifanalysis.Main:main @@ -27,7 +27,7 @@ requirements: host: - biopython >=1.64 - scipy >=1.0.0 - - numpy >=1.4.0,<=1.11 + - numpy 1.11.* - numpy-base - cython - fisher >=0.1.5 @@ -54,7 +54,7 @@ requirements: run: - biopython >=1.64 - scipy >=1.0.0 - - numpy >=1.4.0,<=1.11 + - numpy 1.11.* - numpy-base - cython - fisher >=0.1.5 From b32791cd488a67b7a7780a4457fcfa9dc4ea44b3 Mon Sep 17 00:00:00 2001 From: Philipp Rescheneder Date: Mon, 12 Nov 2018 22:05:15 +0000 Subject: [PATCH 251/546] Qcat (#12066) qcat added --- recipes/qcat/build.sh | 3 +++ recipes/qcat/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/qcat/build.sh create mode 100644 recipes/qcat/meta.yaml diff --git a/recipes/qcat/build.sh b/recipes/qcat/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/qcat/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/qcat/meta.yaml b/recipes/qcat/meta.yaml new file mode 100644 index 0000000000000..9a42c317d7a5e --- /dev/null +++ b/recipes/qcat/meta.yaml @@ -0,0 +1,46 @@ +package: + name: qcat + version: 0.1.0 + +source: + fn: v0.1.0.tar.gz [py3k] + url: https://github.com/nanoporetech/qcat/archive/v0.1.0.tar.gz [py3k] + md5: 69a170e7db9cbd1aa50c9e199fa9bc1d [py3k] + +build: + noarch_python: True + skip: True # [py27] + number: 0 + +requirements: + build: + - python + - setuptools + - pytest-runner + - pyyaml + - biopython + - six + - parasail-python + - pandas + - pysam + - mappy + + run: + - python + - biopython + - six + - pyyaml + - parasail-python + - pandas + - pysam + - mappy + +test: + commands: + - qcat -h + +about: + home: https://github.com/nanoporetech/qcat + license: Mozilla Public License Version 2.0 + summary: "Qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files." + From ed864b95831cd22fe1c695c22c5653e1001b9bbb Mon Sep 17 00:00:00 2001 From: nh3 Date: Tue, 13 Nov 2018 00:48:27 +0000 Subject: [PATCH 252/546] scanpy-scripts: pin scanpy version requirement to 1.3.2 (#12062) * Bump version * Fix scanpy version requirement to v1.3.2 --- recipes/scanpy-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 939d849976c70..c123d4d0e4d7f 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 5d00666986d933d0bcddfdbef24cba86decf1ae5bf46df71fe53e87fc701ac71 build: - number: 0 + number: 1 noarch: generic requirements: @@ -19,7 +19,7 @@ requirements: - python>=3.6 - pandas>=0.21 - matplotlib>=3.0.0 - - scanpy>=1.3.2 + - scanpy==1.3.2 test: commands: From 77a0dc083983bf760fdde0fc3d810a359092687e Mon Sep 17 00:00:00 2001 From: Philipp Rescheneder Date: Tue, 13 Nov 2018 01:12:19 +0000 Subject: [PATCH 253/546] Clean up parasail-python meta.yaml (#12067) --- recipes/parasail-python/meta.yaml | 23 +---------------------- 1 file changed, 1 insertion(+), 22 deletions(-) diff --git a/recipes/parasail-python/meta.yaml b/recipes/parasail-python/meta.yaml index e8fffa2383117..bb68a86190189 100644 --- a/recipes/parasail-python/meta.yaml +++ b/recipes/parasail-python/meta.yaml @@ -10,40 +10,25 @@ source: md5: 109fc497924030eebda60bde33f0976b build: - number: 1 -# noarch: python - #script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + number: 2 requirements: host: - python -# - numpy -# - pip -# - setuptools -# - zlib build: - python - numpy - pip - setuptools - {{ compiler('c') }} - #- {{ compiler('cxx') }} - #- gcc # [linux] - #- llvm # [osx] - m4 - autoconf - automake - libtool - zlib -# - autoreconf -# host: -# - numpy -# - pip -# - python run: - numpy - python - #- libgcc # [linux] - zlib test: @@ -54,11 +39,5 @@ about: home: https://github.com/jeffdaily/parasail-python license: BSD license_family: BSD - license_file: summary: pairwise sequence alignment library - doc_url: - dev_url: -#extra: -# recipe-maintainers: -# - your-github-id-here From 08caadf4561c426aed61abb64208af128b975eea Mon Sep 17 00:00:00 2001 From: Philipp Rescheneder Date: Tue, 13 Nov 2018 01:14:54 +0000 Subject: [PATCH 254/546] Update qcat to version 1.0.0 (#12068) * Update qcat to version 1.0.0 * Remove fn from qcat meta.yaml --- recipes/qcat/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/qcat/meta.yaml b/recipes/qcat/meta.yaml index 9a42c317d7a5e..56d71997b93de 100644 --- a/recipes/qcat/meta.yaml +++ b/recipes/qcat/meta.yaml @@ -1,11 +1,10 @@ package: name: qcat - version: 0.1.0 + version: 1.0.0 source: - fn: v0.1.0.tar.gz [py3k] - url: https://github.com/nanoporetech/qcat/archive/v0.1.0.tar.gz [py3k] - md5: 69a170e7db9cbd1aa50c9e199fa9bc1d [py3k] + url: https://github.com/nanoporetech/qcat/archive/v1.0.0.tar.gz + md5: 9f896c61e55265be5da31a2a6c30fcda build: noarch_python: True From 9085cf113b7592f9ea0dd0c56a88c53772bd1fed Mon Sep 17 00:00:00 2001 From: Jillian Rowe Date: Tue, 13 Nov 2018 09:47:25 +0300 Subject: [PATCH 255/546] Feature/demuxlet (#12057) --- recipes/demuxlet/Makefile.am.new | 28 + recipes/demuxlet/Makefile.am.patch | 31 + recipes/demuxlet/Makefile.new | 875 +++++++++++++++++++++++++++++ recipes/demuxlet/build.sh | 22 + recipes/demuxlet/meta.yaml | 62 ++ 5 files changed, 1018 insertions(+) create mode 100644 recipes/demuxlet/Makefile.am.new create mode 100644 recipes/demuxlet/Makefile.am.patch create mode 100644 recipes/demuxlet/Makefile.new create mode 100644 recipes/demuxlet/build.sh create mode 100644 recipes/demuxlet/meta.yaml diff --git a/recipes/demuxlet/Makefile.am.new b/recipes/demuxlet/Makefile.am.new new file mode 100644 index 0000000000000..615e2d1d95e28 --- /dev/null +++ b/recipes/demuxlet/Makefile.am.new @@ -0,0 +1,28 @@ +## Additional flags to pass to aclocal when it is invoked automatically at +## make time. The ${ACLOCAL_FLAGS} variable is picked up from the environment +## to provide a way for the user to supply additional arguments. +ACLOCAL_AMFLAGS = -I m4 ${ACLOCAL_FLAGS} + +AM_CPPFLAGS = -fopenmp -I ${PREFIX} -I ${PREFIX}/htslib -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -Wl,--no-as-needed -ldl + +noinst_HEADERS = \ + Constant.h pException.h \ + genomeLoci.h \ + bcf_variant_key.h bcf_filter_arg.h + +bin_PROGRAMS = demuxlet + +## vcfast files +demuxlet_SOURCES = \ + Error.cpp PhredHelper.cpp params.cpp \ + hts_utils.cpp bcf_ordered_reader.cpp interval.cpp interval_tree.cpp utils.cpp genome_interval.cpp \ + reference_sequence.cpp \ + bcf_chunked_reader.cpp genomeChunk.cpp \ + sam_filtered_reader.cpp sc_drop_seq.cpp \ + bcf_filtered_reader.cpp \ + filter.cpp \ + tsv_reader.cpp \ + cmd_cram_demuxlet.cpp + +demuxlet_LDADD = ../htslib/libhts.a -ldl -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto -ldeflate +#demuxlet_LDFLAGS = -Wl,--no-as-needed -ldl diff --git a/recipes/demuxlet/Makefile.am.patch b/recipes/demuxlet/Makefile.am.patch new file mode 100644 index 0000000000000..0b0a9f214b09b --- /dev/null +++ b/recipes/demuxlet/Makefile.am.patch @@ -0,0 +1,31 @@ +*** Makefile.am 2018-11-11 08:43:09.000000000 +0300 +--- Makefile.am 2018-11-11 11:35:35.000000000 +0300 +*************** +*** 3,9 **** + ## to provide a way for the user to supply additional arguments. + ACLOCAL_AMFLAGS = -I m4 ${ACLOCAL_FLAGS} + +! AM_CPPFLAGS = -fopenmp -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 + + noinst_HEADERS = \ + Constant.h pException.h \ +--- 3,9 ---- + ## to provide a way for the user to supply additional arguments. + ACLOCAL_AMFLAGS = -I m4 ${ACLOCAL_FLAGS} + +! AM_CPPFLAGS = -fopenmp -I ${PREFIX} -I ${PREFIX}/htslib -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -Wl,--no-as-needed -ldl + + noinst_HEADERS = \ + Constant.h pException.h \ +*************** demuxlet_SOURCES = \ +*** 24,27 **** + tsv_reader.cpp \ + cmd_cram_demuxlet.cpp + +! demuxlet_LDADD = ../htslib/libhts.a -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto +--- 24,28 ---- + tsv_reader.cpp \ + cmd_cram_demuxlet.cpp + +! demuxlet_LDADD = ../htslib/libhts.a -ldl -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto -ldeflate +! #demuxlet_LDFLAGS = -Wl,--no-as-needed -ldl diff --git a/recipes/demuxlet/Makefile.new b/recipes/demuxlet/Makefile.new new file mode 100644 index 0000000000000..e631859e25c2b --- /dev/null +++ b/recipes/demuxlet/Makefile.new @@ -0,0 +1,875 @@ +# Makefile.in generated by automake 1.15.1 from Makefile.am. +# Makefile. 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info-am install install-am install-binPROGRAMS install-data \ + install-data-am install-dvi install-dvi-am install-exec \ + install-exec-am install-html install-html-am install-info \ + install-info-am install-man install-pdf install-pdf-am \ + install-ps install-ps-am install-strip installcheck \ + installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-compile \ + mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \ + tags tags-am uninstall uninstall-am uninstall-binPROGRAMS + +.PRECIOUS: Makefile + + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/recipes/demuxlet/build.sh b/recipes/demuxlet/build.sh new file mode 100644 index 0000000000000..e3074671145b1 --- /dev/null +++ b/recipes/demuxlet/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +set -x -e + +cd htslib +./configure --prefix=$(pwd) --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3 +make +make install + +cd .. + +cd demuxlet +export CFLAGS="${CFLAGS} -I${PREFIX}/include -I ${PREFIX}/include/htslib -ldl -ldeflate -fno-strict-aliasing" +#export LDFLAGS="-ldl" +export CXXFLAGS="${CXXFLAGS} -ldl -ldeflate" +export INCLUDE_PATH="${PREFIX}/include:${PREFIX}/include/htslib" +export LD_LIBRARY_PATH="${PREFIX}/lib" +autoreconf -vfi + +CXXFLAGS="-I${PREFIX}/htslib ${CXXFLAGS}" ./configure --prefix=${PREFIX} +CXXFLAGS="${CXXFLAGS}" PREFIX=${PREFIX} make +make install diff --git a/recipes/demuxlet/meta.yaml b/recipes/demuxlet/meta.yaml new file mode 100644 index 0000000000000..3c84e6292e834 --- /dev/null +++ b/recipes/demuxlet/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "demuxlet" %} +{% set version = "1.0" %} +{% set sha256 = "6ca1427b08461eac292623041d4808c7216e18e5ac0eade0c8245930853b68ff" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 1 + skip: True # [osx] + +source: + - url: https://github.com/statgen/demuxlet/archive/b99026f9298f46d897a23f6e7909e462e1b1fa1b.zip + sha256: {{ sha256 }} + folder: demuxlet + patches: + - Makefile.am.patch + - url: https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 + sha256: e04b877057e8b3b8425d957f057b42f0e8509173621d3eccaedd0da607d9929a + folder: htslib + + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - libtool + - autoconf + - automake + host: + - curl + - bzip2 + - xz + - zlib + - libdeflate + - samtools + - htslib + - zlib + - libtool + run: + - libtool + - samtools + - htslib + - zlib + - curl + - bzip2 + - xz + - zlib + - libdeflate + +test: + commands: + - demuxlet -help 2>&1 | grep 'Detailed' + +about: + home: https://github.com/statgen/demuxlet + license: GPL3 + license_file: demuxlet/LICENSE + summary: Genetic multiplexing of barcoded single cell RNA-seq + dev_url: https://github.com/statgen/demuxlet + doc_url: https://github.com/statgen/demuxlet From 3b9c866ea246c46c753aa7d44443381fa56024f6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 23:57:59 -0700 Subject: [PATCH 256/546] Update r-nodiv to 1.3.0 (#12073) --- recipes/r-nodiv/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/r-nodiv/meta.yaml b/recipes/r-nodiv/meta.yaml index cca6ec2d2434a..2d889266b1126 100644 --- a/recipes/r-nodiv/meta.yaml +++ b/recipes/r-nodiv/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.0' %} +{% set version = '1.3.0' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,12 +11,12 @@ source: url: - {{ cran_mirror }}/src/contrib/nodiv_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/nodiv/nodiv_{{ version }}.tar.gz - sha256: cb5517dcf6fd1b614891ddef0c555dabc0df07419fcc68f982c984660ba6b02d + sha256: 03e8674619d95b7c4175520c57da95078f56cb207a5a8649fab93c7a5dc31dfc build: merge_build_host: True # [win] - number: 2 + number: 0 rpaths: - lib/R/lib/ From 884fbad48582bfce5607c62f28b325c610e8c2ac Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 12 Nov 2018 23:58:13 -0700 Subject: [PATCH 257/546] Update r-rnexml to 2.2.0 (#12072) --- recipes/r-rnexml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-rnexml/meta.yaml b/recipes/r-rnexml/meta.yaml index 2c81456bc27cc..1b3241b0b5148 100644 --- a/recipes/r-rnexml/meta.yaml +++ b/recipes/r-rnexml/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.1.2' %} +{% set version = '2.2.0' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,7 +11,7 @@ source: url: - {{ cran_mirror }}/src/contrib/RNeXML_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/RNeXML/RNeXML_{{ version }}.tar.gz - sha256: 860dcdce074cd120a5d6cc1f253d4a409965f9d5326568310d3013e550ada52b + sha256: 182108109ce35f80eae67c5b5114a566fd56b69be65863e05fdb06b5036b2842 build: merge_build_host: True # [win] From c464fb26b53518eef1e221696d171d7dcb577807 Mon Sep 17 00:00:00 2001 From: Philipp Rescheneder Date: Tue, 13 Nov 2018 07:50:50 +0000 Subject: [PATCH 258/546] Remove skip (#12074) --- recipes/qcat/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/qcat/meta.yaml b/recipes/qcat/meta.yaml index 56d71997b93de..afd7ebe078086 100644 --- a/recipes/qcat/meta.yaml +++ b/recipes/qcat/meta.yaml @@ -7,8 +7,7 @@ source: md5: 9f896c61e55265be5da31a2a6c30fcda build: - noarch_python: True - skip: True # [py27] + noarch: python number: 0 requirements: From bd844919eefa30fd34ae51c4968760e0ce8b4811 Mon Sep 17 00:00:00 2001 From: Laurent Gil Date: Tue, 13 Nov 2018 08:10:54 +0000 Subject: [PATCH 259/546] Remove perl-cgi dependency (not required anymore to run ensembl-vep) (#12059) --- recipes/ensembl-vep/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml index 88544b483519e..0466e32409dbf 100644 --- a/recipes/ensembl-vep/meta.yaml +++ b/recipes/ensembl-vep/meta.yaml @@ -25,7 +25,6 @@ requirements: - htslib - perl-bioperl >=1.7.2 - perl-bio-db-hts >=2.7 - - perl-cgi - perl-dbi - perl-dbd-mysql - perl-io-compress From 577dd81a4ceaa4efb5ab4bfe44c0f3ed4060436f Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Tue, 13 Nov 2018 19:49:21 +0800 Subject: [PATCH 260/546] Update ngless to 0.10.0 (#12075) Trivial update: version and checksum update only --- recipes/ngless/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ngless/meta.yaml b/recipes/ngless/meta.yaml index 7f557726aee4c..cf3526252f625 100644 --- a/recipes/ngless/meta.yaml +++ b/recipes/ngless/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ngless" %} -{% set version = "0.9.1" %} -{% set md5 = "808e091b8b99eac4488a236606e9f19c" %} +{% set version = "0.10.0" %} +{% set md5 = "8cfdf8c1641f1238ecf187d03c0cd335" %} package: name: {{ name }} From 1aadcad6e22ce7184ff3a80c891ed578b259e9dc Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Tue, 13 Nov 2018 15:40:47 +0100 Subject: [PATCH 261/546] Update PureCLIP to v1.2.0 (#12080) --- recipes/pureclip/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pureclip/meta.yaml b/recipes/pureclip/meta.yaml index a61b1365ccca1..ee0d13fd753ba 100644 --- a/recipes/pureclip/meta.yaml +++ b/recipes/pureclip/meta.yaml @@ -1,7 +1,7 @@ {% set name = "PureCLIP" %} -{% set version = "1.1.2" %} -{% set sha256_linux64_static = "b00842db8062f12cd7047948bf684fcfa33ee194ea7edb97dc7a1ffd1c94c2fa" %} -{% set sha256_osx = "d63cdd61b8e0395fc7a9b360ab1e2419c8e939556d8465e4e5bcf78b362d1634" %} +{% set version = "1.2.0" %} +{% set sha256_linux64_static = "d998c6d894bfbf6b2ea6b2127b5ff9a39f6a029727cb33fbc5b793ded8388c75" %} +{% set sha256_osx = "c9a81df2cdd682106f51ce326ce2c08f824f2717cf01ee5fc8fb2ded135e98f2" %} package: name: {{ name | lower }} From fdb6c1919a9fdb104781c96f0d2e14a171355476 Mon Sep 17 00:00:00 2001 From: Ehsan Haghshenas Date: Tue, 13 Nov 2018 23:46:06 -0800 Subject: [PATCH 262/546] Lordfast (#12083) * update lordfast to v0.0.10 --- recipes/lordfast/meta.yaml | 62 +++++++++++++++++++------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/recipes/lordfast/meta.yaml b/recipes/lordfast/meta.yaml index 4201fbd6f3ffb..fbe5a4ec50388 100644 --- a/recipes/lordfast/meta.yaml +++ b/recipes/lordfast/meta.yaml @@ -1,31 +1,31 @@ -{% set version = "0.0.9" %} -{% set sha256 = "dd8b61be6997d25a8a63cb8c3ffb72595f4bdf839f3a945c9409502ac9874f44" %} - -package: - name: lordfast - version: {{ version }} - -source: - url: https://github.com/vpc-ccg/lordfast/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 0 - -requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - host: - - zlib - run: - - zlib -test: - commands: - - lordfast -v - -about: - home: https://github.com/vpc-ccg/lordfast - license: GPL-3.0 - summary: Sensitive and Fast Alignment Search Tool for Long Read sequencing Data - +{% set version = "0.0.10" %} +{% set sha256 = "80cd7640fcb20d18143fd950db7ef05a6395db82c7ca8064e90a27ad00af932f" %} + +package: + name: lordfast + version: {{ version }} + +source: + url: https://github.com/vpc-ccg/lordfast/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib +test: + commands: + - lordfast -v + +about: + home: https://github.com/vpc-ccg/lordfast + license: GPL-3.0 + summary: Sensitive and Fast Alignment Search Tool for Long Read sequencing Data + From d507101ac88aec333cf6474273b1e93922480e5b Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Wed, 14 Nov 2018 11:15:27 +0100 Subject: [PATCH 263/546] Add legacy comet-ms 2016013 (#12085) --- recipes/comet/2016013/build.sh | 17 +++++++++++++++++ recipes/comet/2016013/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 recipes/comet/2016013/build.sh create mode 100644 recipes/comet/2016013/meta.yaml diff --git a/recipes/comet/2016013/build.sh b/recipes/comet/2016013/build.sh new file mode 100644 index 0000000000000..c570c1bba93a7 --- /dev/null +++ b/recipes/comet/2016013/build.sh @@ -0,0 +1,17 @@ +#!/usr/bin/env bash +set -e +set -x + +platform="$(uname)" +if [ "$platform" = "Darwin" ]; then + unzip comet_source_"$PKG_VERSION".zip + sed -i bak -e 's/ -static//' Makefile + make +elif [ "$platform" = "Linux" ]; then + mv comet."$PKG_VERSION".linux.exe comet.exe +fi +chmod 755 comet.exe +mkdir -p "$PREFIX"/bin +cp comet.exe "$PREFIX"/bin/comet +cd "$PREFIX"/bin/ +ln -s comet comet.exe diff --git a/recipes/comet/2016013/meta.yaml b/recipes/comet/2016013/meta.yaml new file mode 100644 index 0000000000000..59b7159b1be70 --- /dev/null +++ b/recipes/comet/2016013/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "comet-ms" %} +{% set version = "2016013" %} +{% set sha256_src_bin_bundle = "c16bfaf49ed8d22b39ffdeebc68cd111e197d4218e4ba9fed906f797e0845f9b" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://sourceforge.net/projects/{{ name }}/files/comet_{{ version }}.zip + sha256: {{ sha256_src_bin_bundle }} + +build: + number: 1 + +requirements: + build: + - {{ compiler('cxx') }} + +test: + commands: + - comet.exe -p && rm comet.params.new + - comet -p && rm comet.params.new + +about: + home: http://comet-ms.sourceforge.net/ + license: Apache License 2.0 + summary: 'Comet is a command line tool that does MS/MS database search.' + +extra: + identifiers: + - doi:10.1007/s13361-015-1179-x + - doi:10.1002/pmic.201200439 From 0ce7acadbbc31e464c141e40b1402bcc32a77d45 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 14 Nov 2018 14:02:57 +0100 Subject: [PATCH 264/546] add eden (#11824) * added eden 1.1 version used in blockclust * Update meta.yaml * eden checksum and test * added zlib requirement * add include and lib paths to build.sh * add include and lib paths to build.sh * modify makefile flags using sed * modify makefile flags using sed * use c++ * Update build.sh * Update build.sh * LDFLAGS not used in makefile * add eden * remove CXX * add more flags * Update build.sh * Update meta.yaml * Create conda_build_config.yaml * add LD_LIBRARY_PATH * Update build.sh * Update build.sh * Delete conda_build_config.yaml * removed -static * Update meta.yaml --- recipes/eden/1.1/build.sh | 16 ++++++++++++++++ recipes/eden/1.1/meta.yaml | 27 +++++++++++++++++++++++++++ recipes/eden/v1.1/build.sh | 6 ++++++ recipes/eden/v1.1/meta.yaml | 25 +++++++++++++++++++++++++ 4 files changed, 74 insertions(+) create mode 100644 recipes/eden/1.1/build.sh create mode 100644 recipes/eden/1.1/meta.yaml create mode 100644 recipes/eden/v1.1/build.sh create mode 100644 recipes/eden/v1.1/meta.yaml diff --git a/recipes/eden/1.1/build.sh b/recipes/eden/1.1/build.sh new file mode 100644 index 0000000000000..fb1e9c0684aa7 --- /dev/null +++ b/recipes/eden/1.1/build.sh @@ -0,0 +1,16 @@ +#!/bin/sh +export LD_LIBRARY_PATH="$PREFIX/lib:$LD_LIBRARY_PATH" +export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" +export CPPFLAGS="$CPPFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export LIBRARY_PATH="${PREFIX}/lib:$LIBRARY_PATH" + +export OBABEL="${LDFLAGS}" + +sed -i.bak "s/CXXFLAGS=/CXXFLAGS+=/" Makefile +sed -i.bak "s|-c EDeN.cc|$CPPFLAGS -c EDeN.cc|" Makefile +sed -i.bak "s/CXX=g++\|-static//g" Makefile +cat Makefile +make +mkdir -p ${PREFIX}/bin +cp EDeN ${PREFIX}/bin diff --git a/recipes/eden/1.1/meta.yaml b/recipes/eden/1.1/meta.yaml new file mode 100644 index 0000000000000..b020e5c5624f5 --- /dev/null +++ b/recipes/eden/1.1/meta.yaml @@ -0,0 +1,27 @@ +package: + name: eden + version: 1.1 + +source: + url: https://github.com/bgruening/download_store/raw/master/EDeN/EDeN-1.1.0.tar.gz + sha256: 6709b7dac2dc90f6d914fda33ecc807390a136306e04c63b0ae6f764081db050 + +build: + number: 0 + skip: True # [osx] + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - zlib + +test: + commands: + - EDeN -h 2>&1 | grep "OPTIONS" >/dev/null + +about: + home: http://dtai.cs.kuleuven.be/ml/systems/nspdk + license: GNUv3 + summary: Explicit Decomposition with Neighborhoods diff --git a/recipes/eden/v1.1/build.sh b/recipes/eden/v1.1/build.sh new file mode 100644 index 0000000000000..c7784a4f43501 --- /dev/null +++ b/recipes/eden/v1.1/build.sh @@ -0,0 +1,6 @@ +#!/bin/sh +export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" +sed -i "s|-c EDeN.cc|$CFLAGS -c EDeN.cc|" Makefile +make +mkdir -p ${PREFIX}/bin +cp EDeN ${PREFIX}/bin diff --git a/recipes/eden/v1.1/meta.yaml b/recipes/eden/v1.1/meta.yaml new file mode 100644 index 0000000000000..9fddb966e3a10 --- /dev/null +++ b/recipes/eden/v1.1/meta.yaml @@ -0,0 +1,25 @@ +package: + name: eden + version: 1.1 + +source: + url: https://github.com/bgruening/download_store/raw/master/EDeN/EDeN-1.1.0.tar.gz + sha256: 6709b7dac2dc90f6d914fda33ecc807390a136306e04c63b0ae6f764081db050 + +build: + number: 0 + +requirements: + build: + - {{ compiler('cxx') }} + host: + - zlib + +test: + commands: + - EDeN -h 2>&1 | grep "OPTIONS" >/dev/null + +about: + home: http://dtai.cs.kuleuven.be/ml/systems/nspdk + license: GNUv3 + summary: Explicit Decomposition with Neighborhoods From 96b6553b5b4d4ba9790a5756141dedb6b4e14d73 Mon Sep 17 00:00:00 2001 From: Joachim Wolff Date: Wed, 14 Nov 2018 14:08:55 +0100 Subject: [PATCH 265/546] Update to version 5 of HiCMatrix (#12082) --- recipes/hicmatrix/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hicmatrix/meta.yaml b/recipes/hicmatrix/meta.yaml index 037cd550a5e6e..ba7ce0c91fcab 100644 --- a/recipes/hicmatrix/meta.yaml +++ b/recipes/hicmatrix/meta.yaml @@ -1,10 +1,10 @@ package: name: hicmatrix - version: '4' + version: '5' source: - url: https://github.com/deeptools/HiCMatrix/archive/4.tar.gz - sha256: 6bcb5c72d4f3a310acda829b3c5a98573ed69d016f8185297ebd72a4430c2bcc + url: https://github.com/deeptools/HiCMatrix/archive/5.tar.gz + sha256: 27ac7eb9b6c0781d498815af829df7baad73125636f192cb4d5bd9fa0d2beb8d build: number: 0 From 3b869d91b7da72dbe3bf2593ed34a3047f282fdb Mon Sep 17 00:00:00 2001 From: pvanheus Date: Wed, 14 Nov 2018 15:09:25 +0200 Subject: [PATCH 266/546] Recipe for ncbi_taxid / diamond_add_taxonomy (#12064) * Recipe for ncbi_taxid / diamond_add_taxonomy * Shift testing to run_test.sh * Renamed throughout to diamond_add_taxonomy * Remove ncbi_taxid * Remove run_test.sh, switch to extended-base container --- recipes/diamond_add_taxonomy/meta.yaml | 40 ++++++++++++++++++++++++ recipes/diamond_add_taxonomy/run_test.sh | 6 ++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/diamond_add_taxonomy/meta.yaml create mode 100755 recipes/diamond_add_taxonomy/run_test.sh diff --git a/recipes/diamond_add_taxonomy/meta.yaml b/recipes/diamond_add_taxonomy/meta.yaml new file mode 100644 index 0000000000000..aebe6c2ba50d9 --- /dev/null +++ b/recipes/diamond_add_taxonomy/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "diamond_add_taxonomy" %} +{% set version = "0.1.0" %} +{% set sha256 = "1315ea9088ebff2a0ce75390a50a992624ce7d3e8267c2842ada3c4fe61589be" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/pvanheus/{{ name }}/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + skip: True # [py<36] + script: "{{ PYTHON }} -m pip install --no-deps . -vvv" + number: 0 + +requirements: + host: + - python + - pip + run: + - python + - click + - ete3 + +test: + commands: + - diamond_add_taxonomy --help |grep DIAMOND_OUTPUT_FILE >/dev/null 2>&1 + +about: + home: https://github.com/pvanheus/diamond_add_taxonomy + summary: 'Utility to work with NCBI taxonomy database including tool to annotate DIAMOND results with taxonomy lineage' + license: MIT +extra: + container: + # click needs locale + extended-base: True + recipe-maintainers: + - pvanheus diff --git a/recipes/diamond_add_taxonomy/run_test.sh b/recipes/diamond_add_taxonomy/run_test.sh new file mode 100755 index 0000000000000..3d19acc444ff5 --- /dev/null +++ b/recipes/diamond_add_taxonomy/run_test.sh @@ -0,0 +1,6 @@ +#!/bin/sh + +export LC_ALL=en_US.utf-8 +export LANG=en_US.utf-8 + +diamond_add_taxonomy --help |grep DIAMOND_OUTPUT_FILE >/dev/null 2>&1 From 9a49a533ea8ca66595cc4ad178c363bd4257b048 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 14 Nov 2018 14:38:01 +0100 Subject: [PATCH 267/546] remove eden v1.1 --- recipes/eden/v1.1/build.sh | 6 ------ recipes/eden/v1.1/meta.yaml | 25 ------------------------- 2 files changed, 31 deletions(-) delete mode 100644 recipes/eden/v1.1/build.sh delete mode 100644 recipes/eden/v1.1/meta.yaml diff --git a/recipes/eden/v1.1/build.sh b/recipes/eden/v1.1/build.sh deleted file mode 100644 index c7784a4f43501..0000000000000 --- a/recipes/eden/v1.1/build.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/sh -export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" -sed -i "s|-c EDeN.cc|$CFLAGS -c EDeN.cc|" Makefile -make -mkdir -p ${PREFIX}/bin -cp EDeN ${PREFIX}/bin diff --git a/recipes/eden/v1.1/meta.yaml b/recipes/eden/v1.1/meta.yaml deleted file mode 100644 index 9fddb966e3a10..0000000000000 --- a/recipes/eden/v1.1/meta.yaml +++ /dev/null @@ -1,25 +0,0 @@ -package: - name: eden - version: 1.1 - -source: - url: https://github.com/bgruening/download_store/raw/master/EDeN/EDeN-1.1.0.tar.gz - sha256: 6709b7dac2dc90f6d914fda33ecc807390a136306e04c63b0ae6f764081db050 - -build: - number: 0 - -requirements: - build: - - {{ compiler('cxx') }} - host: - - zlib - -test: - commands: - - EDeN -h 2>&1 | grep "OPTIONS" >/dev/null - -about: - home: http://dtai.cs.kuleuven.be/ml/systems/nspdk - license: GNUv3 - summary: Explicit Decomposition with Neighborhoods From f1a797648977a57691b9e9c6719472806bef7037 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Wed, 14 Nov 2018 19:42:01 +0100 Subject: [PATCH 268/546] python-tripal: 3.1 release (#12088) * 3.1 release * 3.1.1 * reset build number --- recipes/python-tripal/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/python-tripal/meta.yaml b/recipes/python-tripal/meta.yaml index 2b2c199280deb..45d469afda526 100644 --- a/recipes/python-tripal/meta.yaml +++ b/recipes/python-tripal/meta.yaml @@ -1,14 +1,14 @@ package: name: python-tripal - version: "3.0" + version: "3.1.1" source: - url: https://files.pythonhosted.org/packages/d9/c9/99cec61435f81812501b8598dbf18f76ba410b8c27f4b63a2e27b84dc235/tripal-3.0.tar.gz - sha256: 0f6002457d264b9ae42864e17e816dc41127573c0503709ee9dbf425d1a9ac10 + url: https://files.pythonhosted.org/packages/eb/f2/0040bb7056a1fbb7b5a6f4bf3300a6b582fab16b815dec8e0f46eb087557/tripal-3.1.1.tar.gz + sha256: 83f303d895bbe0d69ef2daaf3308a13578ca56871c2bc054ff82999f1ddaa932 build: noarch: python - number: 1 + number: 0 requirements: host: @@ -18,7 +18,6 @@ requirements: - wrapt - click - pyyaml - run: - python - requests >=2.4.3 From 20356ed298b74ee91e03ba703ff95f7668ff6636 Mon Sep 17 00:00:00 2001 From: Aaron Petkau Date: Wed, 14 Nov 2018 14:31:22 -0600 Subject: [PATCH 269/546] Update staramr to 0.3.0 (#12089) --- recipes/staramr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/staramr/meta.yaml b/recipes/staramr/meta.yaml index 5d7551047c6cd..9ba4f5220be2c 100644 --- a/recipes/staramr/meta.yaml +++ b/recipes/staramr/meta.yaml @@ -1,8 +1,8 @@ {% set name = "staramr" %} -{% set version = "0.2.2" %} +{% set version = "0.3.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "27f8e5da33342429dd3e0dccba4ab6198a1df2787f5570298615ec661bb68428" %} +{% set hash_value = "ab9b5acbed55f0cff57ee67e5288981c2002f6befd808a7ed65f4f3d98c97ca0" %} package: name: '{{ name|lower }}' From dfb14ef5efa30a411f84dd92b151695e4aef11c7 Mon Sep 17 00:00:00 2001 From: Tara Furstenau Date: Wed, 14 Nov 2018 13:50:20 -0700 Subject: [PATCH 270/546] add new recipe for wgfast (#11767) * add wgfast recipe --- recipes/wgfast/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/wgfast/meta.yaml diff --git a/recipes/wgfast/meta.yaml b/recipes/wgfast/meta.yaml new file mode 100644 index 0000000000000..ed7e56aa08896 --- /dev/null +++ b/recipes/wgfast/meta.yaml @@ -0,0 +1,47 @@ +{% set version="1.0.3" %} +{% set sha256="43d7b0d593a484bec4a5ebbc77dcf8ffd645ee11fd79b778dcdd02b20dd576c1" %} +package: + name: 'wgfast' + version: {{ version }} + +source: + url: https://github.com/FofanovLab/wgfast/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: true # [osx] + script: "{{ PYTHON }} -m pip install . -v" + entry_points: + - wgfast = wgfast.main:main + - wgfast_prep = wgfast.wgfast_prep:main + +requirements: + build: + - python==3.6.0 + host: + - python==3.6.0 + - pip + run: + - python==3.6.0 + - biopython + - dendropy # -c bioconda + - samtools # -c bioconda + - bwa==0.7.8 + - bbmap # -c bioconda + - raxml # -c bioconda + - picard # bioconda + +test: + commands: + - wgfast --help + - wgfast_prep --help + +about: + home: https://github.com/jasonsahl/wgfast + summary: 'The whole genome focused array SNP typing (WG-FAST) pipeline' + license: 'GPL v3' + license_file: LICENSE + license_family: 'GPL' + + From 9ee7e65d3e842aadca7be7fc2d9ace8a764a0b6e Mon Sep 17 00:00:00 2001 From: Hugo Varet Date: Thu, 15 Nov 2018 11:37:35 +0100 Subject: [PATCH 271/546] rm_sartools_blacklist (#12092) --- build-fail-blacklist | 1 - recipes/r-sartools/meta.yaml | 5 +++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index b01b60c035c27..ed1007a4effb9 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -784,7 +784,6 @@ recipes/r-quorts recipes/r-raceid3 recipes/r-rBLAST recipes/r-rubic -recipes/r-sartools recipes/r-scimpute recipes/r-seurat-scripts recipes/r-sleuth diff --git a/recipes/r-sartools/meta.yaml b/recipes/r-sartools/meta.yaml index fe2d93e920c64..6dfe2d8ec97ce 100644 --- a/recipes/r-sartools/meta.yaml +++ b/recipes/r-sartools/meta.yaml @@ -20,7 +20,7 @@ requirements: - r-base - r-knitr - bioconductor-deseq2 - - bioconductobioconductor-edger + - bioconductor-edger - r-rmarkdown - r-bit64 - r-blob @@ -29,7 +29,7 @@ requirements: - r-base >=3.3.0 - r-knitr - bioconductor-deseq2 >=1.12.0 - - bioconductobioconductor-edger >=3.12.0 + - bioconductor-edger >=3.12.0 - r-rmarkdown >=1.4 - r-bit64 - r-blob @@ -55,3 +55,4 @@ extra: - bgruening - daler - jdblischak + - hvaret From 39541672242d17df3a443b2b90c7c6424c734e15 Mon Sep 17 00:00:00 2001 From: Simon van Heeringen Date: Thu, 15 Nov 2018 14:06:38 +0100 Subject: [PATCH 272/546] bump build of genomepy (#12093) * bump build * test locale --- recipes/genomepy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genomepy/meta.yaml b/recipes/genomepy/meta.yaml index 2274213df5803..e83ec5e7cb6fb 100644 --- a/recipes/genomepy/meta.yaml +++ b/recipes/genomepy/meta.yaml @@ -9,7 +9,7 @@ source: sha256: e4624898ce7eb012af19cae3dc074bdc75e23cfcc966e5b9397caaeb51b72dbc build: - number: 1 + number: 2 requirements: host: @@ -47,7 +47,7 @@ test: - genomepy commands: - - LC_ALL=en_US.utf8 genomepy -h || LC_ALL=en_US.UTF-8 genomepy -h + - genomepy -h extra: container: From 2b4e99438e09a27058b664f3477857f84dc0e725 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 15 Nov 2018 06:46:48 -0700 Subject: [PATCH 273/546] Update perl-xml-semanticdiff to 1.0007 (#12030) * Update perl-xml-semanticdiff to 1.0007 * Update meta.yaml --- recipes/perl-xml-semanticdiff/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/perl-xml-semanticdiff/meta.yaml b/recipes/perl-xml-semanticdiff/meta.yaml index 636b5d3272e18..cdc4a0defe45a 100644 --- a/recipes/perl-xml-semanticdiff/meta.yaml +++ b/recipes/perl-xml-semanticdiff/meta.yaml @@ -1,29 +1,33 @@ package: name: perl-xml-semanticdiff - version: "1.0004" + version: "1.0007" source: - url: http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/XML-SemanticDiff-1.0004.tar.gz - md5: 0d13434cbc3eb2721b45c942ddb05d97 + url: https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-SemanticDiff-1.0007.tar.gz + sha256: 05fdefefbbc3f6b62fc7c9b5fabafb6b695ed68f0a3d958577251d1f0402a0f5 build: - number: 2 + number: 0 requirements: host: - perl - - perl-module-build + - perl-digest-md5 - perl-xml-parser + - perl-test + - perl-encode + - perl-module-build run: - perl + - perl-digest-md5 + - perl-encode - perl-xml-parser test: # Perl 'use' tests imports: - XML::SemanticDiff - - XML::SemanticDiff::BasicHandler about: home: http://metacpan.org/pod/XML-SemanticDiff From d50bef95d103a3607ff6d8f5c8fef09f30d42429 Mon Sep 17 00:00:00 2001 From: Alexander Junge Date: Thu, 15 Nov 2018 14:59:21 +0100 Subject: [PATCH 274/546] Add CoCoScore v0.2.0 (#12094) --- recipes/cocoscore/meta.yaml | 44 +++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/cocoscore/meta.yaml diff --git a/recipes/cocoscore/meta.yaml b/recipes/cocoscore/meta.yaml new file mode 100644 index 0000000000000..a7512cd05e048 --- /dev/null +++ b/recipes/cocoscore/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "cocoscore" %} +{% set version = "0.2.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: be0a0ae38edd4f3b51e1e9ac1a697facf0dcb8ede4389bdd578a7bcefe3188b9 + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + skip: True # [py27 or py34] + +requirements: + host: + - fasttext ==0.1.0 + - gensim >=3.4.0 + - pandas >=0.23.0 + - pip + - python + - scikit-learn >=0.19.1 + run: + - fasttext ==0.1.0 + - gensim >=3.4.0 + - pandas >=0.23.0 + - python + - scikit-learn >=0.19.1 + +test: + imports: + - cocoscore + - cocoscore.ml + - cocoscore.ml.feature + - cocoscore.tagger + - cocoscore.tools + +about: + home: https://github.com/JungeAlexander/cocoscore + license: MIT + license_family: MIT + summary: 'CoCoScore: context-aware co-occurrence scores for biomedical text mining applications' From a8bdc571aa314089f8d8710d6277035e07a4e32a Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Thu, 15 Nov 2018 18:12:11 +0100 Subject: [PATCH 275/546] Genenotebook v0.1.8 (#12095) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 --- recipes/genenotebook/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index d4bc0b71b5c55..b4c355bf72503 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.7' %} -{% set sha256 = 'a9b0a987c25a18d1d009a9fbd58833843c2780418165db3f613cca09cb002364' %} +{% set version = '0.1.8' %} +{% set sha256 = '953fa9fbf7b6d0e3e7a16a565f17ac5953ed119b212fb5cd8bcc72b3829ac33f' %} package: name: {{ name|lower }} From c63f0f6e4beaf5bbad61d56c59fdce5676e87128 Mon Sep 17 00:00:00 2001 From: Mikhail Kolmogorov Date: Thu, 15 Nov 2018 11:53:25 -0800 Subject: [PATCH 276/546] flye-2.3.7 (#12099) --- recipes/flye/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml index a7209d2fe888b..eab47337fc0fc 100644 --- a/recipes/flye/meta.yaml +++ b/recipes/flye/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.6" %} +{% set version = "2.3.7" %} package: name: flye @@ -6,10 +6,10 @@ package: source: url: https://github.com/fenderglass/Flye/archive/{{ version }}.tar.gz - sha256: 0793cb8963743b3ce84f701e1a63a08b7bbb5fb9342f19b2eefad92ceee546f2 + sha256: e18707c6f029c9c863e93559bdc970892a1f9fd30ae6f74a96f7b68e9a9fae52 build: - number: 3 + number: 0 skip: True # [not py27] requirements: From 3cea9de5a15b856dba0f9d22b8b1b041cfe6c761 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 15 Nov 2018 14:50:22 -0700 Subject: [PATCH 277/546] Update perl-file-slurp to 9999.24 (#12008) --- recipes/perl-file-slurp/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-file-slurp/meta.yaml b/recipes/perl-file-slurp/meta.yaml index 883d099d44f94..7c05ed347563f 100644 --- a/recipes/perl-file-slurp/meta.yaml +++ b/recipes/perl-file-slurp/meta.yaml @@ -1,17 +1,17 @@ {% set name = "perl-file-slurp" %} -{% set version = "9999.19" %} -{% set sha256 = "ce29ebe995097ebd6e9bc03284714cdfa0c46dc94f6b14a56980747ea3253643" %} +{% set version = "9999.24" %} +{% set sha256 = "fd480c3d474f477580940b26e0bce900ca5cb92c143c3bb3549882c1d7f823cf" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/U/UR/URI/File-Slurp-9999.19.tar.gz + url: https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB/File-Slurp-9999.24.tar.gz sha256: {{ sha256 }} build: - number: 3 + number: 0 requirements: host: From a7b797fb9ca3033ea82871929e7af149f44a5732 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 15 Nov 2018 15:04:22 -0700 Subject: [PATCH 278/546] Update perl-io-all to 0.87 (#11985) * Update perl-io-all to 0.87 * Adding tests --- recipes/perl-io-all/meta.yaml | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/recipes/perl-io-all/meta.yaml b/recipes/perl-io-all/meta.yaml index e0ba653c21b45..9c116be710428 100644 --- a/recipes/perl-io-all/meta.yaml +++ b/recipes/perl-io-all/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-io-all - version: "0.86" + version: "0.87" source: - url: http://search.cpan.org/CPAN/authors/id/I/IN/INGY/IO-All-0.86.tar.gz - md5: b257d3f742867825d018e74f5a5d549b + url: https://cpan.metacpan.org/authors/id/F/FR/FREW/IO-All-0.87.tar.gz + sha256: 54e21d250c0229127e30b77a3461e10077854ec244f26fb670f1b445ed4c4d5b build: - number: 1 + number: 0 requirements: host: @@ -18,9 +18,24 @@ requirements: run: - perl - perl-scalar-list-utils - - perl-extutils-makemaker -# no tests so far + +test: + # Perl 'use' tests + imports: + - IO::All + - IO::All::Base + - IO::All::DBM + - IO::All::Dir + - IO::All::File + - IO::All::Filesys + - IO::All::Link + - IO::All::MLDBM + - IO::All::Pipe + - IO::All::STDIO + - IO::All::Socket + - IO::All::String + - IO::All::Temp about: home: https://github.com/ingydotnet/io-all-pm From 86cb77629bc7af2c160f125949eb497957e311bb Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 15 Nov 2018 15:17:24 -0700 Subject: [PATCH 279/546] Update meta-sparse to 0.1.11 (#11995) * Update meta-sparse to 0.1.11 * remove fn --- recipes/meta-sparse/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/meta-sparse/meta.yaml b/recipes/meta-sparse/meta.yaml index a153b27d38d14..846f2d8632313 100644 --- a/recipes/meta-sparse/meta.yaml +++ b/recipes/meta-sparse/meta.yaml @@ -1,14 +1,13 @@ package: name: meta-sparse - version: "0.1.2" + version: "0.1.11" source: - fn: meta-sparse-0.1.2.tar.gz - url: https://files.pythonhosted.org/packages/dc/40/fa1652a2470889411c51cd295228434d55db14704e8d0f46bb661830822b/meta-sparse-0.1.2.tar.gz - md5: 45d5318465363740ae0873265b4b4056 + url: https://files.pythonhosted.org/packages/81/fd/ed7a13bb0ce85adab65eece9741bc377b527dca5f5ce033e69d1eabbda5d/meta-sparse-0.1.11.tar.gz + sha256: 120ea1c261ca740fd7383502f293d7b449f666f791d2029c54a4da9e2f7f4da1 build: - number: 2 + number: 0 skip: True # [not py27] entry_points: - sparse = SPARSE.SPARSE:SPARSE From fb7c910f4737b30ab3d54e84544cecca249ab8e6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 15 Nov 2018 22:53:32 -0700 Subject: [PATCH 280/546] Update perl-params-validate to 1.29 (#11971) * Update perl-params-validate to 1.29 * Update perl-params-validate to 1.29 * Update meta.yaml --- recipes/perl-params-validate/meta.yaml | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/recipes/perl-params-validate/meta.yaml b/recipes/perl-params-validate/meta.yaml index 5b9d4c91f418d..08784dfa625d8 100644 --- a/recipes/perl-params-validate/meta.yaml +++ b/recipes/perl-params-validate/meta.yaml @@ -1,28 +1,37 @@ package: name: perl-params-validate - version: 1.08 + version: 1.29 source: - url: http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Params-Validate-1.08.tar.gz - md5: 5edfb0ffd92cbb0e2646ddf23d4516e9 + url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/Params-Validate-1.29.tar.gz + sha256: 49a68dfb430bea028042479111d19068e08095e5a467e320b7ab7bde3d729733 build: - number: 2 + number: 0 requirements: build: - {{ compiler('c') }} host: - perl - - perl-module-build - - perl-scalar-list-utils - - perl-module-implementation + - perl-extutils-makemaker + - perl-file-temp + - perl-lib + - perl-base - perl-test-fatal + - perl-module-implementation + - perl-module-build + - perl-carp + - perl-test-requires + - perl-exporter + - perl-xsloader run: - perl + - perl-exporter - perl-module-implementation - - perl-scalar-list-utils + - perl-xsloader + - perl-carp test: imports: From 681a9abadd951a642e4d394883f93b897618787e Mon Sep 17 00:00:00 2001 From: Petter Uvesten Date: Fri, 16 Nov 2018 08:00:28 +0100 Subject: [PATCH 281/546] Add humann2 v. 0.11.2 recipe (#12096) * Add humann2 v. 0.11.2 recipe * Set build number to 0 * Move most recent recipe to root --- recipes/humann2/build.sh | 5 +++ recipes/humann2/meta.yaml | 84 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 recipes/humann2/build.sh create mode 100644 recipes/humann2/meta.yaml diff --git a/recipes/humann2/build.sh b/recipes/humann2/build.sh new file mode 100644 index 0000000000000..7da76de21b8d3 --- /dev/null +++ b/recipes/humann2/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +$PYTHON setup.py install \ + --bypass-dependencies-install \ + --single-version-externally-managed --record=record.txt diff --git a/recipes/humann2/meta.yaml b/recipes/humann2/meta.yaml new file mode 100644 index 0000000000000..dbf4df78b9b06 --- /dev/null +++ b/recipes/humann2/meta.yaml @@ -0,0 +1,84 @@ +package: + name: humann2 + version: "0.11.2" + +build: + number: 0 + skip: True # [not py27 and not py34] + entry_points: + - humann2 = humann2.humann2:main + - humann2_databases = humann2.tools.humann2_databases:main + - humann2_config = humann2.tools.humann2_config:main + - humann2_join_tables = humann2.tools.join_tables:main + - humann2_split_table = humann2.tools.split_table:main + - humann2_rename_table = humann2.tools.rename_table:main + - humann2_renorm_table = humann2.tools.renorm_table:main + - humann2_regroup_table = humann2.tools.regroup_table:main + - humann2_infer_taxonomy = humann2.tools.infer_taxonomy:main + - humann2_humann1_kegg = humann2.tools.humann2_humann1_kegg:main + - humann2_rna_dna_norm = humann2.tools.rna_dna_norm:main + - humann2_strain_profiler = humann2.tools.strain_profiler:main + - humann2_reduce_table = humann2.tools.reduce_table:main + - humann2_unpack_pathways = humann2.tools.merge_abundance:main + - humann2_test = humann2.tests.humann2_test:main + - humann2_build_custom_database = humann2.tools.build_custom_database:main + - humann2_genefamilies_genus_level = humann2.tools.genefamilies_genus_level:main + - humann2_split_stratified_table = humann2.tools.split_stratified_table:main + - humann2_associate = humann2.tools.humann2_associate:main + - humann2_barplot = humann2.tools.humann2_barplot:main + - humann2_benchmark = humann2.tools.humann2_benchmark:main + +source: + url: https://files.pythonhosted.org/packages/f2/c6/01ef12082fa44f06c5329bacb49c6dbeb4a04c66a60b0f64e4a9f1fb824a/humann2-0.11.2.tar.gz + sha256: e38dd7e04705f15b00159b68f4b2e9645806f83d39127e33ca08c236d4a4f86b + +requirements: + host: + - python + - setuptools + run: + - python + - bowtie2 >=2.2.5 + - metaphlan2 >=2.6.0 + - diamond >=0.7.10,<0.9.0 + - samtools + - biom-format + - matplotlib + - scipy + - numpy + +test: + imports: + - humann2 + - humann2.quantify + - humann2.search + - humann2.tests + - humann2.tools + commands: + - humann2 --help + - humann2_databases --help + - humann2_config --help + - humann2_join_tables --help + - humann2_split_table --help + - humann2_rename_table --help + - humann2_renorm_table --help + - humann2_regroup_table --help + - humann2_infer_taxonomy --help 2>&1 | grep "HUMAnN2" + - humann2_humann1_kegg --help + - humann2_rna_dna_norm --help + - humann2_strain_profiler --help + - humann2_reduce_table --help + - humann2_unpack_pathways --help + - humann2_test --help + - humann2_build_custom_database --help + - humann2_genefamilies_genus_level --help + - humann2_split_stratified_table --help + - humann2_associate --help + - humann2_barplot --help + - humann2_benchmark --help + +about: + home: http://huttenhower.sph.harvard.edu/humann2 + license: MIT + summary: 'HUMAnN2: The HMP Unified Metabolic Analysis Network 2' + license_family: MIT From f9e98772525719d0d8194b09b27d5458317ea9a2 Mon Sep 17 00:00:00 2001 From: bensellak Date: Fri, 16 Nov 2018 11:05:44 +0000 Subject: [PATCH 282/546] r-classdiscovery (#12105) * r-oompabase * r-classdiscovery * Remove oompabase * Fixed Dependency Biobase --- recipes/r-classdiscovery/build.sh | 38 +++++++++++++ recipes/r-classdiscovery/meta.yaml | 91 ++++++++++++++++++++++++++++++ 2 files changed, 129 insertions(+) create mode 100644 recipes/r-classdiscovery/build.sh create mode 100644 recipes/r-classdiscovery/meta.yaml diff --git a/recipes/r-classdiscovery/build.sh b/recipes/r-classdiscovery/build.sh new file mode 100644 index 0000000000000..d869cbc54c1f7 --- /dev/null +++ b/recipes/r-classdiscovery/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/ClassDiscovery + mv * $PREFIX/lib/R/library/ClassDiscovery + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-classdiscovery/meta.yaml b/recipes/r-classdiscovery/meta.yaml new file mode 100644 index 0000000000000..ff955ae1f1e50 --- /dev/null +++ b/recipes/r-classdiscovery/meta.yaml @@ -0,0 +1,91 @@ +{% set version = '3.3.9' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-classdiscovery + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/ClassDiscovery_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ClassDiscovery/ClassDiscovery_{{ version }}.tar.gz + sha256: b71c459e0224a71e8342086c71af07f6f87213cd254fb2a8a6e76d328c9e8a43 + +build: + merge_build_host: True # [win] + # If this is a new build for the same version, increment the build number. + number: 0 + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +# Suggests: xtable +requirements: + build: + - {{posix}}zip # [win] + + host: + - r-base + - bioconductor-biobase + - r-cluster + - r-mclust + - r-oompabase >=3.0.1 + - r-oompadata + + run: + - r-base + - bioconductor-biobase + - r-cluster + - r-mclust + - r-oompabase >=3.0.1 + - r-oompadata + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('ClassDiscovery')" # [not win] + - "\"%R%\" -e \"library('ClassDiscovery')\"" # [win] + + # You can also put a file called run_test.py, run_test.sh, or run_test.bat + # in the recipe that will be run at test time. + + # requires: + # Put any additional test requirements here. + +about: + home: http://oompa.r-forge.r-project.org/ + license: Apache (== 2.0) + summary: 'Defines the classes used for "class discovery" problems in the OOMPA project (). + Class discovery primarily consists of unsupervised clustering methods with attempts + to assess their statistical significance. ' + + license_family: APACHE + +# The original CRAN metadata for this package was: + +# Package: ClassDiscovery +# Version: 3.3.9 +# Date: 2018-09-27 +# Title: Classes and Methods for "Class Discovery" with Microarrays or Proteomics +# Author: Kevin R. Coombes +# Maintainer: Kevin R. Coombes +# Depends: R (>= 3.0), cluster, oompaBase (>= 3.0.1) +# Imports: methods, stats, graphics, grDevices, mclust, oompaData, Biobase +# Suggests: xtable +# Description: Defines the classes used for "class discovery" problems in the OOMPA project (). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. +# License: Apache License (== 2.0) +# LazyLoad: yes +# biocViews: Microarray, Clustering +# URL: http://oompa.r-forge.r-project.org/ +# NeedsCompilation: no +# Packaged: 2018-10-03 11:25:11 UTC; Kevin +# Repository: CRAN +# Date/Publication: 2018-10-03 22:02:55 UTC + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml From 52f70f5ab6733e5cf199ac02bd10ed59f3a45df3 Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Fri, 16 Nov 2018 20:11:31 +0800 Subject: [PATCH 283/546] R lncpipereporter (#12102) * ADD lncPipeReporter * update * update --- recipes/r-lncpipereporter/build.sh | 2 + recipes/r-lncpipereporter/meta.yaml | 60 +++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 recipes/r-lncpipereporter/build.sh create mode 100644 recipes/r-lncpipereporter/meta.yaml diff --git a/recipes/r-lncpipereporter/build.sh b/recipes/r-lncpipereporter/build.sh new file mode 100644 index 0000000000000..e3921285a046d --- /dev/null +++ b/recipes/r-lncpipereporter/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +R CMD INSTALL --build . diff --git a/recipes/r-lncpipereporter/meta.yaml b/recipes/r-lncpipereporter/meta.yaml new file mode 100644 index 0000000000000..da98f5148fd39 --- /dev/null +++ b/recipes/r-lncpipereporter/meta.yaml @@ -0,0 +1,60 @@ +package: + name: 'r-lncpipereporter' + version: '0.1.1' +source: + url: + - 'https://github.com/bioinformatist/LncPipeReporter/archive/v0.1.1.tar.gz' + sha256: e7c6fc1865b323cfad0f23bec8ee5ead7692b4a30287cf7fd51c0d44d44e1257 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - {{ compiler('c') }} + host: + - r-base + - r-devtools + - r-ggplot2 + - r-plotly + - r-data.table + - r-ggsci + - r-heatmaply + - r-ggbiplot + - bioconductor-edger + - r-knitr + - r-flexdashboard + - r-dt + - r-cowplot + - r-htmlwidgets + - r-rmarkdown + - bioconductor-noiseq + - bioconductor-deseq2=1.20.0 + run: + - r-base + - r-devtools + - r-ggplot2 + - r-plotly + - r-data.table + - r-ggsci + - r-heatmaply + - r-ggbiplot + - bioconductor-edger + - r-knitr + - r-flexdashboard + - r-dt + - r-cowplot + - r-htmlwidgets + - r-rmarkdown + - bioconductor-noiseq + - bioconductor-deseq2=1.20.0 + +test: + commands: + - '$R -e "library(LncPipeReporter)"' +about: + date: '2017-12-20' + summary: 'Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report' + home: 'https://github.com/bioinformatist/LncPipeReporter' + license: 'GPL-2' From 1240f243e417c1397a684d0c85f0c03caa79fe91 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Fri, 16 Nov 2018 23:06:42 +0800 Subject: [PATCH 284/546] seqkit 0.9.2 (#12110) --- recipes/seqkit/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 83fa55e0c9a37..2dfee145e243c 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.1" %} +{% set version = "0.9.2" %} package: name: seqkit @@ -15,13 +15,13 @@ build: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: 8607754ac2207cbf861da78c9ade6e6b # [osx] + md5: 929ae9ec2fc18eec41da7ef569ee5031 # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_386.tar.gz # [linux] - md5: 65a73a13e408159a3b635f6cf59a40cd # [linux] + md5: b7ffec6f73e206b0ed5a57b7632e73ef # [linux] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux64] - md5: fcc7e59b42f9afa18ade7c331fa9b7c2 # [linux64] + md5: db44546b38add64094f664a23b56b73c # [linux64] test: commands: From 89bb0665f56ddfdab53f39f33a3c71dbf5872372 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 16 Nov 2018 10:29:16 -0500 Subject: [PATCH 285/546] Update fastq-scan to v0.3 (#12109) --- recipes/fastq-scan/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fastq-scan/meta.yaml b/recipes/fastq-scan/meta.yaml index 4047d0bd173c2..71fee3dd07e38 100644 --- a/recipes/fastq-scan/meta.yaml +++ b/recipes/fastq-scan/meta.yaml @@ -1,6 +1,6 @@ {% set name="fastq-scan" %} -{% set version = "0.2" %} -{% set sha256 = "0f5235fe6b358b29c7e9330e5db0ae5f25b01ddf6703426d6d8a529503d920cc" %} +{% set version = "0.3" %} +{% set sha256 = "e63cc9efa157e5dc65173b0fce1c87a8fdbaf7be2f493b6e1fc40d128510d101" %} package: name: {{ name }} From 128fb20c378ae302b7191f536078b17d9fb714aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Fri, 16 Nov 2018 18:34:48 +0200 Subject: [PATCH 286/546] Add perl-clone-choose (#12108) --- recipes/perl-clone-choose/build.sh | 19 ++++++++++++++++ recipes/perl-clone-choose/meta.yaml | 34 +++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 recipes/perl-clone-choose/build.sh create mode 100644 recipes/perl-clone-choose/meta.yaml diff --git a/recipes/perl-clone-choose/build.sh b/recipes/perl-clone-choose/build.sh new file mode 100644 index 0000000000000..67918fe672fe6 --- /dev/null +++ b/recipes/perl-clone-choose/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-clone-choose/meta.yaml b/recipes/perl-clone-choose/meta.yaml new file mode 100644 index 0000000000000..1d65e60d523e2 --- /dev/null +++ b/recipes/perl-clone-choose/meta.yaml @@ -0,0 +1,34 @@ +{% set name = "perl-clone-choose" %} +{% set version = "0.010" %} +{% set sha256 = "5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://cpan.metacpan.org/authors/id/H/HE/HERMES/Clone-Choose-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl + - perl-test-without-module + - perl-extutils-makemaker + - perl-storable + + run: + - perl + - perl-storable + +test: + imports: + - Clone::Choose + +about: + home: https://metacpan.org/release/Clone-Choose + license: perl_5 + summary: 'Choose appropriate clone utility' From f9fca588fd343e9a50f497a7a4bee65a0a7eb6a0 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 13:38:14 -0700 Subject: [PATCH 287/546] Update perl-hash-merge to 0.300 (#11941) * Update perl-hash-merge to 0.300 * Update perl-hash-merge to 0.300 * Update meta.yaml --- recipes/perl-hash-merge/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/perl-hash-merge/meta.yaml b/recipes/perl-hash-merge/meta.yaml index 28e418d6ce704..f00a6182b4d6b 100644 --- a/recipes/perl-hash-merge/meta.yaml +++ b/recipes/perl-hash-merge/meta.yaml @@ -1,24 +1,24 @@ package: name: perl-hash-merge - version: "0.200" + version: "0.300" source: - url: http://cpan.metacpan.org/authors/id/R/RE/REHSACK/Hash-Merge-0.200.tar.gz - md5: 54b5743103fb3b3986a384b5424f21f4 + url: https://cpan.metacpan.org/authors/id/R/RE/REHSACK/Hash-Merge-0.300.tar.gz + sha256: 402fd52191d51415bb7163b7673fb4a108e3156493d7df931b8db4b2af757c40 build: - number: 1 + number: 0 requirements: host: - perl - - perl-clone + - perl-clone-choose - perl-extutils-makemaker - perl-test-simple run: - perl - - perl-clone + - perl-clone-choose test: imports: From 1e7d0199b5e14c6aad62439de8c8858553362ad7 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 13:44:36 -0700 Subject: [PATCH 288/546] Update perl-file-slurper to 0.012 (#11910) * Update perl-file-slurper to 0.012 * Adding dependencies --- recipes/perl-file-slurper/meta.yaml | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/recipes/perl-file-slurper/meta.yaml b/recipes/perl-file-slurper/meta.yaml index d8a027c8a7139..b8e2b58fb342c 100644 --- a/recipes/perl-file-slurper/meta.yaml +++ b/recipes/perl-file-slurper/meta.yaml @@ -1,20 +1,31 @@ package: name: perl-file-slurper - version: "0.008" + version: "0.012" source: - url: https://cpan.metacpan.org/authors/id/L/LE/LEONT/File-Slurper-0.008.tar.gz - md5: 6e4f8ab76e38dc3f3fec6a0f575bf132 + url: https://cpan.metacpan.org/authors/id/L/LE/LEONT/File-Slurper-0.012.tar.gz + sha256: 4efb2ea416b110a1bda6f8133549cc6ea3676402e3caf7529fce0313250aa578 build: - number: 2 + number: 0 requirements: host: - perl + - perl-encode + - perl-extutils-makemaker + - perl-test-warnings + - perl-file-temp + - perl-exporter + - perl-constant + - perl-carp run: - perl + - perl-constant + - perl-encode + - perl-exporter + - perl-carp test: # Perl 'use' tests From a4685384fee3d83fca0572dfb237582d0f91027c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 14:22:06 -0700 Subject: [PATCH 289/546] Update perl-moo to 2.003004 (#11897) * Update perl-moo to 2.003004 * Update meta.yaml --- recipes/perl-moo/meta.yaml | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/recipes/perl-moo/meta.yaml b/recipes/perl-moo/meta.yaml index dedbbcc7c5cef..f7f3a81c6d350 100644 --- a/recipes/perl-moo/meta.yaml +++ b/recipes/perl-moo/meta.yaml @@ -1,29 +1,36 @@ package: name: perl-moo - version: "2.001000" + version: "2.003004" source: - url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Moo-2.001000.tar.gz - md5: 25d1b88c9246ac323a267bf0d32fbfdb + url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Moo-2.003004.tar.gz + sha256: f8bbb625f8e963eabe05cff9048fdd72bdd26777404ff2c40bc690f558be91e1 build: - number: 2 + number: 0 requirements: host: - perl - - perl-class-method-modifiers - - perl-devel-globaldestruction - - perl-module-runtime - perl-role-tiny - - perl-test-fatal + - perl-exporter + - perl-module-runtime + - perl-sub-quote + - perl-test-fatal >=0.003 + - perl-devel-globaldestruction + - perl-class-method-modifiers + - perl-extutils-makemaker + - perl-moose run: - perl - - perl-class-method-modifiers - - perl-devel-globaldestruction - - perl-module-runtime - perl-role-tiny + - perl-exporter + - perl-module-runtime + - perl-sub-quote + - perl-devel-globaldestruction + - perl-class-method-modifiers + - perl-moose test: # Perl 'use' tests From 5ed598bd45b7dc220733e143a06cc397745ab970 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 16 Nov 2018 23:59:53 +0100 Subject: [PATCH 290/546] Add deeptoolsintervals (#12114) * Add deeptoolsintervals * blah * No nose in the mulled container --- recipes/deeptoolsintervals/build.sh | 3 +++ recipes/deeptoolsintervals/meta.yaml | 30 ++++++++++++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 recipes/deeptoolsintervals/build.sh create mode 100644 recipes/deeptoolsintervals/meta.yaml diff --git a/recipes/deeptoolsintervals/build.sh b/recipes/deeptoolsintervals/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/deeptoolsintervals/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml new file mode 100644 index 0000000000000..bbb3d6d9fc274 --- /dev/null +++ b/recipes/deeptoolsintervals/meta.yaml @@ -0,0 +1,30 @@ +{% set name = "deeptoolsintervals" %} +{% set version = "0.1.7" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 4682808360a5b50b69b28ec1f9231dfe9443638d0a262f8a4a1403c30f1592be + +build: + number: 0 + +requirements: + build: + - "{{ compiler('c') }}" + host: + - python + run: + - python + +test: + imports: + - deeptoolsintervals + +about: + home: https://github.com/deeptools/deeptools_intervals + license: GPL3 + summary: A python module creating/accessing GTF-based interval trees with associated meta-data From 4d91d8d560eb58986c0572ef12ef2a53bb02bd18 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Sat, 17 Nov 2018 02:27:21 +0100 Subject: [PATCH 291/546] Fix octopus binary "invalid instruction" (-march too new) (#11822) * This attempts to make the binary more portable by only requiring Sandybridge. * Fix march set to native --- recipes/octopus/fix_march_set_to_native.patch | 12 ++++++++++++ recipes/octopus/meta.yaml | 4 +++- 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 recipes/octopus/fix_march_set_to_native.patch diff --git a/recipes/octopus/fix_march_set_to_native.patch b/recipes/octopus/fix_march_set_to_native.patch new file mode 100644 index 0000000000000..b6ab6a8885dce --- /dev/null +++ b/recipes/octopus/fix_march_set_to_native.patch @@ -0,0 +1,12 @@ +diff -rNu octopus-0.5.2-beta.orig/src/CMakeLists.txt octopus-0.5.2-beta/src/CMakeLists.txt +--- octopus-0.5.2-beta.orig/src/CMakeLists.txt 2018-10-29 08:36:32.000000000 -0600 ++++ octopus-0.5.2-beta/src/CMakeLists.txt 2018-11-13 15:54:06.000000000 -0700 +@@ -639,7 +639,7 @@ + else() + add_executable(octopus main.cpp ${OCTOPUS_SOURCES} ${INCLUDE_SOURCES}) + target_compile_features(octopus PRIVATE cxx_thread_local) +- target_compile_options(octopus PRIVATE -ffast-math -funroll-loops -march=native) ++ target_compile_options(octopus PRIVATE -ffast-math -funroll-loops) + target_include_directories(octopus PUBLIC ${octopus_SOURCE_DIR}/lib ${octopus_SOURCE_DIR}/src) + target_link_libraries(octopus tandem ranger) + if (NOT BUILD_SHARED_LIBS) diff --git a/recipes/octopus/meta.yaml b/recipes/octopus/meta.yaml index 36a6a4f081dd3..50cc2b6b726e7 100644 --- a/recipes/octopus/meta.yaml +++ b/recipes/octopus/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 # Not building on osx CircleCI and unsure how to fix; does not pick # up 7.2 compilers skip: true # [osx] @@ -15,6 +15,8 @@ build: source: url: https://github.com/luntergroup/{{ name }}/archive/v0.5.2-beta.tar.gz sha256: {{ sha256 }} + patches: + - fix_march_set_to_native.patch requirements: build: From ac08d97bff32243c33f4c25b79046308225f09bf Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 18:52:13 -0700 Subject: [PATCH 292/546] Update perl-bio-asn1-entrezgene to 1.73 (#11914) * Update perl-bio-asn1-entrezgene to 1.73 * Update perl-bio-asn1-entrezgene to 1.73 * Update meta.yaml --- recipes/perl-bio-asn1-entrezgene/meta.yaml | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/recipes/perl-bio-asn1-entrezgene/meta.yaml b/recipes/perl-bio-asn1-entrezgene/meta.yaml index d5c95fb58cdd7..79ca2ab72fa76 100644 --- a/recipes/perl-bio-asn1-entrezgene/meta.yaml +++ b/recipes/perl-bio-asn1-entrezgene/meta.yaml @@ -1,22 +1,34 @@ package: name: perl-bio-asn1-entrezgene - version: 1.72 + version: 1.73 source: - url: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/Bio-ASN1-EntrezGene-1.72.tar.gz - md5: ea51d9d1774e0873e702909bf7ccf0cb + url: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/Bio-ASN1-EntrezGene-1.73.tar.gz + sha256: f9e778db705ce5c35ad2798e38a8490b644edfdc14253aa1b74a1f5e79fc6a4b build: - number: 2 + number: 0 requirements: host: - perl + - perl-parent + - perl-base + - perl-data-dumper + - perl-extutils-makemaker + - perl-lib + - perl-carp - perl-bioperl-core + - perl-test-most run: - perl + - perl-parent + - perl-base + - perl-data-dumper + - perl-carp - perl-bioperl-core + - perl-test-most test: imports: From a15d051c4a5a683a25e8b64262c610341eceee3d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 22:57:26 -0700 Subject: [PATCH 293/546] Update perl-file-slurp to 9999.25 (#12127) --- recipes/perl-file-slurp/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-file-slurp/meta.yaml b/recipes/perl-file-slurp/meta.yaml index 7c05ed347563f..5d6982f0bb436 100644 --- a/recipes/perl-file-slurp/meta.yaml +++ b/recipes/perl-file-slurp/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-file-slurp" %} -{% set version = "9999.24" %} -{% set sha256 = "fd480c3d474f477580940b26e0bce900ca5cb92c143c3bb3549882c1d7f823cf" %} +{% set version = "9999.25" %} +{% set sha256 = "c7ea97bae61bc68404476ce69277f6f796d31ab58c9c40ee390d9d5a1c5ce3c1" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB/File-Slurp-9999.24.tar.gz + url: https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB/File-Slurp-9999.25.tar.gz sha256: {{ sha256 }} build: From fda11a3ab0e5b4ad750e04de22f4f0fcb4c830e2 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 22:58:34 -0700 Subject: [PATCH 294/546] Update manta to 1.5.0 (#12126) --- recipes/manta/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/manta/meta.yaml b/recipes/manta/meta.yaml index e659051dc136b..70ffbd4261d8b 100644 --- a/recipes/manta/meta.yaml +++ b/recipes/manta/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "1.4.0" %} +{% set version = "1.5.0" %} package: name: manta version: '{{ version }}' source: url: https://github.com/Illumina/manta/releases/download/v{{ version }}/manta-{{ version }}.centos6_x86_64.tar.bz2 - md5: 50a4c1a7abf6b50459940a9be0a7ace0 + sha256: 2e4200d80dde9b4c7e24fb6ee73c50c99d20528709da5726efdba69d63a05a0f build: - number: 1 + number: 0 skip: True # [not py27 or osx] requirements: host: From c7029cda0775a60f7d6bce75717b5fc60d06eea3 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:00:14 -0700 Subject: [PATCH 295/546] Update nanocomp to 1.0.0 (#12124) --- recipes/nanocomp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanocomp/meta.yaml b/recipes/nanocomp/meta.yaml index 23340b010b70c..d8322d17376ea 100644 --- a/recipes/nanocomp/meta.yaml +++ b/recipes/nanocomp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.23.1" %} +{% set version = "1.0.0" %} package: name: nanocomp @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanocomp/NanoComp-{{ version }}.tar.gz - sha256: f221bd2e693711d94e761b49099f5d349d3ecf1118287eb7f9178522f5a70f10 + sha256: 1d20f5b0d944da84fa32a94a65193b7cd2502bf915b25f61b9680be0ffde54cd build: entry_points: From ee4beb56711cc301af8d77b6d42f9f07364aff62 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:00:36 -0700 Subject: [PATCH 296/546] Update masurca to 3.2.9 (#12121) --- recipes/masurca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index b69b9bad8ed48..97d1ae58f96cc 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "masurca" %} -{% set version = "3.2.8" %} +{% set version = "3.2.9" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/alekseyzimin/masurca/releases/download/{{ version }}/MaSuRCA-{{ version }}.tar.gz - sha256: b9ab27803d2a0bd8426b5c2e949874e9bc31c9cca8f7f0c8b487664d04cd0fe8 + sha256: 461b4d67d2b2cf30c6e020d9a4a63837f13d2994206d5541bba461beb72fd79a build: number: 0 From 27aab18452c4cb42a70a021afeeedd1af6ea53c8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:32:03 -0700 Subject: [PATCH 297/546] Update beagle-lib to 3.1.1 (#12119) --- recipes/beagle-lib/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/beagle-lib/meta.yaml b/recipes/beagle-lib/meta.yaml index f8f7543abb91f..83cd71d527631 100644 --- a/recipes/beagle-lib/meta.yaml +++ b/recipes/beagle-lib/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "3.1.0" %} -{% set sha256 = "f680bdace45dffbb175688aa8bf679710e4e60d000bbf332860de757d4e1c411" %} +{% set version = "3.1.1" %} +{% set sha256 = "3ddb7f39863389816f6289f5da2fe921d0d4efe85dcf349fae3a2718cc14f0fb" %} package: name: beagle-lib version: '{{version}}' source: - url: https://github.com/beagle-dev/beagle-lib/archive/v3.1.0.tar.gz + url: https://github.com/beagle-dev/beagle-lib/archive/v3.1.1.tar.gz sha256: '{{sha256}}' #patches: # [osx] # - osx_jni.patch # [osx] From d958dae81cb6cbf0eda3b1eb798b3132f030d3e8 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:32:15 -0700 Subject: [PATCH 298/546] Update r-spocc to 0.9.0 (#12118) --- recipes/r-spocc/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/r-spocc/meta.yaml b/recipes/r-spocc/meta.yaml index 3f383680a45ac..25cef2935a288 100644 --- a/recipes/r-spocc/meta.yaml +++ b/recipes/r-spocc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.8.0' %} +{% set version = '0.9.0' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,12 +11,12 @@ source: url: - {{ cran_mirror }}/src/contrib/spocc_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/spocc/spocc_{{ version }}.tar.gz - sha256: 7c0d1fca1ff3b5281bdbf34e90dd3611646dcc559176370f41aab2cfa71b9503 + sha256: 5e1f4defa7b537d91c59f989537ed7b7e9d5afa439a64e247044d61c1f6af1ab build: merge_build_host: True # [win] - number: 3 + number: 0 rpaths: - lib/R/lib/ From 60c7d93452bf6463021251597d54d1cebe096c88 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:32:25 -0700 Subject: [PATCH 299/546] Update kallisto to 0.45.0 (#12117) --- recipes/kallisto/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index 8fe7ca78e8336..9b0f287f8ae07 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.44.0" %} +{% set version = "0.45.0" %} package: name: kallisto @@ -6,10 +6,10 @@ package: source: url: https://github.com/pachterlab/kallisto/archive/v{{ version }}.tar.gz - sha256: 35a81201a56f4557697e6fe693dc6b701bbbd0a7b2b6e1c6c845ef816d67ca29 + sha256: 42cf3949065e286e0a184586e160a909d7660825dbbb25ca350cb1dd82aafa57 build: - number: 2 + number: 0 requirements: build: From 3aec4b4bc81626e00c45d01f1b80de2958689276 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:32:36 -0700 Subject: [PATCH 300/546] Update validators to 0.12.3 (#12116) --- recipes/validators/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/validators/meta.yaml b/recipes/validators/meta.yaml index 92fc3dc2b3f98..c41f8b57a302f 100644 --- a/recipes/validators/meta.yaml +++ b/recipes/validators/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.12.2" %} -{% set sha256 = "172ac45f7d1944ce4beca3c5c53ca7c83e9759e39fd3fedc1cf28e2130268706" %} +{% set version = "0.12.3" %} +{% set sha256 = "cb9c61250ee23a68e8b5f75319c3cd3668af83112fed4f72dfe352f65fe5387c" %} package: name: validators @@ -7,7 +7,7 @@ package: source: url: https://pypi.python.org/packages/source/v/validators/validators-{{version}}.tar.gz - sha256: 172ac45f7d1944ce4beca3c5c53ca7c83e9759e39fd3fedc1cf28e2130268706 + sha256: cb9c61250ee23a68e8b5f75319c3cd3668af83112fed4f72dfe352f65fe5387c build: noarch: python From 64536031af32a942eb7c3329702ec6037644ca4c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:32:51 -0700 Subject: [PATCH 301/546] Update illumina-interop to 1.1.7 (#12115) --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 9eb0523ee0a45..33b767ae2f5d3 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.6" %} -{% set sha256 = "05784a5cb8be8d8a888e3b359e541f379b3463cabf246d7b9705a2f6eb741b5d" %} +{% set version = "1.1.7" %} +{% set sha256 = "1c5bce541b7654f892b368ee8a34af109322ecdfe819d081b7fc122b3fb7f21e" %} package: name: illumina-interop From 8151eedfc8123bee6cb5eccaced9db3ce8a9f036 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:33:08 -0700 Subject: [PATCH 302/546] Update umi_tools to 0.5.5 (#12123) --- recipes/umi_tools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/umi_tools/meta.yaml b/recipes/umi_tools/meta.yaml index a1170710e8034..dd956c581c625 100644 --- a/recipes/umi_tools/meta.yaml +++ b/recipes/umi_tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "umi_tools" %} -{% set version = "0.5.4" %} -{% set sha256hash = "80e2f5f07d2d689cf8639920bcaef531eff8cdc3ef73f37cfef068b3e5400878" %} +{% set version = "0.5.5" %} +{% set sha256hash = "d9422bb69b876ccc20dac346054d6e5cb1f8f48613e76a55486a54bc9e8abccb" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256hash }} build: - number: 3 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" entry_points: - umi_tools = umi_tools.umi_tools:main From 84df0f297b099177976f3d339628ad6f3b598817 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 16 Nov 2018 23:33:20 -0700 Subject: [PATCH 303/546] Update tiptoft to 1.0.0 (#12122) --- recipes/tiptoft/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/tiptoft/meta.yaml b/recipes/tiptoft/meta.yaml index dcd837c5c9563..d37a4aa19c86b 100644 --- a/recipes/tiptoft/meta.yaml +++ b/recipes/tiptoft/meta.yaml @@ -1,13 +1,13 @@ {% set name = "tiptoft" %} -{% set version = "0.1.4" %} -{% set hash_value = "167b7194599d6eea7b2c0fa596d0a224991cba867aa4fd067e5677b0e6bfbabf" %} +{% set version = "1.0.0" %} +{% set hash_value = "271badd22f2a8e239f0c1a89b06380176535b22f48470ae87aa716c177cddd7b" %} package: name: '{{ name|lower }}' version: '{{ version }}' source: - url: https://files.pythonhosted.org/packages/e3/78/f8771c111c68508507fe83f15b4d7c1811ae31262918b0860a9526f8c7ab/tiptoft-0.1.4.tar.gz + url: https://files.pythonhosted.org/packages/56/fd/07cee0bceaead935df9a7a53e9ab568dad323052bc742c15c51d53cfb1ee/tiptoft-1.0.0.tar.gz sha256: {{ hash_value }} build: From 7b5cc933c2493bec97430ab2e5a304634c34b089 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Sat, 17 Nov 2018 04:28:05 -0500 Subject: [PATCH 304/546] Update: TitanCNA with fix for hg38 plotting (#12130) --- recipes/bioconductor-titancna/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 54c5b6158c281..78f67541c81fa 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -6,13 +6,13 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: https://github.com/gavinha/TitanCNA/archive/8fb529d.tar.gz + url: https://github.com/gavinha/TitanCNA/archive/e214ca3.tar.gz # - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' # - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' # - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 81c071a64caa2c2384a9e25170ac9844183e2f2bf03d2a5c808e44d594cd4400 + sha256: 990137a1b3ae6c6a94fb3ee7735171188393b34006d5053f6eb9746ea47ee82a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ From 9210bc60d2311cedbbc2cd81066aa40e569c11e4 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Sat, 17 Nov 2018 11:49:14 +0100 Subject: [PATCH 305/546] blockclust (#12111) * added eden 1.1 version used in blockclust * Update meta.yaml * eden checksum and test * added zlib requirement * add include and lib paths to build.sh * add include and lib paths to build.sh * modify makefile flags using sed * modify makefile flags using sed * use c++ * Update build.sh * Update build.sh * LDFLAGS not used in makefile * remove v1.1 * add blockclust 1.1.0 recipe * skip osx build * added tarball url and checksum; removed conda_build_config.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/blockclust/build.sh | 7 ++++++ recipes/blockclust/meta.yaml | 41 ++++++++++++++++++++++++++++++++ recipes/blockclust/post-link.sh | 10 ++++++++ recipes/blockclust/pre-unlink.sh | 1 + 4 files changed, 59 insertions(+) create mode 100644 recipes/blockclust/build.sh create mode 100644 recipes/blockclust/meta.yaml create mode 100644 recipes/blockclust/post-link.sh create mode 100644 recipes/blockclust/pre-unlink.sh diff --git a/recipes/blockclust/build.sh b/recipes/blockclust/build.sh new file mode 100644 index 0000000000000..cbfd77d026b22 --- /dev/null +++ b/recipes/blockclust/build.sh @@ -0,0 +1,7 @@ +sed -i.bak "s/CXX=g++//" Makefile +make +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/share/blockclust_data +cp blockclust scripts/blockclust.py scripts/blockclust_plot.r ${PREFIX}/bin +cp blockclust_data/blockclust.config blockclust_data/rfam_map.txt ${PREFIX}/share/blockclust_data + diff --git a/recipes/blockclust/meta.yaml b/recipes/blockclust/meta.yaml new file mode 100644 index 0000000000000..799fb5c3fac4c --- /dev/null +++ b/recipes/blockclust/meta.yaml @@ -0,0 +1,41 @@ +package: + name: blockclust + version: 1.1.0 + +source: + url: https://github.com/pavanvidem/blockclust/archive/c4b8a985fcb615b2b4356a242ff1bc60b672f8e1.tar.gz + sha256: 6fcac1a735505642d206c30acec203794e5a942d7f798b8a815dae888feb7f81 + +build: + number: 0 + skip: True # [osx] + +requirements: + build: + - {{ compiler('cxx') }} + host: + - python + - r-base + run: + - python + - r-base + - scikit-learn >=0.20.0 + - r-dendextend >=1.8.0 + - mcl >=14.137 + - eden >=1.1 + - pysam >=0.15.0 + - gnu-wget + +test: + commands: + - blockclust 2>&1 | grep classification + +about: + home: https://github.com/pavanvidem/blockclust + license: GPL + license_file: LICENSE + summary: Efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. + +extra: + identifiers: + - doi:10.1093/bioinformatics/btu270 diff --git a/recipes/blockclust/post-link.sh b/recipes/blockclust/post-link.sh new file mode 100644 index 0000000000000..aa1bbab0fbab2 --- /dev/null +++ b/recipes/blockclust/post-link.sh @@ -0,0 +1,10 @@ +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz -P ${PREFIX}/share/blockclust_data +wget https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz -P ${PREFIX}/share/blockclust_data + +for i in ${PREFIX}/share/blockclust_data/*.tar.gz; do tar -xf $i -C ${PREFIX}/share/blockclust_data;rm $i;done diff --git a/recipes/blockclust/pre-unlink.sh b/recipes/blockclust/pre-unlink.sh new file mode 100644 index 0000000000000..71cf1bfb98fa0 --- /dev/null +++ b/recipes/blockclust/pre-unlink.sh @@ -0,0 +1 @@ +rm -rf ${PREFIX}/share/blockclust_data From 6256c41e1e66c4f8a5f13e88e04dff99d9871139 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 17 Nov 2018 18:33:38 -0700 Subject: [PATCH 306/546] Update chewbbaca to 2.0.16 (#12132) --- recipes/chewbbaca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index cc04d2e1f1dec..3f68b24b51f7e 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,6 +1,6 @@ {% set name='chewBBACA' %} -{% set version='2.0.15' %} -{% set sha256='26333b802d69e91b43c1d78c9cc235e89d787b299d3624f29be344e52d2285b1' %} +{% set version='2.0.16' %} +{% set sha256='4686714a1828fd24008e14ab8c7d1fe3f3b0b1888739383ee35a2805c329b462' %} package: name: {{ name|lower }} From d31caba456a6c6a4373a7a48c06467bed39c8e22 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 17 Nov 2018 18:33:49 -0700 Subject: [PATCH 307/546] Update abeona to 0.40.0 (#12131) --- recipes/abeona/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index 73ed9ec00de34..45eeeb68c215b 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.39.3" %} -{% set sha256 = "2acf5851b025a29f8f97d96377349ffa5bb04ac2e5ad4cc1ef375b79fa55f724" %} +{% set version = "0.40.0" %} +{% set sha256 = "cd1372a78ed5e3335eb2bca0a433e46b274d70f8a2e8cf5153fff9404af242f0" %} package: name: abeona From bf06c820e17ace5377c19c54bdc2aa1fdad55eae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 18 Nov 2018 12:20:13 +0100 Subject: [PATCH 308/546] ping to eden 1.1 (#12134) --- recipes/blockclust/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/blockclust/meta.yaml b/recipes/blockclust/meta.yaml index 799fb5c3fac4c..6e23250fde49b 100644 --- a/recipes/blockclust/meta.yaml +++ b/recipes/blockclust/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 6fcac1a735505642d206c30acec203794e5a942d7f798b8a815dae888feb7f81 build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -22,7 +22,7 @@ requirements: - scikit-learn >=0.20.0 - r-dendextend >=1.8.0 - mcl >=14.137 - - eden >=1.1 + - eden 1.1 - pysam >=0.15.0 - gnu-wget From bc059246d9b4358fff92e2324cd77a8561bed64b Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sun, 18 Nov 2018 21:17:28 +0000 Subject: [PATCH 309/546] clean swap file (#12137) --- .../bioconductor-complexheatmap/.meta.yaml.swp | Bin 12288 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 recipes/bioconductor-complexheatmap/.meta.yaml.swp diff --git a/recipes/bioconductor-complexheatmap/.meta.yaml.swp b/recipes/bioconductor-complexheatmap/.meta.yaml.swp deleted file mode 100644 index 4e0394ca668b5188a04b2d76d619e9f2bd689e87..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeI2zmMER6vro&X^&@At#yWGR!8rKw7%=g9SI;u#8Mzu*pLB+?assGJ z?@WLRFaajO1egF5U;<2l3H;9qg!Y2?1Z#Y1T<2_jUU=d;e)59}FaajO1egF5U;<2l z2`~XBzyz286F7$iR3XIAPYdz+MI?{^|4)AZ|MiRzKSAF?-$DGV z=ojb_^gZ+y^ab=OltXu*2znm60{wkih~JNfC(@GCUE`K;YOd);O zw$=qd1ogIaIbzvT7Ah#@5;j(j4oKCqwSi2~c=N%bLbr3|V|kk#$xxAeeN(M_dsD58 zh`wtY<&IN18;2%y!-vXJ=Nb|FG!L}zRIMM7RNmWM53BYvqi{%MWTDFv^O%6Jwa&?S zLfALnc}rfqwJ(>~dn%P}&{>7hrpZZx@lZz`TenU|Vtu7?P0G_?kyN3nlhcXEeVKHQa9O}*F>x7Y@>nfRU2^U6 zfo?y?_S69(@EtGv5Uw-lFX^n)b&(23A9dPMgEIpD5-q|>$&$(I-DK==tqRp(Wx6IK zm&&;q!${c_t5h!cioI-+FN?+YvRK{3#~!VAcNQzPBHAf(MD1MtUr(ENd4jU{;E>np zL-)ZVzJZMl%Ejvk2ws}>iTiZgVslmdbsmuOI6bKxBA~;l{u-Q7M=!>!kcxi*GmWQ< From 226accc10591f754ce1e38565c52ac79a8c8e660 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 15:04:00 -0700 Subject: [PATCH 310/546] Update corset to 1.07 (#12143) --- recipes/corset/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/corset/meta.yaml b/recipes/corset/meta.yaml index 3830fa45eb0aa..f69fb1efbca1c 100644 --- a/recipes/corset/meta.yaml +++ b/recipes/corset/meta.yaml @@ -1,16 +1,16 @@ {% set name = "corset" %} -{% set version = "1.06" %} +{% set version = "1.07" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 source: - url: https://github.com/Oshlack/Corset/archive/version-1.06.tar.gz - md5: decc3bc6b499d6d7ac448ff3683e07aa + url: https://github.com/Oshlack/Corset/archive/version-1.07.tar.gz + sha256: 9df143e6dd88e13e8af97d137a96730390f3f4c5044332b581b5bb18bc664e50 requirements: build: From 033d2455e2ba31a19e37ed635d7bcc60273c47f1 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 15:17:37 -0700 Subject: [PATCH 311/546] Update peddy to 0.4.3 (#12144) --- recipes/peddy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peddy/meta.yaml b/recipes/peddy/meta.yaml index f51edb0d727cf..d84f111a11beb 100644 --- a/recipes/peddy/meta.yaml +++ b/recipes/peddy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.2" %} -{% set sha256 = "f931a45ddc2831411d139e31bfd711862dc5c7ab413d07192a89b7468a5df9c0" %} +{% set version = "0.4.3" %} +{% set sha256 = "69c41c3bc42d4d7979de0a098f960dfcd7fbca91117400cec70b4c64a0bfeb5a" %} package: name: peddy From ab600c7ff43a26b53ced35d474a636758f82167e Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Sun, 18 Nov 2018 23:28:47 +0100 Subject: [PATCH 312/546] blockclust latest source and added cloudpickle as requirement (#12142) --- recipes/blockclust/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/blockclust/meta.yaml b/recipes/blockclust/meta.yaml index 6e23250fde49b..b433c046fb521 100644 --- a/recipes/blockclust/meta.yaml +++ b/recipes/blockclust/meta.yaml @@ -3,11 +3,11 @@ package: version: 1.1.0 source: - url: https://github.com/pavanvidem/blockclust/archive/c4b8a985fcb615b2b4356a242ff1bc60b672f8e1.tar.gz - sha256: 6fcac1a735505642d206c30acec203794e5a942d7f798b8a815dae888feb7f81 + url: https://github.com/pavanvidem/blockclust/archive/23cb198228d3ce2f5ecab49e9e85dfce44b14e67.tar.gz + sha256: ab54fd935333c1bc7cebed05a3e26d935530f85376b77623f8e846969872bb0e build: - number: 1 + number: 2 skip: True # [osx] requirements: @@ -25,6 +25,7 @@ requirements: - eden 1.1 - pysam >=0.15.0 - gnu-wget + - cloudpickle 0.5.6 test: commands: From 2a525a392b72e7986e9d12b646648bb53f3433cb Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 15:59:09 -0700 Subject: [PATCH 313/546] Update nanomath to 0.22.0 (#12149) --- recipes/nanomath/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nanomath/meta.yaml b/recipes/nanomath/meta.yaml index 34386713a1b40..65278d091b0f0 100644 --- a/recipes/nanomath/meta.yaml +++ b/recipes/nanomath/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.21.0" %} +{% set version = "0.22.0" %} package: name: nanomath @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/n/nanomath/nanomath-{{ version }}.tar.gz - sha256: 2ebf33cde4ded3d97803ce95a0c6405e5a42c2baaf1d47dc6cdf1adae088bcb6 + sha256: 5766b7f8594c43be51fe5c83bb39eacc143b1466890c82c7d49e2f69c0459924 build: - number: 2 + number: 0 skip: True # [py27] requirements: From 0d03cbdfcc87cc879728af6d888815dc84aa3349 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 16:22:48 -0700 Subject: [PATCH 314/546] Update pymvpa to 2.6.5 (#12152) --- recipes/pymvpa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pymvpa/meta.yaml b/recipes/pymvpa/meta.yaml index 22486e08778dd..6b176f939e274 100644 --- a/recipes/pymvpa/meta.yaml +++ b/recipes/pymvpa/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.6.4" %} -{% set sha256 = "2f4ced9dfb4b770fa2d808ea9f85579b9164bdc25ec52a455a97cabbbd059a07" %} +{% set version = "2.6.5" %} +{% set sha256 = "ea0f4c4f81ec9679cc80a1ae7c598a1365fdb8f909a2d3e9941bca787f9c0544" %} package: name: pymvpa From 5160daa2bcb45e0fd8a17abd71c40f2d9f12dbd4 Mon Sep 17 00:00:00 2001 From: Diogo Silva Date: Sun, 18 Nov 2018 23:31:04 +0000 Subject: [PATCH 315/546] Updated to version 1.4.0 (#12138) * Updated to version 1.4.0 * Resetting build number to 0 and build->host --- recipes/flowcraft/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/flowcraft/meta.yaml b/recipes/flowcraft/meta.yaml index a0d778fa0a72e..45de4e2c7cee3 100644 --- a/recipes/flowcraft/meta.yaml +++ b/recipes/flowcraft/meta.yaml @@ -1,8 +1,8 @@ {% set name = "flowcraft" %} -{% set version = "1.3.1" %} +{% set version = "1.4.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "b0dd1e65600e807abb1c0219fdad13ae47cf35ee6dfc3eb4d22cffa2aff936b6" %} +{% set hash_value = "77d9acaed50208c9bee0d9e0551951771dd0394cf2ef0b77509f46aaac840273" %} package: name: '{{ name|lower }}' @@ -13,14 +13,14 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 1 + number: 0 skip: True # [py27] entry_points: - flowcraft = flowcraft.flowcraft:main script: python setup.py install --single-version-externally-managed --record=record.txt requirements: - build: + host: - python - setuptools - pympler @@ -35,13 +35,14 @@ requirements: - argparse - jinja2 - requests - - nextflow >=0.27 + - nextflow >=0.28 test: imports: - flowcraft - flowcraft.generator - flowcraft.generator.components + - flowcraft.generator.recipes - flowcraft.templates - flowcraft.templates.flowcraft_utils commands: From a7b5ad49801a30fee3e3f1cf812cd9807efd9f41 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 17:33:26 -0700 Subject: [PATCH 316/546] Update transdecoder to 5.5.0 (#12172) --- recipes/transdecoder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/transdecoder/meta.yaml b/recipes/transdecoder/meta.yaml index 4d4a24de3f5c5..5dcda9321a309 100644 --- a/recipes/transdecoder/meta.yaml +++ b/recipes/transdecoder/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "5.3.0" %} -{% set sha256 = "60dc0e6e31902bede257b8f8cdbf34750a9866323f4c7788f4ef80b0ad782077" %} +{% set version = "5.5.0" %} +{% set sha256 = "c800d9226350817471e9f51267c91f7cab99dbc9b26c980527fc1019e7d90a76" %} package: name: transdecoder From 24b13b3f86602bd94a080e2f21ff1b6aa77536d2 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 17:57:50 -0700 Subject: [PATCH 317/546] Update gridss to 2.0.1 (#12190) --- recipes/gridss/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gridss/meta.yaml b/recipes/gridss/meta.yaml index 90f85ef7787a5..cd4db791f49c0 100644 --- a/recipes/gridss/meta.yaml +++ b/recipes/gridss/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.9.0" %} -{% set sha256 = "ec608fb1a9e487aafccf4ddafe3f6bf2472963783b85cae8b486f83dfddfd6bb" %} +{% set version = "2.0.1" %} +{% set sha256 = "f04a02fd35b91cb4fbb53d1a6fc4dac25913549cbad44b54e199e3b6ca629c11" %} package: name: gridss From 08419ada7c46521a41118200eaf7a4c13cdffb2c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 18:07:05 -0700 Subject: [PATCH 318/546] Update tracer to 1.7.1 (#12189) --- recipes/tracer/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/tracer/meta.yaml b/recipes/tracer/meta.yaml index 0a5fe849799b8..76566150f25a4 100644 --- a/recipes/tracer/meta.yaml +++ b/recipes/tracer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tracer" %} -{% set version = "1.7.0" %} +{% set version = "1.7.1" %} {% set build = 1 %} about: @@ -18,8 +18,8 @@ build: noarch: generic source: - url: https://github.com/beast-dev/tracer/releases/download/v1.7/Tracer_v1.7.0.tgz - sha256: 439bf13f35f1ad1cf3c4dc4bd816fab8616424bfc20ba72441a55d91b4e89a84 + url: https://github.com/beast-dev/tracer/releases/download/v1.7.1/Tracer_v1.7.1.tgz + sha256: 200d7ffa1e48994b71245994e299847ac2be72d3d5c37d9048418557e1d8c12e requirements: run: From 9a3c810fc92658510dbc1ec411a0e9d12e5b41c5 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 18:07:23 -0700 Subject: [PATCH 319/546] Update flowcraft to 1.4.0 (#12179) From e5689df68ebeed8e48106882f4aa11a2e23eed1a Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 18:07:33 -0700 Subject: [PATCH 320/546] Update seqbuster to 3.2 (#12182) --- recipes/seqbuster/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/seqbuster/meta.yaml b/recipes/seqbuster/meta.yaml index 7838b2d81df87..9e713d93967ef 100644 --- a/recipes/seqbuster/meta.yaml +++ b/recipes/seqbuster/meta.yaml @@ -5,11 +5,11 @@ about: package: name: seqbuster - version: '3.1a' + version: '3.2' source: - url: https://github.com/lpantano/seqbuster/archive/miraligner-3.1a.tar.gz - md5: 79d245a651ee7fada51facfbb4a830ff + url: https://github.com/lpantano/seqbuster/archive/miraligner-3.2.tar.gz + sha256: 16419d453fd56bd6eb9164be4353a71c5859fac85a9f165edf73a0bf1048d505 build: number: 0 From 550c490594cb42d0e1976757560c2b36c0cd08f4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 18:17:25 -0700 Subject: [PATCH 321/546] Update perl-io-compress to 2.081 (#12201) --- recipes/perl-io-compress/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-io-compress/meta.yaml b/recipes/perl-io-compress/meta.yaml index b3700f24a4011..4f57e75f8973e 100644 --- a/recipes/perl-io-compress/meta.yaml +++ b/recipes/perl-io-compress/meta.yaml @@ -1,13 +1,13 @@ package: name: perl-io-compress - version: 2.069 + version: 2.081 source: - url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/IO-Compress-2.069.tar.gz - md5: b26925161e3f01919f60344d1bbb49c4 + url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/IO-Compress-2.081.tar.gz + sha256: 5211c775544dc8c511af08edfb1c0c22734daa2789149c2a88d68e17b43546d9 build: - number: 5 + number: 0 requirements: build: From 6125e7ef78debfecc26475f8fe23425fbf7b69c4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 20:48:08 -0700 Subject: [PATCH 322/546] Update twobitreader to 3.1.6 (#12205) * Update twobitreader to 3.1.6 * Update meta.yaml --- recipes/twobitreader/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/twobitreader/meta.yaml b/recipes/twobitreader/meta.yaml index d1ffbf690273e..5c1ae9effb9ca 100644 --- a/recipes/twobitreader/meta.yaml +++ b/recipes/twobitreader/meta.yaml @@ -1,13 +1,14 @@ package: name: twobitreader - version: "3.1.4" + version: "3.1.6" build: - number: 1 + number: 0 + noarch: python source: - url: https://pypi.python.org/packages/4c/95/133326b21354b8592d1b6be6d594a17cebf1070325222075df2630d77da4/twobitreader-3.1.4.tar.gz - md5: 1672e7e515d057a93cc2dd6c8d487458 + url: https://files.pythonhosted.org/packages/9b/90/eb2dc9f097a0a0d60e3ef46bb6e3dee74aef4f5225fe8ab3b0cd0b480204/twobitreader-3.1.6.tar.gz + sha256: 42bbbe9b06e4b9c1d96406b94802da7c90ca41d9ea740e90bf76546f21982b49 requirements: host: From 96267d393edc0910568e2c1acffeed0ff71587c6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 20:48:26 -0700 Subject: [PATCH 323/546] Update gtfparse to 1.2.0 (#12186) * Update gtfparse to 1.2.0 * remove compiler --- recipes/gtfparse/meta.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index 417c8d0db0d07..11889e8f1196c 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,8 +1,8 @@ {% set name = "gtfparse" %} -{% set version = "1.0.7" %} +{% set version = "1.2.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "568d2c52d9d2594d785e06e46c8590f8596ffe597275d42bffda661c7aeddb78" %} +{% set hash_value = "2f27aa2b87eb43d613edabf27f9c11147dc595c8683b440ac1d88e9acdb85873" %} package: name: '{{ name|lower }}' @@ -14,11 +14,9 @@ source: build: noarch: python - number: 1 + number: 0 requirements: - build: - - {{ compiler('cxx') }} host: - python - numpy >=1.7,<2.0 From 5487298c62048dc2cdc9cedb4c6f3081d935495a Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sun, 18 Nov 2018 23:41:10 -0700 Subject: [PATCH 324/546] Update htseq to 0.11.0 (#12177) * Update htseq to 0.11.0 * add compiler --- recipes/htseq/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index afc3fa58f3d90..b43384f7e7448 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -1,15 +1,18 @@ package: name: htseq - version: "0.9.1" + version: "0.11.0" source: - url: https://pypi.python.org/packages/fd/94/b7c8c1dcb7a3c3dcbde66b8d29583df4fa0059d88cc3592f62d15ef539a2/HTSeq-0.9.1.tar.gz - md5: fc71e021bf284a68f5ac7533a57641ac + url: https://files.pythonhosted.org/packages/c9/e7/598b33395ac7c9417a7d7cfcb2d04cbfc2e410199cc7f938eed287bb5eae/HTSeq-0.11.0.tar.gz + sha256: 19145fd3359baa4a8dd5c93470aa0a77e16da3ffde8e4e10fa8df4191df5cd29 build: - number: 1 + number: 0 requirements: + build: + - {{ compiler('c') }} + host: - python - setuptools From d5414a8eeba8c201460d9f5e85958a44e068c187 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 19 Nov 2018 00:10:36 -0700 Subject: [PATCH 325/546] Update htseq to 0.11.0 (#12239) [testing co-author] * Update htseq to 0.11.0 * add compiler Co-authored-by: Bjoern Gruening From 634a179fb98daa52304f0cbee18a75c25259815b Mon Sep 17 00:00:00 2001 From: Tobias Rausch Date: Mon, 19 Nov 2018 10:17:26 +0100 Subject: [PATCH 326/546] alfred v0.1.16 (#12240) * alfred v0.1.16 * makefile patch * makefile patch --- recipes/alfred/Makefile.patch | 22 ++++++++++++---------- recipes/alfred/meta.yaml | 8 ++++---- 2 files changed, 16 insertions(+), 14 deletions(-) diff --git a/recipes/alfred/Makefile.patch b/recipes/alfred/Makefile.patch index 484c81138cb53..0ca2a08034fe0 100644 --- a/recipes/alfred/Makefile.patch +++ b/recipes/alfred/Makefile.patch @@ -1,23 +1,29 @@ diff --git a/opt/dev/alfred/Makefile b/Makefile -index e76eead8e..d0866c3e9 100644 +index aaa52e5f7..644ae81f4 100644 --- a/opt/dev/alfred/Makefile +++ b/Makefile -@@ -1,64 +1,21 @@ +@@ -1,66 +1,20 @@ DEBUG ?= 0 STATIC ?= 0 -# Submodules -PWD = $(shell pwd) -EBROOTHTSLIB ?= ${PWD}/src/htslib/ -- ++CXXFLAGS += -isystem ${PREFIX} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive ++LDFLAGS += -L${PREFIX}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time ++LDFLAGS += -lhts -lz -llzma -lbz2 ++CXXFLAGS += -O3 -fno-tree-vectorize -DNDEBUG + -# Install dir -prefix = ${PWD} -exec_prefix = $(prefix) -bindir ?= $(exec_prefix)/bin - - # Flags +-# Flags -CXX=g++ --CXXFLAGS += -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing +-CXXFLAGS = ${CMDCXXFLAGS} +-CXXFLAGS += -isystem ${EBROOTHTSLIB} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive +-LDFLAGS = ${CMDLDFLAGS} -LDFLAGS += -L${EBROOTHTSLIB} -L${EBROOTHTSLIB}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - -# Additional flags for release/debug @@ -38,11 +44,7 @@ index e76eead8e..d0866c3e9 100644 - SUBMODULES += .htslib -endif - -+CXXFLAGS += -isystem ${PREFIX} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive -+LDFLAGS += -L${PREFIX}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+LDFLAGS += -lhts -lz -llzma -lbz2 -+CXXFLAGS += -O3 -fno-tree-vectorize -DNDEBUG - +- -# External sources -HTSLIBSOURCES = $(wildcard src/htslib/*.c) $(wildcard src/htslib/*.h) SOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index d029f68ee0eb1..d405ad1c00873 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.15" %} -{% set sha256 = "a5a18129019821fac8b346166820d70604190ba36f5a8051f11433de8e9f8478" %} +{% set version = "0.1.16" %} +{% set sha256 = "57950cbcb996db71e5b699f9f55951203888748d920dc2a7d32faa22fd58c554" %} package: name: alfred @@ -8,8 +8,8 @@ package: source: url: https://github.com/tobiasrausch/alfred/archive/v{{ version }}.tar.gz sha256: '{{ sha256 }}' -# patches: -# - Makefile.patch + patches: + - Makefile.patch build: number: 0 From 7b002aef003c2253bcbcc740d5664b82e7d7fee0 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 19 Nov 2018 12:57:00 -0700 Subject: [PATCH 327/546] Update scrm to 1.7.3 (#12150) * Update scrm to 1.7.3 * Update scrm to 1.7.3 --- recipes/scrm/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/scrm/meta.yaml b/recipes/scrm/meta.yaml index c723d84eb7316..1bb7bdc413a8b 100644 --- a/recipes/scrm/meta.yaml +++ b/recipes/scrm/meta.yaml @@ -1,14 +1,14 @@ build: - number: 1 + number: 0 skip: True # [osx] package: name: scrm - version: "1.7.2" + version: "1.7.3" source: - url: https://github.com/scrm/scrm/releases/download/v1.7.2/scrm-src.tar.gz - md5: eb55770072d2bd6f42cddc8e1d9bd30f + url: https://github.com/scrm/scrm/releases/download/v1.7.3/scrm-src.tar.gz + sha256: 92c10ada715fb9bb06352a18cf508436b6845215c475feee33cc65582d43b195 requirements: build: From 808f4e4a672f783f76be971c8f31a8f5f6264c90 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Mon, 19 Nov 2018 14:58:50 -0500 Subject: [PATCH 328/546] Mob suite update 1.4.8 --> 1.4.9 (#12244) We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs. --- recipes/mob_suite/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/mob_suite/meta.yaml b/recipes/mob_suite/meta.yaml index 081320d8e6fc0..ba42f98f28ff1 100644 --- a/recipes/mob_suite/meta.yaml +++ b/recipes/mob_suite/meta.yaml @@ -1,5 +1,4 @@ -{% set version = "1.4.8" %} - +{% set version = "1.4.9" %} package: name: mob_suite @@ -12,7 +11,7 @@ build: source: url: https://github.com/phac-nml/mob-suite/archive/{{ version }}.tar.gz - sha256: 261bc84c4db9e4d65b7f120660ae7935be6e53e2459e4dc47232de8543b643e1 + sha256: 8bb2442737a11fc2c6b45c6a371b05ccb2defa6b57a77150aa141795367acd0c requirements: From 75b2b118c51354942dffb283f6b80bd7fee6b029 Mon Sep 17 00:00:00 2001 From: Carlos Date: Mon, 19 Nov 2018 21:09:51 +0100 Subject: [PATCH 329/546] PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 --- recipes/peptide-shaker/meta.yaml | 5 +++-- recipes/peptide-shaker/peptide-shaker.py | 2 +- recipes/searchgui/meta.yaml | 4 ++-- recipes/searchgui/searchgui.py | 2 +- 4 files changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 4ad480af43673..e6c2eb492148d 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,5 +1,6 @@ {% set name = "PeptideShaker" %} -{% set version = "1.16.32" %} +{% set version = "1.16.35" %} + # Do not forget to update the version string in the peptide-shaker.py file about: @@ -22,7 +23,7 @@ build: source: url: http://genesis.ugent.be/maven2/eu/isas/peptideshaker/{{ name }}/{{ version }}/{{ name }}-{{ version }}.zip - sha256: 4db6d3d4c23d0bf5679fe7514e5e8be39775c2cb7ff541ee7cd0d5fceac6b0ef + sha256: 701159ade190af573d7894d9c81dae4f709482a84863f3a052e9bf3b9a8f5ce0 requirements: host: diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index b2719b60397a0..39cb4e270311d 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -13,7 +13,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'PeptideShaker-1.16.32.jar' +jar_file = 'PeptideShaker-1.16.35.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 9d7e2003e0cbd..156d513f828a0 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SearchGUI" %} -{% set version = "3.3.6" %} +{% set version = "3.3.9" %} # Do not forget to update the version string in the searchgui.py file about: @@ -17,7 +17,7 @@ build: source: url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz - sha256: 6e22b4c2d37ef8e3e9edc2a07194b25aad69c0b38746651d64b795111e6c13c9 + sha256: 86295699c475abff84fd0c3b80627ca468578e581e8f85d2b8cca633593de53e requirements: host: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index c99de69aa287a..5b53c00a3f933 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -13,7 +13,7 @@ from os import access from os import getenv from os import X_OK -jar_file = 'SearchGUI-3.3.6.jar' +jar_file = 'SearchGUI-3.3.9.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] From 618955c35f26a79d007874a6597f3f67213efa4c Mon Sep 17 00:00:00 2001 From: Bob Harris Date: Mon, 19 Nov 2018 17:26:16 -0500 Subject: [PATCH 330/546] First attempt at a recipe for ncrf (#12101) * First attempt at a recipe for ncrf * changed from copies to symlinks * including absolute path in symlinks --- recipes/ncrf/build.sh | 18 ++++++++++++++++++ recipes/ncrf/meta.yaml | 26 ++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/ncrf/build.sh create mode 100644 recipes/ncrf/meta.yaml diff --git a/recipes/ncrf/build.sh b/recipes/ncrf/build.sh new file mode 100644 index 0000000000000..e18c1dfc05f32 --- /dev/null +++ b/recipes/ncrf/build.sh @@ -0,0 +1,18 @@ +#!/bin/sh + +mkdir -p $PREFIX/bin + +make + +chmod +x NCRF + +mv NCRF $PREFIX/bin + +chmod +x *.py +cp *.py $PREFIX/bin/ +ln -s $PREFIX/bin/ncrf_to_bed.py $PREFIX/bin/ncrf_to_bed +ln -s $PREFIX/bin/ncrf_summary.py $PREFIX/bin/ncrf_summary +ln -s $PREFIX/bin/ncrf_sort.py $PREFIX/bin/ncrf_sort +ln -s $PREFIX/bin/ncrf_cat.py $PREFIX/bin/ncrf_cat +ln -s $PREFIX/bin/ncrf_resolve_overlaps.py $PREFIX/bin/ncrf_resolve_overlaps +ln -s $PREFIX/bin/ncrf_consensus_filter.py $PREFIX/bin/ncrf_consensus_filter diff --git a/recipes/ncrf/meta.yaml b/recipes/ncrf/meta.yaml new file mode 100644 index 0000000000000..02ecbadaa6c29 --- /dev/null +++ b/recipes/ncrf/meta.yaml @@ -0,0 +1,26 @@ +package: + name: ncrf + version: "1.0.4" + +build: + number: 0 + skip: True # [not py27] + +source: + url: https://github.com/makovalab-psu/NoiseCancellingRepeatFinder/archive/v1.00.04.tar.gz + sha256: fae5700393100736ad0d69cd8aa5d4c967674b12c8536bfb7fd647960397aba9 + +requirements: + build: + - {{ compiler('c') }} + run: + - python +test: + commands: + - NCRF --version 2>&1 | grep 1.00.04 > /dev/null + +about: + home: https://github.com/makovalab-psu/NoiseCancellingRepeatFinder + license: MIT + summary: Noise-Cancelling Repeat Finder, Uncovering tandem repeats in error-prone long-read sequencing data. + From 48621b35dd46ae404a305118b7f55b35020f9327 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Armin=20T=C3=B6pfer?= Date: Mon, 19 Nov 2018 23:32:28 +0100 Subject: [PATCH 331/546] PacBio: Update `pbmm2` to version 0.11.0 (#12246) --- recipes/pbmm2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pbmm2/meta.yaml b/recipes/pbmm2/meta.yaml index cc5585c18757b..c16a37c72a13b 100644 --- a/recipes/pbmm2/meta.yaml +++ b/recipes/pbmm2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbmm2" %} -{% set version = "0.10.1" %} -{% set sha256 = "ed566ed7a67bbf4b89aa86e188031c19618f0f0bc7cc6a6ee40e5f7348ccd88a" %} +{% set version = "0.11.0" %} +{% set sha256 = "75e9b927bc63a5d2bfd42c707c4814d2fdc2603c52b9947760846065755a81a9" %} package: name: {{ name }} @@ -22,7 +22,7 @@ extra: - mhsieh build: - number: 1 + number: 0 requirements: build: From b3b7c3cf1cd4cb7a4be1537436c5c40936e42a8e Mon Sep 17 00:00:00 2001 From: Simon van Heeringen Date: Tue, 20 Nov 2018 06:21:06 +0100 Subject: [PATCH 332/546] Gimmemotifs version 0.13.0 (#12245) * new release to fix numpy incompatibility * GimmeMotifs 0.13.0 release test * numpy 1.15 * version 0.13.0 * Fix about:home and extra: --- recipes/gimmemotifs/conda_build_config.yaml | 2 +- recipes/gimmemotifs/meta.yaml | 24 +++++++++++---------- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/recipes/gimmemotifs/conda_build_config.yaml b/recipes/gimmemotifs/conda_build_config.yaml index 980c459f1c44e..1043105c954dc 100644 --- a/recipes/gimmemotifs/conda_build_config.yaml +++ b/recipes/gimmemotifs/conda_build_config.yaml @@ -1,2 +1,2 @@ numpy: - - 1.13 + - 1.15 diff --git a/recipes/gimmemotifs/meta.yaml b/recipes/gimmemotifs/meta.yaml index d2f9d2da50d52..4bf8ae6def78c 100644 --- a/recipes/gimmemotifs/meta.yaml +++ b/recipes/gimmemotifs/meta.yaml @@ -1,21 +1,20 @@ -{% set version = "0.12.0" %} +{% set version = "0.13.0" %} package: name: gimmemotifs version: {{ version }} source: - url: https://github.com/simonvh/gimmemotifs/archive/0.12.0.tar.gz - sha256: 199df912e7551045bba9af8be005a201bd7d3c8a45a00b283e884e1263983513 + url: https://github.com/vanheeringen-lab/gimmemotifs/releases/download/{{ version }}/gimmemotifs-{{ version }}.tar.gz + sha256: ccaa9ec2b58f22fd7fb07680de0d4e7fc3d9eff2ec2aed26c0d89abb94cb69ca build: - number: 1 + number: 0 requirements: build: - {{ compiler('c') }} host: - #skipping py27 until configparser is fixed at conda-forge - python >=3 - setuptools - numpy @@ -33,7 +32,6 @@ requirements: - xdg - diskcache - python-xxhash - - configparser # [py27] - six - future - pillow @@ -44,13 +42,16 @@ requirements: - gadem - trawler - weeder + - xxmotif + - meme - tqdm - genomepy + - ncurses run: - python >=3 - scipy >=0.9.0 - - {{ pin_compatible('numpy', max_pin='x.x') }} + - {{ pin_compatible('numpy') }} - matplotlib >=2.0 - jinja2 - pyyaml >=3.10 @@ -64,7 +65,6 @@ requirements: - xdg - diskcache - python-xxhash - - configparser # [py27] - six - future - pillow @@ -75,10 +75,12 @@ requirements: - gadem - trawler - weeder - - meme # [py27] + - xxmotif + - meme - ghostscript - tqdm - genomepy + - ncurses test: imports: @@ -88,10 +90,10 @@ test: - gimme --help about: - home: https://github.com/simonvh/gimmemotifs + home: https://github.com/vanheeringen-lab/gimmemotifs license: MIT summary: Motif prediction pipeline and various motif-related tools -en_c+xtra: +extra: identifiers: - biotools:gimmemotifs From be29b0a15254ac106862f3f350939c3e96fa4f6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Armin=20T=C3=B6pfer?= Date: Tue, 20 Nov 2018 14:43:13 +0100 Subject: [PATCH 333/546] PacBio: Update `isoseq3` to version 3.1.0 (#12263) --- recipes/isoseq3/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/isoseq3/meta.yaml b/recipes/isoseq3/meta.yaml index 0d917c839d810..72ce228e86e88 100644 --- a/recipes/isoseq3/meta.yaml +++ b/recipes/isoseq3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "isoseq3" %} -{% set version = "3.0.0" %} -{% set sha256 = "bf43b4f7c2f7a825c954e8445b66fe3cbc6ca0d95361c11acb5e855ba19040c7" %} +{% set version = "3.1.0" %} +{% set sha256 = "863594fd859d7b6d9e93d8528e9ccd1980a262808a1e0ead5f2941363a825992" %} package: name: {{ name }} @@ -22,7 +22,7 @@ extra: - mhsieh build: - number: 2 + number: 0 skip: True # [osx] requirements: From 61793c94d38564ea6c0b76c961e4dc543100c22f Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Tue, 20 Nov 2018 16:36:33 +0100 Subject: [PATCH 334/546] add python to host section (#12264) --- recipes/ncrf/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/ncrf/meta.yaml b/recipes/ncrf/meta.yaml index 02ecbadaa6c29..60432af773359 100644 --- a/recipes/ncrf/meta.yaml +++ b/recipes/ncrf/meta.yaml @@ -13,6 +13,8 @@ source: requirements: build: - {{ compiler('c') }} + host: + - python run: - python test: From fb2ef22ea8c762f3bc6c509398cf31564a5a0d80 Mon Sep 17 00:00:00 2001 From: lowandrew Date: Tue, 20 Nov 2018 11:00:39 -0500 Subject: [PATCH 335/546] Update confindr to 0.4.7 (#12266) --- recipes/confindr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/confindr/meta.yaml b/recipes/confindr/meta.yaml index 24e6ff35ce578..b0b17679bfa41 100644 --- a/recipes/confindr/meta.yaml +++ b/recipes/confindr/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.6" %} -{% set sha256 = "8a387955ae904883c3cbcee26d9e1b5f1203c24fbdd3daa1400530a60bff87e6" %} +{% set version = "0.4.7" %} +{% set sha256 = "deb64931cccc26a5d9058b93ea7cbd27c52d833f7f6e5712a37c24331b7ca97a" %} package: name: confindr From fd478dd32b79d7d0ac8bc31d3688e487decd8ac9 Mon Sep 17 00:00:00 2001 From: aemiol <38737287+aemiol@users.noreply.github.com> Date: Tue, 20 Nov 2018 14:51:29 -0500 Subject: [PATCH 336/546] new build of GRiD (#12269) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml --- recipes/grid/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/grid/meta.yaml b/recipes/grid/meta.yaml index 0fb46766cf4b3..842e7bc083768 100644 --- a/recipes/grid/meta.yaml +++ b/recipes/grid/meta.yaml @@ -4,12 +4,12 @@ package: build: skip: True # [osx] - number: 2 + number: 3 source: url: https://github.com/ohlab/GRiD/archive/1.1.tar.gz - sha256: d0cf0fc2407d4678e38c3bf9f895771d73a67505b9f27b065692785186b88b3f - + sha256: 85db19227e0cc988f55e246368443509ea757981e174a5508c4491d5b5f2a62b + requirements: run: - parallel From 13453d3f5a6b174cdaeadd77999315b582440571 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 20 Nov 2018 23:59:39 +0100 Subject: [PATCH 337/546] peptideshaker, searchgui: version bump (#12136) * peptideshaker, searchgui: version bump solving https://github.com/compomics/searchgui/issues/192 * Update peptide-shaker.py * searchgui: added c compiler for building test if linking errors go away this way * searchgui: removed noarch --- recipes/peptide-shaker/meta.yaml | 2 +- recipes/searchgui/meta.yaml | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index e6c2eb492148d..2f036aee73d48 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -19,7 +19,7 @@ package: build: noarch: generic - number: 1 + number: 0 source: url: http://genesis.ugent.be/maven2/eu/isas/peptideshaker/{{ name }}/{{ version }}/{{ name }}-{{ version }}.zip diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 156d513f828a0..ea1837a7b3a51 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -12,8 +12,7 @@ package: version: {{ version }} build: - noarch: generic - number: 1 + number: 0 source: url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz @@ -21,6 +20,8 @@ source: requirements: host: + build: + - {{ compiler('c') }} run: - openjdk >=6 - mono >=4.0.0 From 883c48f1d274caf623221e9cb6f09a560e94cf73 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Wed, 21 Nov 2018 06:13:42 -0500 Subject: [PATCH 338/546] Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273) --- recipes/bcbio-nextgen-vm/meta.yaml | 6 +++--- recipes/bcbio-nextgen/meta.yaml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/bcbio-nextgen-vm/meta.yaml b/recipes/bcbio-nextgen-vm/meta.yaml index 9d42d67d9be6f..770e9de602f98 100644 --- a/recipes/bcbio-nextgen-vm/meta.yaml +++ b/recipes/bcbio-nextgen-vm/meta.yaml @@ -3,12 +3,12 @@ package: version: '0.1.0a' build: - number: 131 + number: 132 skip: True # [not py27] source: - url: https://github.com/bcbio/bcbio-nextgen-vm/archive/d61850b.tar.gz - sha256: 053b0843a38ad98b22ab643313bef9c117aaac1aba34cb2f97dc7e8b81a1705d + url: https://github.com/bcbio/bcbio-nextgen-vm/archive/d246f7a.tar.gz + sha256: adf32f77253b7ab72755ceaebedab5634be56d7f721c5e782afa58e0fab902f2 requirements: host: diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index db0b44b865e75..a2bac0868362d 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -3,13 +3,13 @@ package: version: '1.1.2a' build: - number: 0 + number: 1 skip: true # [not py27] source: #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz - url: https://github.com/bcbio/bcbio-nextgen/archive/8d40ce7.tar.gz - sha256: 138f2ce9d5ceb4183e066cb3af1e46208a15968fade11b7162ede8c3085e3295 + url: https://github.com/bcbio/bcbio-nextgen/archive/3a2e565.tar.gz + sha256: cec1148e2f3411aaee84047fb4c83a545bc3863ae8f770be1e85844854b2ba39 requirements: host: From 45a317dbf7629795bffad25ee6222babe481f12f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 21 Nov 2018 16:48:08 +0100 Subject: [PATCH 339/546] Make snakemake a noarch package. (#12274) * noarch: python in combination with version constraint * Cleanup deps and simplify version definition. --- recipes/snakemake-minimal/meta.yaml | 18 ++++++------------ recipes/snakemake/meta.yaml | 14 ++++---------- 2 files changed, 10 insertions(+), 22 deletions(-) diff --git a/recipes/snakemake-minimal/meta.yaml b/recipes/snakemake-minimal/meta.yaml index 227d972de3694..0d72f355a726a 100644 --- a/recipes/snakemake-minimal/meta.yaml +++ b/recipes/snakemake-minimal/meta.yaml @@ -2,15 +2,15 @@ package: name: snakemake-minimal - version: {{ version }} + version: "5.3.0" source: - url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz + url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ PKG_VERSION }}.tar.gz sha256: 612a16f2bba580c47183e4f752ed40b034852541ca3e96e480d01fb30ad9570c build: - number: 1 - skip: True # [py27] + number: 2 + noarch: python script: python -m pip install --no-deps --ignore-installed . entry_points: - snakemake = snakemake:main @@ -18,17 +18,11 @@ build: requirements: host: - - python + - python >=3.5 - pip - setuptools - - wrapt - - requests - - ratelimiter - - configargparse - - appdirs - - datrie run: - - python + - python >=3.5 - setuptools - wrapt - requests diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index b749ff6aa22f2..3f38f91fbf699 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -2,18 +2,15 @@ package: name: snakemake - version: {{ version }} + version: "5.3.0" build: - number: 1 - skip: True # [py27] + number: 2 + noarch: generic requirements: - host: - - python run: - - python - - snakemake-minimal ={{ version }} + - snakemake-minimal ={{ PKG_VERSION }} # optional dependencies needed for the full experience # require this dropbox version to ensure that a conda doesn't pick up the # outdated version available @@ -25,12 +22,9 @@ requirements: - aioeasywebdav # pandas is optional, but required for many workflows - pandas - - ratelimiter - - configargparse - python-irodsclient - google-cloud-storage - boto3 - - aioeasywebdav - jsonschema - jinja2 - pygraphviz From 541bed6dc5f26f1eabc51642a04ac512db239945 Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Wed, 21 Nov 2018 20:15:59 +0100 Subject: [PATCH 340/546] Genenotebook v0.1.9 (#12277) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 --- recipes/genenotebook/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index b4c355bf72503..0d6216b3ad5ef 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.8' %} -{% set sha256 = '953fa9fbf7b6d0e3e7a16a565f17ac5953ed119b212fb5cd8bcc72b3829ac33f' %} +{% set version = '0.1.9' %} +{% set sha256 = '84ad8a7a5653b9ed8c90ef18ed73836c3a787047783449c8c3e496cc75985ad9' %} package: name: {{ name|lower }} From 2f3fb39498fa74a930bfcefa6e76e32e09c5dcbb Mon Sep 17 00:00:00 2001 From: Fabien Pertuy Date: Wed, 21 Nov 2018 22:44:13 +0100 Subject: [PATCH 341/546] Create r-airr recipe (#12284) * Create r-airr recipe using bgruening/conda_r_skeleton_helper * Update meta.yaml --- recipes/r-airr/build.sh | 8 +++++++ recipes/r-airr/meta.yaml | 51 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 recipes/r-airr/build.sh create mode 100644 recipes/r-airr/meta.yaml diff --git a/recipes/r-airr/build.sh b/recipes/r-airr/build.sh new file mode 100644 index 0000000000000..addd4f5d649f7 --- /dev/null +++ b/recipes/r-airr/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/airr + mv * $PREFIX/lib/R/library/airr +fi diff --git a/recipes/r-airr/meta.yaml b/recipes/r-airr/meta.yaml new file mode 100644 index 0000000000000..54d115276d7b7 --- /dev/null +++ b/recipes/r-airr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = '1.2.0' %} + +package: + name: r-airr + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/airr_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/airr/airr_{{ version }}.tar.gz + sha256: 306cd7084b1ef0617af62e5815df538f2dcd6d6aaabb593df6f579e8ab5c5cef + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-readr + - r-stringi + - r-yaml + run: + - r-base + - r-readr + - r-stringi + - r-yaml + +test: + commands: + - $R -e "library('airr')" + +about: + home: http://docs.airr-community.org + license: CC BY 4.0 + summary: Schema definitions and read, write and validation tools for data formatted in accordance + with the AIRR Data Representation schemas defined by the AIRR Community . + license_family: CC + +extra: + recipe-maintainers: + - johanneskoester + - bgruening + - daler + - jdblischak + - cbrueffer + - dbast + - PertuyF From 938155dcc9a7bfc0447451ef34973d40a89d09b4 Mon Sep 17 00:00:00 2001 From: Joerg Fallmann Date: Thu, 22 Nov 2018 09:14:33 +0100 Subject: [PATCH 342/546] Findbin::Real added (#12291) --- recipes/perl-findbin-real/build.sh | 9 +++++++++ recipes/perl-findbin-real/meta.yaml | 28 ++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 recipes/perl-findbin-real/build.sh create mode 100644 recipes/perl-findbin-real/meta.yaml diff --git a/recipes/perl-findbin-real/build.sh b/recipes/perl-findbin-real/build.sh new file mode 100644 index 0000000000000..7b82d4fb337a6 --- /dev/null +++ b/recipes/perl-findbin-real/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CPATH=${PREFIX}/include +export LIBRARY_PATH=${PREFIX}/lib + +perl Makefile.PL INSTALLDIRS=site +make +make test +make install diff --git a/recipes/perl-findbin-real/meta.yaml b/recipes/perl-findbin-real/meta.yaml new file mode 100644 index 0000000000000..7a23270b65d7e --- /dev/null +++ b/recipes/perl-findbin-real/meta.yaml @@ -0,0 +1,28 @@ +package: + name: perl-findbin-real + version: "1.05" + +source: + url: https://cpan.metacpan.org/authors/id/S/ST/STRO/FindBin-Real-1.05.tar.gz + md5: 686a6d7027237b6984ae8318ed203366 + +build: + number: 0 + +requirements: + host: + - perl + - zlib + run: + - perl + - zlib + +test: + # Perl 'use' tests + imports: + - FindBin::Real + +about: + home: https://metacpan.org/pod/FindBin::Real + license: perl_5 + summary: 'Locates the full path to the script bin directory to allow the use of paths relative to the bin directory.' From 64c76f7712cba39d117074553a6918ace0b9150c Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 22 Nov 2018 09:54:47 +0100 Subject: [PATCH 343/546] Added version bump to 1.3 (#12292) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index c4221407f2a3c..2908184fcb768 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "1.2" %} -{% set sha256 = "74589eacd8829ad2566ca360bb66a49f35645d9899f90cb0e5834eed2cf567f2" %} +{% set version = "1.3" %} +{% set sha256 = "2a993d57e3ccb3af79559e1faf6ba17f4df6965b1b47c5bd797fa6e0430df802" %} package: name: {{ name|lower }} From acae943bfc8b8454106b14b6b305ca3499eabf2e Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Thu, 22 Nov 2018 10:01:46 +0100 Subject: [PATCH 344/546] ngs-bits 2018_11 (#12262) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2018_11 --- recipes/ngs-bits/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index 5e131c1693b7b..814de1d7fd8a3 100644 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2018_10" %} +{% set version = "2018_11" %} package: name: ngs-bits @@ -10,7 +10,7 @@ build: source: git_rev: ngs-bits-{{ version }}.tgz url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: 8e63f1895b3775d828262aea46b63841a7bc8178d8f6f8416b9e984eb43721af + sha256: 1b6ba783080db176ca5334603a8c0c7416ed1db129789510a66b9c6f8efaf15a requirements: build: From e6d4fc9f367055c5124ef1c43d0767f708492595 Mon Sep 17 00:00:00 2001 From: aemiol <38737287+aemiol@users.noreply.github.com> Date: Thu, 22 Nov 2018 05:07:07 -0500 Subject: [PATCH 345/546] minor edit in grid (#12287) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid --- recipes/grid/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/grid/meta.yaml b/recipes/grid/meta.yaml index 842e7bc083768..28a816d0afbf1 100644 --- a/recipes/grid/meta.yaml +++ b/recipes/grid/meta.yaml @@ -4,11 +4,11 @@ package: build: skip: True # [osx] - number: 3 + number: 4 source: url: https://github.com/ohlab/GRiD/archive/1.1.tar.gz - sha256: 85db19227e0cc988f55e246368443509ea757981e174a5508c4491d5b5f2a62b + sha256: 9ba8bd0e3ea6cc029a4a560bc07c98fe2aacab1364f2185961f2db4eac8c9aa6 requirements: run: From e2ef8950712ab53f89c274e1aa22f55c0622ad49 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 22 Nov 2018 12:54:41 +0100 Subject: [PATCH 346/546] Fred2 update (#12259) * Update FRED2 Recipe --- recipes/fred2/build.sh | 5 ++--- recipes/fred2/meta.yaml | 15 +++++++-------- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/recipes/fred2/build.sh b/recipes/fred2/build.sh index 8cfa4a6b3a75f..d60ecfabf51ea 100644 --- a/recipes/fred2/build.sh +++ b/recipes/fred2/build.sh @@ -1,3 +1,2 @@ -#Patch away the install requires, we're getting these through conda directly -sed -i 's/install_requires/#install_requires/g' setup.py -$PYTHON setup.py install \ No newline at end of file +#!/usr/bin/env bash +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/fred2/meta.yaml b/recipes/fred2/meta.yaml index b41d0e8c2eb83..86a932bc48b68 100644 --- a/recipes/fred2/meta.yaml +++ b/recipes/fred2/meta.yaml @@ -1,19 +1,17 @@ {% set name = "fred2" %} -{% set version = "2.0.2" %} -{% set sha256 = "223f139b35357e25d98644eb2668b9140f1489f4befd1e337a83fa6253cc0d54" %} +{% set version = "2.0.3" %} +{% set sha256 = "539df6920f08bf3cb3866c390f837f65d4fd3318dfe99df8c4bc1e3e8ec27323" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/FRED-2/Fred2/archive/{{ version }}.tar.gz + url: https://github.com/FRED-2/Fred2/archive/v{{ version }}.tar.gz sha256: '{{ sha256 }}' build: - noarch: python - number: 2 - + number: 1 skip: True # [not py27] requirements: @@ -24,7 +22,8 @@ requirements: - pandas - pyvcf - biopython - - mysql-python + - pymysql + run: - python - setuptools @@ -32,7 +31,7 @@ requirements: - pandas - pyvcf - biopython - - mysql-python + - pymysql test: commands: From d55d3a2173c9b7abb36f4fda0301a3ee442d3743 Mon Sep 17 00:00:00 2001 From: Jorrit Boekel Date: Thu, 22 Nov 2018 14:36:06 +0100 Subject: [PATCH 347/546] msstitch version 2.9 (#12296) --- recipes/msstitch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/msstitch/meta.yaml b/recipes/msstitch/meta.yaml index ced498888d77b..d83ab10facf05 100644 --- a/recipes/msstitch/meta.yaml +++ b/recipes/msstitch/meta.yaml @@ -1,10 +1,10 @@ package: name: msstitch - version: "2.8" + version: "2.9" source: - url: https://files.pythonhosted.org/packages/7f/b4/61f8c5ee5cfd71d985b3f69cd1be9239f2f7b5f73d34c5e8e07771816aa6/msstitch-2.8.tar.gz - sha256: 715444b247a44aca214fd3cebc02565f0b04077dc234754aed183fb1403d5326 + url: https://files.pythonhosted.org/packages/e9/c2/a6f965f8e4dbfd2e819126b96110940903215df1a4d5cad5d84c821eb484/msstitch-2.9.tar.gz + sha256: 0096958917e597cbe998b8eefab6be7c3af5d490a2e4a0f722311cb6bdeb07b8 build: skip: True # [py2k or osx] From 22717eb74a8ed846a19021d98b64701e57bc6dd9 Mon Sep 17 00:00:00 2001 From: Chris-Lowe-Integrity <43525473+Chris-Lowe-Integrity@users.noreply.github.com> Date: Thu, 22 Nov 2018 10:08:22 -0500 Subject: [PATCH 348/546] r-mvr (#12300) This is a non-parametric method for joint adaptive mean-variance regularization and variance sta- bilization of high-dimensional data. --- recipes/r-mvr/build.sh | 38 ++++++++++++++++++++++ recipes/r-mvr/meta.yaml | 71 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 recipes/r-mvr/build.sh create mode 100644 recipes/r-mvr/meta.yaml diff --git a/recipes/r-mvr/build.sh b/recipes/r-mvr/build.sh new file mode 100644 index 0000000000000..93b209296dee1 --- /dev/null +++ b/recipes/r-mvr/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/MVR + mv * $PREFIX/lib/R/library/MVR + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-mvr/meta.yaml b/recipes/r-mvr/meta.yaml new file mode 100644 index 0000000000000..fb648f26e3d46 --- /dev/null +++ b/recipes/r-mvr/meta.yaml @@ -0,0 +1,71 @@ +{% set version = '1.33.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-mvr + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/MVR_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/MVR/MVR_{{ version }}.tar.gz + sha256: e8ada15c6e98e55fdd0785df6a7ef798dd22acde5dff42715725972bd421fff9 + +build: + merge_build_host: True # [win] + + number: 0 + + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + - r-statmod + + run: + - r-base + - {{native}}gcc-libs # [win] + - r-statmod + +test: + commands: + + - $R -e "library('MVR')" # [not win] + - "\"%R%\" -e \"library('MVR')\"" # [win] + + + # requires: + + +about: + home: https://github.com/jedazard/MVR + license: GPL (>= 3) | file LICENSE + summary: 'This is a non-parametric method for joint adaptive mean-variance regularization and + variance stabilization of high-dimensional data. It is suited for handling difficult + problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among + those are that the variance is often a function of the mean, variable-specific estimators + of variances are not reliable, and tests statistics have low powers due to a lack + of degrees of freedom. Key features include: (i) Normalization and/or variance stabilization + of the data, (ii) Computation of mean-variance-regularized t-statistics (F-statistics + to follow), (iii) Generation of diverse diagnostic plots, (iv) Computationally efficient + implementation using C/C++ interfacing and an option for parallel computing to enjoy + a faster and easier experience in the R environment.' + + license_family: GPL3 + From b4eef1c88420a86ff65c9674242f65f38efacd66 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 22 Nov 2018 15:39:11 +0000 Subject: [PATCH 349/546] Bump to Gromacs 2018.3 + re-enable OSX build (#12299) * Gromacs 2018.3 + re-enable osx build See also #7825 on OSX build Include RRID for Gromacs (see bioconda/bioconda-utils#252) * disabled ocl-icd on osx; not available (or needed?) https://anaconda.org/conda-forge/ocl-icd --- recipes/gromacs/meta.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/gromacs/meta.yaml b/recipes/gromacs/meta.yaml index 72209e6f80cfe..9d14425fac8e0 100644 --- a/recipes/gromacs/meta.yaml +++ b/recipes/gromacs/meta.yaml @@ -5,19 +5,19 @@ about: package: name: gromacs - version: 2018.2 + version: 2018.3 build: number: 0 - skip: True # [osx] +# skip: True # [osx] # See http://manual.gromacs.org/documentation/ # for latest release. Note that version scheme changed from # 5.1 to 2016.x and 2018.x source: - url: https://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz - md5: 7087462bb08393aec4ce3192fa4cd8df - sha256: 4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857 + url: https://ftp.gromacs.org/pub/gromacs/gromacs-2018.3.tar.gz + md5: c82634a31d0ec7dc8a128f404149440e + sha256: 4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291 requirements: build: @@ -25,13 +25,13 @@ requirements: - cmake host: - openmp # [linux] - - ocl-icd + - ocl-icd # [linux] - libhwloc 1.* - fftw - perl - python >=2.7,<3 run: - - ocl-icd + - ocl-icd # [linux] - openmp # [linux] - fftw - libhwloc 1.* @@ -45,3 +45,4 @@ extra: identifiers: - biotools:gromacs - doi:10.1016/j.softx.2015.06.001 + - rrid:RRID:SCR_014565 From e3ceb27623f6cfeb948b68a8bf9568f27b5eefa5 Mon Sep 17 00:00:00 2001 From: Joachim Wolff Date: Thu, 22 Nov 2018 17:30:11 +0100 Subject: [PATCH 350/546] pyGenomeTracks update of dependencies (#12279) * Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list * Increase build number * Update meta.yaml * Exclude Python 3.5 --- recipes/pygenometracks/meta.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/recipes/pygenometracks/meta.yaml b/recipes/pygenometracks/meta.yaml index 42b3eee029632..60375f33e3a46 100644 --- a/recipes/pygenometracks/meta.yaml +++ b/recipes/pygenometracks/meta.yaml @@ -7,32 +7,32 @@ source: sha256: ee998574c74d5176039eea35da8ab7f71d05c61e7a75421905d59a3336d301d7 build: - number: 0 + number: 1 script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt - skip: True # [py3k] + skip: True # [py35] requirements: host: - python - setuptools - - numpy 1.13.* - - matplotlib 2.1.* + - numpy >=1.15 + - matplotlib - intervaltree >=2.1.0 - pybigwig >=0.3.4 - - pytest - configparser >=3.5.0 # [py2k] - future >=0.16.0 - - hicexplorer >=2.1.4 + - hicmatrix >=5 + - pysam run: - python - - numpy 1.13.* - - matplotlib 2.1.* + - numpy >=1.15 + - matplotlib - intervaltree >=2.1.0 - pybigwig >=0.3.4 - - pytest - configparser >=3.5.0 # [py2k] - - future >=0.16.0 - - hicexplorer >=2.1.4 + - future >=0.17.0 + - hicmatrix >=5 + - pysam test: imports: From 5711e1c425fe45dbc2277c05c35fc213afeb03e6 Mon Sep 17 00:00:00 2001 From: Stian Soiland-Reyes Date: Thu, 22 Nov 2018 18:11:15 +0000 Subject: [PATCH 351/546] Gromacs 2018.4 (#12302) --- recipes/gromacs/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/gromacs/meta.yaml b/recipes/gromacs/meta.yaml index 9d14425fac8e0..ce0dd2473e76b 100644 --- a/recipes/gromacs/meta.yaml +++ b/recipes/gromacs/meta.yaml @@ -5,7 +5,7 @@ about: package: name: gromacs - version: 2018.3 + version: 2018.4 build: number: 0 @@ -15,9 +15,9 @@ build: # for latest release. Note that version scheme changed from # 5.1 to 2016.x and 2018.x source: - url: https://ftp.gromacs.org/pub/gromacs/gromacs-2018.3.tar.gz - md5: c82634a31d0ec7dc8a128f404149440e - sha256: 4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291 + url: http://ftp.gromacs.org/pub/gromacs/gromacs-2018.4.tar.gz + md5: 7bede4c1a656531fc43b95805e9a5a94 + sha256: 6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891 requirements: build: From ca52beeaa7973df2b06063c063c866b5bbe015f5 Mon Sep 17 00:00:00 2001 From: alexeigurevich Date: Thu, 22 Nov 2018 21:12:01 +0300 Subject: [PATCH 352/546] quast 5.0.2 (#12303) --- recipes/quast/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index 9b17e70d5da72..1d323e7094d12 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -1,6 +1,6 @@ {% set name = "quast" %} -{% set version = "5.0.1" %} -{% set hash = "d273954e8a16002b86c807d0bcb2a65c" %} +{% set version = "5.0.2" %} +{% set hash = "2b31aac010f5c04d5367f1bf718516ae" %} package: name: {{ name|lower }} From cd36147e93314d4b82aa59ca2f53f140573266d0 Mon Sep 17 00:00:00 2001 From: richjstark <30689565+richjstark@users.noreply.github.com> Date: Thu, 22 Nov 2018 18:21:02 +0000 Subject: [PATCH 353/546] Update meta.yaml (#12275) * Update meta.yaml r-rsqlite version dependency added * Update meta.yaml Updated build number to 1 --- recipes/bioconductor-decipher/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 0b5c4695c2753..76009fe5dbf21 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: 1eb5d11ad330a58dba102faedec531947ad33206b41164c259314eca6edc89e5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -24,7 +24,7 @@ requirements: - bioconductor-xvector - 'r-base =3.4.1' - r-dbi - - 'r-rsqlite >=1.1' + - 'r-rsqlite >=1.1,<2.1.1' run: - 'bioconductor-biostrings =2.46.0' - bioconductor-iranges @@ -32,7 +32,7 @@ requirements: - bioconductor-xvector - 'r-base =3.4.1' - r-dbi - - 'r-rsqlite >=1.1' + - 'r-rsqlite >=1.1,<2.1.1' build: - {{ compiler('c') }} - make From f935cd6a46281fb45048a98be4b77f1ce3dea117 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Thu, 22 Nov 2018 20:31:48 +0200 Subject: [PATCH 354/546] Use the extended-base container because of wget issues when downloading databases (#12297) --- recipes/eggnog-mapper/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/eggnog-mapper/meta.yaml b/recipes/eggnog-mapper/meta.yaml index 896c318e6773f..0a8f554736d2e 100644 --- a/recipes/eggnog-mapper/meta.yaml +++ b/recipes/eggnog-mapper/meta.yaml @@ -11,7 +11,7 @@ source: - setup.patch build: - number: 1 + number: 2 skip: True # [not py27] requirements: @@ -34,3 +34,8 @@ about: home: https://github.com/jhcepas/eggnog-mapper license: GPL summary: Fast genome-wide functional annotation through orthology assignment + +extra: + container: + # need wget with more options than the busybox one + extended-base: True From 33501560308992fd3e43f791be2a505fbc80efb9 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 22 Nov 2018 11:34:02 -0700 Subject: [PATCH 355/546] Update duphold to 0.1.0 (#12257) --- recipes/duphold/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/duphold/meta.yaml b/recipes/duphold/meta.yaml index 7cef8c9dc144c..cd13ea7e1850f 100644 --- a/recipes/duphold/meta.yaml +++ b/recipes/duphold/meta.yaml @@ -1,6 +1,6 @@ {% set name = "duphold" %} -{% set version = "0.0.9" %} -{% set sha256hash = "6dbca07fce926d4252ce048dc79580068da5b21a7a8776e5a3098276fea72595" %} +{% set version = "0.1.0" %} +{% set sha256hash = "f044f13b2d65bdd04e94426b213bc1822ccc6cf92e7a752e805c1876de33a993" %} package: name: {{ name|lower }} From 4dd70c14878e830fd8d0753457aae09319309cd2 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 22 Nov 2018 11:34:36 -0700 Subject: [PATCH 356/546] Update flashlfq to 0.1.109 (#12256) --- recipes/flashlfq/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/flashlfq/meta.yaml b/recipes/flashlfq/meta.yaml index 69022bc4d2b66..1ed2ddedd14b1 100644 --- a/recipes/flashlfq/meta.yaml +++ b/recipes/flashlfq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.108" %} -{% set sha256 = "5c21a262490a01cc6a1dcffd6eee8034e2033600dff91a2cd8616014dda075e8" %} +{% set version = "0.1.109" %} +{% set sha256 = "b6347071865f3adcad1666b41142321fed99051149679ecedba2719c5956631d" %} source: @@ -11,7 +11,7 @@ package: version: '{{version}}' build: - number: 1 + number: 0 requirements: build: From 828d7a4dc347394e3ace86a7028804b4f6f0a6ae Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 22 Nov 2018 11:35:01 -0700 Subject: [PATCH 357/546] Update planemo to 0.57.0 (#12251) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 9034e8987cea2..f2a965d2a7e7b 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "planemo" %} -{% set version = "0.56.0" %} +{% set version = "0.57.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b790bd73eb6be68e57b986b5149427fba3328808e98ffb2a26e80f02df789736 + sha256: 8ed5ee7f4a133ea2025698167ded71338bb896c1ece7a2dd5bca749d1f1d158f build: number: 0 From 2fdda45310c5a1c93b65e7019a97700ecdcacb1c Mon Sep 17 00:00:00 2001 From: Tom Smith Date: Thu, 22 Nov 2018 18:35:53 +0000 Subject: [PATCH 358/546] Update meta.yaml (#12258) From e2159019dfd797d8c77c09c5a6971a10fc46a7a4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 22 Nov 2018 11:42:20 -0700 Subject: [PATCH 359/546] Update scalpel to 0.5.4 (#12249) * Update scalpel to 0.5.4 * Fix url --- recipes/scalpel/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/scalpel/meta.yaml b/recipes/scalpel/meta.yaml index 308d19b7c00ba..5b1b6df389526 100644 --- a/recipes/scalpel/meta.yaml +++ b/recipes/scalpel/meta.yaml @@ -1,13 +1,13 @@ package: name: scalpel - version: '0.5.3' + version: '0.5.4' source: - url: http://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz - md5: 682c9f1cd6ab2cb11c6866f303c673f0 + url: http://downloads.sourceforge.net/project/scalpel/scalpel-0.5.4.tar.gz + sha256: 506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0 build: - number: 2 + number: 0 skip: True # [osx] requirements: From 5a520088d1b266d1e0568b30f4acb131effe33f6 Mon Sep 17 00:00:00 2001 From: aemiol <38737287+aemiol@users.noreply.github.com> Date: Thu, 22 Nov 2018 13:56:49 -0500 Subject: [PATCH 360/546] edit grid (#12298) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * minor edit to recipe grid --- recipes/grid/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/grid/meta.yaml b/recipes/grid/meta.yaml index 28a816d0afbf1..b5e54074b5c45 100644 --- a/recipes/grid/meta.yaml +++ b/recipes/grid/meta.yaml @@ -1,14 +1,13 @@ package: name: grid - version: "1.1" + version: "1.2" build: skip: True # [osx] - number: 4 source: - url: https://github.com/ohlab/GRiD/archive/1.1.tar.gz - sha256: 9ba8bd0e3ea6cc029a4a560bc07c98fe2aacab1364f2185961f2db4eac8c9aa6 + url: https://github.com/ohlab/GRiD/archive/1.2.tar.gz + sha256: be730aed472c72f41d6d7ef0d1f545bbd68d06ee092a8ca9da96fa6e68038db1 requirements: run: From bcd13e67305448af2b25fb8ec6040129d04b273b Mon Sep 17 00:00:00 2001 From: Simon van Heeringen Date: Thu, 22 Nov 2018 21:31:11 +0100 Subject: [PATCH 361/546] added feather to deps (#12293) --- recipes/gimmemotifs/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/gimmemotifs/meta.yaml b/recipes/gimmemotifs/meta.yaml index 4bf8ae6def78c..a05e22a68e469 100644 --- a/recipes/gimmemotifs/meta.yaml +++ b/recipes/gimmemotifs/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ccaa9ec2b58f22fd7fb07680de0d4e7fc3d9eff2ec2aed26c0d89abb94cb69ca build: - number: 0 + number: 1 requirements: build: @@ -47,6 +47,7 @@ requirements: - tqdm - genomepy - ncurses + - feather-format run: - python >=3 @@ -81,6 +82,7 @@ requirements: - tqdm - genomepy - ncurses + - feather-format test: imports: From de421ce02f03640d9bb5095ad93b684d73c2b584 Mon Sep 17 00:00:00 2001 From: Fabien Pertuy Date: Thu, 22 Nov 2018 22:15:07 +0100 Subject: [PATCH 362/546] R tigger (#12286) * Create recipe for r-tigger (#12271) * Create recipe for r-tigger using bgruening/conda_r_skeleton_helper. * Delete bld.bat * Remove windows support --- recipes/r-tigger/build.sh | 34 ++++++++++++++++++ recipes/r-tigger/meta.yaml | 73 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 recipes/r-tigger/build.sh create mode 100644 recipes/r-tigger/meta.yaml diff --git a/recipes/r-tigger/build.sh b/recipes/r-tigger/build.sh new file mode 100644 index 0000000000000..55e85eb9a5789 --- /dev/null +++ b/recipes/r-tigger/build.sh @@ -0,0 +1,34 @@ +#!/bin/bash +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/tigger + mv * $PREFIX/lib/R/library/tigger + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-tigger/meta.yaml b/recipes/r-tigger/meta.yaml new file mode 100644 index 0000000000000..d36d6978a81d3 --- /dev/null +++ b/recipes/r-tigger/meta.yaml @@ -0,0 +1,73 @@ +{% set version = '0.3.1' %} + +package: + name: r-tigger + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/tigger_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/tigger/tigger_{{ version }}.tar.gz + sha256: 2dc221be0a01a608bb9b0cd5e0cd44e257e14f7add46cd97fab729620e55c8ab + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-alakazam >=0.2.11 + - r-doparallel + - r-dplyr >=0.7.0 + - r-foreach + - r-ggplot2 >=2.0.0 + - r-gridextra + - r-gtools + - r-iterators + - r-lazyeval + - r-rlang + - r-shazam >=0.1.10 + - r-stringi + - r-tidyr + run: + - r-base + - r-alakazam >=0.2.11 + - r-doparallel + - r-dplyr >=0.7.0 + - r-foreach + - r-ggplot2 >=2.0.0 + - r-gridextra + - r-gtools + - r-iterators + - r-lazyeval + - r-rlang + - r-shazam >=0.1.10 + - r-stringi + - r-tidyr + +test: + commands: + - $R -e "library('tigger')" + +about: + home: http://tigger.readthedocs.io + license: CC BY-SA 4.0 + summary: 'Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing + data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information + is then used to correct existing V allele calls from among the sample sequences. + Citations: Gadala-Maria, et al (2015) .' + license_family: CC + +extra: + recipe-maintainers: + - johanneskoester + - bgruening + - daler + - jdblischak + - cbrueffer + - dbast + - PertuyF From 9da5a6ea298d9c08b8140c7ca60cf9ac08c8cb11 Mon Sep 17 00:00:00 2001 From: Scott Gigante Date: Fri, 23 Nov 2018 00:44:31 -0500 Subject: [PATCH 363/546] update scprep to v0.8.1 (#12306) --- recipes/scprep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scprep/meta.yaml b/recipes/scprep/meta.yaml index 88c4cbab699a3..f6fdd2ae1eb5b 100644 --- a/recipes/scprep/meta.yaml +++ b/recipes/scprep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scprep" %} -{% set version = "0.7.1" %} +{% set version = "0.8.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 916f21dbda25f085378c5e44d28cfc4bd91ccedbbdc09b77d15cb81e31e18fe3 + sha256: 4da05d30f5841c977a091a66e5367d85ad3c64f7b8b51ff84a3847fce322fb49 build: number: 0 From a5a52c04a699ae1f1103df08414244c5311756b6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 23 Nov 2018 02:53:07 -0700 Subject: [PATCH 364/546] Update nanoget to 1.7.5 (#12252) * Update nanoget to 1.7.5 * Bump to version 1.7.6 should fix the README.md problem --- recipes/nanoget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanoget/meta.yaml b/recipes/nanoget/meta.yaml index 0fe8847ba3ec7..e3e55354f38ba 100644 --- a/recipes/nanoget/meta.yaml +++ b/recipes/nanoget/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.4" %} +{% set version = "1.7.6" %} package: name: nanoget @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanoget/nanoget-{{ version }}.tar.gz - sha256: 08f27ccf86006fc2c7345f5f41c098c1bf8992364d78abc118b5ce92696d6e65 + sha256: 4458fdf523fbd4e96167e30824718617e9b161b076edbad76ca7ca66b47e35fb build: number: 0 From dcb60f4d0ba5a4cbf737c932ca8017d8c9f7bcac Mon Sep 17 00:00:00 2001 From: M Bernt Date: Fri, 23 Nov 2018 11:48:24 +0100 Subject: [PATCH 365/546] gffcompare: version bump (#12308) --- recipes/gffcompare/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gffcompare/meta.yaml b/recipes/gffcompare/meta.yaml index 2781c16b18ad2..9b02c6e2265c1 100644 --- a/recipes/gffcompare/meta.yaml +++ b/recipes/gffcompare/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gffcompare" %} -{% set version = "0.10.5" %} -{% set sha256hash = "fce3b8c469f6d9225552f9905f865306f302bb9edd466f7e2a94dff2db313583" %} +{% set version = "0.10.6" %} +{% set sha256hash = "98fd98b3035d0a8971f46b7947f2f1dbe034e4add71bbfaaade454927fce9784" %} package: name: {{ name }} From 035fbee74a1af3315b918961e26d4368ddc7e997 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Fri, 23 Nov 2018 07:12:25 -0500 Subject: [PATCH 366/546] Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307) * Update: cromwell (36), bcbio (Cromwell Docker runs) * Pin java to 8 to avoid compile errors on 11 --- recipes/bcbio-nextgen/meta.yaml | 6 +++--- recipes/cromwell/meta.yaml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index a2bac0868362d..56acbf2c81d95 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -3,13 +3,13 @@ package: version: '1.1.2a' build: - number: 1 + number: 2 skip: true # [not py27] source: #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz - url: https://github.com/bcbio/bcbio-nextgen/archive/3a2e565.tar.gz - sha256: cec1148e2f3411aaee84047fb4c83a545bc3863ae8f770be1e85844854b2ba39 + url: https://github.com/bcbio/bcbio-nextgen/archive/00180f8.tar.gz + sha256: 6e1947cc4c1788a7e10712a61a14f1137c6f1c387023e8efbad76b26a8cbc4fd requirements: host: diff --git a/recipes/cromwell/meta.yaml b/recipes/cromwell/meta.yaml index f8f2c6750b47f..3e9a05db60bc1 100644 --- a/recipes/cromwell/meta.yaml +++ b/recipes/cromwell/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "35" %} -{% set sha256 = "5ef5afb286a04bf63ab175082597bd9ced5001db35ef34f9a596232aaf2a132c" %} +{% set version = "36" %} +{% set sha256 = "6e668caa2568510312ede7a3f75f4880937a2542c2697e44f43d50e04f9ca581" %} package: name: cromwell @@ -15,11 +15,11 @@ source: requirements: host: - - openjdk >=8 + - openjdk >=8,<9 - sbt - scala run: - - openjdk >=8 + - openjdk >=8,<9 - python - findutils From 90649fecc04082f7bbcd274f3109dde091e8e3fc Mon Sep 17 00:00:00 2001 From: Joachim Wolff Date: Fri, 23 Nov 2018 16:13:42 +0100 Subject: [PATCH 367/546] HiCExplorer update to version 2.2-beta (#12309) * HiCExplorer update to version 2.2-beta * Remove of '-' from version number * Numpy set to 1.15 * Update meta.yaml --- recipes/hicexplorer/meta.yaml | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/recipes/hicexplorer/meta.yaml b/recipes/hicexplorer/meta.yaml index 22945e3f2545b..93140cf733a8d 100644 --- a/recipes/hicexplorer/meta.yaml +++ b/recipes/hicexplorer/meta.yaml @@ -1,21 +1,22 @@ package: name: hicexplorer - version: '2.1.4' + version: '2.2beta' source: - url: https://github.com/deeptools/HiCExplorer/archive/2.1.4.tar.gz - sha256: 83dec8e0388cb185a51fa6cfb055be084be0f8a2912bba18f5bc159d19831698 + url: https://github.com/deeptools/HiCExplorer/archive/2.2-beta.tar.gz + sha256: fbdcb0697323489999cfaad609721afa4c89401f0917fd51a1c2bf8cbacfb817 build: - number: 3 + number: 0 + skip: True #[py35] requirements: host: - python - setuptools - - numpy + - numpy >=1.15 - scipy - - matplotlib 2.1.* + - matplotlib >=2.2.* - pysam - intervaltree - biopython @@ -24,15 +25,17 @@ requirements: - pandas - jinja2 - configparser # [not py>34] - - cooler <=0.7.6 + - cooler >=0.7.11 - six - future - unidecode + - hicmatrix + - pygenometracks run: - python - - numpy + - numpy >=1.15 - scipy - - matplotlib 2.1.* + - matplotlib >=2.2.* - pysam - intervaltree - biopython @@ -41,10 +44,12 @@ requirements: - pandas - jinja2 - configparser # [not py>34] - - cooler <=0.7.6 + - cooler >=0.7.11 - six - future - unidecode + - hicmatrix + - pygenometracks test: imports: From 178b7802b8fc5d3989b99036df434c4b5b7df8c8 Mon Sep 17 00:00:00 2001 From: Andreas Heger Date: Fri, 23 Nov 2018 20:55:14 +0000 Subject: [PATCH 368/546] upgrade to version 2.8.1 (#12316) --- recipes/ruffus/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ruffus/meta.yaml b/recipes/ruffus/meta.yaml index 794d5d51f719d..4988f6e1cdaa6 100644 --- a/recipes/ruffus/meta.yaml +++ b/recipes/ruffus/meta.yaml @@ -1,10 +1,10 @@ package: name: ruffus - version: 2.8 + version: 2.8.1 source: - url: https://files.pythonhosted.org/packages/ac/c7/5652e44a3644dfdf8cdfa17c2bb7933896dddec99888f57bf2adbbcca226/ruffus-2.8.0.tar.gz - sha256: 609e76e88de2d11362ed2a312917508f14daf56413fd1b3c7d5a96aaa14bb5e9 + url: https://files.pythonhosted.org/packages/18/24/05e8fe590d08bd9e6122c6a87425ff741c79edf01d2873f92028e860e547/ruffus-2.8.1.tar.gz + sha256: 90bc1e57ffb95be11e9c4461a406fee63395898beacd35a1dce9dd2c468c2582 build: noarch: python From c0d2bd05d833a7975c8c18b49dfb2420f8cac6c5 Mon Sep 17 00:00:00 2001 From: Fabien Pertuy Date: Sat, 24 Nov 2018 00:04:21 +0100 Subject: [PATCH 369/546] Create Airr recipe (#12318) * Create AIRR recipe using conda skeleton pypi. * Add noarch python * Clean host requirements --- recipes/airr/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/airr/meta.yaml diff --git a/recipes/airr/meta.yaml b/recipes/airr/meta.yaml new file mode 100644 index 0000000000000..53d6f1be86401 --- /dev/null +++ b/recipes/airr/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "airr" %} +{% set version = "1.2.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: b6c523cee7822b327bfcc637e6261bda27a0d4148bc46a73fef745199ee5fcb9 + +build: + number: 0 + noarch: python + entry_points: + - airr-tools=airr.tools:main + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv " + +requirements: + host: + - pip + - python + run: + - pandas >=0.18.0 + - python + - pyyaml >=3.12 + - setuptools >=2.0 + - yamlordereddictloader >=0.4.0 + +test: + imports: + - airr + - airr.specs + - tests + commands: + - airr-tools --help + +about: + home: http://docs.airr-community.org + license: CC BY 4.0 + license_family: CC + summary: 'AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data. + Citations: AIRR standards .' + +extra: + recipe-maintainers: + - PertuyF From 43e0663c75be6f85427dd425730826f6dd7ad3a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C5=BDiga=20Avsec?= Date: Sat, 24 Nov 2018 13:00:04 +0100 Subject: [PATCH 370/546] Added nimnexus [v0.1] (#12133) * added nimnexus * Fix sha * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/nimnexus/build.sh | 53 ++++++++++++++++++++++++++++++++++++++ recipes/nimnexus/meta.yaml | 36 ++++++++++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 recipes/nimnexus/build.sh create mode 100644 recipes/nimnexus/meta.yaml diff --git a/recipes/nimnexus/build.sh b/recipes/nimnexus/build.sh new file mode 100644 index 0000000000000..419668ec5d9cd --- /dev/null +++ b/recipes/nimnexus/build.sh @@ -0,0 +1,53 @@ +#!/bin/bash +set -eu -o pipefail + +# Build script based off of mosdepth build +# https://github.com/brentp/mosdepth/blob/master/scripts/install.sh + +NIM_VERSION=v0.19.0 +NIMBLE_VERSION=v0.9.0 +export base=$(pwd) + +# Install nim +git clone -b $NIM_VERSION --depth 1 git://github.com/nim-lang/nim nim-$NIM_VERSION/ +cd nim-$NIM_VERSION +git clone -b $NIM_VERSION --depth 1 git://github.com/nim-lang/csources csources/ + +cd csources +# Fix compiler references to use conda set CC +export LINKER=$CC +sed -i.bak '/^CC=/s/^/#/g' build.sh +sed -i.bak '/^LINKER=/s/^/#/g' build.sh +sh build.sh +cd .. +rm -rf csources +bin/nim c koch +./koch boot -d:release + +export PATH=$base/nim-$NIM_VERSION/bin/:$PATH:$base/nimble/src:$PATH + +cd $base +echo $PATH + +set -x + +git clone -b $NIMBLE_VERSION --depth 1 git://github.com/nim-lang/nimble.git +cd nimble +nim c src/nimble + +cd $base +git clone --depth 1 git://github.com/brentp/hts-nim.git +cd hts-nim +grep -v requires hts.nimble > k.nimble && mv k.nimble hts.nimble +nimble install -y + +echo $(which nimble) +echo $(pwd) + +set -x +cd $base +nimble --nimbleDir:$base/.nimble install -y + +mkdir -p $PREFIX/bin +chmod a+x nimnexus +cp nimnexus $PREFIX/bin diff --git a/recipes/nimnexus/meta.yaml b/recipes/nimnexus/meta.yaml new file mode 100644 index 0000000000000..de686600677ab --- /dev/null +++ b/recipes/nimnexus/meta.yaml @@ -0,0 +1,36 @@ +{% set name = "nimnexus" %} +{% set version = "0.1.0" %} +{% set revision = "52aed74" %} +{% set sha256hash = "c59d7804a35902acc47b5d60a28692dfdc1c38902df7074b70ae92008e4dbd43" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/avsecz/{{ name }}/archive/{{ revision }}.tar.gz + sha256: {{ sha256hash }} + +build: + number: 2 + skip: True # [osx] + +requirements: + build: + - {{ compiler('c') }} + host: + - pcre + - htslib + run: + - pcre + - htslib + +test: + commands: + - nimnexus trim -h + - nimnexus dedup -h + +about: + home: https://github.com/avsecz/nimnexus + license: MIT + summary: command-line tools for processing ChIP-nexus data From f2dc191522f3b859f80fdb8ed52dea266b81e362 Mon Sep 17 00:00:00 2001 From: Mehmet Tekman Date: Sat, 24 Nov 2018 14:12:52 +0100 Subject: [PATCH 371/546] [WIP] Add R-loom (#12320) * initial WIP skeleton * Update meta.yaml * Update meta.yaml * Update meta.yaml * try osx --- recipes/r-loom/build.sh | 1 + recipes/r-loom/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/r-loom/build.sh create mode 100644 recipes/r-loom/meta.yaml diff --git a/recipes/r-loom/build.sh b/recipes/r-loom/build.sh new file mode 100644 index 0000000000000..aea5b12eaa821 --- /dev/null +++ b/recipes/r-loom/build.sh @@ -0,0 +1 @@ +R CMD INSTALL --build . diff --git a/recipes/r-loom/meta.yaml b/recipes/r-loom/meta.yaml new file mode 100644 index 0000000000000..a6d211f10850a --- /dev/null +++ b/recipes/r-loom/meta.yaml @@ -0,0 +1,48 @@ +package: + name: r-loom + # package is neccesary until CRAN release + version: 0.2.0.1 + +source: + url: https://github.com/mojaveazure/loomR/archive/df0144bd2bbceca6fadef9edc1bbc5ca672d4739.tar.gz + sha256: 6264448baf4fd9a569eb5a832598c4a224382ef26c0a7fbd061a8c901672f0ac + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-devtools + - r-hdf5r + - r-iterators + - r-itertools + - r-matrix + run: + - r-base + - r-hdf5r + - r-iterators + - r-itertools + - r-matrix +test: + commands: + - $R -e "library(loomR)" + +about: + home: https://github.com/mojaveazure/loomR + license: GPL-3 + summary: "An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files." + license_family: GPL3 + +extra: + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak From 94dead7d7f7799dd215d1fbbe75d055e76375e15 Mon Sep 17 00:00:00 2001 From: Fabien Pertuy Date: Sat, 24 Nov 2018 15:21:06 +0100 Subject: [PATCH 372/546] Create Changeo recipe (#12321) * Create changeo recipe using conda skeleton pypi. * EDIT about section * ADD noarch generic * Update noarch to python * Clean host requirements * Add test for scripts * Change requirement to python>=3.4 * Add noarch pyton --- recipes/changeo/meta.yaml | 55 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 recipes/changeo/meta.yaml diff --git a/recipes/changeo/meta.yaml b/recipes/changeo/meta.yaml new file mode 100644 index 0000000000000..dc1f68fd8ff11 --- /dev/null +++ b/recipes/changeo/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "changeo" %} +{% set version = "0.4.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 7d19ac3873acf83abe6115b7f4787629a622b0fc3095e8a3ab4b35a675d163e2 + +build: + noarch: python + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + +requirements: + host: + - pip + - python >=3.4 + run: + - airr >=1.2.1 + - biopython >=1.65 + - numpy >=1.8 + - pandas >=0.15 + - presto >=0.5.10 + - python >=3.4 + - pyyaml >=3.12 + - scipy >=0.14 + - setuptools >=2.0 + +test: + imports: + - changeo + commands: + - AlignRecords.py --version + - AssignGenes.py --version + - BuildTrees.py --version + - ConvertDb.py --version + - CreateGermlines.py --version + - DefineClones.py --version + - MakeDb.py --version + - ParseDb.py --version + + +about: + home: http://changeo.readthedocs.io + license: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) + license_family: CC + summary: 'A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data. + Citations: Gupta, et al (2015) .' + +extra: + recipe-maintainers: + - PertuyF From 8d6f86bb5f18305cbedb3fc8e5ff8dd378d7a00f Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Sat, 24 Nov 2018 18:10:55 -0500 Subject: [PATCH 373/546] r-corbi (#12325) --- recipes/r-corbi/build.sh | 38 +++++++++++++++++++++++ recipes/r-corbi/meta.yaml | 64 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 recipes/r-corbi/build.sh create mode 100644 recipes/r-corbi/meta.yaml diff --git a/recipes/r-corbi/build.sh b/recipes/r-corbi/build.sh new file mode 100644 index 0000000000000..a3609d7f0dfdb --- /dev/null +++ b/recipes/r-corbi/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/Corbi + mv * $PREFIX/lib/R/library/Corbi + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-corbi/meta.yaml b/recipes/r-corbi/meta.yaml new file mode 100644 index 0000000000000..5fc2e814be8be --- /dev/null +++ b/recipes/r-corbi/meta.yaml @@ -0,0 +1,64 @@ +{% set version = '0.4-2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-corbi + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/Corbi_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/Corbi/Corbi_{{ version }}.tar.gz + sha256: fc7adee4866c5fbcdc0b051bb3e910df0400651b7c6b749dbd51f94c6f440840 + +build: + merge_build_host: True # [win] + + number: 0 + + + rpaths: + - lib/R/lib/ + - lib/ + + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{ compiler('fortran') }} + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + - r-crf + - r-matrix + - r-mpmi + + run: + - r-base + - {{native}}gcc-libs # [win] + - r-crf + - r-matrix + - r-mpmi + +test: + commands: + - $R -e "library('Corbi')" # [not win] + - "\"%R%\" -e \"library('Corbi')\"" # [win] + +about: + home: https://github.com/wulingyun/Corbi + license: GPL (>= 2) + summary: Provides a bundle of basic and fundamental bioinformatics tools, such as network querying + and alignment, subnetwork extraction and search, network biomarker identification. + license_family: GPL3 + + From 0b3caddb203a9ecb7fb0fdbeb12847cd05455d02 Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Sat, 24 Nov 2018 20:45:19 -0500 Subject: [PATCH 374/546] r-nam (#12327) --- recipes/r-nam/build.sh | 34 ++++++++++++++++++++ recipes/r-nam/meta.yaml | 69 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 recipes/r-nam/build.sh create mode 100644 recipes/r-nam/meta.yaml diff --git a/recipes/r-nam/build.sh b/recipes/r-nam/build.sh new file mode 100644 index 0000000000000..f98a41ea93092 --- /dev/null +++ b/recipes/r-nam/build.sh @@ -0,0 +1,34 @@ +#!/bin/bash +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/NAM + mv * $PREFIX/lib/R/library/NAM + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-nam/meta.yaml b/recipes/r-nam/meta.yaml new file mode 100644 index 0000000000000..ac8f3537750eb --- /dev/null +++ b/recipes/r-nam/meta.yaml @@ -0,0 +1,69 @@ +{% set version = '1.6.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-nam + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/NAM_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/NAM/NAM_{{ version }}.tar.gz + sha256: a45ecf3286f7c17028d38a8389b7173b1ec38047768cec64a5e961649964ad2c + +build: + merge_build_host: True # [win] + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + - r-rcpp + - r-randomforest + + run: + - r-base + - {{native}}gcc-libs # [win] + - r-rcpp + - r-randomforest + +test: + commands: + - $R -e "library('NAM')" # [not win] + - "\"%R%\" -e \"library('NAM')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=NAM + license: GPL-3 + summary: Designed for association studies in nested association mapping (NAM) panels, experimental + and random panels. The method is described by Xavier et al. (2015) . + It includes tools for genome-wide associations of multiple populations, marker quality + control, population genetics analysis, genome-wide prediction, solving mixed models + and finding variance components through likelihood and Bayesian methods. + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + +extra: + recipe-maintainers: + - johanneskoester + - bgruening + - daler + - jdblischak + - cbrueffer + - dbast + - Chris-Lowe-Integrity From a4b1778659994f3d98a8771ffbc95869c1bcd098 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 24 Nov 2018 20:49:01 -0500 Subject: [PATCH 375/546] Update pybedtools to 0.8.0 (#12324) * Update pybedtools to 0.8.0 * rm cython requirement --- recipes/pybedtools/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/pybedtools/meta.yaml b/recipes/pybedtools/meta.yaml index 4b5f5b187ce23..28fdb83d3b66e 100644 --- a/recipes/pybedtools/meta.yaml +++ b/recipes/pybedtools/meta.yaml @@ -1,13 +1,13 @@ package: name: pybedtools - version: '0.7.10' + version: '0.8.0' source: - url: https://pypi.python.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz - md5: f003c67e22c48b77f070538368ece70c + url: https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz + sha256: 4eebd2cd1764ee1c604fd881703c3e329195485350b987b7fb8db42d232984f6 build: - number: 3 + number: 0 requirements: build: @@ -18,7 +18,6 @@ requirements: - pysam >=0.8.1 - setuptools - pandas - - cython - zlib run: From 4213b7d00d20795c48d66efea43f3d98db357588 Mon Sep 17 00:00:00 2001 From: Jorrit Boekel Date: Sun, 25 Nov 2018 23:30:11 +0100 Subject: [PATCH 376/546] MSGFplus does not work with newer Java (#12330) * Trying to not use a very new java version since the latest versions have dropped some classes * Increment build --- recipes/msgf_plus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/msgf_plus/meta.yaml b/recipes/msgf_plus/meta.yaml index f65a9683bd8a7..a567108cd3ae8 100644 --- a/recipes/msgf_plus/meta.yaml +++ b/recipes/msgf_plus/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/sangtaekim/msgfplus/releases/download/v2017.07.21/v20170721.zip @@ -12,7 +12,7 @@ source: requirements: run: - - openjdk + - openjdk<11 - python test: From ee468fe68820b635bd09ca2f04538daa5c67362e Mon Sep 17 00:00:00 2001 From: John Didion Date: Sun, 25 Nov 2018 17:30:38 -0500 Subject: [PATCH 377/546] Update atropos to 1.1.21 (#12322) --- recipes/atropos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/atropos/meta.yaml b/recipes/atropos/meta.yaml index ae12fcb123c4d..df37a7057119f 100644 --- a/recipes/atropos/meta.yaml +++ b/recipes/atropos/meta.yaml @@ -1,6 +1,6 @@ {% set name = "atropos" %} -{% set version = "1.1.19" %} -{% set hash = "297513f59574a5570a7477b9aacf9abe389790c144738bad93cf744b5099b010" %} +{% set version = "1.1.21" %} +{% set hash = "8178af467734b299960edae15d8835a2228ba0cc1b718af436c7d86041fbd4ec" %} package: name: {{ name }} From 056e349643f2c68e39a94175345ef593d06bc227 Mon Sep 17 00:00:00 2001 From: Johannes Alneberg Date: Sun, 25 Nov 2018 23:31:06 +0100 Subject: [PATCH 378/546] Update CONCOCT to 0.4.2 (#12317) * Update CONCOCT to 0.4.2 * Wrong shasum given * Reset build number for new version --- recipes/concoct/concoct.patch | 11 ----------- recipes/concoct/meta.yaml | 11 ++++++----- 2 files changed, 6 insertions(+), 16 deletions(-) delete mode 100644 recipes/concoct/concoct.patch diff --git a/recipes/concoct/concoct.patch b/recipes/concoct/concoct.patch deleted file mode 100644 index a38093efbe2b4..0000000000000 --- a/recipes/concoct/concoct.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- setup.py 2018-10-11 11:19:58.000000000 +0200 -+++ setup.py 2018-10-11 11:20:24.000000000 +0200 -@@ -36,7 +36,7 @@ - 'pandas>=0.11.0', - 'biopython>=1.62b', - 'scikit-learn>=0.13.1', -- 'nose==1.3.0'], -+ 'nose'], - entry_points=""" - # -*- Entry points: -*- - """, diff --git a/recipes/concoct/meta.yaml b/recipes/concoct/meta.yaml index 686c2fe4dd8b4..6efcab66b3b36 100644 --- a/recipes/concoct/meta.yaml +++ b/recipes/concoct/meta.yaml @@ -1,16 +1,15 @@ package: name: concoct - version: "0.4.1" + version: "0.4.2" source: - url: https://github.com/BinPro/CONCOCT/archive/9f09f5385ce378406208b07b5102254aa6b61471.tar.gz - sha256: 3eff2a8d2188a9b42e686fcd49e8614b7c9e76daac8320971d276d4e5406b6d5 - patches: - - concoct.patch + url: https://github.com/BinPro/CONCOCT/archive/0.4.2.tar.gz + sha256: 1242460a6d0b53e2aa28a1426213db397f6fd7dcaccd783cf24a2d09c035605c build: preserve_egg_dir: True number: 0 + skip: True # [not py27] requirements: build: @@ -47,6 +46,8 @@ requirements: - openblas test: + commands: + - concoct -h imports: - concoct From 7332d907e5df17fd8197c6033e0ab2adf91977a4 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Mon, 26 Nov 2018 04:58:59 -0500 Subject: [PATCH 379/546] New: gvcfgenotyper for joint calling with Illumina strelka2 (#12331) --- recipes/gvcfgenotyper/build.sh | 11 +++++++++++ recipes/gvcfgenotyper/meta.yaml | 32 ++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/gvcfgenotyper/build.sh create mode 100644 recipes/gvcfgenotyper/meta.yaml diff --git a/recipes/gvcfgenotyper/build.sh b/recipes/gvcfgenotyper/build.sh new file mode 100644 index 0000000000000..e0b1080ffafc6 --- /dev/null +++ b/recipes/gvcfgenotyper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu -o pipefail + +cd external/htslib-* +./configure --prefix=${PREFIX} --disable-lzma --disable-bz2 +cd ../.. +sed -i.bak 's^-Isrc/c/^-Isrc/c/ -I${PREFIX}/include^' Makefile +sed -i.bak 's^-lpthread^-lpthread -L$(PREFIX)/lib^' Makefile +make +mkdir -p $PREFIX/bin +cp bin/gvcfgenotyper $PREFIX/bin diff --git a/recipes/gvcfgenotyper/meta.yaml b/recipes/gvcfgenotyper/meta.yaml new file mode 100644 index 0000000000000..2f4816fea3317 --- /dev/null +++ b/recipes/gvcfgenotyper/meta.yaml @@ -0,0 +1,32 @@ +{% set version="2018.10.15" %} +{% set hash="e873f57a4df61f24901f2bb2cdf827e1cfcfc663858e56548374b0667d4c9549" %} + +package: + name: gvcfgenotyper + version: {{ version }} + + +source: + url: https://github.com/Illumina/gvcfgenotyper/archive/{{ version }}.tar.gz + sha256: {{ hash }} + +build: + number: 0 + skip: True # [not linux] + +requirements: + build: + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + +test: + commands: + - gvcfgenotyper 2>&1 | grep 'About:' + +about: + home: https://github.com/Illumina/gvcfgenotyper + license: Apache 2.0 + summary: A utility for merging and genotyping Illumina-style GVCFs. From f269fa98ec1134b414a9996a0b0c6fbcaa4183d8 Mon Sep 17 00:00:00 2001 From: Jorrit Boekel Date: Mon, 26 Nov 2018 12:41:26 +0100 Subject: [PATCH 380/546] Apparently we need openJDK to be below 9, not below 11 as in the previous PR (#12332) --- recipes/msgf_plus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/msgf_plus/meta.yaml b/recipes/msgf_plus/meta.yaml index a567108cd3ae8..25ebd5dc122dd 100644 --- a/recipes/msgf_plus/meta.yaml +++ b/recipes/msgf_plus/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 2 + number: 3 source: url: https://github.com/sangtaekim/msgfplus/releases/download/v2017.07.21/v20170721.zip @@ -12,7 +12,7 @@ source: requirements: run: - - openjdk<11 + - openjdk<9 - python test: From 78d41d0f6bd8d0a2b190a9bbf174f9220221988d Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Mon, 26 Nov 2018 14:24:38 +0100 Subject: [PATCH 381/546] Update Picard to 2.18.17. (#12333) --- recipes/picard/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index 6a98ff39cd676..0a6a9ff881ba2 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.18.16" %} -{% set sha256 = "0aae8886ab29b9eeb40118994ad944fed2e1d043b5a5dc497884b5795a42e975" %} +{% set version = "2.18.17" %} +{% set sha256 = "f51f64824072f26dc5d0932376929b20e6f66ff478810bcf8145792773f5474f" %} package: name: picard From 6beb59cc9471648115ed38fcb5768fabd2b30d61 Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Mon, 26 Nov 2018 15:08:07 +0100 Subject: [PATCH 382/546] Unblacklist IgDiscover (#12335) --- build-fail-blacklist | 2 -- 1 file changed, 2 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index ed1007a4effb9..c808e3f74dc1e 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -310,8 +310,6 @@ recipes/imfusion/0.3.0 recipes/imfusion/0.3.2 recipes/poretools/0.5.1 -# conda.exceptions.PaddingError: Placeholder of length '80' too short in package /opt/conda/conda-bld/igdiscover_1530078817859/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.5/site-packages/sqt/_helpers.cpython-35m-x86_64-linux-gnu.so. -recipes/igdiscover # RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/pyaml/# recipes/hubward From f5824651279da3e14e02a63fe6e729559ce74cbb Mon Sep 17 00:00:00 2001 From: David Seifert <39679069+pb-dseifert@users.noreply.github.com> Date: Mon, 26 Nov 2018 16:12:55 +0100 Subject: [PATCH 383/546] PacBio: Add missing licenses and post-link message (#12334) --- recipes/bam2fastx/meta.yaml | 4 ++-- recipes/bam2fastx/post-link.sh | 32 +++++++++++++++++++++++++++++++ recipes/bax2bam/meta.yaml | 4 ++-- recipes/bax2bam/post-link.sh | 32 +++++++++++++++++++++++++++++++ recipes/blasr/meta.yaml | 4 ++-- recipes/blasr_libcpp/meta.yaml | 4 ++-- recipes/blasr_libcpp/post-link.sh | 32 +++++++++++++++++++++++++++++++ recipes/pbalign/meta.yaml | 4 ++-- recipes/pbalign/post-link.sh | 32 +++++++++++++++++++++++++++++++ recipes/pbbam/meta.yaml | 4 ++-- recipes/pbcopper/post-link.sh | 32 +++++++++++++++++++++++++++++++ 11 files changed, 172 insertions(+), 12 deletions(-) create mode 100644 recipes/bam2fastx/post-link.sh create mode 100644 recipes/bax2bam/post-link.sh create mode 100644 recipes/blasr_libcpp/post-link.sh create mode 100644 recipes/pbalign/post-link.sh create mode 100644 recipes/pbcopper/post-link.sh diff --git a/recipes/bam2fastx/meta.yaml b/recipes/bam2fastx/meta.yaml index 6c6f33dec5d28..7ea7581a6dcbc 100644 --- a/recipes/bam2fastx/meta.yaml +++ b/recipes/bam2fastx/meta.yaml @@ -12,7 +12,7 @@ source: about: home: https://github.com/PacificBiosciences/bam2fastx - license: BSD + license: BSD-3-Clause-Clear summary: Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files extra: @@ -21,7 +21,7 @@ extra: - mhsieh build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/bam2fastx/post-link.sh b/recipes/bam2fastx/post-link.sh new file mode 100644 index 0000000000000..703ab0b671961 --- /dev/null +++ b/recipes/bam2fastx/post-link.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +cat > "${PREFIX}"/.messages.txt <<- EOF + + ############################################################################## + # # + # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # + # necessarily ISO compliant, intended for Research Use Only and not for use # + # in diagnostic procedures, intended only for command-line users, and # + # possibly newer than the currently available SMRT(R) Analysis builds. While # + # efforts have been made to ensure that releases on Bioconda live up to the # + # quality that PacBio strives for, we make no warranty regarding any # + # Bioconda release. # + # # + # As PacBio tools distributed via Bioconda are not covered by any service # + # level agreement or the like, please *do not* contact a PacBio Field # + # Applications Scientist or PacBio Customer Service for assistance with any # + # Bioconda release. We instead provide an issue tracker for you to report # + # issues to us at: # + # # + # https://github.com/PacificBiosciences/pbbioconda # + # # + # We make no warranty that any such issue will be addressed, # + # to any extent or within any time frame. # + # # + # BSD 3-Clause Clear License # + # # + # Please see https://github.com/PacificBiosciences/pbbioconda for # + # information on License, Copyright and Disclaimer # + # # + ############################################################################## +EOF diff --git a/recipes/bax2bam/meta.yaml b/recipes/bax2bam/meta.yaml index b0d2c1e22710a..3e933df42913d 100644 --- a/recipes/bax2bam/meta.yaml +++ b/recipes/bax2bam/meta.yaml @@ -12,7 +12,7 @@ source: about: home: https://github.com/PacificBiosciences/bax2bam - license: BSD + license: BSD-3-Clause-Clear summary: bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format extra: @@ -21,7 +21,7 @@ extra: - mhsieh build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/bax2bam/post-link.sh b/recipes/bax2bam/post-link.sh new file mode 100644 index 0000000000000..703ab0b671961 --- /dev/null +++ b/recipes/bax2bam/post-link.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +cat > "${PREFIX}"/.messages.txt <<- EOF + + ############################################################################## + # # + # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # + # necessarily ISO compliant, intended for Research Use Only and not for use # + # in diagnostic procedures, intended only for command-line users, and # + # possibly newer than the currently available SMRT(R) Analysis builds. While # + # efforts have been made to ensure that releases on Bioconda live up to the # + # quality that PacBio strives for, we make no warranty regarding any # + # Bioconda release. # + # # + # As PacBio tools distributed via Bioconda are not covered by any service # + # level agreement or the like, please *do not* contact a PacBio Field # + # Applications Scientist or PacBio Customer Service for assistance with any # + # Bioconda release. We instead provide an issue tracker for you to report # + # issues to us at: # + # # + # https://github.com/PacificBiosciences/pbbioconda # + # # + # We make no warranty that any such issue will be addressed, # + # to any extent or within any time frame. # + # # + # BSD 3-Clause Clear License # + # # + # Please see https://github.com/PacificBiosciences/pbbioconda for # + # information on License, Copyright and Disclaimer # + # # + ############################################################################## +EOF diff --git a/recipes/blasr/meta.yaml b/recipes/blasr/meta.yaml index 24861a679be6a..8593216be0558 100644 --- a/recipes/blasr/meta.yaml +++ b/recipes/blasr/meta.yaml @@ -12,7 +12,7 @@ source: about: home: https://github.com/PacificBiosciences/blasr - license: BSD + license: BSD-3-Clause-Clear summary: BLASR - The PacBio long read aligner extra: @@ -21,7 +21,7 @@ extra: - mhsieh build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/blasr_libcpp/meta.yaml b/recipes/blasr_libcpp/meta.yaml index dac5af25c5410..d5eb067a66a9b 100644 --- a/recipes/blasr_libcpp/meta.yaml +++ b/recipes/blasr_libcpp/meta.yaml @@ -12,7 +12,7 @@ source: about: home: https://github.com/PacificBiosciences/blasr_libcpp - license: BSD + license: BSD-3-Clause-Clear summary: blasr_libcpp is a support library used by blasr and other PacBio tools extra: @@ -21,7 +21,7 @@ extra: - mhsieh build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/blasr_libcpp/post-link.sh b/recipes/blasr_libcpp/post-link.sh new file mode 100644 index 0000000000000..703ab0b671961 --- /dev/null +++ b/recipes/blasr_libcpp/post-link.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +cat > "${PREFIX}"/.messages.txt <<- EOF + + ############################################################################## + # # + # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # + # necessarily ISO compliant, intended for Research Use Only and not for use # + # in diagnostic procedures, intended only for command-line users, and # + # possibly newer than the currently available SMRT(R) Analysis builds. While # + # efforts have been made to ensure that releases on Bioconda live up to the # + # quality that PacBio strives for, we make no warranty regarding any # + # Bioconda release. # + # # + # As PacBio tools distributed via Bioconda are not covered by any service # + # level agreement or the like, please *do not* contact a PacBio Field # + # Applications Scientist or PacBio Customer Service for assistance with any # + # Bioconda release. We instead provide an issue tracker for you to report # + # issues to us at: # + # # + # https://github.com/PacificBiosciences/pbbioconda # + # # + # We make no warranty that any such issue will be addressed, # + # to any extent or within any time frame. # + # # + # BSD 3-Clause Clear License # + # # + # Please see https://github.com/PacificBiosciences/pbbioconda for # + # information on License, Copyright and Disclaimer # + # # + ############################################################################## +EOF diff --git a/recipes/pbalign/meta.yaml b/recipes/pbalign/meta.yaml index 5ef9b585a54c5..bc34b0f91408f 100644 --- a/recipes/pbalign/meta.yaml +++ b/recipes/pbalign/meta.yaml @@ -12,7 +12,7 @@ source: about: home: https://github.com/PacificBiosciences/pbalign - license: BSD + license: BSD-3-Clause-Clear summary: Python wrapper for producing PBBAM valid alignments extra: @@ -24,7 +24,7 @@ extra: build: skip: True # [not py27] - number: 1 + number: 2 requirements: host: diff --git a/recipes/pbalign/post-link.sh b/recipes/pbalign/post-link.sh new file mode 100644 index 0000000000000..703ab0b671961 --- /dev/null +++ b/recipes/pbalign/post-link.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +cat > "${PREFIX}"/.messages.txt <<- EOF + + ############################################################################## + # # + # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # + # necessarily ISO compliant, intended for Research Use Only and not for use # + # in diagnostic procedures, intended only for command-line users, and # + # possibly newer than the currently available SMRT(R) Analysis builds. While # + # efforts have been made to ensure that releases on Bioconda live up to the # + # quality that PacBio strives for, we make no warranty regarding any # + # Bioconda release. # + # # + # As PacBio tools distributed via Bioconda are not covered by any service # + # level agreement or the like, please *do not* contact a PacBio Field # + # Applications Scientist or PacBio Customer Service for assistance with any # + # Bioconda release. We instead provide an issue tracker for you to report # + # issues to us at: # + # # + # https://github.com/PacificBiosciences/pbbioconda # + # # + # We make no warranty that any such issue will be addressed, # + # to any extent or within any time frame. # + # # + # BSD 3-Clause Clear License # + # # + # Please see https://github.com/PacificBiosciences/pbbioconda for # + # information on License, Copyright and Disclaimer # + # # + ############################################################################## +EOF diff --git a/recipes/pbbam/meta.yaml b/recipes/pbbam/meta.yaml index 46952bb831ba9..15521802e00d9 100644 --- a/recipes/pbbam/meta.yaml +++ b/recipes/pbbam/meta.yaml @@ -12,7 +12,7 @@ source: about: home: https://github.com/PacificBiosciences/pbbam - license: BSD + license: BSD-3-Clause-Clear summary: PacBio BAM C++ library extra: @@ -21,7 +21,7 @@ extra: - mhsieh build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/pbcopper/post-link.sh b/recipes/pbcopper/post-link.sh new file mode 100644 index 0000000000000..703ab0b671961 --- /dev/null +++ b/recipes/pbcopper/post-link.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +cat > "${PREFIX}"/.messages.txt <<- EOF + + ############################################################################## + # # + # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # + # necessarily ISO compliant, intended for Research Use Only and not for use # + # in diagnostic procedures, intended only for command-line users, and # + # possibly newer than the currently available SMRT(R) Analysis builds. While # + # efforts have been made to ensure that releases on Bioconda live up to the # + # quality that PacBio strives for, we make no warranty regarding any # + # Bioconda release. # + # # + # As PacBio tools distributed via Bioconda are not covered by any service # + # level agreement or the like, please *do not* contact a PacBio Field # + # Applications Scientist or PacBio Customer Service for assistance with any # + # Bioconda release. We instead provide an issue tracker for you to report # + # issues to us at: # + # # + # https://github.com/PacificBiosciences/pbbioconda # + # # + # We make no warranty that any such issue will be addressed, # + # to any extent or within any time frame. # + # # + # BSD 3-Clause Clear License # + # # + # Please see https://github.com/PacificBiosciences/pbbioconda for # + # information on License, Copyright and Disclaimer # + # # + ############################################################################## +EOF From d42206b39f2ae44345089507f83cf99fea3171c0 Mon Sep 17 00:00:00 2001 From: Jorrit Boekel Date: Mon, 26 Nov 2018 17:08:09 +0100 Subject: [PATCH 384/546] Bioconductor DEqMS package (#12336) * Bioconductor DEqMS package * Limma version could be set lower (checked with the bioconductor recipe page) to include limma in bioconda --- recipes/bioconductor-deqms/build.sh | 4 ++++ recipes/bioconductor-deqms/meta.yaml | 36 ++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 recipes/bioconductor-deqms/build.sh create mode 100644 recipes/bioconductor-deqms/meta.yaml diff --git a/recipes/bioconductor-deqms/build.sh b/recipes/bioconductor-deqms/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-deqms/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deqms/meta.yaml b/recipes/bioconductor-deqms/meta.yaml new file mode 100644 index 0000000000000..7c5d1da90baa3 --- /dev/null +++ b/recipes/bioconductor-deqms/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "DEqMS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 43415cf52b11a83771f6eb5b308cce83 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,RColorBrewer,utils,ggrepel,pheatmap,ExperimentHub +requirements: + host: + - 'bioconductor-limma >=3.34.0,<3.40.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-limma >=3.34.0,<3.40.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.' + From 28f9135accf514d6b52ac6a4630e4a3f452c6a20 Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Mon, 26 Nov 2018 17:54:45 +0100 Subject: [PATCH 385/546] Genenotebook v0.1.10 (#12337) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 --- recipes/genenotebook/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index 0d6216b3ad5ef..a62a79d6745fc 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.9' %} -{% set sha256 = '84ad8a7a5653b9ed8c90ef18ed73836c3a787047783449c8c3e496cc75985ad9' %} +{% set version = '0.1.10' %} +{% set sha256 = 'd077a80de4f157ab4bd385337bc4be8eddd1c865585e89d63e259637916b097c' %} package: name: {{ name|lower }} From dbca09a9fa1f7e643e875df8fc5f4cced59713ed Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 26 Nov 2018 18:00:31 +0100 Subject: [PATCH 386/546] removed cloudpickle requirement for blockclust (#12242) * blockclust latest source and added cloudpickle as requirement * removed cloudpickle requirement for blockclust * added a tagged release to the source * back to source url but with release tarball and checksum --- recipes/blockclust/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/blockclust/meta.yaml b/recipes/blockclust/meta.yaml index b433c046fb521..39858b6cb9910 100644 --- a/recipes/blockclust/meta.yaml +++ b/recipes/blockclust/meta.yaml @@ -3,11 +3,11 @@ package: version: 1.1.0 source: - url: https://github.com/pavanvidem/blockclust/archive/23cb198228d3ce2f5ecab49e9e85dfce44b14e67.tar.gz - sha256: ab54fd935333c1bc7cebed05a3e26d935530f85376b77623f8e846969872bb0e + url: https://github.com/pavanvidem/blockclust/archive/v1.1.0.tar.gz + sha256: 2376c567f17537da4ac6eba1f75dd1f56079ea406e7e801c5de1ac9e82c08219 build: - number: 2 + number: 3 skip: True # [osx] requirements: From 61234944e4e8922a257d8d17a8adb73af5ef7b10 Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Mon, 26 Nov 2018 15:36:41 -0500 Subject: [PATCH 387/546] R guilds (#12341) --- recipes/r-guilds/build.sh | 38 ++++++++++++++++++++++ recipes/r-guilds/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 recipes/r-guilds/build.sh create mode 100644 recipes/r-guilds/meta.yaml diff --git a/recipes/r-guilds/build.sh b/recipes/r-guilds/build.sh new file mode 100644 index 0000000000000..e940c57cf48b3 --- /dev/null +++ b/recipes/r-guilds/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/GUILDS + mv * $PREFIX/lib/R/library/GUILDS + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-guilds/meta.yaml b/recipes/r-guilds/meta.yaml new file mode 100644 index 0000000000000..7e532b6b5a6a3 --- /dev/null +++ b/recipes/r-guilds/meta.yaml @@ -0,0 +1,64 @@ +{% set version = '1.3' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-guilds + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/GUILDS_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/GUILDS/GUILDS_{{ version }}.tar.gz + sha256: 0dd59a52afcae6624d3b37639c016efc0b3752db5f61378cbecb8f6437e8867e + +build: + merge_build_host: True # [win] + + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('cxx') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + - r-rcpp >=0.11.0 + - r-pracma + + run: + - r-base + - {{native}}gcc-libs # [win] + - r-rcpp >=0.11.0 + - r-pracma + +test: + commands: + + - $R -e "library('GUILDS')" # [not win] + - "\"%R%\" -e \"library('GUILDS')\"" # [win] + +about: + home: https://github.com/thijsjanzen/GUILDS + license: GPL-2 + summary: A collection of sampling formulas for the unified neutral model of biogeography and + biodiversity. Alongside the sampling formulas, it includes methods to perform maximum + likelihood optimization of the sampling formulas, methods to generate data given + the neutral model, and methods to estimate the expected species abundance distribution. + Sampling formulas included in the GUILDS package are the Etienne Sampling Formula + (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in + dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned + on guild size (Janzen et al. 2015). + license_family: GPL2 From 4ea921318f6d2a1a3581f1b3baf5b8d5862e8075 Mon Sep 17 00:00:00 2001 From: "Gherman V. Uritskiy" Date: Mon, 26 Nov 2018 16:41:57 -0500 Subject: [PATCH 388/546] Strict rec (#12113) * added metawrap * fixed perl and jdk * added more strict req * fixed java and perl * removed extra boost --- recipes/metawrap/build.sh | 31 +++++++++++++++ recipes/metawrap/meta.yaml | 80 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 111 insertions(+) create mode 100644 recipes/metawrap/build.sh create mode 100644 recipes/metawrap/meta.yaml diff --git a/recipes/metawrap/build.sh b/recipes/metawrap/build.sh new file mode 100644 index 0000000000000..cbb3a3d2c18aa --- /dev/null +++ b/recipes/metawrap/build.sh @@ -0,0 +1,31 @@ +echo "# Paths to custon pipelines and scripts of metaWRAP" > bin/config-metawrap + +echo 'mw_path=$(which metawrap)' >> bin/config-metawrap +echo 'bin_path=${mw_path%/*}' >> bin/config-metawrap +echo 'SOFT=${bin_path}/metawrap-scripts' >> bin/config-metawrap +echo 'PIPES=${bin_path}/metawrap-modules' >> bin/config-metawrap +echo '' >> bin/config-metawrap + +echo "# OPTIONAL databases (see 'Databases' section of metaWRAP README for details)" >> bin/config-metawrap +echo "# path to kraken standard database" >> bin/config-metawrap +echo "KRAKEN_DB=/path/to/database" >> bin/config-metawrap +echo "" >> bin/config-metawrap + +echo "# path to indexed human genome (see metaWRAP website for guide). This insludes files hg38.bitmask and hg38.srprism.*" >> bin/config-metawrap +echo "BMTAGGER_DB=/path/to/database" >> bin/config-metawrap +echo "" >> bin/config-metawrap + +echo "# paths to BLAST databases" >> bin/config-metawrap +echo "BLASTDB=/path/to/database/NCBI_nt" >> bin/config-metawrap +echo "TAXDUMP=/path/to/database/NCBI_tax" >> bin/config-metawrap + +chmod +x bin/config-metawrap + + +# copying over all necessary files +mkdir -p $PREFIX/bin/ +cp bin/metaWRAP $PREFIX/bin/ +cp bin/metawrap $PREFIX/bin/ +cp bin/config-metawrap $PREFIX/bin/ +cp -r bin/metawrap-modules $PREFIX/bin/ +cp -r bin/metawrap-scripts $PREFIX/bin/ diff --git a/recipes/metawrap/meta.yaml b/recipes/metawrap/meta.yaml new file mode 100644 index 0000000000000..c621842ccd0eb --- /dev/null +++ b/recipes/metawrap/meta.yaml @@ -0,0 +1,80 @@ +{% set name = "metawrap" %} +{% set version = "1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/bxlab/metaWRAP/archive/v{{ version }}.tar.gz + md5: face9197bb696b037d7b2acdf27c668a + +build: + number: 0 + skip: True # [osx] + +requirements: + build: + + run: + - bcftools 1.6 + - biopython 1.69 + - blast 2.7.* + - bmfilter 3.101 + - bmtagger 3.101 + - bmtool 3.101 + - boost 1.64.0 + - bowtie2 2.3.* + - brewer2mpl 1.4.1 + - bwa 0.7.15 + - cairo 1.14.8 + - checkm-genome 1.* + - concoct 0.4.0 + - fastqc 0.11.5 + - gnutls 3.5.15 + - icu 58.2 + - openjdk + - kraken + - krona 2.7 + - libgfortran-ng 7.2.0 + - libopenblas 0.2.20 + - matplotlib 1.5.1 + - maxbin2 2.2.* + - megahit 1.1.2 + - metabat2 2.12.1 + - numpy 1.10.4 + - pandas 0.23.4 + - perl 5.26.2 + - perl-bioperl 1.6.924 + - pplacer 1.1.alpha17 + - prokka 1.* + - qt 4.8.5 + - quast 4.* + - readline 6.2 + - r-recommended 3.3.2 + - r-ggplot2 2.2.1 + - salmon 0.9.* + - samtools 1.6 + - scikit-learn 0.16.1 + - scipy 0.17.1 + - seaborn 0.8.1 + - spades 3.* + - srprism 2.4.24 + - subprocess32 3.2.7 + - taxator-tk 1.3.3e + - tk 8.5.19 + - trim-galore 0.4.* + - xorg-libxrender 0.9.10 + +test: + commands: + - metawrap -h + - metawrap read_qc -h + - which config-metawrap + +about: + home: https://github.com/bxlab/metaWRAP + license: MIT + summary: "MetaWRAP is a pipeline for genome-resolved metagenomic data analysis" + + From a7b9026bb9460da2afbd5e2df1467811d9f172e5 Mon Sep 17 00:00:00 2001 From: Philipp Rescheneder Date: Mon, 26 Nov 2018 22:56:41 +0000 Subject: [PATCH 389/546] Update qcat to v1.0.1 (#12343) --- recipes/qcat/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/qcat/meta.yaml b/recipes/qcat/meta.yaml index afd7ebe078086..a490ac8e855ed 100644 --- a/recipes/qcat/meta.yaml +++ b/recipes/qcat/meta.yaml @@ -1,10 +1,10 @@ package: name: qcat - version: 1.0.0 + version: 1.0.1 source: - url: https://github.com/nanoporetech/qcat/archive/v1.0.0.tar.gz - md5: 9f896c61e55265be5da31a2a6c30fcda + url: https://github.com/nanoporetech/qcat/archive/v1.0.1.tar.gz + md5: 52bbfb23801e744cd666c7fa291f6411 build: noarch: python From 260f58e0f02d5558780195d5c8bbf289a724e4f4 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Tue, 27 Nov 2018 11:12:13 +0200 Subject: [PATCH 390/546] Add better error checking (#12345) --- recipes/diamond_add_taxonomy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/diamond_add_taxonomy/meta.yaml b/recipes/diamond_add_taxonomy/meta.yaml index aebe6c2ba50d9..150d63439ce2e 100644 --- a/recipes/diamond_add_taxonomy/meta.yaml +++ b/recipes/diamond_add_taxonomy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "diamond_add_taxonomy" %} -{% set version = "0.1.0" %} -{% set sha256 = "1315ea9088ebff2a0ce75390a50a992624ce7d3e8267c2842ada3c4fe61589be" %} +{% set version = "0.1.2" %} +{% set sha256 = "b6ef999133e1299e9a4aeee0c944efa6ef62c941456a0426fb0e9477370c0aca" %} package: name: {{ name|lower }} From 6833dc7c411c3ec20165e083d8193e2c7dda3afc Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Tue, 27 Nov 2018 12:32:54 +0100 Subject: [PATCH 391/546] Add mhcnames python package (#12349) --- recipes/mhcnames/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/mhcnames/meta.yaml diff --git a/recipes/mhcnames/meta.yaml b/recipes/mhcnames/meta.yaml new file mode 100644 index 0000000000000..0fee7ffa3695e --- /dev/null +++ b/recipes/mhcnames/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "mhcnames" %} +{% set version = "0.4.8" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 0a18de129eaa4bf8ce802e5e2d856806639ab17b392688ea13dc20ec6d3cc8a2 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + +requirements: + host: + - pip + - python + - six >=1.9.0 + run: + - python + - six >=1.9.0 + +test: + imports: + - mhcnames + +about: + home: https://github.com/hammerlab/mhcnames + license: Apache License Version 2.0 + summary: Python library for MHC nomenclature parsing + +extra: + recipe-maintainers: + - lkuchenb From 456c2a02c48d199669777ed793ae425aa7d5eaa9 Mon Sep 17 00:00:00 2001 From: Leon Kuchenbecker Date: Tue, 27 Nov 2018 13:06:18 +0100 Subject: [PATCH 392/546] Add MHCflurry pMHC class I binding affinity prediction tool (#12346) --- recipes/mhcflurry/meta.yaml | 70 +++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 recipes/mhcflurry/meta.yaml diff --git a/recipes/mhcflurry/meta.yaml b/recipes/mhcflurry/meta.yaml new file mode 100644 index 0000000000000..5b52409960e1d --- /dev/null +++ b/recipes/mhcflurry/meta.yaml @@ -0,0 +1,70 @@ +{% set name = "mhcflurry" %} +{% set version = "1.2.2" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 561ccb2a0f1548db6c88055f0c6fffac10e70ab4b6b48ccf5126acac54a23f17 + +build: + number: 0 + noarch: python + entry_points: + - mhcflurry-downloads = mhcflurry.downloads_command:run + - mhcflurry-predict = mhcflurry.predict_command:run + - mhcflurry-class1-train-allele-specific-models = mhcflurry.train_allele_specific_models_command:run + - mhcflurry-class1-select-allele-specific-models = mhcflurry.select_allele_specific_models_command:run + - mhcflurry-calibrate-percentile-ranks = mhcflurry.calibrate_percentile_ranks_command:run + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + +requirements: + host: + - appdirs + - keras >=2.0.9 + - mhcnames + - numpy >=1.11 + - pandas >=0.20.3 + - pip + - python + - pyyaml + - scikit-learn + - six + - tensorflow >=1.1.0 + - tqdm + run: + - appdirs + - keras >=2.0.9 + - mhcnames + - numpy >=1.11 + - pandas >=0.20.3 + - python + - pyyaml + - scikit-learn + - six + - tensorflow >=1.1.0 + - tqdm + +test: + imports: + - mhcflurry + commands: + - mhcflurry-downloads --help + - mhcflurry-predict --help + - mhcflurry-class1-train-allele-specific-models --help + - mhcflurry-class1-select-allele-specific-models --help + - mhcflurry-calibrate-percentile-ranks --help + +about: + home: https://github.com/hammerlab/mhcflurry + license: Apache License Version 2.0 + summary: Peptide-MHC I binding affinity prediction + doc_url: http://openvax.github.io/mhcflurry/ + +extra: + recipe-maintainers: + - lkuchenb + identifiers: + - doi:10.1016/j.cels.2018.05.014 From cf1a74b59a80dcdc653af00bf05fd71f70cc116e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Tue, 27 Nov 2018 22:19:05 +0100 Subject: [PATCH 393/546] Bump pilon (#12354) --- recipes/pilon/meta.yaml | 6 +++--- recipes/pilon/pilon.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pilon/meta.yaml b/recipes/pilon/meta.yaml index 98e5b212d7144..8c94ebb10183f 100644 --- a/recipes/pilon/meta.yaml +++ b/recipes/pilon/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.22" %} +{% set version = "1.23" %} package: name: pilon @@ -6,11 +6,11 @@ package: source: url: https://github.com/broadinstitute/pilon/releases/download/v{{ version }}/pilon-{{ version }}.jar - md5: 3c45568dc1b878a9a0316410ec62ab04 + sha256: bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185 build: noarch: generic - number: 1 + number: 0 requirements: run: diff --git a/recipes/pilon/pilon.py b/recipes/pilon/pilon.py index 66d01118d744d..dbdf7bd332d38 100755 --- a/recipes/pilon/pilon.py +++ b/recipes/pilon/pilon.py @@ -11,7 +11,7 @@ import sys import subprocess from os import access, getenv, X_OK -jar_file = 'pilon-1.22.jar' +jar_file = 'pilon-1.23.jar' default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] From 6e7d9f53296959a59f6b5fb22a1bcef1d4fc6a12 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:44:15 -0700 Subject: [PATCH 394/546] Update pronto to 0.11.1 (#12377) --- recipes/pronto/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pronto/meta.yaml b/recipes/pronto/meta.yaml index cda52ea258173..8e090a0ba2848 100644 --- a/recipes/pronto/meta.yaml +++ b/recipes/pronto/meta.yaml @@ -1,10 +1,10 @@ package: name: pronto - version: "0.11.0" + version: "0.11.1" source: - url: https://files.pythonhosted.org/packages/a1/f4/a6e7bc04ba94fffe82ec4b3e73c9c3b7eb7fabbd1189871376059ed241e4/pronto-0.11.0.zip - sha256: 78fb9f876e46e635e3e43232edecbcfcae2c5650e3cee506016ae99e1e9131eb + url: https://files.pythonhosted.org/packages/c7/cb/5739ba20fc5aeb246318fb5559fc7c80a56cba15ea77e6f6694a069a84a1/pronto-0.11.1.zip + sha256: ec6fd512b3f509aefc67169f1fd8da7f4b34b600dfc21c606530906b15e99eda # patches: # List any patch files here # - fix.patch From eab103be0a0eea5e03100ee6b74f0d3e113568b4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:46:15 -0700 Subject: [PATCH 395/546] Update perl-json-xs to 4.0 (#12373) --- recipes/perl-json-xs/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-json-xs/meta.yaml b/recipes/perl-json-xs/meta.yaml index 42826267b4b98..dd2119ef75e3e 100644 --- a/recipes/perl-json-xs/meta.yaml +++ b/recipes/perl-json-xs/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-json-xs" %} -{% set version = "3.04" %} -{% set sha256 = "65d8836bd8ea6f0b7bffc70b2212156adc3e2ffa587e27e548d576893f097c2c" %} +{% set version = "4.0" %} +{% set sha256 = "479f4afca6d21d679101954a8144cf42e3ff8780c336ea8b748cf2a77ef62804" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/JSON-XS-3.04.tar.gz + url: https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/JSON-XS-4.0.tar.gz sha256: {{ sha256 }} build: From 3aec1c761bf654f341e8a48e2b06ee4130580b4e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:47:00 -0700 Subject: [PATCH 396/546] Update planemo to 0.57.1 (#12370) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index f2a965d2a7e7b..2391b69eadafb 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "planemo" %} -{% set version = "0.57.0" %} +{% set version = "0.57.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8ed5ee7f4a133ea2025698167ded71338bb896c1ece7a2dd5bca749d1f1d158f + sha256: 2346ebef56797d3fc1987b9baaeec8512f3426bb000e1a261791cd70da2efbc3 build: number: 0 From 4f800e56b098412e5a6f04358246d09f41ed49ff Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:47:36 -0700 Subject: [PATCH 397/546] Update snippy to 4.3.6 (#12372) --- recipes/snippy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml index 09e0b9c62865b..35e9674500894 100644 --- a/recipes/snippy/meta.yaml +++ b/recipes/snippy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "snippy" %} -{% set version = "4.3.5" %} -{% set sha256 = "eca58b15459739532c21bc1723efd668aab73e85c2671f6519de67b5d3acb0cf" %} +{% set version = "4.3.6" %} +{% set sha256 = "a55ade10d853e2eb9ab29e1301cb534a3cf3ca5711cd349e203706652bd2db20" %} package: name: '{{ name }}' From d9ee685ca0353fd17b665c83e671982c1a7a40e2 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:47:47 -0700 Subject: [PATCH 398/546] Update intarna to 2.3.1 (#12367) --- recipes/intarna/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 4bf73f9039b9c..8f919a5020d73 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -1,4 +1,4 @@ -{% set INTARNA_VERSION = "2.3.0" %} +{% set INTARNA_VERSION = "2.3.1" %} {% set VRNA_VERSION = "2.4.9" %} package: @@ -15,7 +15,7 @@ build: source: url: "https://github.com/BackofenLab/IntaRNA/releases/download/v{{INTARNA_VERSION}}/intaRNA-{{INTARNA_VERSION}}.tar.gz" - sha256: b787e740fe60111388ee781e1b52d835100c3cbefaf5aa9d1d50ca5b9dd61917 + sha256: ee674ea3d50b272e5a5831e467c94abbdefa327a1faae9420ad137663055d8e8 requirements: build: From 0070e865a5068e90a29da4e057c71e58dafd9752 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:48:31 -0700 Subject: [PATCH 399/546] Update agfusion to 1.231 (#12366) --- recipes/agfusion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/agfusion/meta.yaml b/recipes/agfusion/meta.yaml index 478a1bd175bee..0c4f398831e63 100644 --- a/recipes/agfusion/meta.yaml +++ b/recipes/agfusion/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.23" %} -{% set sha256 = "b11225f03c24b130a148abef08d516da35c1a55a038b826550ddade14eafa222" %} +{% set version = "1.231" %} +{% set sha256 = "68ee568a0d9abf6b5d18bdad311488d2de0c5ba20b93ed2c63e63795d95017a4" %} From 9eec5e96b2fbc7f5ae9a29f666b51ba87236c79f Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:49:16 -0700 Subject: [PATCH 400/546] Update bioconda-utils to 0.15.0 (#12359) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index cea1a83e24b96..0b53a59635981 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.9" %} -{% set sha256 = "b23f1836f40bcde939dadd3d5ff43af596cb9835c9fffddd9e6d70ec392db4af" %} +{% set version = "0.15.0" %} +{% set sha256 = "9f8891d99956dc7c7b4f30b5b7039702fc2fa7f9fd974a628ae94e10e4007b60" %} package: name: bioconda-utils From 8f4b7dfa9e5a1be55489061bd220b6cefbd34060 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:49:45 -0700 Subject: [PATCH 401/546] Update mapdamage2 to 2.0.9 (#12358) --- recipes/mapdamage2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mapdamage2/meta.yaml b/recipes/mapdamage2/meta.yaml index 62cf4f47ce470..e94dd4ae73117 100644 --- a/recipes/mapdamage2/meta.yaml +++ b/recipes/mapdamage2/meta.yaml @@ -1,14 +1,14 @@ package: name: mapdamage2 - version: "2.0.8" + version: "2.0.9" build: noarch: python number: 0 source: - url: https://github.com/ginolhac/mapDamage/archive/2.0.8.tar.gz - sha256: 69b8f0f6f41ef7f6f7c9d5451f5a647ea12f983464676e8e032efc3dcbc7392b + url: https://github.com/ginolhac/mapDamage/archive/2.0.9.tar.gz + sha256: 25fadf8a1a0a1f6fcd0df283201edcb308bc6ee35264f6ac81a8efe8b7357508 patches: - makefile.patch - composition.patch From ff93b4f0066536f4b49d28691571e096c0c4e7bc Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:50:28 -0700 Subject: [PATCH 402/546] Update scanpy to 1.3.4 (#12357) --- recipes/scanpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scanpy/meta.yaml b/recipes/scanpy/meta.yaml index 4f7b3b207ec23..7d833365d3d58 100644 --- a/recipes/scanpy/meta.yaml +++ b/recipes/scanpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scanpy" %} -{% set version = "1.3.3" %} +{% set version = "1.3.4" %} package: name: {{ name|lower }} @@ -9,7 +9,7 @@ build: skip: True # [not py36] source: url: https://github.com/theislab/scanpy/archive/{{ version }}.tar.gz - sha256: a1ade2079498c2cc8df3da85e94330f64955f4a8f9266829aa0093b4f3aef2f5 + sha256: 8a4afd47e6b21a0d414f54243505bb8a5e8b7e9635bd138bdab6ed1c174e18c2 requirements: host: From 3a5fe2702d0bd6fd7377d8d661c7499027658c0e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:56:27 -0700 Subject: [PATCH 403/546] Update goatools to 0.8.11 (#12361) --- recipes/goatools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/goatools/meta.yaml b/recipes/goatools/meta.yaml index cb3538b6aec7a..4d20869195748 100644 --- a/recipes/goatools/meta.yaml +++ b/recipes/goatools/meta.yaml @@ -1,11 +1,11 @@ -{% set version = "0.8.9" %} +{% set version = "0.8.11" %} package: name: goatools version: '{{version}}' source: url: https://pypi.io/packages/source/g/goatools/goatools-{{version}}.tar.gz - sha256: 846531b8c95aec1ffe952cceed9816524626f6fbfd4059a6d469e75cc6207f0e + sha256: ec742f1a8c8847af56444a166d352716f6c68496dc6a886d0e58b59889de7e95 build: noarch: python From 45c1e508afac9ec9d31c1149f8b8fc797dcf89dd Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 15:56:44 -0700 Subject: [PATCH 404/546] Update perl-math-random-mt-auto to 6.23 (#12362) --- recipes/perl-math-random-mt-auto/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-random-mt-auto/meta.yaml b/recipes/perl-math-random-mt-auto/meta.yaml index 45c65a1854343..2aa4802587e56 100644 --- a/recipes/perl-math-random-mt-auto/meta.yaml +++ b/recipes/perl-math-random-mt-auto/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-random-mt-auto" %} -{% set version = "6.22" %} -{% set sha256 = "1f2ae9752ba908c126dc2bd3c27cb286543121997f87c5bce578fb2e7f51f01f" %} +{% set version = "6.23" %} +{% set sha256 = "58bcb5ad3162964ff5a0c4d2dcbaa0202c2c85d9c470496f3b7a998757776313" %} package: name: {{ name }} From 6e22f040b901afdd73344810f8dc6cc77d28e15c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:38:49 -0700 Subject: [PATCH 405/546] Update kipoi to 0.6.3 (#12374) --- recipes/kipoi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kipoi/meta.yaml b/recipes/kipoi/meta.yaml index ca44d38f95673..fbd460892a27b 100644 --- a/recipes/kipoi/meta.yaml +++ b/recipes/kipoi/meta.yaml @@ -1,8 +1,8 @@ {% set name = "kipoi" %} -{% set version = "0.6.0" %} +{% set version = "0.6.3" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "dd44a074221042e3a891274333042b45d2202ab2fa207bac187462619051c976" %} +{% set hash_value = "b4e52933cfd62a5eab18b3077f7b7dadf49031906b27973f74ebff10168df969" %} package: name: '{{ name|lower }}' From 6c5f1440740bc6aa0553049b31c3b8ea687b7904 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:39:55 -0700 Subject: [PATCH 406/546] Update kipoi_veff to 0.2.1 (#12364) --- recipes/kipoi_veff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kipoi_veff/meta.yaml b/recipes/kipoi_veff/meta.yaml index db0599c8dc175..c04d1706107f0 100644 --- a/recipes/kipoi_veff/meta.yaml +++ b/recipes/kipoi_veff/meta.yaml @@ -1,8 +1,8 @@ {% set name = "kipoi_veff" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "5c13c1b44b5512325c87efcade325701c0fbeb348dc8b8652204781a2f1cfd59" %} +{% set hash_value = "d5f157f1743c4bd2694f6e2de40a1c2abdc94a95d6f98cf60b99c9aaeea64490" %} package: name: '{{ name|lower }}' From 2591786c771451b15f42cf7e77100c5b2829fb39 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:44:09 -0700 Subject: [PATCH 407/546] Update perl-object-insideout to 4.05 (#12380) --- recipes/perl-object-insideout/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-object-insideout/meta.yaml b/recipes/perl-object-insideout/meta.yaml index d376f40f30ef7..65dc7c0a80a30 100644 --- a/recipes/perl-object-insideout/meta.yaml +++ b/recipes/perl-object-insideout/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-object-insideout" %} -{% set version = "4.04" %} -{% set sha256 = "b2ba9bb624cf25fd0090e631e7c415dc9ea011b8aa0b613390fecc919f62f606" %} +{% set version = "4.05" %} +{% set sha256 = "9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4" %} package: name: {{ name }} From 1cda255d8748a63ca28fc052ff11fe8a3caa9481 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:44:19 -0700 Subject: [PATCH 408/546] Update sevenbridges-python to 0.17.1 (#12379) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 8443ea0c386ec..a13909bc02004 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.17.0" %} -{% set sha256 = "2fb224b48ac1dc2e3954344429031aafa190ae1021dd9ec55ad1f4ae0deec1c8" %} +{% set version = "0.17.1" %} +{% set sha256 = "269259e74d972a7f34b4c58d37d9d903a48c347d738080a76dc9a2e0f2efb48b" %} package: name: sevenbridges-python From 9156c7e18f7c335aa8d6b8052e1dc99a3f7868d9 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:44:36 -0700 Subject: [PATCH 409/546] Update nanosv to 1.2.3 (#12378) --- recipes/nanosv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanosv/meta.yaml b/recipes/nanosv/meta.yaml index ca4587d521707..4a361d913233f 100644 --- a/recipes/nanosv/meta.yaml +++ b/recipes/nanosv/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.2" %} +{% set version = "1.2.3" %} package: name: nanosv @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanosv/NanoSV-{{ version }}.tar.gz - sha256: d8d858b8cc7f23341f91abb2be1d3b48586c7b10ad9dbf68fb735bdda1e7ab69 + sha256: d1f2d89cece444007bff0be88a22434cbdab75a3de560d188f004ad4b5ae3c8b build: number: 0 From 78564608b578242f4a9d3eb6ee1c4c8d2851f38d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:44:57 -0700 Subject: [PATCH 410/546] Update starfish to 0.0.30 (#12368) --- recipes/starfish/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/starfish/meta.yaml b/recipes/starfish/meta.yaml index 954112757b991..99e50ab934664 100644 --- a/recipes/starfish/meta.yaml +++ b/recipes/starfish/meta.yaml @@ -1,4 +1,4 @@ -{% set STARFISH_VERSION = "0.0.29" %} +{% set STARFISH_VERSION = "0.0.30" %} package: name: starfish @@ -6,7 +6,7 @@ package: source: url: https://github.com/spacetx/starfish/archive/{{ STARFISH_VERSION }}.zip - sha256: 2c9dd59f5ee0dc0b5b0f3780a27770236682c79c1fea194532eba7253bef4ba6 + sha256: de9fb705ae5db39e91fc0caf9331e559645b7fd949a7ac6e422a194aece93568 build: noarch: python From e2f5360a62e6357fd3fbfd93645dca51bcb50e48 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:45:25 -0700 Subject: [PATCH 411/546] Update clust to 1.8.10 (#12356) --- recipes/clust/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clust/meta.yaml b/recipes/clust/meta.yaml index 12a12a163c0bd..dc8f4dd49c015 100644 --- a/recipes/clust/meta.yaml +++ b/recipes/clust/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clust" %} -{% set version = "1.8.9" %} +{% set version = "1.8.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 68a74dc267662e245facde8192ffbfc341626a089553a7f58c1954e7deb7ba1e + sha256: d2f93848e20d88cacc3856f7c4ab17fc2ad668d05f6cb0f56f265797d2b70230 build: number: 0 From ef2cd271a018e40af209e334c369b9f625ff25ce Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:45:35 -0700 Subject: [PATCH 412/546] Update pypairs to 2.0.6 (#12381) --- recipes/pypairs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypairs/meta.yaml b/recipes/pypairs/meta.yaml index adbfd48b53c36..411df7a4bd440 100644 --- a/recipes/pypairs/meta.yaml +++ b/recipes/pypairs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypairs" %} -{% set version = "2.0.5" %} +{% set version = "2.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 902eeb0714d1102776160acbd60dd5efb4cbbfbcf49123b3a001b8d572c7e19f + sha256: 39546c372405f22cefd2b00fdbf0bb2bd6abe779d88a35f82f4b746807446bcb build: number: 0 From 2be40963157844ba7b91b03e14d5753a9d0737f4 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 16:48:41 -0700 Subject: [PATCH 413/546] Update khmer to 3.0.0a2 (#12360) --- recipes/khmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/khmer/meta.yaml b/recipes/khmer/meta.yaml index ff07bd969ab05..e7de239d0d8fb 100644 --- a/recipes/khmer/meta.yaml +++ b/recipes/khmer/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.0.0a1" %} -{% set sha256 = "312a08f48e178cc4ff37dac9469ecfeeca348d5d99e51248dbfef9aba65aa68c" %} +{% set version = "3.0.0a2" %} +{% set sha256 = "6a53de499ffd4a808c40973894ec4400d82d8b9e34ad012c4903578edb4be9e1" %} package: name: khmer From 075fc9d475bf114b2e52213f4ff9a406ddf3a966 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 18:36:09 -0700 Subject: [PATCH 414/546] Update flashlfq to 0.1.110 (#12385) --- recipes/flashlfq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flashlfq/meta.yaml b/recipes/flashlfq/meta.yaml index 1ed2ddedd14b1..0474c809ebb45 100644 --- a/recipes/flashlfq/meta.yaml +++ b/recipes/flashlfq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.109" %} -{% set sha256 = "b6347071865f3adcad1666b41142321fed99051149679ecedba2719c5956631d" %} +{% set version = "0.1.110" %} +{% set sha256 = "2dcbf9c749bce876482ab40f06748f3febd475a81931e3f27a8f95aad02aed47" %} source: From 81a73afa8267c11fcc51bf4ea976bab5577a10d7 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 18:36:21 -0700 Subject: [PATCH 415/546] Update perl-algorithm-cluster to 1.57 (#12384) --- recipes/perl-algorithm-cluster/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-algorithm-cluster/meta.yaml b/recipes/perl-algorithm-cluster/meta.yaml index 015253af53c92..cbb5186b5e7e4 100644 --- a/recipes/perl-algorithm-cluster/meta.yaml +++ b/recipes/perl-algorithm-cluster/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-algorithm-cluster - version: "1.56" + version: "1.57" source: - url: http://cpan.metacpan.org/authors/id/M/MD/MDEHOON/Algorithm-Cluster-1.56.tar.gz - sha256: 604f72d44ebf76d2bff08a07d7ec0121ea4eb8442215de99e9d1bc1658b8bf6b + url: https://cpan.metacpan.org/authors/id/M/MD/MDEHOON/Algorithm-Cluster-1.57.tar.gz + sha256: 7033c23d602c98ac4ae67061e684b19c116ead4b5326001ff9d10cf19b9fc71e build: number: 0 From 29874ec0ff56bd8519ff509a2992eed70b2b4fee Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 18:37:21 -0700 Subject: [PATCH 416/546] Update arvados-python-client to 1.2.0.20181121194423 (#12382) --- recipes/arvados-python-client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index 417aa1718be1f..8f014a5d12167 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.2.0.20181109162613" %} +{% set version="1.2.0.20181121194423" %} package: name: arvados-python-client @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - sha256: 09465ea4079c8e9eb72a37db8e3abb33546c43a8a662ba02b557734a952fa318 + sha256: e2f24382a74c40533c41431398fa83b1bb3c70bfa843c661cddcb89b8ccdad70 build: number: 0 From 0cf946e7d95803d7b11c85efdea5a0759793072c Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 18:37:46 -0700 Subject: [PATCH 417/546] Update avro-cwl to 1.8.9 (#12355) * Update avro-cwl to 1.8.9 * Set noarch: python --- recipes/avro-cwl/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/avro-cwl/meta.yaml b/recipes/avro-cwl/meta.yaml index 408d25e12245b..109f737039c12 100644 --- a/recipes/avro-cwl/meta.yaml +++ b/recipes/avro-cwl/meta.yaml @@ -1,7 +1,7 @@ -{% set version = "1.8.4" %} +{% set version = "1.8.9" %} build: - number: 1 + number: 0 package: name: avro-cwl @@ -9,7 +9,10 @@ package: source: url: https://pypi.io/packages/source/a/avro-cwl/avro-cwl-{{ version }}.tar.gz - sha256: 0334de2f44166b449bd2ea29d525ffe531146d7e2aad84c2b0eee081f636c7f4 + sha256: d4900657133cc21e530f2b1c7881699b3828d94c4b28942876feeb7d7fed91f0 + +build: + noarch: python requirements: host: From 1470fedf2c1833c14811067e43ae1601990c88f7 Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Tue, 27 Nov 2018 21:45:04 -0500 Subject: [PATCH 418/546] r-breakaway (#12386) --- recipes/r-breakaway/build.sh | 38 ++++++++++++++++++++++++ recipes/r-breakaway/meta.yaml | 54 +++++++++++++++++++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 recipes/r-breakaway/build.sh create mode 100644 recipes/r-breakaway/meta.yaml diff --git a/recipes/r-breakaway/build.sh b/recipes/r-breakaway/build.sh new file mode 100644 index 0000000000000..f3cff13ed0cb9 --- /dev/null +++ b/recipes/r-breakaway/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/breakaway + mv * $PREFIX/lib/R/library/breakaway + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-breakaway/meta.yaml b/recipes/r-breakaway/meta.yaml new file mode 100644 index 0000000000000..51ba870fc121f --- /dev/null +++ b/recipes/r-breakaway/meta.yaml @@ -0,0 +1,54 @@ +{% set version = '3.0' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-breakaway + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/breakaway_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/breakaway/breakaway_{{ version }}.tar.gz + sha256: ecce9505a84658bf85ba286b5e2a2a7e8f08d849b9ca73faf8e988ede23b7078 + +build: + merge_build_host: True #[win] + + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{posix}}zip # [win] + + host: + - r-base + + run: + - r-base + +test: + commands: + + - $R -e "library('breakaway')" # [not win] + - "\"%R%\" -e \"library('breakaway')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=breakaway + license: GPL-2 + summary: Species richness estimation is an important problem in biodiversity analysis. This + package provides methods for total species richness estimation (observed plus unobserved) + and a method for modelling total diversity with covariates. breakaway() estimates + total (observed plus unobserved) species richness. Microbial diversity datasets + are characterized by a large number of rare species and a small number of highly + abundant species. The class of models implemented by breakaway() is flexible enough + to model both these features. breakaway_nof1() implements a similar procedure however + does not require a singleton count. betta() provides a method for modelling total + diversity with covariates in a way that accounts for its estimated nature and thus + accounts for unobserved taxa, and betta_random() permits random effects modelling. + license_family: GPL2 From dd4040af8e07c9f275b1ace2a249e2cfd16f4a3e Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Tue, 27 Nov 2018 22:56:46 -0500 Subject: [PATCH 419/546] R sads (#12388) --- recipes/r-sads/build.sh | 38 +++++++++++++++++++++++ recipes/r-sads/meta.yaml | 66 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 recipes/r-sads/build.sh create mode 100644 recipes/r-sads/meta.yaml diff --git a/recipes/r-sads/build.sh b/recipes/r-sads/build.sh new file mode 100644 index 0000000000000..ca1e998b13940 --- /dev/null +++ b/recipes/r-sads/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/sads + mv * $PREFIX/lib/R/library/sads + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-sads/meta.yaml b/recipes/r-sads/meta.yaml new file mode 100644 index 0000000000000..f076b95a9a55a --- /dev/null +++ b/recipes/r-sads/meta.yaml @@ -0,0 +1,66 @@ +{% set version = '0.4.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-sads + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/sads_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/sads/sads_{{ version }}.tar.gz + sha256: 89d3d0d0729162cd5138a0049b66ad49581aca4594c1bdf824172f7bb76cdbc8 + +build: + merge_build_host: True # [win] + + number: 0 + + + rpaths: + - lib/R/lib/ + - lib/ + + +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + - r-guilds + - r-mass + - r-vgam + - r-bbmle >=1.0.19 + - r-poilog + + run: + - r-base + - {{native}}gcc-libs # [win] + - r-guilds + - r-mass + - r-vgam + - r-bbmle >=1.0.19 + - r-poilog + +test: + commands: + + - $R -e "library('sads')" # [not win] + - "\"%R%\" -e \"library('sads')\"" # [win] + + +about: + home: http://piLaboratory.github.io/sads, https://github.com/piklprado/sads + license: GPL-2 + summary: Maximum likelihood tools to fit and compare models of species abundance distributions + and of species rank-abundance distributions. + license_family: GPL2 From f2c84759d4cb483898d01ae93aa29d6a0403259b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Tue, 27 Nov 2018 23:03:43 -0700 Subject: [PATCH 420/546] Update python-sortedcontainers to 2.1.0 (#12383) --- recipes/python-sortedcontainers/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/python-sortedcontainers/meta.yaml b/recipes/python-sortedcontainers/meta.yaml index 5350a0f8c5b6a..16cdf0ca93c44 100644 --- a/recipes/python-sortedcontainers/meta.yaml +++ b/recipes/python-sortedcontainers/meta.yaml @@ -1,11 +1,11 @@ -{% set version = "2.0.5" %} +{% set version = "2.1.0" %} package: name: "python-sortedcontainers" version: {{ version }} source: - url: https://files.pythonhosted.org/packages/b9/30/accbf5c09c5fa25a3d5f762761e0d7ece6fdb12f2a9c43b840f73cef43ef/sortedcontainers-2.0.5.tar.gz - sha256: b74f2756fb5e23512572cc76f0fe0832fd86310f77dfee54335a35fb33f6b950 + url: https://files.pythonhosted.org/packages/29/e0/135df2e733790a3d3bcda970fd080617be8cea3bd98f411e76e6847c17ef/sortedcontainers-2.1.0.tar.gz + sha256: 974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a build: number: 0 noarch: python From d590842621dae8af8f70a4fd91e683d7f3f4db40 Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Wed, 28 Nov 2018 01:24:44 -0500 Subject: [PATCH 421/546] r-ebimetagenomics (#12339) --- recipes/r-ebimetagenomics/build.sh | 38 ++++++++++++++++++++ recipes/r-ebimetagenomics/meta.yaml | 56 +++++++++++++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 recipes/r-ebimetagenomics/build.sh create mode 100644 recipes/r-ebimetagenomics/meta.yaml diff --git a/recipes/r-ebimetagenomics/build.sh b/recipes/r-ebimetagenomics/build.sh new file mode 100644 index 0000000000000..1050b4fc4fb00 --- /dev/null +++ b/recipes/r-ebimetagenomics/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/ebimetagenomics + mv * $PREFIX/lib/R/library/ebimetagenomics + + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-ebimetagenomics/meta.yaml b/recipes/r-ebimetagenomics/meta.yaml new file mode 100644 index 0000000000000..0f07c563ad840 --- /dev/null +++ b/recipes/r-ebimetagenomics/meta.yaml @@ -0,0 +1,56 @@ +{% set version = '0.6' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-ebimetagenomics + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/ebimetagenomics_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/ebimetagenomics/ebimetagenomics_{{ version }}.tar.gz + sha256: 9d27d9ba816383732b837aa745141856a748b1bca0d781b088c3d91b0e3d5f49 + +build: + merge_build_host: True # [win] + + number: 0 + + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{posix}}zip # [win] + + host: + - r-base + - r-breakaway + - r-sads + - r-vegan + + run: + - r-base + - r-breakaway + - r-sads + - r-vegan + +test: + commands: + + - $R -e "library('ebimetagenomics')" # [not win] + - "\"%R%\" -e \"library('ebimetagenomics')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=ebimetagenomics + license: LGPL-3 + summary: 'Functions for querying the EBI Metagenomics Portal . + The current main focus is on taxa abundance data, but the intention is that this + package should evolve into a general purpose package for working with EBI Metagenomics + data using R. ' + + license_family: LGPL From 079e75ed92f5e4b6cb58cde28efce7342368bd13 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 28 Nov 2018 00:34:50 -0700 Subject: [PATCH 422/546] pin armadilo on major version (#12389) --- recipes/fastspar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fastspar/meta.yaml b/recipes/fastspar/meta.yaml index 2777bc58f355b..6f013e7bc1477 100644 --- a/recipes/fastspar/meta.yaml +++ b/recipes/fastspar/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{sha256}} build: - number: 0 + number: 1 requirements: build: @@ -28,7 +28,7 @@ requirements: run: - gsl - - armadillo >=6.7 + - {{ pin_compatible('armadillo', min_pin='x.x', max_pin='x') }} - openblas - openmp >=4.0 - gnu-getopt # [osx] From 9bd996b15b3bfe1b64179d8d3e52a8744d60d82d Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Wed, 28 Nov 2018 08:53:00 +0100 Subject: [PATCH 423/546] IgDiscover version 0.11 (#12351) * IgDiscover version 0.11 * IgDiscover requires Python 3.6 * Fix build on macOS with a small patch * Remove unneeded host dependencies --- recipes/igdiscover/clusterplot.tab.gz | Bin 304 -> 0 bytes recipes/igdiscover/cpucount-osx.patch | 10 ++++++ recipes/igdiscover/meta.yaml | 47 +++++++++++--------------- 3 files changed, 30 insertions(+), 27 deletions(-) delete mode 100644 recipes/igdiscover/clusterplot.tab.gz create mode 100644 recipes/igdiscover/cpucount-osx.patch diff --git a/recipes/igdiscover/clusterplot.tab.gz b/recipes/igdiscover/clusterplot.tab.gz deleted file mode 100644 index 7e99c5234020bb103f2f5e93e0a961c262b7fa67..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 304 zcmV-00nh#)iwFqKJi1x{17mD;b97~LaBOdME_7jH0PU7NZ^A$fhUfIBRH8~YR?C9{ zsZ*`2nNT;T{(sev4FhTfB7&+^C(z;Z`Q!DYBQQ>%`@_E5O&^>0Zk!HZFI(G;!)jQ+ z_Cwdd^__~DYpm*FNEnV~>^U+K-gA*b^japojxPQW=#cR=0.8.0 - - pandas 0.22.* - - numpy >=1.14 - - matplotlib 2.1.* - - snakemake 4.5.* - - cutadapt >=1.16 - - xopen >=0.3 - - seaborn ==0.7.1 - - scipy >=1.0 + - sqt 0.8.* + - pandas 0.23.* + - numpy >=1.15 + - matplotlib-base 3.0.* + - snakemake-minimal 5.3.* + - cutadapt ==1.18 + - xopen >=0.3.5 + - seaborn 0.9.* + - scipy >=1.1 - ruamel.yaml 0.15.* - muscle 3.8.* - pear 0.9.6.* - flash 1.2.* - igblast 1.7.* - - vsearch 2.6.* - host: - - python - - sqt >=0.8.0 - - pandas 0.22.* - - numpy >=1.14 - - matplotlib 2.1.* - - snakemake 4.5.* - - cutadapt >=1.16 - - xopen >=0.3 - - seaborn ==0.7.1 - - scipy >=1.0 - - ruamel.yaml 0.15.* build: - number: 3 - skip: True # [py27] + number: 0 + skip: True # [py<36] script: python -m pip install --no-deps --ignore-installed . test: From 4723dd871ad7a4e2c60acc94efaa4f9daf732f6b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 28 Nov 2018 01:15:36 -0700 Subject: [PATCH 424/546] Update goatools to 0.8.12 (#12391) --- recipes/goatools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/goatools/meta.yaml b/recipes/goatools/meta.yaml index 4d20869195748..a0184334b0190 100644 --- a/recipes/goatools/meta.yaml +++ b/recipes/goatools/meta.yaml @@ -1,11 +1,11 @@ -{% set version = "0.8.11" %} +{% set version = "0.8.12" %} package: name: goatools version: '{{version}}' source: url: https://pypi.io/packages/source/g/goatools/goatools-{{version}}.tar.gz - sha256: ec742f1a8c8847af56444a166d352716f6c68496dc6a886d0e58b59889de7e95 + sha256: b58f77321fc1c3393b7973b1dad7b08897394ae1465c036f91977e65383e5c7c build: noarch: python From edf6f83e25f3706e49c90350dcda0a6d0546cb9e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 28 Nov 2018 01:15:46 -0700 Subject: [PATCH 425/546] Update bioconda-utils to 0.15.1 (#12390) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 0b53a59635981..a7b757dd4da56 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.0" %} -{% set sha256 = "9f8891d99956dc7c7b4f30b5b7039702fc2fa7f9fd974a628ae94e10e4007b60" %} +{% set version = "0.15.1" %} +{% set sha256 = "f1c20353a4e6713fdf2fc3e2697e18082b1ea6e416ef010af1ae001e17e6a156" %} package: name: bioconda-utils From 69594bc98b5882ef99317e6457bddb14c3ae20b1 Mon Sep 17 00:00:00 2001 From: Christopher Lowe Date: Wed, 28 Nov 2018 03:31:21 -0500 Subject: [PATCH 426/546] R ebimetagenomics (#12393) --- recipes/r-ebimetagenomics/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/r-ebimetagenomics/meta.yaml b/recipes/r-ebimetagenomics/meta.yaml index 0f07c563ad840..74f67465ec69e 100644 --- a/recipes/r-ebimetagenomics/meta.yaml +++ b/recipes/r-ebimetagenomics/meta.yaml @@ -18,7 +18,6 @@ build: number: 0 - rpaths: - lib/R/lib/ - lib/ @@ -41,10 +40,10 @@ requirements: test: commands: - - $R -e "library('ebimetagenomics')" # [not win] - "\"%R%\" -e \"library('ebimetagenomics')\"" # [win] + about: home: https://CRAN.R-project.org/package=ebimetagenomics license: LGPL-3 From deca186496286422938648c4dd7fdf29bddd5e07 Mon Sep 17 00:00:00 2001 From: Ralf Weber Date: Wed, 28 Nov 2018 10:27:08 +0000 Subject: [PATCH 427/546] Add dimspy recipes for reference purposes (#12387) * Add dimspy recipes for reference purposes * Remove filename * remove from blacklist * Update build-fail-blacklist --- build-fail-blacklist | 4 ++- recipes/dimspy/1.2.0/build.sh | 3 +++ recipes/dimspy/1.2.0/meta.yaml | 48 ++++++++++++++++++++++++++++++++++ recipes/dimspy/meta.yaml | 14 +++++----- 4 files changed, 61 insertions(+), 8 deletions(-) create mode 100644 recipes/dimspy/1.2.0/build.sh create mode 100644 recipes/dimspy/1.2.0/meta.yaml diff --git a/build-fail-blacklist b/build-fail-blacklist index c808e3f74dc1e..b943bbeea2caf 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -36,10 +36,12 @@ recipes/smalt recipes/perl-file-homedir # needs some special treatment, shorter prefix than normal pkgs -recipes/dimspy/1.1.0 recipes/dimspy +recipes/dimspy/1.2.0 +recipes/dimspy/1.1.0 recipes/dimspy/1.0.0 + #can't find file to patch at input line 3 recipes/erds diff --git a/recipes/dimspy/1.2.0/build.sh b/recipes/dimspy/1.2.0/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/dimspy/1.2.0/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/dimspy/1.2.0/meta.yaml b/recipes/dimspy/1.2.0/meta.yaml new file mode 100644 index 0000000000000..858a71c0277e2 --- /dev/null +++ b/recipes/dimspy/1.2.0/meta.yaml @@ -0,0 +1,48 @@ +package: + name: dimspy + version: "1.2.0" + +source: + url: https://files.pythonhosted.org/packages/ed/a9/915b082888d0d145af747da12cab7bb26ecfe143ec6bced7aac5dedca0c6/dimspy-1.2.0.tar.gz + md5: b4a31230e9d5fd89a0aca601a9bc672b + +build: + skip: True # [py3k] + number: 1 + entry_points: + - dimspy = dimspy.__main__:main + +requirements: + build: + - python + - setuptools + - numpy + - scipy + - fastcluster + - pymzml <=2.0.0 + - h5py + - pythonnet + run: + - python + - numpy + - scipy + - fastcluster + - pymzml <=2.0.0 + - h5py + - pythonnet + +test: + imports: + - dimspy + - dimspy.models + - dimspy.portals + - dimspy.process + + commands: + - dimspy --help + +about: + home: https://github.com/computational-metabolomics/dimspy + license: GPLv3 + summary: 'Python package for data processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data' + license_family: GPL3 diff --git a/recipes/dimspy/meta.yaml b/recipes/dimspy/meta.yaml index be579897be9c2..e6c358f348b0f 100644 --- a/recipes/dimspy/meta.yaml +++ b/recipes/dimspy/meta.yaml @@ -1,25 +1,25 @@ package: name: dimspy - version: "1.2.0" + version: "1.3.0" source: - url: https://files.pythonhosted.org/packages/ed/a9/915b082888d0d145af747da12cab7bb26ecfe143ec6bced7aac5dedca0c6/dimspy-1.2.0.tar.gz - md5: b4a31230e9d5fd89a0aca601a9bc672b + url: https://files.pythonhosted.org/packages/e0/a5/b2bf1c47bb7f31db1a902d9a435a12d982ef47d8493f3246df21ca87d0f7/dimspy-1.3.0.tar.gz + md5: cd15e9aea8f74a7d08e434c5358a6504 build: skip: True # [py3k] - number: 1 + number: 0 entry_points: - dimspy = dimspy.__main__:main requirements: - host: + build: - python - setuptools - numpy - scipy - fastcluster - - pymzml + - pymzml <=2.0.0 - h5py - pythonnet run: @@ -27,7 +27,7 @@ requirements: - numpy - scipy - fastcluster - - pymzml + - pymzml <=2.0.0 - h5py - pythonnet From b83a80624b4a6afc5692ae0b662ca2debe9f0017 Mon Sep 17 00:00:00 2001 From: "Darren J. White" Date: Wed, 28 Nov 2018 11:28:00 +0100 Subject: [PATCH 428/546] Added BioExcel_SeqQC to bioconda-recipes (#12276) --- recipes/BioExcel_SeqQC/build.sh | 3 +++ recipes/BioExcel_SeqQC/meta.yaml | 38 ++++++++++++++++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 recipes/BioExcel_SeqQC/build.sh create mode 100644 recipes/BioExcel_SeqQC/meta.yaml diff --git a/recipes/BioExcel_SeqQC/build.sh b/recipes/BioExcel_SeqQC/build.sh new file mode 100644 index 0000000000000..27fda12b7e24d --- /dev/null +++ b/recipes/BioExcel_SeqQC/build.sh @@ -0,0 +1,3 @@ +#!/usr/bin/env bash + +python setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/BioExcel_SeqQC/meta.yaml b/recipes/BioExcel_SeqQC/meta.yaml new file mode 100644 index 0000000000000..dae625a550c18 --- /dev/null +++ b/recipes/BioExcel_SeqQC/meta.yaml @@ -0,0 +1,38 @@ +package: + name: bioexcel_seqqc + version: "0.5" + +source: + url: https://github.com/bioexcel/BioExcel_SeqQC/archive/v0.5.tar.gz + md5: dd6f6f6fc2938ade62b0bf55b5e9cc34 + +build: + number: 0 + noarch: python + +requirements: + host: + - python >=3 + - setuptools + run: + - python >=3 + - pyyaml + - fastqc + - cutadapt + +test: + imports: + - bioexcel_seqqc + - bioexcel_seqqc.runfastqc + - bioexcel_seqqc.runtrim + - bioexcel_seqqc.seqqcutils + + commands: + - bioexcel_seqqc -h + +about: + home: https://github.com/bioexcel/bioexcel_seqqc + license: Apache Software License + license_family: APACHE + license_file: LICENSE + summary: Sequence Quality Control pipeline/modules From 8c50fa9f6b67c2f311cdd81c294ce218df31f09a Mon Sep 17 00:00:00 2001 From: David Seifert <39679069+pb-dseifert@users.noreply.github.com> Date: Wed, 28 Nov 2018 14:14:58 +0100 Subject: [PATCH 429/546] PacBio: Update pbalign to 0.3.2 (#12396) * PacBio: Update pbalign to 0.3.2 Closes: PacificBiosciences/pbbioconda#39 --- recipes/pbalign/build.sh | 5 +++++ recipes/pbalign/meta.yaml | 9 +++++---- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/recipes/pbalign/build.sh b/recipes/pbalign/build.sh index e45c73d5420b0..49b1a2924a450 100644 --- a/recipes/pbalign/build.sh +++ b/recipes/pbalign/build.sh @@ -1,3 +1,8 @@ #!/usr/bin/env bash +# pysam metadata is broken, falsely advertising itself +# as 0.15.0 instead of 0.15.1, in turn tripping up +# the setuptools load_entry_point check +sed -i.bak 's/pysam >= 0\.15\.1/pysam >= 0.15.0/g' setup.py + $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/pbalign/meta.yaml b/recipes/pbalign/meta.yaml index bc34b0f91408f..8749afa2348e3 100644 --- a/recipes/pbalign/meta.yaml +++ b/recipes/pbalign/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbalign" %} -{% set version = "0.3.1" %} -{% set sha256 = "8ee9be02959e50504dac4308ce7573ed6d4dd74f59fbe11534f9805a55f64c2d" %} +{% set version = "0.3.2" %} +{% set sha256 = "4555b4c3997e982f195fd66d581e1dfd8e30af7df900b53e89da046476635edc" %} package: name: {{ name }} @@ -24,7 +24,7 @@ extra: build: skip: True # [not py27] - number: 2 + number: 0 requirements: host: @@ -32,7 +32,8 @@ requirements: - setuptools run: - python - - pysam >=0.13 + - setuptools + - pysam >=0.15.1 - pbcore >=1.6.5 - pbcommand >=1.1.1 - blasr >=5.3.2 From 34ae6f388d22c937d985fbe879700166a3ebf8c3 Mon Sep 17 00:00:00 2001 From: Antoine Limasset Date: Wed, 28 Nov 2018 15:41:45 +0100 Subject: [PATCH 430/546] add bgreat to bioconda (#12350) * bgreat addition * zlib in build should not be needed --- recipes/bgreat2/build.sh | 11 +++++++++++ recipes/bgreat2/meta.yaml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 recipes/bgreat2/build.sh create mode 100644 recipes/bgreat2/meta.yaml diff --git a/recipes/bgreat2/build.sh b/recipes/bgreat2/build.sh new file mode 100644 index 0000000000000..2ac735379b52a --- /dev/null +++ b/recipes/bgreat2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +export CFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" +export CPATH=${PREFIX}/include + + +make zobu="-L${PREFIX}/lib " + +mkdir -p $PREFIX/bin +cp bgreat $PREFIX/bin diff --git a/recipes/bgreat2/meta.yaml b/recipes/bgreat2/meta.yaml new file mode 100644 index 0000000000000..bea2fa699dee0 --- /dev/null +++ b/recipes/bgreat2/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "2.0.0" %} + + +package: + name: bgreat + version: '{{version}}' + +source: + url: "https://github.com/Malfoy/BGREAT2/archive/1.0.tar.gz" + sha256: bc60e755a3205b725834f37d7509062879415f03730b424cbac06b776eb977cc + +build: + number: 0 + skip: true # [osx] + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - zlib + +test: + commands: + - bgreat + +about: + home: https://github.com/Malfoy/BGREAT2 + license: AGPL-3.0 + summary: BGREAT2 is a read mapping tool for NGS sequencing data that align reads on a de Bruijn graph. Preliminary version described at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1103-9 and used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336) From 7e7e7180c87a7322efb36e252c77c00d1f279c2a Mon Sep 17 00:00:00 2001 From: Antoine Limasset Date: Wed, 28 Nov 2018 15:42:39 +0100 Subject: [PATCH 431/546] btrim integration to conda (#12395) --- recipes/btrim/build.sh | 6 ++++++ recipes/btrim/meta.yaml | 28 ++++++++++++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 recipes/btrim/build.sh create mode 100644 recipes/btrim/meta.yaml diff --git a/recipes/btrim/build.sh b/recipes/btrim/build.sh new file mode 100644 index 0000000000000..99a633977504f --- /dev/null +++ b/recipes/btrim/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +make; + +mkdir -p $PREFIX/bin +cp btrim $PREFIX/bin diff --git a/recipes/btrim/meta.yaml b/recipes/btrim/meta.yaml new file mode 100644 index 0000000000000..0a17434ff4980 --- /dev/null +++ b/recipes/btrim/meta.yaml @@ -0,0 +1,28 @@ +{% set version = "1.0.0" %} + + +package: + name: btrim + version: '{{version}}' + +source: + url: "https://github.com/Malfoy/BTRIM/archive/1.0.0.tar.gz" + sha256: 4e3eb67ef16fddafee0eab5b24b332d9a87a9bd07007da31b52c3874d76de530 + +build: + number: 0 + skip: true # [osx] + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + +test: + commands: + - btrim + +about: + home: https://github.com/Malfoy/BTRIM + license: AGPL-3.0 + summary: This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336) From b6df1029c90b786f4cae2e7f0965377f67c73ffc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 28 Nov 2018 17:02:44 +0100 Subject: [PATCH 432/546] Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399) --- recipes/r-sleuth/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/r-sleuth/meta.yaml b/recipes/r-sleuth/meta.yaml index 927b1a41ed814..bbbdb911ca0bd 100644 --- a/recipes/r-sleuth/meta.yaml +++ b/recipes/r-sleuth/meta.yaml @@ -1,15 +1,18 @@ package: name: r-sleuth version: 0.30.0 + source: - url: https://github.com/pachterlab/sleuth/archive/v0.30.0.tar.gz + url: https://github.com/pachterlab/sleuth/archive/v{{ PKG_VERSION }}.tar.gz sha256: c25158dff35416865931f7c95f02c64be764c5b2ce964fe9f40972d96150ddb2 + build: number: 0 skip: true # [win32] rpaths: - lib/R/lib/ - lib/ + requirements: host: - r-base @@ -39,13 +42,16 @@ requirements: - r-reshape2 - r-shiny - r-tidyr + test: commands: - '$R -e "library(''sleuth'')"' + about: home: http://pachterlab.github.io/sleuth license: GPLv3 summary: "Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto." + extra: recipe-maintainers: - MathiasHaudgaard From 7512af951137e91e0cc115053ab1c6ed789e5ddd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Armin=20T=C3=B6pfer?= Date: Wed, 28 Nov 2018 17:07:20 +0100 Subject: [PATCH 433/546] PacBio: Update `pbsv2` to version 2.1.0 (#12400) --- recipes/pbsv/meta.yaml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/recipes/pbsv/meta.yaml b/recipes/pbsv/meta.yaml index de3a9d8ebaeec..0c478eecb0047 100644 --- a/recipes/pbsv/meta.yaml +++ b/recipes/pbsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbsv" %} -{% set version = "2.0.2" %} -{% set sha256 = "ef5c6f8e00d2ec3a2a2bcabd66b857aa48563b9495f77d5679476c14fb59cb43" %} +{% set version = "2.1.0" %} +{% set sha256 = "774655ea7403790b46f129f4b0e2b08d6d4e10bb7f23b693c75c790a1745de5b" %} package: name: {{ name }} @@ -25,10 +25,6 @@ build: number: 0 skip: True # [osx] -requirements: - run: - - minimap2 >=2.11 - test: commands: - pbsv -h From 0354d8cc1318e070941f0a4066ca5adfbd0efb82 Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Wed, 28 Nov 2018 17:25:25 +0100 Subject: [PATCH 434/546] Genenotebook v0.1.11 (#12398) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 --- recipes/genenotebook/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index a62a79d6745fc..e867b83b3df64 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.10' %} -{% set sha256 = 'd077a80de4f157ab4bd385337bc4be8eddd1c865585e89d63e259637916b097c' %} +{% set version = '0.1.11' %} +{% set sha256 = '43abfe033d7280a179506b50a636fd595bb4dd1d93348c03ca9270b48cbcc555' %} package: name: {{ name|lower }} From 3b58e2cab6b57b996dbb4ac3ad62f4e92a79d418 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 28 Nov 2018 20:14:23 +0100 Subject: [PATCH 435/546] prosolo: new package version 0.6.0 (#12397) --- recipes/prosolo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/prosolo/meta.yaml b/recipes/prosolo/meta.yaml index 282916fc2819e..eeea33b61be3f 100644 --- a/recipes/prosolo/meta.yaml +++ b/recipes/prosolo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: prosolo @@ -9,7 +9,7 @@ build: source: url: https://github.com/prosolo/prosolo/archive/v{{ version }}.tar.gz - sha256: a778c5cab84b38842b7a80772c85e8bc590e25caca0f405711af7f60e8762ba6 + sha256: 4ba1193d2632516d31e39efec6fc53fd86406bb50578668c6ada30112e64285c requirements: build: From 93573abc1606752b7b443fb157e887b92adf0629 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 28 Nov 2018 15:45:42 -0700 Subject: [PATCH 436/546] Update sevenbridges-python to 0.17.2 (#12404) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index a13909bc02004..cef3dc838c8d8 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.17.1" %} -{% set sha256 = "269259e74d972a7f34b4c58d37d9d903a48c347d738080a76dc9a2e0f2efb48b" %} +{% set version = "0.17.2" %} +{% set sha256 = "81560d9ba686cf50d2adaf74b1ea5aa1b38dd10b39fe71311f3ac214447d882c" %} package: name: sevenbridges-python From 1f0a2b1365b6de3005f57bc0d7075f2792c74d94 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Wed, 28 Nov 2018 17:35:09 -0600 Subject: [PATCH 437/546] Add recipe for ICED (#12406) --- recipes/iced/meta.yaml | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 recipes/iced/meta.yaml diff --git a/recipes/iced/meta.yaml b/recipes/iced/meta.yaml new file mode 100644 index 0000000000000..b400c6e07fcec --- /dev/null +++ b/recipes/iced/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "iced" %} +{% set version = "0.5.0" %} +{% set sha256 = "6a227483989bb3522b499f4a221bf1aff3f3e2439da922d7383a3d2b02c2ca9b" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://github.com/hiclib/{{ name }}/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed" + +requirements: + build: + - {{ compiler('cxx') }} + host: + - pip + - python + - numpy >=1.9 + run: + - python + - numpy >=1.9 + - scipy >=0.14 + - pandas + - scikit-learn + - cython + - matplotlib + +test: + imports: + - iced + +about: + home: https://github.com/hiclib/iced + license: new BSD + license_family: BSD + license_file: COPYING + summary: "The python module iced implements the ICE normalization of hic data." From a1d194e75eaadece3a07f896aa5c5778abc3344c Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Wed, 28 Nov 2018 20:29:48 -0600 Subject: [PATCH 438/546] Downgrade version for iced (#12409) --- recipes/iced/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/iced/meta.yaml b/recipes/iced/meta.yaml index b400c6e07fcec..9292eec084047 100644 --- a/recipes/iced/meta.yaml +++ b/recipes/iced/meta.yaml @@ -1,6 +1,6 @@ {% set name = "iced" %} -{% set version = "0.5.0" %} -{% set sha256 = "6a227483989bb3522b499f4a221bf1aff3f3e2439da922d7383a3d2b02c2ca9b" %} +{% set version = "0.4.2" %} +{% set sha256 = "6a199d713b1d8211c843afa8ec0caa83c640212470e735ebde3729c344537690" %} package: name: "{{ name }}" From 9f150d3fc50e731043092b8ed33f09b735591c37 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Wed, 28 Nov 2018 22:12:51 -0600 Subject: [PATCH 439/546] Update recipe for libstatgen 1.0.5 (#12348) * Add recipe for libstatgen-1.0.5 --- recipes/libstatgen/build.sh | 9 ++++++++ recipes/libstatgen/gcc_zlib.patch | 33 +++++++++++++++++++++++++++++ recipes/libstatgen/meta.yaml | 35 +++++++++++++++++++++++++++++++ 3 files changed, 77 insertions(+) create mode 100644 recipes/libstatgen/build.sh create mode 100644 recipes/libstatgen/gcc_zlib.patch create mode 100644 recipes/libstatgen/meta.yaml diff --git a/recipes/libstatgen/build.sh b/recipes/libstatgen/build.sh new file mode 100644 index 0000000000000..4a5a0037e4241 --- /dev/null +++ b/recipes/libstatgen/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CFLAGS="-I$PREFIX/include -I${SRC_DIR}/include" +export LDFLAGS="-L$PREFIX/lib" +export CPATH=${PREFIX}/include:${SRC_DIR}/include + +make +cp libStatGen*.a ${PREFIX}/lib +cp include/* ${PREFIX}/include diff --git a/recipes/libstatgen/gcc_zlib.patch b/recipes/libstatgen/gcc_zlib.patch new file mode 100644 index 0000000000000..501c7fe542e4c --- /dev/null +++ b/recipes/libstatgen/gcc_zlib.patch @@ -0,0 +1,33 @@ +--- bam/SamInterface.cpp 2012-10-24 15:53:29.000000000 -0500 ++++ bam/SamInterface.cpp.new 2018-11-27 02:53:32.764220114 -0600 +@@ -15,12 +15,16 @@ + * along with this program. If not, see . + */ + ++#include ++#define __STDC_LIMIT_MACROS ++#include ++#include ++ ++// using namespace std; ++ + #include "SamInterface.h" + #include "SamRecordHelper.h" + +-#include +-#include +- + SamInterface::SamInterface() + { + } +--- Makefiles/Makefile.include 2018-11-27 03:39:26.853405131 -0600 ++++ Makefiles/Makefile.include.new 2018-11-27 03:40:14.109391148 -0600 +@@ -44,7 +44,7 @@ + ZLIB_AVAIL ?= 1 + + USE_ZLIB = -D__ZLIB_AVAILABLE__ +-ZLIB_LIB = -lz ++ZLIB_LIB = -lz -L${PREFIX}/lib + ifeq ($(ZLIB_AVAIL), 0) + USE_ZLIB = + ZLIB_LIB = diff --git a/recipes/libstatgen/meta.yaml b/recipes/libstatgen/meta.yaml new file mode 100644 index 0000000000000..c523b99a96088 --- /dev/null +++ b/recipes/libstatgen/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "libStatGen" %} +{% set version = "1.0.5" %} +{% set sha256 = "a402777e2999badca177d568565e9cd3775cbe511ef2a449658e96b8b1e4aa7e" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + +source: + url: https://github.com/statgen/libStatGen/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - gcc_zlib.patch + +requirements: + build: + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + +test: + commands: + - test -f ${PREFIX}/lib/libStatGen.a + +about: + home: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen + license: GPL3 + license_file: copyrights/LICENSE.txt + summary: Useful set of classes for creating statistical genetic programs. + dev_url: https://github.com/statgen/libStatGen From ad4f9d68999c90603141178553c8827f09d60a00 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 28 Nov 2018 21:13:58 -0700 Subject: [PATCH 440/546] Update iced to 0.5.0 (#12411) --- recipes/iced/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/iced/meta.yaml b/recipes/iced/meta.yaml index 9292eec084047..b400c6e07fcec 100644 --- a/recipes/iced/meta.yaml +++ b/recipes/iced/meta.yaml @@ -1,6 +1,6 @@ {% set name = "iced" %} -{% set version = "0.4.2" %} -{% set sha256 = "6a199d713b1d8211c843afa8ec0caa83c640212470e735ebde3729c344537690" %} +{% set version = "0.5.0" %} +{% set sha256 = "6a227483989bb3522b499f4a221bf1aff3f3e2439da922d7383a3d2b02c2ca9b" %} package: name: "{{ name }}" From 09336cacb42599eea615f8af3d59a64503f38297 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 28 Nov 2018 21:21:07 -0700 Subject: [PATCH 441/546] Update perl-test2-suite to 0.000116 (#12412) --- recipes/perl-test2-suite/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-test2-suite/meta.yaml b/recipes/perl-test2-suite/meta.yaml index 3f705dc8bc908..4fec4f3d5b034 100644 --- a/recipes/perl-test2-suite/meta.yaml +++ b/recipes/perl-test2-suite/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-test2-suite" %} -{% set version = "0.000115" %} -{% set sha256 = "02be3428a0965aeb21245d44bbadda69b94dc76cd68d5695352c996ac7fc3638" %} +{% set version = "0.000116" %} +{% set sha256 = "8669bc7e680bd6a0dbcb7e24a68d768a49cad99484a4470b1856b9888f88f366" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Test2-Suite-0.000115.tar.gz + url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Test2-Suite-0.000116.tar.gz sha256: {{ sha256 }} build: From 393a334e2deb607647827ddab8b40d4cf693accf Mon Sep 17 00:00:00 2001 From: Antoine Limasset Date: Thu, 29 Nov 2018 13:07:01 +0100 Subject: [PATCH 442/546] fix compatibility with other tools (#12415) --- recipes/btrim/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/btrim/meta.yaml b/recipes/btrim/meta.yaml index 0a17434ff4980..5a320dc26b74f 100644 --- a/recipes/btrim/meta.yaml +++ b/recipes/btrim/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: @@ -6,11 +6,11 @@ package: version: '{{version}}' source: - url: "https://github.com/Malfoy/BTRIM/archive/1.0.0.tar.gz" - sha256: 4e3eb67ef16fddafee0eab5b24b332d9a87a9bd07007da31b52c3874d76de530 + url: "https://github.com/Malfoy/BTRIM/archive/1.0.1.tar.gz" + sha256: 5e183a41dcbc52d6c3820dd521ce70d03bec7c6eb518feb7adf3dde04f1a1d41 build: - number: 0 + number: 1 skip: true # [osx] requirements: From c28dc49162a78784816a5c12f0aa1ae328974007 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Thu, 29 Nov 2018 09:18:30 -0500 Subject: [PATCH 443/546] Restore dexseq python helper scripts (#12352) * Restore dexseq python helper scripts * Add python requirement for helper scripts * Add python noarch to build section * pin it to python2k * Add htseq requirement, support only python <3 for now --- recipes/bioconductor-dexseq/build.sh | 10 +++++++++- recipes/bioconductor-dexseq/meta.yaml | 13 ++++++++++++- 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index da43ce2168312..e5264766ba3a0 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -1,4 +1,12 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . +python_scripts=$PREFIX/lib/R/library/DEXSeq/python_scripts +sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_count.py +sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_prepare_annotation.py +chmod +x $python_scripts/dexseq_count.py +chmod +x $python_scripts/dexseq_prepare_annotation.py +mkdir -p $PREFIX/bin +ln -s $python_scripts/dexseq_count.py $PREFIX/bin/dexseq_count.py +ln -s $python_scripts/dexseq_prepare_annotation.py $PREFIX/bin/dexseq_prepare_annotation.py diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 110aae2fd7724..ce5855cbc77ba 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -5,17 +5,21 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' + source: url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' sha256: e1e9026c07fc26e1eaee06a0dd63d2f765bcd711f350fdb2a2236ad65b1d0bd7 + build: - number: 0 + noarch: python + number: 1 rpaths: - lib/R/lib/ - lib/ + requirements: host: - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' @@ -55,13 +59,20 @@ requirements: - r-rcolorbrewer - r-statmod - r-stringr + - python <3 + - 'htseq >=0.9.1' + test: commands: - '$R -e "library(''{{ name }}'')"' + - dexseq_count.py --help + - dexseq_prepare_annotation.py --help + about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.' + extra: identifiers: - biotools:dexseq From d24d7b00abce0b4587dc88f5f3c95d6880a3d363 Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Thu, 29 Nov 2018 16:11:05 +0100 Subject: [PATCH 444/546] Genenotebook v0.1.12 (#12418) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source --- recipes/genenotebook/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index e867b83b3df64..81503208f72f3 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.11' %} -{% set sha256 = '43abfe033d7280a179506b50a636fd595bb4dd1d93348c03ca9270b48cbcc555' %} +{% set version = '0.1.12' %} +{% set sha256 = 'c2de5968fc66e9db0d18b7bd586db1e0f8c55aa339c341dc427340620bf108ca' %} package: name: {{ name|lower }} From 4824abaa24831712927938ed1cbda04a110cc27a Mon Sep 17 00:00:00 2001 From: ThomasWollmann Date: Thu, 29 Nov 2018 17:08:43 +0100 Subject: [PATCH 445/546] added medpy recipe (#12417) * added medpy recipe * removed osx from build * Update meta.yaml * Update meta.yaml * add boost and a compiler * Update meta.yaml * Update meta.yaml * add itk --- recipes/medpy/meta.yaml | 56 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 recipes/medpy/meta.yaml diff --git a/recipes/medpy/meta.yaml b/recipes/medpy/meta.yaml new file mode 100644 index 0000000000000..da30c4f0afaa8 --- /dev/null +++ b/recipes/medpy/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "MedPy" %} +{% set version = "0.3.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 299d1be28df0b9c35e856177ada7555746d5b94a0f7af34dc3c3dd3671252a6a + +build: + number: 0 + script: + - export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include -I${PYTHON_INCLUDE_DIR}" + - "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + skip: True # [osx] + +requirements: + build: + #- {{ compiler('cxx') }} + host: + - nibabel >=1.3.0 + - numpy >=1.6.1 + - pip + - pydicom >=0.9.7 + - python <3 + - scipy >=0.9.0 + #- boost + run: + - nibabel >=1.3.0 + - numpy >=1.6.1 + - pydicom >=0.9.7 + - python <3 + - itk + - scipy >=0.9.0 + +test: + imports: + - medpy + - medpy.core + - medpy.features + - medpy.filter + #- medpy.graphcut + - medpy.io + - medpy.itkvtk + - medpy.itkvtk.filter + - medpy.itkvtk.utilities + - medpy.metric + - medpy.utilities + +about: + home: https://github.com/loli/medpy + license: GNU General Public (GPL) + license_family: LGPL + summary: Medical image processing in Python From bcc25fe7c5a85c6df3d9ab8f9b418871e57e15f3 Mon Sep 17 00:00:00 2001 From: HenningTimm Date: Thu, 29 Nov 2018 17:16:30 +0100 Subject: [PATCH 446/546] Updated ddrage to version 1.6.1. (#12421) --- recipes/ddrage/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/ddrage/meta.yaml b/recipes/ddrage/meta.yaml index 4163118ac3bad..738926b6d36c1 100644 --- a/recipes/ddrage/meta.yaml +++ b/recipes/ddrage/meta.yaml @@ -1,10 +1,10 @@ package: name: ddrage - version: "1.5.2" + version: "1.6.1" source: - url: https://bitbucket.org/genomeinformatics/rage/get/1.5.2.tar.gz - sha256: 63dba01ac03a14b0ab4828b5cc63b7723bcf05441231d43f93d82b4a401fd7de + url: https://bitbucket.org/genomeinformatics/rage/get/1.6.1.tar.gz + sha256: 7d5d6f33b011551746426ca0554b8d999b65d2c72ba2b0a398de661f976c11a9 build: @@ -17,7 +17,7 @@ build: - visualize_bbd = ddrage.tools.bbd_visualization:main_standalone - remove_annotation = ddrage.tools.remove_annotation:main - split_by_p7_barcode = ddrage.tools.split_by_p7_barcode:main - build: 1 + build: 0 requirements: @@ -58,7 +58,7 @@ test: about: home: https://bitbucket.org/genomeinformatics/rage license: MIT License - summary: 'Simulator for ddRADseq (double digest restriction site associdated DNA squencing) datasets. Generates reads (FASTQ format) that can be analyzed and validated using a ground truth file (YAML).' + summary: 'Simulator for ddRADseq (double digest restriction site associated DNA sequencing) datasets. Generates reads (FASTQ format) that can be analyzed and validated using a ground truth file (YAML).' license_family: MIT extra: From f0826ecc0f551cf34a3acb37d35b933aabce9adb Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Thu, 29 Nov 2018 17:37:38 +0100 Subject: [PATCH 447/546] Add r-mcpcounter recipe. (#12261) * Add MCPcounter recipe. * fix lint: remove 'fn' * fix license_file, version number and doi --- recipes/r-mcpcounter/build.sh | 1 + recipes/r-mcpcounter/meta.yaml | 42 ++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100755 recipes/r-mcpcounter/build.sh create mode 100755 recipes/r-mcpcounter/meta.yaml diff --git a/recipes/r-mcpcounter/build.sh b/recipes/r-mcpcounter/build.sh new file mode 100755 index 0000000000000..cd627a36da09e --- /dev/null +++ b/recipes/r-mcpcounter/build.sh @@ -0,0 +1 @@ +$R CMD INSTALL --build ./Source diff --git a/recipes/r-mcpcounter/meta.yaml b/recipes/r-mcpcounter/meta.yaml new file mode 100755 index 0000000000000..8161cf72d2412 --- /dev/null +++ b/recipes/r-mcpcounter/meta.yaml @@ -0,0 +1,42 @@ +package: + name: r-mcpcounter + # no releases on the github page. Future updates unlikely. + version: 0 + +source: + url: + - https://github.com/ebecht/MCPcounter/archive/a79614eee002c88c64725d69140c7653e7c379b4.tar.gz + sha256: cc2e842f629c0cc881ffc3273cd429528dd98241fc71de2e983b726db17255d1 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-roxygen2 >=6.0.1 + - r-curl >=2.6 + + run: + - r-base >=2.6.0 + - r-curl >=2.6 + +test: + commands: + - $R -e "library('MCPcounter')" + +about: + home: https://github.com/ebecht/MCPcounter + license: GPL-3 + summary: "Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression" + license_family: GPL + license_file: Source/License + +extra: + recipe-maintainers: + - grst + identifiers: + - doi:10.1186/s13059-016-1070-5 From 6468e1b5dc91959c9494e4b8f597070d1967f9a1 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Thu, 29 Nov 2018 14:26:28 -0500 Subject: [PATCH 448/546] Update DEXSeq requirements to force compatible HTSeq version (#12423) --- recipes/bioconductor-dexseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index ce5855cbc77ba..41631be4ebe99 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -15,7 +15,7 @@ source: build: noarch: python - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -60,7 +60,7 @@ requirements: - r-statmod - r-stringr - python <3 - - 'htseq >=0.9.1' + - 'htseq >=0.6.1,<0.10.0' # dexseq_count.py performes an overly simplistic version check test: commands: From c2e55df081bd1e8449bc64949d2d3f6d1a080f63 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 29 Nov 2018 12:56:52 -0700 Subject: [PATCH 449/546] ARB: Pin glib (#11782) * Pin glib * Update meta.yaml * Update meta.yaml * Work around CB3 issues * Work around bioconda-utils lint false positive * Disable lint check should_not_be_noarch * Can't reference other packages built in recipe from anything but run * Move perl to host section. Maybe that helps. * constraining interpreter version breaks with CB3? * disable perl version constraint :( --- recipes/arb-bio/meta.yaml | 127 ++++++++++++++++++++++++++++---------- 1 file changed, 95 insertions(+), 32 deletions(-) diff --git a/recipes/arb-bio/meta.yaml b/recipes/arb-bio/meta.yaml index 8b3c6503bc870..ae6f4c7efb1ac 100644 --- a/recipes/arb-bio/meta.yaml +++ b/recipes/arb-bio/meta.yaml @@ -25,12 +25,16 @@ source: - gsed.patch build: - number: 4 + number: 5 +# constraining to perl >= 5.23 does not work via requirements, resulting in a +# broken build string. constraining via skip also doesn't work - the suggested +# approach leads to str < int compare failure during lint. +# => let's just hope no one tries building this with an old perl. +# skip: True # [perl <5.23] requirements: build: - {{ compiler('cxx') }} - - {{ compiler('c') }} - pkg-config - time - lynx @@ -51,34 +55,13 @@ requirements: - libxslt - libpng - xerces-c - - perl >=5.23 - run: - # libs: - - openmotif - - glib - - gettext - - xorg-libxi - - xorg-libxmu - - xorg-libxp - - xorg-libxaw - - xorg-libxpm - - xorg-libxft - - libpng - # tools: - - gnuplot - - muscle - - mafft - - raxml - - mrbayes - - phylip - - phyml 3.2.0* - - fasttree - - sed >=4.4 - - xfig - - fig2dev - # We build a binary perl module. ABI compatability seems to be maintained - # at minor version (5.26.x), so we pin accordingly: - - {{ pin_compatible("perl", min_pin="x.x", max_pin="x.x") }} + # Perl is a problem. We must always have a perl version that was compiled with the + # same compiler we are using. Otherwise we run into e.g. "-fstack-protector-strong" type + # issues. Make-Maker uses the flags from the perl build time for the makefile it generates, + # so those flags must work for us as well. + - perl + + test: requires: - conda @@ -93,27 +76,107 @@ outputs: - name: libarbdb script: install_libarbdb.sh requirements: - run: + build: + - {{ compiler('cxx') }} + host: - glib + # We must have perl in the host sections of all output packages because + # `pin_compatible` will fail otherwise. Probably another bug. + - perl + run: - gettext + - {{ pin_compatible("glib", max_pin="x") }} + build: + run_exports: + - {{ pin_subpackage("libarbdb", exact=True) }} - name: arb-bio-tools script: install_tools.sh requirements: + build: + - {{ compiler('cxx') }} + host: + - glib + - perl # see above run: - - {{ pin_subpackage('libarbdb', exact=True) }} + - {{ pin_subpackage("libarbdb", exact=True) }} + - name: arb-bio script: install_main.sh requirements: + # We have to restate everything we used above in the top level requirements here. + # Lacking proper documentation of anything in conda build 3, all of this is trial + # and error. The run dependencies stated at the top level are not applied to the + # arb-bio output even though it shares the name with the toplevel. + # We also can't use YAML anchors to reference what we wrote above because conda + # build breaks YAML by parsing the outputs section again at a later point. + # Horrible mess.... + build: + - {{ compiler('cxx') }} + - pkg-config + - time + - lynx + - xorg-makedepend + - sed >=4.4 + - tar + host: + - openmotif-dev + - glib + - gettext + - pthread-stubs + - xorg-libxi + - xorg-libxp + - xorg-libxaw + - xorg-libxpm + - xorg-libxmu + - libtiff + - libxslt + - libpng + - xerces-c + - perl run: - {{ pin_subpackage('arb-bio-tools', exact=True) }} + # We build a binary perl module. ABI compatability seems to be maintained + # at minor version (5.26.x), so we pin accordingly: + - {{ pin_compatible("perl", max_pin="x.x") }} + - gettext + - openmotif + - xorg-libxi + - xorg-libxmu + - xorg-libxp + - xorg-libxaw + - xorg-libxpm + - xorg-libxft + - xorg-libxt + - libpng + # tools: + - gnuplot + - muscle + - mafft + - raxml + - mrbayes + - phylip + - phyml 3.2.0* + - fasttree + - sed >=4.4 + - xfig + - fig2dev - name: arb-bio-devel script: install_devel.sh requirements: + build: + - {{ compiler('cxx') }} run: - {{ pin_subpackage('arb-bio', exact=True) }} + - openmotif-dev about: home: http://www.arb-home.de license: ARB licence_file: arb_LICENSE.txt summary: ARB 6 Sequence Analysis Suite + +extra: + recipe-maintainers: + - epruesse + skip-lints: + - should_not_be_noarch # false positive, `noarch: False` added by CB3 for outputs From 0a6c94b67dc215c216d27bdf853f3af4a1d5b890 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 29 Nov 2018 21:02:33 +0100 Subject: [PATCH 450/546] Update meta.yaml (#12426) --- recipes/percolator/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/percolator/meta.yaml b/recipes/percolator/meta.yaml index 45dd449771c14..69d5069d4a7f6 100644 --- a/recipes/percolator/meta.yaml +++ b/recipes/percolator/meta.yaml @@ -7,7 +7,7 @@ source: md5: fcb37bc5fcd0149cc775c3e72ff3dc24 build: - number: 5 + number: 6 skip: True # [osx] requirements: From e19312d7a4ad081549c7d7471b02e106a83518c6 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 29 Nov 2018 21:09:43 +0100 Subject: [PATCH 451/546] stacks: fix for fix 'fixing' @ in exe_path (#12420) * stacks: fix for fix 'fixing' @ in exe_path the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580 tried to solve the problem with the @ in the exe_path by setting this variable empty. But the perl scripts - append a / to the empty string and (i.e. the bin path gets /binary) - check for file presence (problem: neither binary nor /binary are present) Now I quote the @ in the exe_path. * stacks: add refmap bugfix --- recipes/stacks/2.2/build.sh | 5 ++++- recipes/stacks/2.2/meta.yaml | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/stacks/2.2/build.sh b/recipes/stacks/2.2/build.sh index e12933bd0370c..8b03fa8e13605 100644 --- a/recipes/stacks/2.2/build.sh +++ b/recipes/stacks/2.2/build.sh @@ -20,8 +20,11 @@ cp -p scripts/{convert_stacks.pl,extract_interpop_chars.pl} "$PREFIX/bin/" # after installation the exe_dir is set to the absolute binary path # this is not necessary and leads to an error if there are characters # like @ included (Galaxy) + +# furthermore a bug in ref_map v2.2 is fixed for i in ref_map.pl denovo_map.pl do - sed -i -e 's/\(my $exe_path\s\+= \).*/\1"";/' "$PREFIX/bin/$i" + sed -i -e "s/^\(my \$exe_path\s\+=[^@]\+\)/\1\\\\/" "$PREFIX/bin/$i" + sed -i -e "s/_alpha/-alpha/" "$PREFIX/bin/$i" done diff --git a/recipes/stacks/2.2/meta.yaml b/recipes/stacks/2.2/meta.yaml index 69ba4f7effd61..92e123ed36a61 100644 --- a/recipes/stacks/2.2/meta.yaml +++ b/recipes/stacks/2.2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: sha256: {{ hash }} From 9d6bf3d72f570c09627addd729d6e8b5eb3513fd Mon Sep 17 00:00:00 2001 From: Rens Holmer Date: Thu, 29 Nov 2018 21:10:23 +0100 Subject: [PATCH 452/546] Genenotebook v0.1.13 (#12424) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * v0.1.13 --- recipes/genenotebook/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index 81503208f72f3..7e100ac3803d6 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'GeneNoteBook' %} -{% set version = '0.1.12' %} -{% set sha256 = 'c2de5968fc66e9db0d18b7bd586db1e0f8c55aa339c341dc427340620bf108ca' %} +{% set version = '0.1.13' %} +{% set sha256 = '1f8c62d339d9b7c09009c592609fbc5b2ec5c0d80c3c3d3c575e662df93763e0' %} package: name: {{ name|lower }} From 7f65fcbb0ec8b652a8beec63329fccc806a41a19 Mon Sep 17 00:00:00 2001 From: Caleb Easterly Date: Thu, 29 Nov 2018 20:46:33 -0500 Subject: [PATCH 453/546] metaQuantome (#12413) replaces metaquant, which is now deprecated. --- recipes/metaquantome/LICENSE | 201 +++++++++++++++++++++++++++++++++ recipes/metaquantome/meta.yaml | 54 +++++++++ 2 files changed, 255 insertions(+) create mode 100644 recipes/metaquantome/LICENSE create mode 100644 recipes/metaquantome/meta.yaml diff --git a/recipes/metaquantome/LICENSE b/recipes/metaquantome/LICENSE new file mode 100644 index 0000000000000..261eeb9e9f8b2 --- /dev/null +++ b/recipes/metaquantome/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/recipes/metaquantome/meta.yaml b/recipes/metaquantome/meta.yaml new file mode 100644 index 0000000000000..252c41617a981 --- /dev/null +++ b/recipes/metaquantome/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "metaquantome" %} +{% set version = "0.99.2" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "f4083204442beebd06fce19a46383b399c38d8c6db9d2cf9c5873124359ad2f8" %} + +package: + name: '{{ name }}' + version: '{{ version }}' + +source: + url: https://github.com/galaxyproteomics/{{ name }}/archive/v{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' + +build: + noarch: python + number: 0 + script: python setup.py install --single-version-externally-managed --record=record.txt + +requirements: + host: + - python >=3 + - setuptools + run: + - python >=3 + - ete3 3.1.* + - goatools 0.7.* + - statsmodels 0.8.* + - biopython >=1.70 + - pandas 0.23.* + - r-gplots 3.0.* + - r-ggplot2 + - r-base + - r-jsonlite + - libiconv + +test: + import: + - metaquantome + + commands: + - metaquantome -h + - metaquantome expand -h + - metaquantome filter -h + - metaquantome stat -h + - metaquantome viz -h + +about: + home: 'https://github.com/galaxyproteomics/metaquant' + license: Apache Software License + license_family: APACHE + license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE' + summary: Quantitative metaproteomics analysis of taxonomy and function. + dev_url: 'https://github.com/galaxyproteomics/metaquant' From 5da3a3a7fbfff7be9400b127d3ccf8914a9a69e3 Mon Sep 17 00:00:00 2001 From: Martin Steinegger Date: Thu, 29 Nov 2018 21:44:40 -0500 Subject: [PATCH 454/546] New MMseqs2 release 7-4e23d (#12432) New mmseqs2 release 7-4e23d --- recipes/mmseqs2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mmseqs2/meta.yaml b/recipes/mmseqs2/meta.yaml index 29a051780c126..802b667af7b97 100644 --- a/recipes/mmseqs2/meta.yaml +++ b/recipes/mmseqs2/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6-f5a1c" %} -{% set sha256 = "41a7b3114a2f54796e0d4e423045ee1bc3372834f75c72956e5c9eda520db586" %} +{% set version = "7-4e23d" %} +{% set sha256 = "39b04ea60741ca209c37be129b852b5024fed1691817e6eb1e80e382f7261724" %} package: name: mmseqs2 From 72cb85330a32b8b719ecf24914e744cd4d989b68 Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Fri, 30 Nov 2018 00:29:26 -0500 Subject: [PATCH 455/546] update spades to 3.13.0 (#12408) * update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure --- recipes/spades/3.11.1/meta.yaml | 2 +- recipes/spades/3.12.0/build.sh | 12 ++++++++ recipes/spades/3.12.0/meta.yaml | 49 +++++++++++++++++++++++++++++++++ recipes/spades/meta.yaml | 9 +++--- 4 files changed, 66 insertions(+), 6 deletions(-) create mode 100644 recipes/spades/3.12.0/build.sh create mode 100644 recipes/spades/3.12.0/meta.yaml diff --git a/recipes/spades/3.11.1/meta.yaml b/recipes/spades/3.11.1/meta.yaml index 78667670300ec..d196842926d15 100644 --- a/recipes/spades/3.11.1/meta.yaml +++ b/recipes/spades/3.11.1/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474 # [linux] build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/spades/3.12.0/build.sh b/recipes/spades/3.12.0/build.sh new file mode 100644 index 0000000000000..528c0d0ecc04c --- /dev/null +++ b/recipes/spades/3.12.0/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +set -e -o pipefail + +outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $outdir +mkdir -p $PREFIX/bin + +cp -r bin $outdir +cp -r share $outdir + +ln -s $outdir/bin/* $PREFIX/bin diff --git a/recipes/spades/3.12.0/meta.yaml b/recipes/spades/3.12.0/meta.yaml new file mode 100644 index 0000000000000..8392711adb22b --- /dev/null +++ b/recipes/spades/3.12.0/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "3.12.0" %} + +package: + name: spades + version: {{ version }} + +source: + # We currently cannot build SPAdes from source, because it requires g++ 5.3.1 or later, + # which bioconda does not yet support. Therefore, we fetch the statically compiled binaries. + url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Darwin.tar.gz # [osx] + sha256: e2a4f589c190767310545300386c7e2841ebdfe3775850cd52879ef01d376575 # [osx] + url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Linux.tar.gz # [linux] + sha256: 5e8988b0cfd8b5a84b718e1e5af21524c7b1369bcba337dfebeed9c22a4f7141 # [linux] + +build: + number: 1 + +requirements: + run: + - python + +test: + commands: + - spades.py --version + - rnaspades.py --version + - truspades.py --version + - dipspades.py --version + - metaspades.py --version + - plasmidspades.py --version + - spades.py --test && rm -rf spades_test + - spades-kmercount -h + +about: + home: http://cab.spbu.ru/software/spades/ + license: GPLv2 + license_family: GPL + license_file: share/spades/LICENSE + summary: | + SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. + dev_url: https://github.com/ablab/spades + doc_url: http://cab.spbu.ru/files/release{{version}}/manual.html +extra: + recipe-maintainers: + - druvus + - notestaff + identifiers: + - biotools:Spades + - doi:10.1089/cmb.2012.0021 + - doi:10.1101/gr.213959.116 diff --git a/recipes/spades/meta.yaml b/recipes/spades/meta.yaml index 8392711adb22b..bc4459e9048c9 100644 --- a/recipes/spades/meta.yaml +++ b/recipes/spades/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.12.0" %} +{% set version = "3.13.0" %} package: name: spades @@ -8,12 +8,12 @@ source: # We currently cannot build SPAdes from source, because it requires g++ 5.3.1 or later, # which bioconda does not yet support. Therefore, we fetch the statically compiled binaries. url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Darwin.tar.gz # [osx] - sha256: e2a4f589c190767310545300386c7e2841ebdfe3775850cd52879ef01d376575 # [osx] + sha256: 86dac86962b6d26891eb9b1d173d8dd5ce957482013880f6d75b751b7bb274a0 # [osx] url: https://github.com/ablab/spades/releases/download/v{{ version }}/SPAdes-{{ version }}-Linux.tar.gz # [linux] - sha256: 5e8988b0cfd8b5a84b718e1e5af21524c7b1369bcba337dfebeed9c22a4f7141 # [linux] + sha256: 3666b256e2239adbdf9d8b3e3e6a60b2d8d51878b892ea6a821b033a5ef0d03b # [linux] build: - number: 1 + number: 0 requirements: run: @@ -24,7 +24,6 @@ test: - spades.py --version - rnaspades.py --version - truspades.py --version - - dipspades.py --version - metaspades.py --version - plasmidspades.py --version - spades.py --test && rm -rf spades_test From f4fca6ff692cd430a833a26c07cceb85bd622282 Mon Sep 17 00:00:00 2001 From: Vlad Saveliev Date: Fri, 30 Nov 2018 17:22:38 +1100 Subject: [PATCH 456/546] Update Crossmap to 0.3.1 (#12439) * Update Crossmap to 0.3.1 --- recipes/crossmap/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/crossmap/meta.yaml b/recipes/crossmap/meta.yaml index 26983f1b2f5bb..74b6087702b8f 100644 --- a/recipes/crossmap/meta.yaml +++ b/recipes/crossmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "CrossMap" %} -{% set version = "0.2.8" %} -{% set sha256hash = "783a89f7378495dc0f1dbbb1b56b780cc4aeeb20d683c2721560952305083c47" %} +{% set version = "0.3.1" %} +{% set sha256hash = "49e57b7b2b9b32a939288af446c20fcaae201a8509c26a24f76539a12d76f9b3" %} package: name: {{ name|lower }} @@ -12,8 +12,7 @@ source: build: number: 0 - # CrossMap is very particular about Python version. - skip: True # [not py27] + skip: True # [py27] requirements: host: @@ -32,6 +31,7 @@ requirements: - pysam >=0.11.1,<0.14.0 - bx-python - ucsc-wigtobigwig + - pybigwig test: commands: From 772c25f6e844d045df52577c4cee353dc11d86b2 Mon Sep 17 00:00:00 2001 From: Caleb Easterly Date: Fri, 30 Nov 2018 02:07:51 -0500 Subject: [PATCH 457/546] Make metaquantome dependencies more specific (#12442) * less stringent deps * bump build * pin goatools * test extra pins --- recipes/metaquantome/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/metaquantome/meta.yaml b/recipes/metaquantome/meta.yaml index 252c41617a981..9120c67b9cbb0 100644 --- a/recipes/metaquantome/meta.yaml +++ b/recipes/metaquantome/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 0 + number: 2 script: python setup.py install --single-version-externally-managed --record=record.txt requirements: @@ -26,11 +26,12 @@ requirements: - ete3 3.1.* - goatools 0.7.* - statsmodels 0.8.* - - biopython >=1.70 + - biopython - pandas 0.23.* + - numpy 1.15.* - r-gplots 3.0.* - r-ggplot2 - - r-base + - r-base 3.4.* - r-jsonlite - libiconv From 8a8ab7df66c51f6701e8baef6be502bc59273a51 Mon Sep 17 00:00:00 2001 From: Antoine Limasset Date: Fri, 30 Nov 2018 12:23:24 +0100 Subject: [PATCH 458/546] integration of bcool to bioconda (#12422) --- recipes/bcool/build.sh | 4 ++++ recipes/bcool/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 recipes/bcool/build.sh create mode 100644 recipes/bcool/meta.yaml diff --git a/recipes/bcool/build.sh b/recipes/bcool/build.sh new file mode 100644 index 0000000000000..d6811373c6d1d --- /dev/null +++ b/recipes/bcool/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +cp src/Bcool_conda $PREFIX/bin/bcool diff --git a/recipes/bcool/meta.yaml b/recipes/bcool/meta.yaml new file mode 100644 index 0000000000000..cd6f7d6bc9f9c --- /dev/null +++ b/recipes/bcool/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.0" %} + + +package: + name: bcool + version: '{{version}}' + +source: + url: "https://github.com/Malfoy/BCOOL/archive/1.0.0.tar.gz" + sha256: ae92f117d7a2f355b5956e8ac389ea7d96e69bc2cd518da3eb86cd176225959e + +build: + number: 0 + skip: true # [osx] + skip: True # [py27] + +requirements: + run: + - python + - bgreat + - ntcard + - bcalm + - btrim + + +test: + commands: + - bcool + +about: + home: https://github.com/Malfoy/BCOOL + license: AGPL-3.0 + summary: BCOOL is a read corrector for NGS sequencing data that align reads on a de Bruijn graph. Version described at (https://arxiv.org/abs/1711.03336) presented at RECOMB-seq 2018 From ce980b92fd9840fcc4ac6c55246c54442d72b444 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 30 Nov 2018 04:42:15 -0700 Subject: [PATCH 459/546] Update hifive to 1.5.7 (#12433) --- recipes/hifive/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hifive/meta.yaml b/recipes/hifive/meta.yaml index 51c34b18b8059..7d6118e627e13 100644 --- a/recipes/hifive/meta.yaml +++ b/recipes/hifive/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.5.6" %} -{% set sha256 = "6c9e7c6e4090f0ee10af83db8744cbe023ee772e2bd71c07506f4a66b58690bc" %} +{% set version = "1.5.7" %} +{% set sha256 = "a903d209eeedba4f9f415a260f2080b469ca460b16a97c9663274bf90f1f6093" %} package: name: hifive @@ -11,7 +11,7 @@ source: build: skip: true # [not py27] - number: 2 + number: 0 script: python setup.py install --single-version-externally-managed --record=record.txt requirements: From 248c5353030d40e174e4cd2994c218a3256094f5 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 30 Nov 2018 04:42:33 -0700 Subject: [PATCH 460/546] Update scvi to 0.2.3 (#12434) --- recipes/scvi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scvi/meta.yaml b/recipes/scvi/meta.yaml index 93fca5376e73f..4d7e8e1874c82 100644 --- a/recipes/scvi/meta.yaml +++ b/recipes/scvi/meta.yaml @@ -1,8 +1,8 @@ {% set name = "scvi" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "ff083ab9a348eba86f376c1eb2a40ca7d4babad03dffb55edd4e939972e84749" %} +{% set hash_value = "4818582145b61b7720d905896aa4784c532061d34c4b305f3ea8b5752c08ed9e" %} package: name: '{{ name|lower }}' From 4ac33b48c03abb0dfad594d31aaec6f8ef419348 Mon Sep 17 00:00:00 2001 From: John Blischak Date: Fri, 30 Nov 2018 06:42:57 -0500 Subject: [PATCH 461/546] Update Subread from 1.6.2 to 1.6.3. (#12425) * Update Subread from 1.6.2 to 1.6.3. * Subread executable coverageCount has been removed. https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ --- recipes/subread/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/subread/meta.yaml b/recipes/subread/meta.yaml index c141d77550fe9..e0c032a091676 100644 --- a/recipes/subread/meta.yaml +++ b/recipes/subread/meta.yaml @@ -4,14 +4,14 @@ about: summary: High-performance read alignment, quantification, and mutation discovery package: name: subread - version: 1.6.2 + version: 1.6.3 build: number: 0 source: - url: https://downloads.sourceforge.net/project/subread/subread-1.6.2/subread-1.6.2-source.tar.gz - sha256: 77b4896c1c242967c5883a06c0a5576a5ff220008a12aa60af9669d2f9a87d7a + url: https://downloads.sourceforge.net/project/subread/subread-1.6.3/subread-1.6.3-source.tar.gz + sha256: 2d9f3ae072e32ec64095fc6b211c287d0f3496cbe6ac72b255c42cbd41778e1a requirements: build: @@ -32,7 +32,6 @@ test: - txUnique || [[ $? == 1 ]] - qualityScores - subread-fullscan || [[ $? == 255 ]] - - coverageCount extra: identifiers: From db233428e7f68bf06e84ce7ef64aefa194ada65a Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Fri, 30 Nov 2018 16:23:27 +0000 Subject: [PATCH 462/546] UCSC Cell Browser 0.4.23 (#12347) * Starting files for ucsc-cell-browser * Customised recipe for ucsc-cell-browser * meta update for ucsc-cell-browser * Changes cbTrackHub to cbHub * Point to static release * Moves to 0.25 * Updates sha hash for ucsc-browser * Reverts to 0.1.9 * At ebi * Update meta.yaml * pins numpy to last know working version * Back to 0.25, no numpy pinning. * Remove git, pin python and numpy. Add build section. * Update meta.yaml * Update meta.yaml * Move to 0.4.20 without skeleton on provisional commit * Typo on executable name * Moves to release version and adds dependencies for converters --- recipes/ucsc-cell-browser/build.sh | 5 ++++ recipes/ucsc-cell-browser/meta.yaml | 40 +++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/ucsc-cell-browser/build.sh create mode 100644 recipes/ucsc-cell-browser/meta.yaml diff --git a/recipes/ucsc-cell-browser/build.sh b/recipes/ucsc-cell-browser/build.sh new file mode 100644 index 0000000000000..582f86f9151e9 --- /dev/null +++ b/recipes/ucsc-cell-browser/build.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +$PYTHON setup.py install +mkdir -p $PREFIX/bin +cp -rp src/cbImportSeurat $PREFIX/bin diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml new file mode 100644 index 0000000000000..b5c2b94d53d5f --- /dev/null +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -0,0 +1,40 @@ +{% set version = '0.4.23' %} + +package: + name: ucsc-cell-browser + version: {{ version }} + +source: + url: https://github.com/maximilianh/cellBrowser/archive/v{{ version }}.tar.gz + sha256: e2a019f8bb150f8d115b0dd1f75a76831c9e96898c42d70b42f37ff61f01641e + +build: + number: 0 + noarch: python + +requirements: + host: + - python >=3.6 + run: + - python >=3.6 + - numpy + - r-data.table + - anndata + +test: + commands: + - which cbBuild + - which cbGuessGencode + - which cbImportSeurat + - which cbMarkerAnnotate + - which cbScanpy + - which cbImportScanpy + - which cbImportCellranger + - which cbTool + - which cbUpgrade + +about: + home: http://cells.ucsc.edu + license: GPL + license_file: LICENSE + summary: A browser for single-cell data, main site at http://cells.ucsc.edu From f3518899ef92b7411870c863d8f5cf270ae6a40b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 30 Nov 2018 10:29:58 -0700 Subject: [PATCH 463/546] Update libstatgen to 1.0.14 (#12437) --- recipes/libstatgen/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/libstatgen/meta.yaml b/recipes/libstatgen/meta.yaml index c523b99a96088..bbcd8114ac8bc 100644 --- a/recipes/libstatgen/meta.yaml +++ b/recipes/libstatgen/meta.yaml @@ -1,6 +1,6 @@ {% set name = "libStatGen" %} -{% set version = "1.0.5" %} -{% set sha256 = "a402777e2999badca177d568565e9cd3775cbe511ef2a449658e96b8b1e4aa7e" %} +{% set version = "1.0.14" %} +{% set sha256 = "70a504c5cc4838c6ac96cdd010644454615cc907df4e3794c999baf958fa734b" %} package: name: {{ name|lower }} From f88aca7aa45a0ecebb226f486fc41898c19be5c3 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 30 Nov 2018 10:30:13 -0700 Subject: [PATCH 464/546] Update arvados-python-client to 1.2.1 (#12438) --- recipes/arvados-python-client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index 8f014a5d12167..2b2449792ddfb 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.2.0.20181121194423" %} +{% set version="1.2.1" %} package: name: arvados-python-client @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - sha256: e2f24382a74c40533c41431398fa83b1bb3c70bfa843c661cddcb89b8ccdad70 + sha256: ab4b19a5c76538cc882ef600625540e7ce7059415f9c8a2bb6613f32f8f70469 build: number: 0 From 0f3cb75ad58abb785defc38c836feb4a56194517 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 30 Nov 2018 10:31:17 -0700 Subject: [PATCH 465/546] Update tirmite to 1.1.3 (#12435) --- recipes/tirmite/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml index 90bedbb9990af..dc286f4c1d1dd 100644 --- a/recipes/tirmite/meta.yaml +++ b/recipes/tirmite/meta.yaml @@ -1,8 +1,8 @@ {% set name = "tirmite" %} -{% set version = "1.1.1" %} +{% set version = "1.1.3" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "b56ff33626253e95edc27af9503febc1ac5becaf00921acb2477b0d010790412" %} +{% set hash_value = "6fa2cea73b40e0faa813a19957801629e971bcc9bd4c4feb2f4f67ce0031039e" %} package: name: '{{ name|lower }}' @@ -53,4 +53,4 @@ about: dev_url: '' extra: - recipe-maintainers: 'Adam Taranto' \ No newline at end of file + recipe-maintainers: 'Adam Taranto' From 287f873bf20e4d965d830b507b501bc5beccd9eb Mon Sep 17 00:00:00 2001 From: Caleb Easterly Date: Fri, 30 Nov 2018 14:04:44 -0500 Subject: [PATCH 466/546] Bump metaquantome (#12449) * less stringent deps * bump build * pin goatools * test extra pins * bump metaquantome to 0.99.3 --- recipes/metaquantome/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metaquantome/meta.yaml b/recipes/metaquantome/meta.yaml index 9120c67b9cbb0..b380fcb37c2fc 100644 --- a/recipes/metaquantome/meta.yaml +++ b/recipes/metaquantome/meta.yaml @@ -1,8 +1,8 @@ {% set name = "metaquantome" %} -{% set version = "0.99.2" %} +{% set version = "0.99.3" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "f4083204442beebd06fce19a46383b399c38d8c6db9d2cf9c5873124359ad2f8" %} +{% set hash_value = "a4084ac12699158b3194202b43341e4dec6bdec6ffdbfbe2e1535dac2d9e02a3" %} package: name: '{{ name }}' From ea4365d62de1d781adc9287f00dd70173072f9dd Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 30 Nov 2018 15:24:48 -0600 Subject: [PATCH 467/546] Update ADAM to 0.25.0 (#12445) --- recipes/adam/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/adam/meta.yaml b/recipes/adam/meta.yaml index 055bb238bda98..ea5c01f23975b 100644 --- a/recipes/adam/meta.yaml +++ b/recipes/adam/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.24.0" %} +{% set version="0.25.0" %} about: home: https://github.com/bigdatagenomics/adam @@ -15,7 +15,7 @@ build: source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark2_2.11/{{ version }}/adam-distribution-spark2_2.11-{{ version }}-bin.tar.gz - sha256: d272553dec2d5f25cea72b05ebf656db7be65b33657e351a0cf55543e2868277 + sha256: 33d8b9047a22fe675732ec63c06c8623b4422ade8c5187c21c60ef04ba31acc8 patches: - adam-shell.patch - adam-submit.patch From f2f210330237bc54f1c171c51a06b61db072a412 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Mon, 3 Dec 2018 14:27:49 -0500 Subject: [PATCH 468/546] Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453) --- recipes/bcbio-nextgen-vm/meta.yaml | 6 +++--- recipes/bcbio-nextgen/meta.yaml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/bcbio-nextgen-vm/meta.yaml b/recipes/bcbio-nextgen-vm/meta.yaml index 770e9de602f98..3ca0c95a8cfe7 100644 --- a/recipes/bcbio-nextgen-vm/meta.yaml +++ b/recipes/bcbio-nextgen-vm/meta.yaml @@ -3,12 +3,12 @@ package: version: '0.1.0a' build: - number: 132 + number: 133 skip: True # [not py27] source: - url: https://github.com/bcbio/bcbio-nextgen-vm/archive/d246f7a.tar.gz - sha256: adf32f77253b7ab72755ceaebedab5634be56d7f721c5e782afa58e0fab902f2 + url: https://github.com/bcbio/bcbio-nextgen-vm/archive/b6bf53d.tar.gz + sha256: 091ea47caa2a6fffe98500fd5ba68999c929e15cf4574ad85ddb2e0e8de4908b requirements: host: diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 56acbf2c81d95..264e69e7950ec 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -3,13 +3,13 @@ package: version: '1.1.2a' build: - number: 2 + number: 3 skip: true # [not py27] source: #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz - url: https://github.com/bcbio/bcbio-nextgen/archive/00180f8.tar.gz - sha256: 6e1947cc4c1788a7e10712a61a14f1137c6f1c387023e8efbad76b26a8cbc4fd + url: https://github.com/bcbio/bcbio-nextgen/archive/f3f23e6.tar.gz + sha256: 2c33edb42bc68c6df562eac612450f70fb1997ca24180ed8c47c8c47e3ca126c requirements: host: From 46ee15ddb34d66df3fecc9f51d51276c0b9f6188 Mon Sep 17 00:00:00 2001 From: mjram0s Date: Mon, 3 Dec 2018 14:34:48 -0600 Subject: [PATCH 469/546] update rgi4.2.2 recipe (#12282) * update to enforce python3.6 and load card.json * remove lines from build.sh * update build number * make PR comment changes * add test to verify db is loaded * update build script * update build script * fix lint errors * fix linting errors * fix liniting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * revert test change --- recipes/rgi/build.sh | 7 +++++++ recipes/rgi/meta.yaml | 30 +++++++++++++++++++++++------- 2 files changed, 30 insertions(+), 7 deletions(-) create mode 100644 recipes/rgi/build.sh diff --git a/recipes/rgi/build.sh b/recipes/rgi/build.sh new file mode 100644 index 0000000000000..01b4738ae2a1b --- /dev/null +++ b/recipes/rgi/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt + +# Load the CARD database JSON file +python `which rgi` load -i card-data/card.json +rm -rf card-data diff --git a/recipes/rgi/meta.yaml b/recipes/rgi/meta.yaml index e5b09d5fb0143..24f9fba638441 100644 --- a/recipes/rgi/meta.yaml +++ b/recipes/rgi/meta.yaml @@ -1,29 +1,44 @@ {% set name = "rgi" %} {% set version = "4.2.2" %} {% set sha256 = "ab4a5614e359884129064ec318d8dda2516052b26aa38cfd480245d24e0c96e7" %} +{% set sha256database = "a98a7cfff770f1eb92b901d96fc82c7884a62bf0a837f896414e16e7ed32a368" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/arpcard/rgi/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} + - url: https://github.com/arpcard/rgi/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + - url: https://card.mcmaster.ca/download/0/broadstreet-v3.0.0.tar.gz + sha256: {{ sha256database }} + folder: card-data build: - skip: True # [win or py27] - number: 0 - script: python setup.py install --single-version-externally-managed --record=record.txt + skip: True # [win or py27 or py34] + number: 1 requirements: build: - {{ compiler('c') }} host: - python - - setuptools - - biopython + - blast ==2.6.0 - six >=1.7.0 - zlib + - prodigal ==2.6.3 + - diamond ==0.8.36 + - biopython >=1.60 + - filetype >=1.0.0 + - pytest >=3.0.0 + - mock >=2.0.0 + - pandas >=0.15.0 + - matplotlib >=2.1.2 + - seaborn >=0.8.1 + - pyfaidx >=0.5.4.1 + - pyahocorasick >=1.1.7 + - setuptools + run: # RGI requires these exact versions of blast prodigal and diamond, or else --alignment_mode DIAMOND fails - python @@ -44,6 +59,7 @@ requirements: test: commands: + - rgi database | grep "3.0.0" - rgi load -h - rgi main -h - rgi tab -h From 7dcdcb781eda64f4b9286186fe046e4736ba7443 Mon Sep 17 00:00:00 2001 From: John Blischak Date: Mon, 3 Dec 2018 15:43:33 -0500 Subject: [PATCH 470/546] Add CRAN R package leapp. (#12428) --- recipes/r-leapp/build.sh | 34 ++++++++++++++++++++++++++++ recipes/r-leapp/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 recipes/r-leapp/build.sh create mode 100644 recipes/r-leapp/meta.yaml diff --git a/recipes/r-leapp/build.sh b/recipes/r-leapp/build.sh new file mode 100644 index 0000000000000..6ceb75d30e228 --- /dev/null +++ b/recipes/r-leapp/build.sh @@ -0,0 +1,34 @@ +#!/bin/bash +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/leapp + mv * $PREFIX/lib/R/library/leapp + if [[ $target_platform == osx-64 ]]; then + pushd $PREFIX + for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do + pushd $libdir || exit 1 + for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do + echo "fixing SHARED_LIB $SHARED_LIB" + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true + install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true + done + popd + done + popd + fi +fi diff --git a/recipes/r-leapp/meta.yaml b/recipes/r-leapp/meta.yaml new file mode 100644 index 0000000000000..39c277634d716 --- /dev/null +++ b/recipes/r-leapp/meta.yaml @@ -0,0 +1,47 @@ +{% set version = '1.2' %} + +package: + name: r-leapp + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/leapp_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/leapp/leapp_{{ version }}.tar.gz + sha256: 27646512c35ee598a377cd39c1493617dd9db11f5f17c62effc315fa60fd38fa + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-mass + - r-corpcor + - bioconductor-sva + + run: + - r-base + - r-mass + - r-corpcor + - bioconductor-sva + +test: + commands: + - $R -e "library('leapp')" + +about: + home: https://CRAN.R-project.org/package=leapp + license: GPL (>= 2) + summary: These functions take a gene expression value matrix, a primary covariate vector, an + additional known covariates matrix. A two stage analysis is applied to counter + the effects of latent variables on the rankings of hypotheses. The estimation and + adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" + is developed in the context of microarray experiments, but may be used as a general + tool for high throughput data sets where dependence may be involved. + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' From 467f9d2418371a4be0dfa270cccebf3033a4ef23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Pedro=20Camargo?= Date: Mon, 3 Dec 2018 18:46:46 -0200 Subject: [PATCH 471/546] Bump DECIPHER to Bioconductor 3.7 (#12463) * Bump DECIPHER to Bioconductor 3.7 * Change r-rsqlite version dependency * Update meta.yaml --- recipes/bioconductor-decipher/meta.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 76009fe5dbf21..af9c4a83d59ad 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.1" %} {% set name = "DECIPHER" %} -{% set bioc = "3.6" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,29 +10,29 @@ source: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1eb5d11ad330a58dba102faedec531947ad33206b41164c259314eca6edc89e5 + sha256: 8bfc5718de78dc4493a44555ea15513d183f9f6644ea9f563ab4a766eb02f1e7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - 'bioconductor-biostrings =2.46.0' + - 'bioconductor-biostrings >=2.35.12' - bioconductor-iranges - bioconductor-s4vectors - bioconductor-xvector - - 'r-base =3.4.1' + - r-base - r-dbi - - 'r-rsqlite >=1.1,<2.1.1' + - 'r-rsqlite >=1.1' run: - - 'bioconductor-biostrings =2.46.0' + - 'bioconductor-biostrings >=2.35.12' - bioconductor-iranges - bioconductor-s4vectors - bioconductor-xvector - - 'r-base =3.4.1' + - r-base - r-dbi - - 'r-rsqlite >=1.1,<2.1.1' + - 'r-rsqlite >=1.1' build: - {{ compiler('c') }} - make From 4a572c6e734ff0b97ee98013ed8e96121e068797 Mon Sep 17 00:00:00 2001 From: Romain Lopez Date: Mon, 3 Dec 2018 13:02:58 -0800 Subject: [PATCH 472/546] updated scVI to 0.2.3 (#12429) From a990df149986fd3de15dd3e8612c9b592c8c9239 Mon Sep 17 00:00:00 2001 From: camytran Date: Mon, 3 Dec 2018 15:05:42 -0600 Subject: [PATCH 473/546] Add recipe for PyAAVF 0.1.0 (#12451) * Add recipe for PyAAVF 0.1.0 * Fix linting error --- recipes/pyaavf/build.sh | 3 +++ recipes/pyaavf/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 recipes/pyaavf/build.sh create mode 100644 recipes/pyaavf/meta.yaml diff --git a/recipes/pyaavf/build.sh b/recipes/pyaavf/build.sh new file mode 100644 index 0000000000000..3786386a73c83 --- /dev/null +++ b/recipes/pyaavf/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/pyaavf/meta.yaml b/recipes/pyaavf/meta.yaml new file mode 100644 index 0000000000000..94f04ab1b8bc8 --- /dev/null +++ b/recipes/pyaavf/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "PyAAVF" %} +{% set version = "0.1.0" %} +{% set file_ext = "tar.gz" %} +{% set sha256 = "b407c27a791ac421b882b2005a7bde17354fce94206f403fdb32483cfe19d154" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + sha256: {{ sha256 }} + +build: + noarch: python + number: 0 + +requirements: + host: + - python + - setuptools + run: + - python + +test: + imports: + - {{ name }} + +about: + home: http://github.com/winhiv/PyAAVF + license: Apache License, Version 2.0 + summary: An amino acid variant format parser for Python. + From 04d9cce0d7d9e40e49a1dc2bbc1ed152ff64f202 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Tue, 4 Dec 2018 05:26:28 +0800 Subject: [PATCH 474/546] seqkit 0.9.3 (#12455) --- recipes/seqkit/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 2dfee145e243c..f5b31b55274b5 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.2" %} +{% set version = "0.9.3" %} package: name: seqkit @@ -10,18 +10,18 @@ about: license: MIT build: - number: 2 + number: 1 skip: False source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: 929ae9ec2fc18eec41da7ef569ee5031 # [osx] + md5: b3107a0c7143e984d736d1837f172cba # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_386.tar.gz # [linux] - md5: b7ffec6f73e206b0ed5a57b7632e73ef # [linux] + md5: 430a22b363821baaac9f89c036edb528 # [linux] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux64] - md5: db44546b38add64094f664a23b56b73c # [linux64] + md5: 60350dbbe497a18dedaf26dfcd226b07 # [linux64] test: commands: From 23365377958b166c10ae157f853e19867758bf74 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Mon, 3 Dec 2018 17:43:26 -0500 Subject: [PATCH 475/546] HTSeq - Pin numpy version (#12467) --- recipes/htseq/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index b43384f7e7448..cbab1da9f1251 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -7,12 +7,12 @@ source: sha256: 19145fd3359baa4a8dd5c93470aa0a77e16da3ffde8e4e10fa8df4191df5cd29 build: - number: 0 + number: 1 requirements: build: - {{ compiler('c') }} - + host: - python - setuptools @@ -23,7 +23,7 @@ requirements: run: - python - - numpy + - {{ pin_compatible('numpy') }} - matplotlib >=1.4 - pysam >=0.9.0 From b64ee93d3a42f9d3b01f9651ead90aef07962f63 Mon Sep 17 00:00:00 2001 From: Ryan Raaum Date: Mon, 3 Dec 2018 17:45:54 -0500 Subject: [PATCH 476/546] update eigensoft to 7.2.1 (#12469) --- recipes/eigensoft/build.sh | 19 +++++++++---------- recipes/eigensoft/meta.yaml | 24 +++++++++++++++--------- 2 files changed, 24 insertions(+), 19 deletions(-) diff --git a/recipes/eigensoft/build.sh b/recipes/eigensoft/build.sh index 8c5d5cad1ec60..21d86f804bd0b 100644 --- a/recipes/eigensoft/build.sh +++ b/recipes/eigensoft/build.sh @@ -1,11 +1,10 @@ -#!/bin/bash -find src -name "*.o" -delete -rm bin/* cd src -export OPENBLAS=$PREFIX -make clean -make -make install -cd .. -mkdir -p $PREFIX/bin -cp bin/* $PREFIX/bin/ +make clobber + +make CFLAGS="-I$PREFIX/include -I../../include" LDFLAGS="-L$PREFIX/lib" all + +# Install (makefile install has hard-coded destination, so have to do this manually) + mkdir -p $PREFIX/bin + cp {baseprog,convertf,mergeit,pca,smshrink} $PREFIX/bin/ + cp {eigensrc/pcatoy,eigensrc/smartrel,eigensrc/smarteigenstrat,eigensrc/twstats} $PREFIX/bin/ + cp {eigensrc/eigenstrat,eigensrc/eigenstratQTL,eigensrc/smartpca} $PREFIX/bin/ diff --git a/recipes/eigensoft/meta.yaml b/recipes/eigensoft/meta.yaml index 506fdd408d9e0..22098bc4d507f 100644 --- a/recipes/eigensoft/meta.yaml +++ b/recipes/eigensoft/meta.yaml @@ -1,29 +1,35 @@ package: name: eigensoft - version: "6.0.1" + version: "7.2.1" + build: - number: 3 - skip: True # [osx] + number: 0 + source: - url: https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/EIG6.0.1.tar.gz - md5: a6ed8f2cb48fe76886dcb97af289596c + url: https://github.com/DReichLab/EIG/archive/v7.2.1.tar.gz + sha256: f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650 + requirements: build: - {{ compiler('c') }} - - {{ compiler('fortran') }} host: - gsl + - openblas run: - gsl + - openblas - perl + test: commands: - - smartpca 2>&1 | grep "no parameters" + - smartpca > /dev/null 2>&1 + about: - home: http://www.hsph.harvard.edu/alkes-price/software/ + home: https://github.com/DReichLab/EIG license: Custom OSS - summary: Population Genetics - Principal Components Analysis (PCA) + summary: The EIGENSOFT package implements methods for analzing population structure and performing stratification correction extra: identifiers: - biotools:Eigensoft + - doi:10.1371/journal.pgen.0020190 From 59ad373d1309a99969ac41e1d5ac10379e1021bc Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Mon, 3 Dec 2018 16:13:46 -0700 Subject: [PATCH 477/546] Update scnic to 0.6.0 (#12436) * Update scnic to 0.6.0 * Work around fastspar insufficient armadillo pin * fix pin --- recipes/scnic/meta.yaml | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/recipes/scnic/meta.yaml b/recipes/scnic/meta.yaml index bccae944ffa3e..efd95b37cefe3 100644 --- a/recipes/scnic/meta.yaml +++ b/recipes/scnic/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.3" %} +{% set version = "0.6.0" %} package: name: scnic @@ -6,7 +6,7 @@ package: source: url: https://github.com/shafferm/SCNIC/archive/{{ version }}.tar.gz - sha256: a2857f96d9887c74c8380d501c1db1d1620c19daf6a0341da38bad4a9d44c51d + sha256: 476868bb0e1703ee4bd29e712e94178f0027b4413fd9428dcf0922baffd3d677 build: number: 0 @@ -27,15 +27,25 @@ requirements: - biom-format - networkx >2 - scikit-bio - - fastspar - - parallel + - fastspar 0.0.6 + # fastspar does not pin armadillo correctly, doing + # that here until fastspar 0.0.7 fixes it + - armadillo 8.* + - tqdm + - matplotlib + - seaborn test: command: - SCNIC_analysis.py --help + - fastspar --help # verify fastspar working correctly about: home: https://github.com/shafferm/SCNIC license: BSD license_file: LICENSE summary: "SCNIC: Sparse Cooccurence Network Investigation for Compositional data" + +extra: + recipe-maintainers: + - shafferm From 839d0fe17d11c9610d870a935d304834c932c680 Mon Sep 17 00:00:00 2001 From: Simon van Heeringen Date: Tue, 4 Dec 2018 08:40:33 +0100 Subject: [PATCH 478/546] GimmeMotifs 0.13.1 (#12471) --- recipes/gimmemotifs/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gimmemotifs/meta.yaml b/recipes/gimmemotifs/meta.yaml index a05e22a68e469..1274b324cbbc3 100644 --- a/recipes/gimmemotifs/meta.yaml +++ b/recipes/gimmemotifs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.13.0" %} +{% set version = "0.13.1" %} package: name: gimmemotifs @@ -6,10 +6,10 @@ package: source: url: https://github.com/vanheeringen-lab/gimmemotifs/releases/download/{{ version }}/gimmemotifs-{{ version }}.tar.gz - sha256: ccaa9ec2b58f22fd7fb07680de0d4e7fc3d9eff2ec2aed26c0d89abb94cb69ca + sha256: ba750eccb2820e8687595d03663848e3a5f8c3b85eb82c41a5f7cd9540f628dc build: - number: 1 + number: 0 requirements: build: From bd69226d335d46e4e63caeaaa2b1ee7963bc763d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 4 Dec 2018 10:35:53 +0000 Subject: [PATCH 479/546] Bumped version to newest, with introspective text (#12461) --- recipes/r-seurat-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-seurat-scripts/meta.yaml b/recipes/r-seurat-scripts/meta.yaml index dd5ffd3ed6546..a99fb53ce094f 100644 --- a/recipes/r-seurat-scripts/meta.yaml +++ b/recipes/r-seurat-scripts/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.0.2" %} +{% set version = "0.0.3" %} package: name: r-seurat-scripts @@ -6,7 +6,7 @@ package: source: url: https://github.com/ebi-gene-expression-group/r-seurat-scripts/archive/v{{ version }}.tar.gz - sha256: 492cd8bab4a1af6d4bdcba43122e3e22eb502137281d6e307f49f43bfc27ded2 + sha256: f2dce203cdbec2d1c3e13209925c40318346e9aaa79379901a1017472b841c00 build: number: 0 From f393daf57d8b3735f20a004251b834ea7c757919 Mon Sep 17 00:00:00 2001 From: Eric Roberts Date: Tue, 4 Dec 2018 06:30:59 -0500 Subject: [PATCH 480/546] Update Segway 2.0.2 recipe to use older depedencies (#11803) * Update Segway 2.0.2 recipe to use older depedencies * Update maximum genomedata version supported * Update build number * Fix missing older dependency information * Update meta.yaml --- recipes/segway/meta.yaml | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/recipes/segway/meta.yaml b/recipes/segway/meta.yaml index f6c03ea1baadb..a0c26f68b7d39 100644 --- a/recipes/segway/meta.yaml +++ b/recipes/segway/meta.yaml @@ -9,36 +9,37 @@ source: build: preserve_egg_dir: True skip: True # [not py27] + number: 3 entry_points: - segway = segway.run:main - segway-task = segway.task:main - segway-layer = segway.layer:main - segway-winner = segway.winner:main - number: 2 requirements: host: - python - setuptools - - genomedata >=1.4.0 + - genomedata <=1.4.1 - gmtk - - textinput - - optbuild - - optplus + - autolog <0.2 + - textinput <=0.1.1 + - optbuild <=0.1.11 + - optplus <=0.1.1 - forked-path - hgtools - - colorbrewer + - colorbrewer <=0.1.1 - drmaa >=0.4a3 - run: - python - - genomedata >=1.4.0 + - genomedata <=1.4.1 - gmtk - - textinput - - optbuild - - optplus + - autolog <0.2 + - textinput <=0.1.1 + - optbuild <=0.1.11 + - optplus <=0.1.1 - forked-path - - colorbrewer + - colorbrewer <=0.1.1 - drmaa >=0.4a3 - ucsc-bedtobigbed From 1e5c8d038d1fc43e08d9c2275219299476d79baa Mon Sep 17 00:00:00 2001 From: Rick Date: Tue, 4 Dec 2018 13:55:39 +0100 Subject: [PATCH 481/546] updating dependencies for reparation_blast (#12443) * updating dependencies for reparation_blast * changed dependency of pysam --- recipes/reparation_blast/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/reparation_blast/meta.yaml b/recipes/reparation_blast/meta.yaml index 783c1558a3d0d..164467b584d2c 100644 --- a/recipes/reparation_blast/meta.yaml +++ b/recipes/reparation_blast/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -20,7 +20,7 @@ requirements: run: - perl - perl-posix - - perl-bioperl + - perl-bioperl >=1.7.2 - samtools - pysam =0.14.1 - plastid From 936f55f7b988823bd2fa589eedb6e4041f031475 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 4 Dec 2018 14:10:00 +0000 Subject: [PATCH 482/546] Added DropletUtils package (#12448) --- recipes/bioconductor-dropletutils/build.sh | 4 ++ .../conda_build_config.yaml | 2 + recipes/bioconductor-dropletutils/meta.yaml | 65 +++++++++++++++++++ 3 files changed, 71 insertions(+) create mode 100644 recipes/bioconductor-dropletutils/build.sh create mode 100644 recipes/bioconductor-dropletutils/conda_build_config.yaml create mode 100644 recipes/bioconductor-dropletutils/meta.yaml diff --git a/recipes/bioconductor-dropletutils/build.sh b/recipes/bioconductor-dropletutils/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-dropletutils/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dropletutils/conda_build_config.yaml b/recipes/bioconductor-dropletutils/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-dropletutils/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-dropletutils/meta.yaml b/recipes/bioconductor-dropletutils/meta.yaml new file mode 100644 index 0000000000000..96949e202fdfe --- /dev/null +++ b/recipes/bioconductor-dropletutils/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.3" %} +{% set name = "DropletUtils" %} +{% set bioc = "3.7" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 63eb07ea6a35a6b52b8990209ce9b0cec5960ecee70e940dd689f2b9a08412ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-beachmat >=1.2.1,<1.4.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomeinfodb >=1.16.0' + - 'bioconductor-genomeinfodbdata >=1.1.0' + - r-base + - r-dplyr + - r-matrix + - 'r-rcpp >=0.12.14' + run: + - 'bioconductor-beachmat >=1.2.1,<1.4.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' + - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomeinfodb >=1.16.0' + - 'bioconductor-genomeinfodbdata >=1.1.0' + - r-base + - r-matrix + - r-plyr + - 'r-rcpp >=0.12.14' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Utilities for Handling Single-Cell Droplet Data.' +extra: + identifiers: + - biotools:DropletUtils From a323ad511b6bd6f0014dc4e9077dcd85930cbd45 Mon Sep 17 00:00:00 2001 From: David Heller Date: Tue, 4 Dec 2018 08:18:52 -0800 Subject: [PATCH 483/546] Create recipe for SVIM (#12272) * add svim recipe * fix bugs in svim recipe * replace source file * remove license file * Lowercase biopython * upgrade to svim 0.4.1 * add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency * fix python version * try to fix lint error * replace "skip: True" with "noarch: python" --- recipes/svim/build.sh | 3 +++ recipes/svim/meta.yaml | 41 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/svim/build.sh create mode 100644 recipes/svim/meta.yaml diff --git a/recipes/svim/build.sh b/recipes/svim/build.sh new file mode 100644 index 0000000000000..04547dc83fe20 --- /dev/null +++ b/recipes/svim/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/svim/meta.yaml b/recipes/svim/meta.yaml new file mode 100644 index 0000000000000..a98c7b38ec8c6 --- /dev/null +++ b/recipes/svim/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.4.1" %} + +package: + name: svim + version: '{{ version }}' + +source: + url: https://github.com/eldariont/svim/archive/v{{ version }}.tar.gz + sha256: 39a90e608157d14c7a4a41efca1548b11e43e5df652d24f32d208c0625f2eba1 + +build: + number: 0 + noarch: python + +requirements: + host: + - python 3.6.* + - pip + run: + - python 3.6.* + - pysam + - numpy + - scipy + - matplotlib + - biopython + - networkx + - ngmlr + - minimap2 + - samtools + +test: + commands: + - svim -h + +about: + home: 'https://github.com/eldariont/svim' + license: GPL-3.0 + license_family: GPL + license_file: LICENSE + summary: SVIM is a structural variant caller for long reads. + From b1962ef731ea4ff79406e12f548925ebef9fca7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Tue, 4 Dec 2018 17:52:40 +0100 Subject: [PATCH 484/546] Update bioconductor-biocgenerics (#12477) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). --- recipes/bioconductor-biocgenerics/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index 737dbe586989b..b0c0c2081048d 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "0.26.0" %} +{% set version = "0.28.0" %} {% set name = "BiocGenerics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 571c491d8a103f13be76b30af72f2bc675f5321bb8acf5e19cfe8ec684871da7 + md5: 39b4dfb1f9526c64ddcb9b994130a7c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit requirements: host: - r-base @@ -25,9 +27,10 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'S4 generic functions needed by many Bioconductor packages.' + extra: identifiers: - - biotools:biocgenerics + - biotools:biocgenerics \ No newline at end of file From 29950e8b1cfbcdb4e92754ef5a395ec8576f9d7e Mon Sep 17 00:00:00 2001 From: Aaron Petkau Date: Tue, 4 Dec 2018 14:38:55 -0600 Subject: [PATCH 485/546] Irida sistr results 0.6.0 (#12478) * Update irida-sistr-results to 0.6.0 * Fixed dependency string --- recipes/irida-sistr-results/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/irida-sistr-results/meta.yaml b/recipes/irida-sistr-results/meta.yaml index e79f65e2e3d38..ad8640fb697ea 100644 --- a/recipes/irida-sistr-results/meta.yaml +++ b/recipes/irida-sistr-results/meta.yaml @@ -1,7 +1,7 @@ {% set name = "irida-sistr-results" %} -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} {% set hash_type = "sha256" %} -{% set hash_value = "a02768e03f37fddc085b0cfedf83f9d125f9961561c0e887de34a8ae546f5222" %} +{% set hash_value = "bcc2178518aee256ce05572ab184bb00de87290e8dfe31f2083e8f75cbe42ea1" %} package: name: '{{ name|lower }}' @@ -24,12 +24,14 @@ requirements: - urllib3 >=1.21.1 - xlsxwriter >=0.9.8 - appdirs >=1.4.3 + - pandas >=0.23.0 run: - python - rauth >=0.7.3 - urllib3 >=1.21.1 - xlsxwriter >=0.9.8 - appdirs >=1.4.3 + - pandas >=0.23.0 test: imports: From 91765ddd685555d73bb8c071514ae98bbef8d7ef Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 5 Dec 2018 09:04:07 +0100 Subject: [PATCH 486/546] Adding recipe for clinvar-tsv v0.1.0. (#12481) --- recipes/clinvar-tsv/meta.yaml | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 recipes/clinvar-tsv/meta.yaml diff --git a/recipes/clinvar-tsv/meta.yaml b/recipes/clinvar-tsv/meta.yaml new file mode 100644 index 0000000000000..e5b6b193fe603 --- /dev/null +++ b/recipes/clinvar-tsv/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.1.0" %} + +package: + name: clinvar-tsv + version: "{{ version }}" + +source: + url: https://github.com/bihealth/clinvar-tsv/archive/v{{ version }}.tar.gz + sha256: 212cced3c4a05eaf7f686d0d76f5cd294c7181529596de6d8a6282bef54ad9dd + +build: + number: 0 + noarch: python + script: python -m pip install --no-deps --ignore-installed . + entry_points: + - clinvar_tsv = clinvar_tsv.__main__:main + +requirements: + host: + - python >=3.5 + - pip + - setuptools + run: + - python >=3.5 + - snakemake-minimal >=5.3.0 + - pysam >=0.15.1 + +test: + imports: + - clinvar_tsv + commands: + - clinvar_tsv --version + - clinvar_tsv --version | grep "{{ version }}" + +about: + home: https://github.com/bihealth/clinvar-tsv + license: MIT + summary: A Snakemake-based program to download ClinVar and convert to easy-to-use TSV files. From bf57aa21e7f0ed19922a9b1c9b5be14e741e3c26 Mon Sep 17 00:00:00 2001 From: Tobias Rausch Date: Wed, 5 Dec 2018 09:46:44 +0100 Subject: [PATCH 487/546] no fixed boost version (#12483) --- recipes/alfred/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index d405ad1c00873..41d18593f976d 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -21,12 +21,12 @@ requirements: host: - zlib - bzip2 - - boost ==1.61.0 + - boost - htslib run: - zlib - bzip2 - - boost ==1.61.0 + - boost - htslib test: From 77b4a54885cd155bebacb8ecb1e196052e27ebf5 Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Wed, 5 Dec 2018 02:30:20 -0800 Subject: [PATCH 488/546] New recipe: pysradb (#12470) --- recipes/pysradb/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/pysradb/meta.yaml diff --git a/recipes/pysradb/meta.yaml b/recipes/pysradb/meta.yaml new file mode 100644 index 0000000000000..6a5ba83900c0b --- /dev/null +++ b/recipes/pysradb/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "pysradb" %} +{% set version = "0.2.2" %} +{% set file_ext = "tar.gz" %} +{% set hash_type = "sha256" %} +{% set hash_value = "15736bec19ca3927b68dd13e3a9ccfab5eee9e586a3d7017b0081605ef37b524" %} + + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} + '{{ hash_type }}': '{{ hash_value }}' + +build: + number: 0 + script: python setup.py install --single-version-externally-managed --record=record.txt + noarch: python + +requirements: + host: + - python + - setuptools + - pandas >=0.23.4 + - tqdm >=4.28 + run: + - python + - pandas >=0.23.4 + - tqdm >=4.28 + +test: + imports: + - pysradb + - pysradb.pysradb + +about: + home: https://github.com/saketkc/pysradb + license: BSD License + license_family: BSD + summary: 'Python package for interacting with SRAdb and downloading datasets from SRA' + description: 'Python package for interacting with SRAdb and downloading datasets from SRA' + doc_url: 'https://saketkc.github.io/pysradb' + +extra: + recipe-maintainers: + - saketkc From 55cb2b557eff86ae9ff565c478020a7c85654083 Mon Sep 17 00:00:00 2001 From: Marco Galardini Date: Wed, 5 Dec 2018 10:31:19 +0000 Subject: [PATCH 489/546] Pyseer 1.2.0 (#12444) * Update pyseer to 1.1.2 * Update pyseer to 1.2.0 * Update pyseer to 1.2.0 Update pyseer to 1.2.0 Update pyseer to 1.2.0 (fixed) * Final touches to pyseer 1.2.0 * Additional update to pyseer recipe --- recipes/pyseer/meta.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/pyseer/meta.yaml b/recipes/pyseer/meta.yaml index 89025123774fe..f23b56b8ffc50 100644 --- a/recipes/pyseer/meta.yaml +++ b/recipes/pyseer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.2" %} +{% set version = "1.2.0" %} package: name: pyseer @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyseer/pyseer-{{ version }}.tar.gz - sha256: 04ca9bf8dc96749be5b2f95b40c95b7ac56e832d62fed910aa4d4ba1ac465ea1 + sha256: 892a6013cfc1883edd140e0a5bec8ce2cb9ef5b34f4cb3a6b7e81a5400a11c16 build: @@ -16,9 +16,11 @@ build: entry_points: - pyseer = pyseer.__main__:main - square_mash = pyseer.mash:main + - similarity_pyseer = pyseer.similarity:main - scree_plot_pyseer = pyseer.scree_plot:main - phandango_mapper = pyseer.kmer_mapping.phandango_plot:main - annotate_hits_pyseer = pyseer.kmer_mapping.annotate_hits:main + - enet_predict_pyseer = pyseer.enet_predict:main requirements: host: @@ -33,6 +35,7 @@ requirements: - pandas - statsmodels - scikit-learn + - glmnet_py - pysam - dendropy - matplotlib @@ -41,6 +44,7 @@ requirements: - bwa - bedtools - bedops + - tqdm test: imports: @@ -51,9 +55,11 @@ test: commands: - pyseer --help - square_mash --help + - similarity_pyseer --help - scree_plot_pyseer --help - phandango_mapper --help - annotate_hits_pyseer --help + - enet_predict_pyseer --help about: home: https://github.com/mgalardini/pyseer From 4d381420c129eee8c15a61e25305e6d90a2a3344 Mon Sep 17 00:00:00 2001 From: Len Trigg Date: Wed, 5 Dec 2018 23:32:19 +1300 Subject: [PATCH 490/546] sentieon: minor version bump to 201808.01 (#12480) --- recipes/sentieon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml index 5d46b8d2a9355..e82154754b4c2 100644 --- a/recipes/sentieon/meta.yaml +++ b/recipes/sentieon/meta.yaml @@ -1,11 +1,11 @@ -{% set version="201808" %} +{% set version="201808.01" %} package: name: sentieon version: {{ version }} source: url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz - sha256: 39843c9ed45b7cfb4de9377e9aea29e9a6966f3175a0582380257d1593c7a6c6 + sha256: 6d77bcd5a35539549b28eccae07b19a3b353d027720536e68f46dcf4b980d5f7 patches: # Fix driver scripts so they resolves location including symlinks - sentieon_symlinks.patch From 75496a9937575351f51a3aa854d149b11f8db5b1 Mon Sep 17 00:00:00 2001 From: asmariyaz23 Date: Wed, 5 Dec 2018 05:41:28 -0500 Subject: [PATCH 491/546] adding java to mutations recipe (#12485) --- recipes/ctat-mutations/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/ctat-mutations/meta.yaml b/recipes/ctat-mutations/meta.yaml index fd807aa12662b..5fb16e57d1118 100644 --- a/recipes/ctat-mutations/meta.yaml +++ b/recipes/ctat-mutations/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-mutations" %} {% set version = "2.0.1" %} -{% set build = "4" %} +{% set build = "5" %} package: name: {{ name }} @@ -23,6 +23,7 @@ requirements: run: - python =2.7 - requests =2.18.4 + - openjdk >=8 - gatk4 - star - picard =2.18.14 From e41b18c560726eaca547564023b902e1e80e2bea Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 5 Dec 2018 04:11:32 -0700 Subject: [PATCH 492/546] Update ncrf to 1.00.06 (#12369) * Update ncrf to 1.00.06 * Update test string --- recipes/ncrf/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ncrf/meta.yaml b/recipes/ncrf/meta.yaml index 60432af773359..35ccd8f951754 100644 --- a/recipes/ncrf/meta.yaml +++ b/recipes/ncrf/meta.yaml @@ -1,14 +1,14 @@ package: name: ncrf - version: "1.0.4" + version: "1.00.06" build: number: 0 skip: True # [not py27] source: - url: https://github.com/makovalab-psu/NoiseCancellingRepeatFinder/archive/v1.00.04.tar.gz - sha256: fae5700393100736ad0d69cd8aa5d4c967674b12c8536bfb7fd647960397aba9 + url: https://github.com/makovalab-psu/NoiseCancellingRepeatFinder/archive/v1.00.06.tar.gz + sha256: 880994d495f3a4603bd9e8397e5488c59da77f3c072c00f6187eb84446f8dd74 requirements: build: @@ -19,7 +19,7 @@ requirements: - python test: commands: - - NCRF --version 2>&1 | grep 1.00.04 > /dev/null + - NCRF --version 2>&1 | grep 1.00.06 about: home: https://github.com/makovalab-psu/NoiseCancellingRepeatFinder From 73227d4962f9617c2cfe62b9adbc19421492eb3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Wed, 5 Dec 2018 15:12:44 +0100 Subject: [PATCH 493/546] Bump umitools (#12486) --- recipes/umitools/build.sh | 10 ---------- recipes/umitools/meta.yaml | 28 +++++++++++++++++++++------- 2 files changed, 21 insertions(+), 17 deletions(-) delete mode 100644 recipes/umitools/build.sh diff --git a/recipes/umitools/build.sh b/recipes/umitools/build.sh deleted file mode 100644 index 6696e36915465..0000000000000 --- a/recipes/umitools/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. - diff --git a/recipes/umitools/meta.yaml b/recipes/umitools/meta.yaml index 942e18ea8ec55..068efae1ce0da 100644 --- a/recipes/umitools/meta.yaml +++ b/recipes/umitools/meta.yaml @@ -1,26 +1,31 @@ +{% set version = "0.3.4" %} + package: - name: umitools - version: "0.3.0" + name: "umitools" + version: "{{ version }}" source: - url: https://pypi.python.org/packages/a0/5c/104c8f5d35abaaff7882b8f398f35e4052d4359762f05b396438095c7518/umitools-0.3.0.tar.gz - md5: 8af92b04cdaa02771a434fabbe211f15 + url: https://pypi.io/packages/source/u/umitools/umitools-{{ version }}.tar.gz + sha256: 43337b9b715495e69f2e46b8e5f997856407560ca9c0cd16a9ee55084ba63b48 build: entry_points: + - umitools=umitools.umitools:main - umi_reformat_fastq=umitools.reformat_umi_fastq:main - umi_reformat_sra_fastq=umitools.reformat_umi_sra_fastq:main - umi_mark_duplicates=umitools.umi_mark_duplicates:main - umi_simulator=umitools.umi_simulator:main skip: True # [py27] - number: 1 + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " requirements: host: - - python - - pysam - editdistance - networkx + - pip + - pysam + - python run: - python @@ -29,7 +34,11 @@ requirements: - networkx test: + imports: + - umitools + commands: + - umitools --help - umi_reformat_fastq --help - umi_reformat_sra_fastq --help - umi_mark_duplicates --help @@ -39,3 +48,8 @@ about: home: https://github.com/weng-lab/umitools license: GPL3 summary: 'A toolset for handling sequencing data with unique molecular identifiers (UMIs)' + +extra: + identifiers: + - doi:10.1186/s12864-018-4933-1 + From c6c2a247bfee5f168087e639f2997a84cf6fddf0 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Wed, 5 Dec 2018 09:13:11 -0500 Subject: [PATCH 494/546] Mob suite version 1.4.9 no arch build number 2 (#12479) * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 --- recipes/mob_suite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/mob_suite/meta.yaml b/recipes/mob_suite/meta.yaml index ba42f98f28ff1..15b7ac08c1333 100644 --- a/recipes/mob_suite/meta.yaml +++ b/recipes/mob_suite/meta.yaml @@ -5,8 +5,8 @@ package: version: {{ version }} build: - number: 0 - skip: True # [not py36] + number: 1 + noarch: python script: python -m pip install --no-deps --ignore-installed . source: @@ -16,11 +16,11 @@ source: requirements: host: - - python + - python >=3.4 - pip - setuptools run: - - python + - python >=3.4 - pycurl >=7.43 - scipy >=1.1 - numpy >=1.11 From a59781d7a38bee9995672fdb64d655c10a0f5a07 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Wed, 5 Dec 2018 07:13:32 -0700 Subject: [PATCH 495/546] Update r-goeveg to 0.4.2 (#12375) * Update r-goeveg to 0.4.2 * Add r-hmisc as dependency --- recipes/r-goeveg/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/r-goeveg/meta.yaml b/recipes/r-goeveg/meta.yaml index 3ec4d5a786da1..ca9cce8e4bff4 100644 --- a/recipes/r-goeveg/meta.yaml +++ b/recipes/r-goeveg/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.3.3' %} +{% set version = '0.4.2' %} package: name: r-goeveg @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/goeveg_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/goeveg/goeveg_{{ version }}.tar.gz - sha256: 8620c9532b66bd77c72b8cedb81106b637ca845f680504c3ed3f81bc0373c6dc + sha256: ca7bdf0a02a7e2c7aad69e580a50cd4bc31991f8137551c8e5a81703e0f5374d build: number: 0 @@ -22,11 +22,14 @@ requirements: - r-fields - r-mgcv - r-vegan + - r-hmisc + run: - r-base - r-fields - r-mgcv - r-vegan + - r-hmisc test: commands: From ea6ec17a180e6407394dbee6755dad7176d9416f Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Wed, 5 Dec 2018 14:53:48 +0000 Subject: [PATCH 496/546] Removes r-seurat-scripts from blacklisting (#12489) * Removes r-seurat-scripts from blacklisting * Unblacklist some non bioconductor packages --- build-fail-blacklist | 4 ---- 1 file changed, 4 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index b943bbeea2caf..79b05a17f36a7 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -785,7 +785,6 @@ recipes/r-raceid3 recipes/r-rBLAST recipes/r-rubic recipes/r-scimpute -recipes/r-seurat-scripts recipes/r-sleuth recipes/r-soap-nmr recipes/r-spieceasi @@ -850,9 +849,6 @@ recipes/r-msqrob recipes/r-probmetab # Not actually bioconductor packages -recipes/bioconductor-sc3-scripts -recipes/bioconductor-scater-scripts -recipes/bioconductor-singlecellexperiment-scripts # post-link error recipes/bioconductor-jaspar2018 From 481b146e134d042c705a6158d6429e2841ebf63d Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 5 Dec 2018 16:21:56 +0100 Subject: [PATCH 497/546] For VarDict-Java, install utility scripts. (#12488) * For VarDict-Java, install utility scripts. Utility script that were previously only shipped with VarDict are not part of VarDict-Java as well, making installation of both packages unnecessary. * Bump build. * Improve variable name. * Make vardict depend on vardict-java for utility scripts. --- recipes/vardict-java/build.sh | 7 +++++-- recipes/vardict-java/meta.yaml | 5 ++++- recipes/vardict/build.sh | 4 ---- recipes/vardict/meta.yaml | 6 +++--- 4 files changed, 12 insertions(+), 10 deletions(-) diff --git a/recipes/vardict-java/build.sh b/recipes/vardict-java/build.sh index ecab6289ab9ae..d652d454b69b0 100644 --- a/recipes/vardict-java/build.sh +++ b/recipes/vardict-java/build.sh @@ -7,5 +7,8 @@ mkdir -p $PREFIX/bin cp lib/*.jar $outdir/lib cp bin/VarDict $outdir/bin/vardict-java -chmod +x $outdir/bin/vardict-java -ln -s $outdir/bin/vardict-java $PREFIX/bin +cp bin/*.{R,pl} $outdir/bin +for executable in vardict-java testsomatic.R teststrandbias.R var2vcf_paired.pl var2vcf_valid.pl; do + chmod +x $outdir/bin/$executable + ln -s $outdir/bin/$executable $PREFIX/bin +done diff --git a/recipes/vardict-java/meta.yaml b/recipes/vardict-java/meta.yaml index fd39ee6fd0388..237e5bd7fb1cb 100644 --- a/recipes/vardict-java/meta.yaml +++ b/recipes/vardict-java/meta.yaml @@ -9,16 +9,19 @@ source: sha256: 36a177b06114ea939d24f7037b6e339b58e572763736a589232f0ced3731735b build: - number: 0 + number: 1 noarch: generic requirements: run: - openjdk + - perl + - r-base test: commands: - vardict-java -h + - var2vcf_paired.pl -h about: home: https://github.com/AstraZeneca-NGS/VarDictJava diff --git a/recipes/vardict/build.sh b/recipes/vardict/build.sh index d91fec4ccc31b..1c9afd0207d22 100644 --- a/recipes/vardict/build.sh +++ b/recipes/vardict/build.sh @@ -12,8 +12,4 @@ chmod a+x $outdir/*.pl chmod a+x $outdir/*.R ln -s $outdir/vardict.pl $PREFIX/bin/vardict ln -s $outdir/vardict.pl $PREFIX/bin -ln -s $outdir/testsomatic.R $PREFIX/bin -ln -s $outdir/teststrandbias.R $PREFIX/bin -ln -s $outdir/var2vcf_valid.pl $PREFIX/bin -ln -s $outdir/var2vcf_paired.pl $PREFIX/bin ln -s $outdir/vardict2mut.pl $PREFIX/bin diff --git a/recipes/vardict/meta.yaml b/recipes/vardict/meta.yaml index b1cd9d5568e10..8bfdd3d919887 100644 --- a/recipes/vardict/meta.yaml +++ b/recipes/vardict/meta.yaml @@ -12,15 +12,15 @@ source: sha256: '{{sha256}}' build: - number: 0 + number: 1 requirements: host: - perl - - r-base + - vardict-java run: - perl - - r-base + - vardict-java test: commands: From 4703f1b0ea9e7b0fde9351fc944d2773ec647d2d Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Wed, 5 Dec 2018 14:02:59 -0500 Subject: [PATCH 498/546] Pin compatible numpy for older HTSEQ versions (#12490) * Pin compatible numpy for older HTSEQ versions This is required to keep older versions of HTSEQ functional * HTSeq - update old versions to build properly with new build system * HTSeq 0.6.1 - Increment build number --- recipes/htseq/0.6.1.post1/meta.yaml | 7 +++-- recipes/htseq/0.6.1/meta.yaml | 4 ++- recipes/htseq/0.7.2/meta.yaml | 7 +++-- recipes/htseq/0.9.1/build.sh | 3 ++ recipes/htseq/0.9.1/meta.yaml | 46 +++++++++++++++++++++++++++++ 5 files changed, 62 insertions(+), 5 deletions(-) create mode 100644 recipes/htseq/0.9.1/build.sh create mode 100644 recipes/htseq/0.9.1/meta.yaml diff --git a/recipes/htseq/0.6.1.post1/meta.yaml b/recipes/htseq/0.6.1.post1/meta.yaml index b659d51bf51d7..2e8b94eb9be63 100644 --- a/recipes/htseq/0.6.1.post1/meta.yaml +++ b/recipes/htseq/0.6.1.post1/meta.yaml @@ -8,10 +8,13 @@ source: build: preserve_egg_dir: True - number: 2 + number: 3 skip: True # [not py27] requirements: + build: + - {{ compiler('c') }} + host: - python - setuptools @@ -19,7 +22,7 @@ requirements: run: - python - - numpy + - {{ pin_compatible('numpy') }} - matplotlib - pysam diff --git a/recipes/htseq/0.6.1/meta.yaml b/recipes/htseq/0.6.1/meta.yaml index 92214d99ba9af..d23079d56530e 100644 --- a/recipes/htseq/0.6.1/meta.yaml +++ b/recipes/htseq/0.6.1/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'A framework to process and analyze data from high-throughput sequencing (HTS) assays' build: - number: 1 + number: 2 skip: True # [py3k or osx] package: @@ -12,6 +12,8 @@ package: version: 0.6.1 requirements: + build: + - {{ compiler('c') }} host: - python - cython diff --git a/recipes/htseq/0.7.2/meta.yaml b/recipes/htseq/0.7.2/meta.yaml index c55069d6520e5..5bf70b398fc3e 100644 --- a/recipes/htseq/0.7.2/meta.yaml +++ b/recipes/htseq/0.7.2/meta.yaml @@ -7,9 +7,12 @@ source: sha256: b9da6d6a9004e8e05a40ecf08f74f765ec0e0be0e835e82205a117aba2ce375b build: - number: 1 + number: 2 requirements: + build: + - {{ compiler('c') }} + host: - python - setuptools @@ -19,7 +22,7 @@ requirements: run: - python - - numpy + - {{ pin_compatible('numpy') }} - matplotlib - pysam >=0.9.0 diff --git a/recipes/htseq/0.9.1/build.sh b/recipes/htseq/0.9.1/build.sh new file mode 100644 index 0000000000000..bf07930878d76 --- /dev/null +++ b/recipes/htseq/0.9.1/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py build install diff --git a/recipes/htseq/0.9.1/meta.yaml b/recipes/htseq/0.9.1/meta.yaml new file mode 100644 index 0000000000000..401d1590b63be --- /dev/null +++ b/recipes/htseq/0.9.1/meta.yaml @@ -0,0 +1,46 @@ +package: + name: htseq + version: "0.9.1" + +source: + url: https://pypi.python.org/packages/fd/94/b7c8c1dcb7a3c3dcbde66b8d29583df4fa0059d88cc3592f62d15ef539a2/HTSeq-0.9.1.tar.gz + md5: fc71e021bf284a68f5ac7533a57641ac + +build: + number: 2 + +requirements: + build: + - {{ compiler('c') }} + + host: + - python + - setuptools + - cython + - numpy + - pysam >=0.9.0 + - swig >=3.0.8 + + run: + - python + - {{ pin_compatible('numpy') }} + - matplotlib >=1.4 + - pysam >=0.9.0 + +test: + # Python imports + imports: + - HTSeq._HTSeq_internal + - HTSeq.StepVector + - HTSeq._version + - HTSeq.scripts.count + - HTSeq.scripts.qa + + commands: + - htseq-count -h + - htseq-qa -h + +about: + home: https://github.com/simon-anders/htseq + license: GPL-3.0 + summary: 'HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.' From 8b0aea96e076f8f47c82642f9061815ce2cc529e Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Wed, 5 Dec 2018 20:33:14 +0100 Subject: [PATCH 499/546] add recipe for r-epic (#12473) --- recipes/r-epic/build.sh | 1 + recipes/r-epic/meta.yaml | 41 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100755 recipes/r-epic/build.sh create mode 100755 recipes/r-epic/meta.yaml diff --git a/recipes/r-epic/build.sh b/recipes/r-epic/build.sh new file mode 100755 index 0000000000000..5bf492ab9fc06 --- /dev/null +++ b/recipes/r-epic/build.sh @@ -0,0 +1 @@ +$R CMD INSTALL --build . diff --git a/recipes/r-epic/meta.yaml b/recipes/r-epic/meta.yaml new file mode 100755 index 0000000000000..28516d95b8e93 --- /dev/null +++ b/recipes/r-epic/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.1" %} + +package: + name: r-epic + version: {{ version }} + +source: + url: + - https://github.com/GfellerLab/EPIC/archive/v{{ version }}.tar.gz + sha256: 95bea4a5bd1fb57a94055198475a2237b2181b2a499a97ec5055637c987d159f + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base >=3.2.0 + - r-roxygen2 >=6.0.1 + + run: + - r-base >=3.2.0 + +test: + commands: + - $R -e "library('EPIC')" + +about: + home: https://github.com/GfellerLab/EPIC + license: other + summary: "Estimate the Proportion of Immune and Cancer cells from bulk gene expression data." + license_family: other + license_file: LICENSE + +extra: + recipe-maintainers: + - grst + identifiers: + - doi:10.7554/eLife.26476.001 From d97ac28e33fc3fbb2a8d458b1632eb0d698c1b36 Mon Sep 17 00:00:00 2001 From: zhanxw Date: Wed, 5 Dec 2018 13:33:41 -0600 Subject: [PATCH 500/546] Add new recipe - RVTESTS (#12465) * Add rvtests * Update pre-req * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create LICENSE * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Create run_test.sh * Update meta.yaml * Delete run_test.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/rvtests/LICENSE | 674 ++++++++++++++++++++++++++++++++++++++ recipes/rvtests/build.sh | 41 +++ recipes/rvtests/meta.yaml | 41 +++ 3 files changed, 756 insertions(+) create mode 100644 recipes/rvtests/LICENSE create mode 100644 recipes/rvtests/build.sh create mode 100644 recipes/rvtests/meta.yaml diff --git a/recipes/rvtests/LICENSE b/recipes/rvtests/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/rvtests/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/rvtests/build.sh b/recipes/rvtests/build.sh new file mode 100644 index 0000000000000..dcea8067b4d76 --- /dev/null +++ b/recipes/rvtests/build.sh @@ -0,0 +1,41 @@ +## export these flags so that zlib.h can be found +#export CFLAGS="-I$PREFIX/include" +#export CXXFLAGS="-I$PREFIX/include" +#export LDFLAGS="-L$PREFIX/lib" + +# Build +(cd third && tar zxf zlib-1.2.8.tar.gz && cd zlib-1.2.8 && ./configure && make) +(cd third && tar jxf tabix-0.2.6.tar.bz2 && ln -s -f tabix-0.2.6 tabix && cd tabix-0.2.6 && sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8:' Makefile && make libtabix.a) +(cd third && tar jxf samtools-0.1.19.tar.bz2 && ln -s -f samtools-0.1.19 samtools && cd samtools-0.1.19 && sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8 -I../../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8 -L../../zlib-1.2.8:' Makefile bcftools/Makefile && make lib-recur) +(sed -i.bak 's:CXX_FLAGS = -O2 -DNDEBUG:CXX_FLAGS = -O2 -DNDEBUG -I../third/zlib-1.2.8:' libsrc/Makefile) + +#export CFLAGS="-I$PREFIX/include" +#export LDFLAGS="-L$PREFIX/lib" +(sed -i.bak 's:^CXX_INCLUDE =:CXX_INCLUDE = -I${PREFIX}/include:' Makefile.common) +(sed -i.bak 's:^CXX_LIB =:CXX_LIB = -L${PREFIX}/lib:' Makefile.common) + +if [[ $(uname -s) == Darwin ]]; then + sed -i.bak '3i\ +#include + ' base/Socket.cpp + sed -i.bak '4i\ +#ifdef _OPENMP +;5i\ +#endif' libVcf/VCFRecord.h + + # clang does not support openmp + sed -i.bak 's:-fopenmp::' libBgen/Makefile + sed -i.bak 's:-fopenmp::' libVcf/Makefile + sed -i.bak 's:-fopenmp::' src/Makefile + + make STATIC_FLAG='' OPENMP_FLAG='' +else + # hack this flag to link against rt, so clock_gettime can be linked + make STATIC_FLAG='-lrt' +fi + +# Install +echo "Install..." +mkdir -p $PREFIX/bin +echo "Copying..." +find executable/ -executable -type f -exec cp {} $PREFIX/bin \; diff --git a/recipes/rvtests/meta.yaml b/recipes/rvtests/meta.yaml new file mode 100644 index 0000000000000..b685fc7dbcbe3 --- /dev/null +++ b/recipes/rvtests/meta.yaml @@ -0,0 +1,41 @@ +package: + name: rvtests + version: "2.0.6" + +build: + number: 1 + skip: True # [osx] + +source: + url: https://github.com/zhanxw/rvtests/archive/v2.0.6.tar.gz + sha256: 72f4419d5d3dd73b8eb58f7ffaabf19a41c99f968ecde9611f9b76f74acc0743 + +channels: + - defaults + - conda-forge + +requirements: + build: + - {{ compiler('cxx') }} + - wget # [not osx] + - zlib + - ruby # [osx] + - curl # [osx] + + host: + - zlib + +test: + commands: + - rvtest --help + +about: + home: https://github.com/zhanxw/rvtests + license: GPL + license_file: LICENSE + summary: Rare variant test software for next generation sequencing data + +extra: + identifiers: + - doi:10.1093/bioinformatics/btw079 + - biotools:rvtests From 8f0e081ba984f7369a5947c2edb8914d630fe2f8 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 5 Dec 2018 22:33:55 +0100 Subject: [PATCH 501/546] Adding recipe for var-agg v0.1.0 (#12482) * Adding recipe for var-agg v0.1.0 * runtime deps do have run-exports defined * move rust into the host section * Adding dependency to clangdev --- recipes/var-agg/build.sh | 9 +++++++++ recipes/var-agg/meta.yaml | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/var-agg/build.sh create mode 100644 recipes/var-agg/meta.yaml diff --git a/recipes/var-agg/build.sh b/recipes/var-agg/build.sh new file mode 100644 index 0000000000000..66e2df35f3fec --- /dev/null +++ b/recipes/var-agg/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash -e + +# circumvent a bug in conda-build >=2.1.18,<3.0.10 +# https://github.com/conda/conda-build/issues/2255 +[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE +[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE + +# build statically linked binary with Rust +C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib cargo install --root $PREFIX diff --git a/recipes/var-agg/meta.yaml b/recipes/var-agg/meta.yaml new file mode 100644 index 0000000000000..0c5e6c826ede9 --- /dev/null +++ b/recipes/var-agg/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.1.0" %} + +package: + name: var-agg + version: {{version}} + +build: + number: 0 + # TODO wait for CB3 gcc, then try again. + skip: true # [osx] + +source: + url: https://github.com/bihealth/var-agg/archive/v{{version}}.tar.gz + sha256: bff4ef0c6ece7f681f159fbf1f92d7d0a33a079a831b96cfc6e0dfb283654634 + +requirements: + build: + - {{ compiler('c') }} + host: + - clangdev + - rust + - zlib + - bzip2 + - xz + +test: + commands: + - var-agg --help + +about: + home: https://github.com/bihealth/var-agg + license: MIT + summary: | + A simple helper for aggregating multi-sample VCF files into "site VCF" files. From 20a3fc3a41cbc87215dd41e8f75d247e74cb0290 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 5 Dec 2018 23:12:28 +0100 Subject: [PATCH 502/546] Adding var-agg v0.1.1. (#12495) --- recipes/var-agg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/var-agg/meta.yaml b/recipes/var-agg/meta.yaml index 0c5e6c826ede9..a38edae939b84 100644 --- a/recipes/var-agg/meta.yaml +++ b/recipes/var-agg/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: var-agg @@ -11,7 +11,7 @@ build: source: url: https://github.com/bihealth/var-agg/archive/v{{version}}.tar.gz - sha256: bff4ef0c6ece7f681f159fbf1f92d7d0a33a079a831b96cfc6e0dfb283654634 + sha256: '35764ff68e7edcad56157cb7a2edfd7edc9a495893e4ff909ef17430e70ea7f4' requirements: build: From 30451246d9815bc0f940a9811ac0a4b07a5185b1 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Thu, 6 Dec 2018 00:11:37 -0500 Subject: [PATCH 503/546] [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441) Salmon v0.12.0 --- version bump and fix OSX build * Considerable updates in terms of features and fixes (check release notes). * Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX). --- recipes/salmon/build.sh | 42 ++++++++++++++++++++++++++++++++++++++++ recipes/salmon/meta.yaml | 8 ++++---- 2 files changed, 46 insertions(+), 4 deletions(-) diff --git a/recipes/salmon/build.sh b/recipes/salmon/build.sh index 82e289fe6e0ba..811109aea9cf0 100644 --- a/recipes/salmon/build.sh +++ b/recipes/salmon/build.sh @@ -8,10 +8,52 @@ set -eu -o pipefail #export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib" #fi +#lint failing 1 +#lint failing 2 +#linter failing 3 +#linter failing 4 +#linter failing 5 +#linter failing 6 +#linter failing 7 +#linter failing 8 +#linter failing 9 +#linter failing 10 +#linter failing 11 +#linter failing 12 +#linter failing 13 +#linter failing 14 +#linter failing 15 +#linter failing 16 +#linter failing 17 +#linter failing 18 +#linter failing 19 +#linter failing 20 +#linter failing 21 (still broken) +#linter failing 22 +#linter failing 23 (good morning) +#linter failing 24 (good afternoon) +#linter failing 25 (PM checkin) +#linter failing 26 (lovely evening) +#linter failing 27 (sighh) +#linter failing 28 (good night) +#linter failing 29 (Morning check) +#linter failing 30 (the big 3-0 ... if this counter eclipses my age, I'll be sad :() +#linter failing 31 (and another one bites the dust?) +#linter failing 32 (powers of 2 are fun!) +#linter failing? 33 (lucky 33?) + mkdir -p $PREFIX/bin mkdir -p $PREFIX/lib mkdir -p build cd build cmake -DCMAKE_BUILD_TYPE=RELEASE -DCONDA_BUILD=TRUE -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX -DBOOST_ROOT=$PREFIX -DBoost_NO_SYSTEM_PATHS=ON .. +make +echo "unit test executable" +./src/unitTests +echo "installing" make install CFLAGS="-L${PREFIX}/lib -I${PREFIX}/include" +../tests/unitTests +echo "cmake-powered unit test" +CTEST_OUTPUT_ON_FAILURE=1 make test + diff --git a/recipes/salmon/meta.yaml b/recipes/salmon/meta.yaml index 97ab8b9003f57..0ac65bf476033 100644 --- a/recipes/salmon/meta.yaml +++ b/recipes/salmon/meta.yaml @@ -1,7 +1,7 @@ -{% set version="0.11.3" %} +{% set version="0.12.0" %} build: - number: 2 + number: 1 about: home: https://github.com/COMBINE-lab/salmon @@ -16,7 +16,7 @@ source: url: https://github.com/COMBINE-lab/salmon/archive/v{{ version }}.tar.gz # work on develop until everything compiles cleanly #url: https://github.com/COMBINE-lab/salmon/archive/develop.tar.gz - md5: 99e95233be7f8510bed5c4d0c46a5074 + md5: 2f07447c0070d1e22fb2b3879eaca810 #patches: salmon_cmake.patch requirements: @@ -32,7 +32,7 @@ requirements: - bzip2 - unzip - jemalloc >=5.1.0 - - tbb + - tbb-devel run: - libboost - icu From 8b9cc9701a4f0e218c2f625fefeeaaa8fb01a4ca Mon Sep 17 00:00:00 2001 From: "Kuan-Hao, Chao" Date: Thu, 6 Dec 2018 15:32:54 +0800 Subject: [PATCH 504/546] Performancean alytics (#12498) * Add bioconductor package RNASeqR * Add performanceanalytics --- r-performanceanalytics/bld.bat | 2 + r-performanceanalytics/build.sh | 11 ++++ r-performanceanalytics/meta.yaml | 99 ++++++++++++++++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 r-performanceanalytics/bld.bat create mode 100644 r-performanceanalytics/build.sh create mode 100644 r-performanceanalytics/meta.yaml diff --git a/r-performanceanalytics/bld.bat b/r-performanceanalytics/bld.bat new file mode 100644 index 0000000000000..b7e1203063141 --- /dev/null +++ b/r-performanceanalytics/bld.bat @@ -0,0 +1,2 @@ +"%R%" CMD INSTALL --build . +IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/r-performanceanalytics/build.sh b/r-performanceanalytics/build.sh new file mode 100644 index 0000000000000..d18bf3dc95d8b --- /dev/null +++ b/r-performanceanalytics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/PerformanceAnalytics + mv * $PREFIX/lib/R/library/PerformanceAnalytics +fi diff --git a/r-performanceanalytics/meta.yaml b/r-performanceanalytics/meta.yaml new file mode 100644 index 0000000000000..2b0ea6e6fb304 --- /dev/null +++ b/r-performanceanalytics/meta.yaml @@ -0,0 +1,99 @@ +{% set version = '1.5.2' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-performanceanalytics + version: {{ version|replace("-", "_") }} + +source: + fn: PerformanceAnalytics_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/PerformanceAnalytics_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/PerformanceAnalytics/PerformanceAnalytics_{{ version }}.tar.gz + sha256: 86d61bb7e23fee837e294f23c55d226dcd3f92906bf0024a362f1df04fa96f05 + +build: + merge_build_host: True # [win] + # If this is a new build for the same version, increment the build number. + number: 0 + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +# Suggests: dygraphs, Hmisc, MASS, quantmod, gamlss, gamlss.dist, robustbase, quantreg, gplots, testthat +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + + host: + - r-base + - r-quadprog + - r-xts >=0.10.0 + - r-zoo + + run: + - r-base + - {{native}}gcc-libs # [win] + - r-quadprog + - r-xts >=0.10.0 + - r-zoo + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('PerformanceAnalytics')" # [not win] + - "\"%R%\" -e \"library('PerformanceAnalytics')\"" # [win] + + # You can also put a file called run_test.py, run_test.sh, or run_test.bat + # in the recipe that will be run at test time. + + # requires: + # Put any additional test requirements here. + +about: + home: https://github.com/braverock/PerformanceAnalytics + license: GPL-2 | GPL-3 + summary: Collection of econometric functions for performance and risk analysis. This package + aims to aid practitioners and researchers in utilizing the latest research in analysis + of non-normal return streams. In general, it is most tested on return (rather than + price) data on a regular scale, but most functions will work with irregular return + data as well, and increasing numbers of functions will work with P&L or price data + where possible. + license_family: GPL3 + +# The original CRAN metadata for this package was: + +# Package: PerformanceAnalytics +# Type: Package +# Title: Econometric Tools for Performance and Risk Analysis +# Authors@R: c( person(given=c("Brian","G."),family="Peterson",role=c("cre","aut","cph"), email="brian@braverock.com") , person(given="Peter",family="Carl",role=c("aut","cph"), email="peter@braverock.com") , person(given="Kris",family="Boudt",role=c("ctb","cph")) , person(given="Ross",family="Bennett",role="ctb") , person(given="Joshua",family="Ulrich",role="ctb") , person(given="Eric",family="Zivot",role="ctb") , person(given="Dries",family="Cornilly",role="ctb") , person(given="Eric",family="Hung",role="ctb") , person(given="Matthieu",family="Lestel",role="ctb") , person(given="Kyle",family="Balkissoon",role="ctb") , person(given="Diethelm",family="Wuertz",role="ctb") ) +# Version: 1.5.2 +# Date: 2018-02-28 $Date$ +# Description: Collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible. +# Imports: methods, quadprog, zoo +# Depends: R (>= 3.0.0), xts (>= 0.10.0) +# Suggests: dygraphs, Hmisc, MASS, quantmod, gamlss, gamlss.dist, robustbase, quantreg, gplots, testthat +# License: GPL-2 | GPL-3 +# URL: https://github.com/braverock/PerformanceAnalytics +# Copyright: (c) 2004-2018 +# RoxygenNote: 6.0.1.9000 +# NeedsCompilation: yes +# Packaged: 2018-03-01 15:16:42.16791 UTC; brian +# Author: Brian G. Peterson [cre, aut, cph], Peter Carl [aut, cph], Kris Boudt [ctb, cph], Ross Bennett [ctb], Joshua Ulrich [ctb], Eric Zivot [ctb], Dries Cornilly [ctb], Eric Hung [ctb], Matthieu Lestel [ctb], Kyle Balkissoon [ctb], Diethelm Wuertz [ctb] +# Maintainer: Brian G. Peterson +# Repository: CRAN +# Date/Publication: 2018-03-02 17:06:04 UTC + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml From 89d5620ac327980f3a5860966dfb2427c70bc6c2 Mon Sep 17 00:00:00 2001 From: "Kuan-Hao, Chao" Date: Thu, 6 Dec 2018 18:22:09 +0800 Subject: [PATCH 505/546] Performancean alytics (#12499) * Add bioconductor package RNASeqR * Add performanceanalytics * Move recipes/r-performanceanalytics and add r-rafalib * Move r-performanceanalytics/ to recipes * Update recipes/r-performanceanalytics * Update r-rafalib * Remove recipes/r-performanceanalytics/bld.bat * Remove recipes/r-performanceanalytics * Update r-performanceanalytics/ * Update r-performanceanalytics/ * Add r-performanceanalytics/ * remove r-performanceanalytics * Add performanceanalytics * Remove r-performanceanalytics --- r-performanceanalytics/bld.bat | 2 - r-performanceanalytics/build.sh | 11 ---- r-performanceanalytics/meta.yaml | 99 -------------------------------- 3 files changed, 112 deletions(-) delete mode 100644 r-performanceanalytics/bld.bat delete mode 100644 r-performanceanalytics/build.sh delete mode 100644 r-performanceanalytics/meta.yaml diff --git a/r-performanceanalytics/bld.bat b/r-performanceanalytics/bld.bat deleted file mode 100644 index b7e1203063141..0000000000000 --- a/r-performanceanalytics/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%R%" CMD INSTALL --build . -IF %ERRORLEVEL% NEQ 0 exit 1 diff --git a/r-performanceanalytics/build.sh b/r-performanceanalytics/build.sh deleted file mode 100644 index d18bf3dc95d8b..0000000000000 --- a/r-performanceanalytics/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then - export DISABLE_AUTOBREW=1 - mv DESCRIPTION DESCRIPTION.old - grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . -else - mkdir -p $PREFIX/lib/R/library/PerformanceAnalytics - mv * $PREFIX/lib/R/library/PerformanceAnalytics -fi diff --git a/r-performanceanalytics/meta.yaml b/r-performanceanalytics/meta.yaml deleted file mode 100644 index 2b0ea6e6fb304..0000000000000 --- a/r-performanceanalytics/meta.yaml +++ /dev/null @@ -1,99 +0,0 @@ -{% set version = '1.5.2' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - -package: - name: r-performanceanalytics - version: {{ version|replace("-", "_") }} - -source: - fn: PerformanceAnalytics_{{ version }}.tar.gz - url: - - {{ cran_mirror }}/src/contrib/PerformanceAnalytics_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/PerformanceAnalytics/PerformanceAnalytics_{{ version }}.tar.gz - sha256: 86d61bb7e23fee837e294f23c55d226dcd3f92906bf0024a362f1df04fa96f05 - -build: - merge_build_host: True # [win] - # If this is a new build for the same version, increment the build number. - number: 0 - - # This is required to make R link correctly on Linux. - rpaths: - - lib/R/lib/ - - lib/ - -# Suggests: dygraphs, Hmisc, MASS, quantmod, gamlss, gamlss.dist, robustbase, quantreg, gplots, testthat -requirements: - build: - - {{ compiler('c') }} # [not win] - - {{native}}toolchain # [win] - - {{posix}}filesystem # [win] - - {{posix}}make - - {{posix}}sed # [win] - - {{posix}}coreutils # [win] - - {{posix}}zip # [win] - - host: - - r-base - - r-quadprog - - r-xts >=0.10.0 - - r-zoo - - run: - - r-base - - {{native}}gcc-libs # [win] - - r-quadprog - - r-xts >=0.10.0 - - r-zoo - -test: - commands: - # You can put additional test commands to be run here. - - $R -e "library('PerformanceAnalytics')" # [not win] - - "\"%R%\" -e \"library('PerformanceAnalytics')\"" # [win] - - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - -about: - home: https://github.com/braverock/PerformanceAnalytics - license: GPL-2 | GPL-3 - summary: Collection of econometric functions for performance and risk analysis. This package - aims to aid practitioners and researchers in utilizing the latest research in analysis - of non-normal return streams. In general, it is most tested on return (rather than - price) data on a regular scale, but most functions will work with irregular return - data as well, and increasing numbers of functions will work with P&L or price data - where possible. - license_family: GPL3 - -# The original CRAN metadata for this package was: - -# Package: PerformanceAnalytics -# Type: Package -# Title: Econometric Tools for Performance and Risk Analysis -# Authors@R: c( person(given=c("Brian","G."),family="Peterson",role=c("cre","aut","cph"), email="brian@braverock.com") , person(given="Peter",family="Carl",role=c("aut","cph"), email="peter@braverock.com") , person(given="Kris",family="Boudt",role=c("ctb","cph")) , person(given="Ross",family="Bennett",role="ctb") , person(given="Joshua",family="Ulrich",role="ctb") , person(given="Eric",family="Zivot",role="ctb") , person(given="Dries",family="Cornilly",role="ctb") , person(given="Eric",family="Hung",role="ctb") , person(given="Matthieu",family="Lestel",role="ctb") , person(given="Kyle",family="Balkissoon",role="ctb") , person(given="Diethelm",family="Wuertz",role="ctb") ) -# Version: 1.5.2 -# Date: 2018-02-28 $Date$ -# Description: Collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible. -# Imports: methods, quadprog, zoo -# Depends: R (>= 3.0.0), xts (>= 0.10.0) -# Suggests: dygraphs, Hmisc, MASS, quantmod, gamlss, gamlss.dist, robustbase, quantreg, gplots, testthat -# License: GPL-2 | GPL-3 -# URL: https://github.com/braverock/PerformanceAnalytics -# Copyright: (c) 2004-2018 -# RoxygenNote: 6.0.1.9000 -# NeedsCompilation: yes -# Packaged: 2018-03-01 15:16:42.16791 UTC; brian -# Author: Brian G. Peterson [cre, aut, cph], Peter Carl [aut, cph], Kris Boudt [ctb, cph], Ross Bennett [ctb], Joshua Ulrich [ctb], Eric Zivot [ctb], Dries Cornilly [ctb], Eric Hung [ctb], Matthieu Lestel [ctb], Kyle Balkissoon [ctb], Diethelm Wuertz [ctb] -# Maintainer: Brian G. Peterson -# Repository: CRAN -# Date/Publication: 2018-03-02 17:06:04 UTC - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 25498b6333a970b0e5807a9c719fde3d729bfa40 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Thu, 6 Dec 2018 11:42:00 +0100 Subject: [PATCH 506/546] Update Picard to 2.18.20. (#12501) --- recipes/picard/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index 0a6a9ff881ba2..4802b49816423 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.18.17" %} -{% set sha256 = "f51f64824072f26dc5d0932376929b20e6f66ff478810bcf8145792773f5474f" %} +{% set version = "2.18.20" %} +{% set sha256 = "f3962a74deda89a9d27204804a6afdeda2ca536c4e1001d5e4aa9e666c77a637" %} package: name: picard From a207acf08dd60ccc2cc06630eab49e01f1d06e0b Mon Sep 17 00:00:00 2001 From: Adam Caprez Date: Thu, 6 Dec 2018 14:54:49 -0600 Subject: [PATCH 507/546] Update vsearch to 2.10.0. (#12504) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index e1eab98ff2aca..e55d4e21cebc0 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.9.1" %} -{% set sha256 = "4c66e1f8399dcd9f64266eb8449c2b3a17a4b2afc6645a420d60c783039339d7" %} +{% set version = "2.10.0" %} +{% set sha256 = "a1ca14a6aaa96d4734572a224624af802973b38bbd3f12a95df1ed4cf918c7d4" %} package: name: vsearch From cda654a0fcac6deaa1aa00cc37e21a6ea13cdf8c Mon Sep 17 00:00:00 2001 From: Michael Roach Date: Fri, 7 Dec 2018 09:15:46 +1030 Subject: [PATCH 508/546] Update Purge Haplotigs to v1.0.4 (#12497) --- recipes/purge_haplotigs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/purge_haplotigs/meta.yaml b/recipes/purge_haplotigs/meta.yaml index ef28e03ac79ea..923c7025c1f9d 100644 --- a/recipes/purge_haplotigs/meta.yaml +++ b/recipes/purge_haplotigs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: purge_haplotigs @@ -6,7 +6,7 @@ package: source: url: https://bitbucket.org/mroachawri/purge_haplotigs/get/v{{ version }}.tar.gz - sha256: cc9828138760989564be266493aeb8715a6602342ac779f9eaca3bc6699dbd7e + sha256: 9fb6b7fbb7358030e8f54bafa77a2b9e2a3a6951fc72a256fe5d9899d7ce219c build: number: 0 From cf3ae11c3a56285988acfd309c706380f6adb043 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:12:06 -0700 Subject: [PATCH 509/546] Update duphold to 0.1.1 (#12516) --- recipes/duphold/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/duphold/meta.yaml b/recipes/duphold/meta.yaml index cd13ea7e1850f..2639b89ca2654 100644 --- a/recipes/duphold/meta.yaml +++ b/recipes/duphold/meta.yaml @@ -1,6 +1,6 @@ {% set name = "duphold" %} -{% set version = "0.1.0" %} -{% set sha256hash = "f044f13b2d65bdd04e94426b213bc1822ccc6cf92e7a752e805c1876de33a993" %} +{% set version = "0.1.1" %} +{% set sha256hash = "fb8fed8ab24a4b2c2c82422d2002fece6d67ece15da178453f0a649e85b1a9dd" %} package: name: {{ name|lower }} From 9dfab4a2794d1801e7a6853c16e6bce7e13fd36b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:12:17 -0700 Subject: [PATCH 510/546] Update starfish to 0.0.31 (#12515) --- recipes/starfish/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/starfish/meta.yaml b/recipes/starfish/meta.yaml index 99e50ab934664..461bd60535c5f 100644 --- a/recipes/starfish/meta.yaml +++ b/recipes/starfish/meta.yaml @@ -1,4 +1,4 @@ -{% set STARFISH_VERSION = "0.0.30" %} +{% set STARFISH_VERSION = "0.0.31" %} package: name: starfish @@ -6,7 +6,7 @@ package: source: url: https://github.com/spacetx/starfish/archive/{{ STARFISH_VERSION }}.zip - sha256: de9fb705ae5db39e91fc0caf9331e559645b7fd949a7ac6e422a194aece93568 + sha256: 3bb8498065d49407240a67ef61739eee1f724a108c9ff032401528a93fd848ab build: noarch: python From ce5b13dd49e693dbb83f47c83d4977c0e4dcca92 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:12:30 -0700 Subject: [PATCH 511/546] Update perl-term-app-roles to 0.02 (#12512) --- recipes/perl-term-app-roles/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-term-app-roles/meta.yaml b/recipes/perl-term-app-roles/meta.yaml index 94c972307364f..c0aba80ac4728 100644 --- a/recipes/perl-term-app-roles/meta.yaml +++ b/recipes/perl-term-app-roles/meta.yaml @@ -1,17 +1,17 @@ {% set name = "perl-term-app-roles" %} -{% set version = "0.01" %} -{% set sha256 = "d34c6b4f39eaf62bcd0b6ed8c70bc4a4e8ff3db2caa07f021158b6fcb2975caf" %} +{% set version = "0.02" %} +{% set sha256 = "bf9b0b76fe7650bd31d8beb41e644918f12bbc8ddb06395532a9eb2f5b665852" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/P/PE/PERLANCAR/Term-App-Roles-0.01.tar.gz + url: https://cpan.metacpan.org/authors/id/P/PE/PERLANCAR/Term-App-Roles-0.02.tar.gz sha256: {{ sha256 }} build: - number: 2 + number: 0 requirements: host: From 0c7323b81d65d428661a09bd538126ef227be1b9 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:12:40 -0700 Subject: [PATCH 512/546] Update perl-dbd-sqlite to 1.60 (#12511) --- recipes/perl-dbd-sqlite/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-dbd-sqlite/meta.yaml b/recipes/perl-dbd-sqlite/meta.yaml index ffcb1fd963d5e..4d5d4477ca336 100644 --- a/recipes/perl-dbd-sqlite/meta.yaml +++ b/recipes/perl-dbd-sqlite/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-dbd-sqlite - version: '1.58' + version: '1.60' source: - url: http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/DBD-SQLite-1.58.tar.gz - sha256: 7120dd99d0338dea2802fda8bfe3fbf10077d5af559f6c67ae35e9270d1a1d3b + url: https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/DBD-SQLite-1.60.tar.gz + sha256: 280b2e30e2d9fcd284febda656b80530c70b38cfcbf3132c94257f1e1d303fc3 build: number: 0 From 349dd1293876cc246c97b7b10ac63acf811f812e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:14:47 -0700 Subject: [PATCH 513/546] Update perl-json to 4.00 (#12509) --- recipes/perl-json/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-json/meta.yaml b/recipes/perl-json/meta.yaml index 08dcd90fa539d..6ee79a5cd7937 100644 --- a/recipes/perl-json/meta.yaml +++ b/recipes/perl-json/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-json - version: "2.97001" + version: "4.00" source: - url: https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/JSON-2.97001.tar.gz - sha256: e277d9385633574923f48c297e1b8acad3170c69fa590e31fa466040fc6f8f5a + url: https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/JSON-4.00.tar.gz + sha256: c4da1f1075878604b7b1f085ff3963e1073ed1c603c3bc9f0b0591e3831a1068 build: number: 0 From d93812ca75c29cb18888a18c3a5a0a2017c87b47 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:15:06 -0700 Subject: [PATCH 514/546] Update kipoi to 0.6.5 (#12508) --- recipes/kipoi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kipoi/meta.yaml b/recipes/kipoi/meta.yaml index fbd460892a27b..7087f07caa71d 100644 --- a/recipes/kipoi/meta.yaml +++ b/recipes/kipoi/meta.yaml @@ -1,8 +1,8 @@ {% set name = "kipoi" %} -{% set version = "0.6.3" %} +{% set version = "0.6.5" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "b4e52933cfd62a5eab18b3077f7b7dadf49031906b27973f74ebff10168df969" %} +{% set hash_value = "4a3d4d703b7b84e9f582bc8e9d8c8d00ea8bca6c10f3eb1217c1cb9b438cbda8" %} package: name: '{{ name|lower }}' From d741550b3143b51f20244a45b3579a5386b784ab Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:15:16 -0700 Subject: [PATCH 515/546] Update illumina-interop to 1.1.8 (#12507) --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 33b767ae2f5d3..447e6622623b6 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.7" %} -{% set sha256 = "1c5bce541b7654f892b368ee8a34af109322ecdfe819d081b7fc122b3fb7f21e" %} +{% set version = "1.1.8" %} +{% set sha256 = "885ee3c0d53ef6f4a3df82ea219b3658c286ab008a2142e6ceb13dac5f7ab410" %} package: name: illumina-interop From a8391f09c392efe2b5689e689ebae7cdcd3be59b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:42:21 -0700 Subject: [PATCH 516/546] Update beagle-lib to 3.1.2 (#12523) --- recipes/beagle-lib/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/beagle-lib/meta.yaml b/recipes/beagle-lib/meta.yaml index 83cd71d527631..360edb6d5fd02 100644 --- a/recipes/beagle-lib/meta.yaml +++ b/recipes/beagle-lib/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "3.1.1" %} -{% set sha256 = "3ddb7f39863389816f6289f5da2fe921d0d4efe85dcf349fae3a2718cc14f0fb" %} +{% set version = "3.1.2" %} +{% set sha256 = "dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275" %} package: name: beagle-lib version: '{{version}}' source: - url: https://github.com/beagle-dev/beagle-lib/archive/v3.1.1.tar.gz + url: https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz sha256: '{{sha256}}' #patches: # [osx] # - osx_jni.patch # [osx] From c58ff1b2c663bcdf8636071fe934c78a926715f6 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 19:42:32 -0700 Subject: [PATCH 517/546] Update pysradb to 0.3.0 (#12522) --- recipes/pysradb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pysradb/meta.yaml b/recipes/pysradb/meta.yaml index 6a5ba83900c0b..1eb18cdcaa9eb 100644 --- a/recipes/pysradb/meta.yaml +++ b/recipes/pysradb/meta.yaml @@ -1,8 +1,8 @@ {% set name = "pysradb" %} -{% set version = "0.2.2" %} +{% set version = "0.3.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "15736bec19ca3927b68dd13e3a9ccfab5eee9e586a3d7017b0081605ef37b524" %} +{% set hash_value = "f8d26b37a1424f642c938654a01c4ae02d2758c9fcc6af2cbb4b291e88c3d8dd" %} package: From d58f5b09409bf62ef781ad82a8f1889de7b04ec7 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 20:03:00 -0700 Subject: [PATCH 518/546] Update bioconda-utils to 0.15.2 (#12525) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index a7b757dd4da56..1b05d619627aa 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.1" %} -{% set sha256 = "f1c20353a4e6713fdf2fc3e2697e18082b1ea6e416ef010af1ae001e17e6a156" %} +{% set version = "0.15.2" %} +{% set sha256 = "a51b1b8e872be08c5f69aaeb55c36379ef4f08039ce51abcabc8167b8577dda2" %} package: name: bioconda-utils From 7ae5b52f9700e46ad3fa2e61e52fa5b0638a79ef Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 20:03:23 -0700 Subject: [PATCH 519/546] Update perl-json-pp to 4.0 (#12524) --- recipes/perl-json-pp/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-json-pp/meta.yaml b/recipes/perl-json-pp/meta.yaml index 21cae40b8c5e7..4d2d2dab696c0 100644 --- a/recipes/perl-json-pp/meta.yaml +++ b/recipes/perl-json-pp/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-json-pp" %} -{% set version = "2.97001" %} -{% set sha256 = "67f54a37778babfe0c0ef21e34f04c152d49729220b38ed300fe8a8d7d1827b4" %} +{% set version = "4.00" %} +{% set sha256 = "bef48e49425398d4cfcef769dc3bfd780897b4c097b6502c19b7b0c83a360f3c" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/JSON-PP-2.97001.tar.gz + url: https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/JSON-PP-4.00.tar.gz sha256: {{ sha256 }} build: From 0cef654c2c60ea539de86b2661a383b9bbdbafba Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 20:03:37 -0700 Subject: [PATCH 520/546] Update perl-term-table to 0.013 (#12529) --- recipes/perl-term-table/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-term-table/meta.yaml b/recipes/perl-term-table/meta.yaml index e5dcd068e1662..b704b6540a402 100644 --- a/recipes/perl-term-table/meta.yaml +++ b/recipes/perl-term-table/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-term-table" %} -{% set version = "0.012" %} -{% set sha256 = "4db6118fbf862bd32a8402e1ee28ce2044d0e0887ef29b726e917ab4258a063a" %} +{% set version = "0.013" %} +{% set sha256 = "ffeb36dcb25c575b9f63657d1591a14af22cd10ba23cc76de9d976b426f4fc40" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.012.tar.gz + url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.013.tar.gz sha256: {{ sha256 }} build: From 457f3c063de79f3b7c8920981ac04c9992257c8d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 20:45:59 -0700 Subject: [PATCH 521/546] Update abyss to 2.1.5 (#12528) --- recipes/abyss/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index 3c21f0155c62a..4e0f73db2246e 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -1,5 +1,5 @@ {% set name = "abyss" %} -{% set version = "2.1.4" %} +{% set version = "2.1.5" %} package: name: {{ name|lower }} @@ -10,7 +10,7 @@ build: source: url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz - sha256: 2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc + sha256: 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757 requirements: build: From c18b5c6cfebb16457e0e8621ea89365e58eb6bcf Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Thu, 6 Dec 2018 20:46:11 -0700 Subject: [PATCH 522/546] Update perl-test2-suite to 0.000117 (#12527) --- recipes/perl-test2-suite/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-test2-suite/meta.yaml b/recipes/perl-test2-suite/meta.yaml index 4fec4f3d5b034..ea4604cf02894 100644 --- a/recipes/perl-test2-suite/meta.yaml +++ b/recipes/perl-test2-suite/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-test2-suite" %} -{% set version = "0.000116" %} -{% set sha256 = "8669bc7e680bd6a0dbcb7e24a68d768a49cad99484a4470b1856b9888f88f366" %} +{% set version = "0.000117" %} +{% set sha256 = "e8877a90655ace2e8302104e0de27faf777397194738b085b209749c091ef154" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Test2-Suite-0.000116.tar.gz + url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Test2-Suite-0.000117.tar.gz sha256: {{ sha256 }} build: From 60827c2a1bbc04012d30ac00860651c03e86201b Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 01:31:02 -0700 Subject: [PATCH 523/546] Update wtforms-alchemy to 0.16.8 (#12505) --- recipes/wtforms-alchemy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/wtforms-alchemy/meta.yaml b/recipes/wtforms-alchemy/meta.yaml index 6a3c3dba76b8c..e60898b10ffb5 100644 --- a/recipes/wtforms-alchemy/meta.yaml +++ b/recipes/wtforms-alchemy/meta.yaml @@ -4,11 +4,11 @@ build: package: name: wtforms-alchemy - version: "0.16.7" + version: "0.16.8" source: - url: https://pypi.python.org/packages/source/W/WTForms-Alchemy/WTForms-Alchemy-0.16.7.tar.gz - sha256: 518e6d725f3b860b0b271e78dc4242cc42cd051b42f9a9a8092b5be968cf3f0e + url: https://files.pythonhosted.org/packages/e9/b6/09d2306b53097d0ff2f1b8dc31b12411fc43f4afcfc0a828b1e2373b5b47/WTForms-Alchemy-0.16.8.tar.gz + sha256: c6ed0b22096542fd3063c00329af56a9a338ba3d9b8656acc6404cfdd8085974 requirements: host: From 50316879298226e818092fe769ed4c6b567b2eee Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 01:31:08 -0700 Subject: [PATCH 524/546] Update perl-carp-clan to 6.07 (#12518) --- recipes/perl-carp-clan/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-carp-clan/meta.yaml b/recipes/perl-carp-clan/meta.yaml index a43a017388d40..0e02416747ec4 100644 --- a/recipes/perl-carp-clan/meta.yaml +++ b/recipes/perl-carp-clan/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-carp-clan" %} -{% set version = "6.06" %} -{% set sha256 = "ea4ac8f611354756d43cb369880032901e9cc4cc7e0bebb7b647186dac00c9d4" %} +{% set version = "6.07" %} +{% set sha256 = "0a08560737d8c5caab36f2684c8512e9771e633d3ab5629db814e1d49e274a3d" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/K/KE/KENTNL/Carp-Clan-6.06.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Carp-Clan-6.07.tar.gz sha256: {{ sha256 }} build: From 104cde3341909df3c3a612b6c5468c55f6015845 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 01:31:15 -0700 Subject: [PATCH 525/546] Update perl-date-manip to 6.75 (#12519) --- recipes/perl-date-manip/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-date-manip/meta.yaml b/recipes/perl-date-manip/meta.yaml index c89330647b032..e56011ae52ba3 100644 --- a/recipes/perl-date-manip/meta.yaml +++ b/recipes/perl-date-manip/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-date-manip" %} -{% set version = "6.73" %} -{% set sha256 = "d39295c7c3f19b43470d1203dded8cb649b41a1098e51b5b7c7cf17b662ca255" %} +{% set version = "6.75" %} +{% set sha256 = "c1fbcfbe2ab1a84e57f191807e87c97985da00926f64d1aae598c8756acbb67d" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/S/SB/SBECK/Date-Manip-6.73.tar.gz + url: https://cpan.metacpan.org/authors/id/S/SB/SBECK/Date-Manip-6.75.tar.gz sha256: {{ sha256 }} build: From c59e3d4e9156408698a5fb6ff5507cc95ea9da87 Mon Sep 17 00:00:00 2001 From: Brad Chapman Date: Fri, 7 Dec 2018 05:43:24 -0500 Subject: [PATCH 526/546] Update: seq2c, multiqc-bcbio (#12533) --- recipes/multiqc-bcbio/meta.yaml | 6 +++--- recipes/seq2c/build.sh | 4 ---- recipes/seq2c/meta.yaml | 10 ++++++---- 3 files changed, 9 insertions(+), 11 deletions(-) diff --git a/recipes/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index 501f27d8a42f2..dbb225c7455ba 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -1,4 +1,4 @@ -{% set tag="374afb6" %} +{% set tag="66c7e1d" %} package: name: multiqc-bcbio @@ -6,11 +6,11 @@ package: source: url: https://github.com/MultiQC/MultiQC_bcbio/archive/{{ tag }}.tar.gz - md5: c29e4fce85472b858d74cd829f0add1e + sha256: 31d4efbd574d61255b0638b29ccad396066c4aeebfc2a6ca323a207857eabf3b build: noarch: python - number: 3 + number: 4 preserve_egg_dir: True requirements: diff --git a/recipes/seq2c/build.sh b/recipes/seq2c/build.sh index 161c67a79661b..f0b89ab7a5e2b 100644 --- a/recipes/seq2c/build.sh +++ b/recipes/seq2c/build.sh @@ -4,10 +4,6 @@ target=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $target mkdir -p $PREFIX/bin -# fix references to handle symlinks -sed -i.bak 's/FindBin::Bin/FindBin::RealBin/' cov2lr.pl -sed -i.bak 's/FindBin::Bin/FindBin::RealBin/' lr2gene.pl - cp -r * $target ln -s $target/seq2cov.pl $PREFIX/bin ln -s $target/cov2lr.pl $PREFIX/bin diff --git a/recipes/seq2c/meta.yaml b/recipes/seq2c/meta.yaml index d22e06c330b57..68ea7324520bf 100644 --- a/recipes/seq2c/meta.yaml +++ b/recipes/seq2c/meta.yaml @@ -1,13 +1,14 @@ package: name: seq2c - version: '2016.03.23' + version: '2018.12.05' source: - url: https://github.com/AstraZeneca-NGS/Seq2C/archive/8e62a3f.tar.gz - sha256: 0b50b6f14a3feed233956a72a631d321e3c8f6328521444886f1b0a8c7f24a5b + url: https://github.com/chapmanb/Seq2C/archive/dd69de2.tar.gz + #url: https://github.com/AstraZeneca-NGS/Seq2C/archive/7b33abe.tar.gz + sha256: 1d181da8433c088dee5b5b133915efc7140633e5cb0136a0bd87e6a8c1f7cc2c build: - number: 1 + number: 0 skip: False requirements: @@ -15,6 +16,7 @@ requirements: - perl run: - perl + - perl-statistics-ttest test: commands: From 7f3cf25db171c4b03891e14ab3da6d720d800e71 Mon Sep 17 00:00:00 2001 From: Tobias Rausch Date: Fri, 7 Dec 2018 12:51:46 +0100 Subject: [PATCH 527/546] tracy v0.3.7 (#12534) --- recipes/tracy/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/tracy/meta.yaml b/recipes/tracy/meta.yaml index fb36eaf480cb3..bf24a6408be0b 100644 --- a/recipes/tracy/meta.yaml +++ b/recipes/tracy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.6" %} -{% set sha256 = "e00f42d0d052941117f678f9ede99ab4da897606b4fa89134c0b2c60ea6798a1" %} +{% set version = "0.3.7" %} +{% set sha256 = "1b7582809595d1a8c6821c84807b839828387f9c01d63f4694a3225fada7e7b4" %} package: name: tracy @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 1 + number: 0 skip: True # [osx] requirements: @@ -21,13 +21,13 @@ requirements: host: - zlib - bzip2 - - boost ==1.61.0 + - boost - htslib - sdsl-lite run: - zlib - bzip2 - - boost ==1.61.0 + - boost - htslib - sdsl-lite From 86fbe7e06314e412c543091be8e3e781aaf6b5bc Mon Sep 17 00:00:00 2001 From: Jorrit Boekel Date: Fri, 7 Dec 2018 15:05:01 +0100 Subject: [PATCH 528/546] Version bump 2.10 (#12535) * Version bump 2.10 * Copy paste error forgot the https --- recipes/msstitch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/msstitch/meta.yaml b/recipes/msstitch/meta.yaml index d83ab10facf05..76addaa82f4ea 100644 --- a/recipes/msstitch/meta.yaml +++ b/recipes/msstitch/meta.yaml @@ -1,10 +1,10 @@ package: name: msstitch - version: "2.9" + version: "2.10" source: - url: https://files.pythonhosted.org/packages/e9/c2/a6f965f8e4dbfd2e819126b96110940903215df1a4d5cad5d84c821eb484/msstitch-2.9.tar.gz - sha256: 0096958917e597cbe998b8eefab6be7c3af5d490a2e4a0f722311cb6bdeb07b8 + url: https://files.pythonhosted.org/packages/af/4e/6a98b424697b6bdf43e089ea0446cddb2e8500cd13a70e439f840c4f500f/msstitch-2.10.tar.gz + sha256: b85c2791484ecd61e8c5832c2c3359921680bbc414f3c6feccd3c82ec4b77cdb build: skip: True # [py2k or osx] From d74bb1fb804331ff0a2da974f4644a6eb24d121d Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Fri, 7 Dec 2018 16:53:22 +0000 Subject: [PATCH 529/546] Missing deps for ucsc-cell-browser 0.4.23 (#12537) * Missing deps for ucsc-cell-browser * Bumps build nuber --- recipes/ucsc-cell-browser/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml index b5c2b94d53d5f..8c151af7ddfd0 100644 --- a/recipes/ucsc-cell-browser/meta.yaml +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -9,7 +9,7 @@ source: sha256: e2a019f8bb150f8d115b0dd1f75a76831c9e96898c42d70b42f37ff61f01641e build: - number: 0 + number: 1 noarch: python requirements: @@ -19,6 +19,8 @@ requirements: - python >=3.6 - numpy - r-data.table + - r-argparser + - r-matrix - anndata test: From 14376531fac5d4ca031a39cf0af611bf9f29348d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 13:31:59 -0700 Subject: [PATCH 530/546] Update vsearch to 2.10.1 (#12540) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index e55d4e21cebc0..4eb9eb4fe8667 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.0" %} -{% set sha256 = "a1ca14a6aaa96d4734572a224624af802973b38bbd3f12a95df1ed4cf918c7d4" %} +{% set version = "2.10.1" %} +{% set sha256 = "fd0726bd0604c00ed8e90d1b5bfe9a1afa42786acb01389e0255c2b418f1bc99" %} package: name: vsearch From 3ac3c1f55e5c0af46af0d0ca38035c19e37a3db2 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Fri, 7 Dec 2018 15:33:13 -0500 Subject: [PATCH 531/546] New recipe for MicroHapDB 0.2 (#12531) * New recipe for MicroHapDB 0.2 * Troubleshoot config * Successful build locally! * Clean up recipe --- recipes/microhapdb/meta.yaml | 39 ++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 recipes/microhapdb/meta.yaml diff --git a/recipes/microhapdb/meta.yaml b/recipes/microhapdb/meta.yaml new file mode 100644 index 0000000000000..c1cb8b54bfe7c --- /dev/null +++ b/recipes/microhapdb/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.2" %} +{% set sha256 = "450faabc3420fc7ed9107c0de3a0643b82352a592bde487c4afc6dc064bc8f7a" %} + +package: + name: microhapdb + version: '{{version}}' + +source: + url: https://github.com/bioforensics/microhapdb/archive/{{ version }}.tar.gz + sha256: '{{sha256}}' + +build: + noarch: python + entry_points: + - microhapdb = microhapdb.cli:main + script: python -m pip install --no-deps --ignore-installed . + number: 0 + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - pandas + +test: + imports: + - microhapdb + requires: + - pytest + - pytest-cov + +about: + home: https://github.com/bioforensics/MicroHapDB/ + license: BSD License + license_family: BSD + summary: Data package providing convenient programmatic access to published microhaplotype data. + dev_url: https://github.com/bioforensics/MicroHapDB/ From 42aaea3191fcfe20b5b3c6c75179b8f5c5531538 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 14:07:41 -0700 Subject: [PATCH 532/546] Update moff to 2.0.2 (#12539) --- recipes/moff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/moff/meta.yaml b/recipes/moff/meta.yaml index d0bd424099135..b0cdff246d06e 100644 --- a/recipes/moff/meta.yaml +++ b/recipes/moff/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: moff @@ -6,7 +6,7 @@ package: source: url: https://github.com/compomics/moFF/archive/{{ version }}.tar.gz - md5: cd8176137643087622554efb2ef265ed + sha256: 42ded39204b4ffd536d2ea9f0b22350ec7a228c6d497d3f3028d3cf6af6810d9 build: number: 0 From 92a75770b1355088dd35cafb300e266f33a4a9e7 Mon Sep 17 00:00:00 2001 From: Sebastian Roskosch Date: Fri, 7 Dec 2018 22:41:26 +0100 Subject: [PATCH 533/546] Update PopDel to version 1.0.5 (#12502) * Update PopDel to version 1.0.5 * Remove Makefile.patch Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead. * Automatically get version from PKG_VERSION --- recipes/popdel/Makefile.patch | 45 ----------------------------------- recipes/popdel/build.sh | 4 +++- recipes/popdel/meta.yaml | 8 +++---- 3 files changed, 6 insertions(+), 51 deletions(-) delete mode 100644 recipes/popdel/Makefile.patch diff --git a/recipes/popdel/Makefile.patch b/recipes/popdel/Makefile.patch deleted file mode 100644 index a31ec8c115409..0000000000000 --- a/recipes/popdel/Makefile.patch +++ /dev/null @@ -1,45 +0,0 @@ ---- Makefile 2018-10-18 15:23:37.903614000 +0200 -+++ MakefileConda 2018-10-18 15:53:03.215652075 +0200 -@@ -1,10 +1,3 @@ --# Use version 4.9 of g++ -- --# Set dependencies, s.t. make detects changes in header files. --%.o: %.cc %.h -- g++ -c $^ -- --CXX=g++ - CC=$(CXX) - - # Set this to include SeqAn libraries, either system wide -@@ -14,14 +7,13 @@ - CXXFLAGS+=-I$(SEQAN_LIB) -DSEQAN_HAS_ZLIB=1 -std=c++14 -DSEQAN_DISABLE_VERSION_CHECK - LDLIBS=-lz -lpthread - --DATE=on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1) --VERSION=1.0.4-$(shell git log --pretty=format:"%h" --date=iso | head -n 1) -+DATE=on 2018-11-09 -+VERSION=1.0.4 - CXXFLAGS+=-DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\" - - # Enable warnings - CXXFLAGS+=-W -Wall -Wno-long-long -pedantic -Wno-variadic-macros -Wno-unused-result - -- - HEADERS=parse_popdel.h insert_histogram_popdel.h workflow_popdel.h utils_popdel.h popdel_view_parameter_parsing.h - HEADERS+=popdel_profile/*.h - HEADERS+=popdel_call/*.h -@@ -30,14 +22,6 @@ - all: CXXFLAGS+=-O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 - all: popdel - --.PHONY: profiling --profiling: CXXFLAGS+=-g -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=1 --profiling: popdel -- --.PHONY: debug --debug: CXXFLAGS+=-g -O0 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=1 --debug: popdel -- - PREFIX = /usr/local - .PHONY: install - install: CXXFLAGS+=-O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 diff --git a/recipes/popdel/build.sh b/recipes/popdel/build.sh index dc77fe956bee6..36448bcdcdb41 100644 --- a/recipes/popdel/build.sh +++ b/recipes/popdel/build.sh @@ -1,4 +1,6 @@ #!/bin/sh -make all +DATE=2018-12-06 + +make CXX=${CXX} VERSION=${PKG_VERSION} DATE=${DATE} mkdir -p ${PREFIX}/bin cp popdel ${PREFIX}/bin diff --git a/recipes/popdel/meta.yaml b/recipes/popdel/meta.yaml index f015eadc03948..d9ed54e867f39 100644 --- a/recipes/popdel/meta.yaml +++ b/recipes/popdel/meta.yaml @@ -1,12 +1,10 @@ package: name: popdel - version: "1.0.4" + version: "1.0.5" source: - url: https://github.com/kehrlab/PopDel/archive/v1.0.4.tar.gz - sha256: eb611363a5279b5d7db0dcc8de9b086f73fd34e1516c762425ea655917e55041 - patches: - - Makefile.patch + url: https://github.com/kehrlab/PopDel/archive/v1.0.5.tar.gz + sha256: 7ab33573780b0f373787cfd9014b7a60d0451049956e072521670708b401109c build: number: 0 From 6980a8e9ca593b91a457211c1bd86583cd85c2af Mon Sep 17 00:00:00 2001 From: Adam Taranto Date: Fri, 7 Dec 2018 13:58:16 -0800 Subject: [PATCH 534/546] Update to teloclip v0.0.3 (#12542) --- recipes/teloclip/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml index d385f33e54ef1..9532ae99ec7b8 100644 --- a/recipes/teloclip/meta.yaml +++ b/recipes/teloclip/meta.yaml @@ -1,8 +1,8 @@ {% set name = "teloclip" %} -{% set version = "0.0.2" %} +{% set version = "0.0.3" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "bee069ec44dec8fd0aff171ddfa146da66a750dea8fa41903cd846f2bdab3ebb" %} +{% set hash_value = "48b25ce0a3dce9f44bc2703ccbcb9738861c260568a9ce1f3687c4aca054b14d" %} package: name: '{{ name|lower }}' @@ -13,10 +13,11 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - noarch: python + skip: True # [py27] number: 0 entry_points: - teloclip=teloclip.run_self:main + - teloclip-extract=teloclip.run_extract:main script: python setup.py install --single-version-externally-managed --record=record.txt requirements: @@ -31,16 +32,17 @@ test: - teloclip commands: - teloclip --help + - teloclip-extract --help about: home: https://github.com/Adamtaranto/teloclip license: MIT License license_family: MIT license_file: '' - summary: Filter SAM file for soft-clipped alignments containing unassembled telomeric repeats. + summary: A tool for the recovery of unassembled telomeres from soft-clipped read alignments. description: '' doc_url: '' dev_url: '' extra: - recipe-maintainers: '' + recipe-maintainers: 'Adam Taranto' From 71d52da17fd290b379d3c8535570aecf27faae77 Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 17:11:22 -0700 Subject: [PATCH 535/546] Update biolite to 1.2.0 (#12544) --- recipes/biolite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/biolite/meta.yaml b/recipes/biolite/meta.yaml index 2a174e9b755ba..8bc2532e4480d 100644 --- a/recipes/biolite/meta.yaml +++ b/recipes/biolite/meta.yaml @@ -1,13 +1,13 @@ package: name: biolite - version: 1.1.0 + version: 1.2.0 source: - url: https://bitbucket.org/caseywdunn/biolite/get/release-1.1.0.zip - sha256: dbfb9cce029098c476d930af179ab0e33c8e9f459c62bb007c0fd9c33fa7b30a + url: https://bitbucket.org/caseywdunn/biolite/get/release-1.2.0.zip + sha256: 61d9268278a50b3ea03b7a4e1a5424beeff2482634ab570d6c66925dac26d9e2 build: - number: 2 + number: 0 skip: True # [not py27] requirements: From fc0dade972c8c1ae2609d882c39b6281e885ff5d Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Fri, 7 Dec 2018 17:11:38 -0700 Subject: [PATCH 536/546] Update kneaddata to 0.7.2 (#12543) --- recipes/kneaddata/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kneaddata/meta.yaml b/recipes/kneaddata/meta.yaml index 4ec0c24f538a4..25b3c845713ea 100644 --- a/recipes/kneaddata/meta.yaml +++ b/recipes/kneaddata/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.2" %} package: name: kneaddata @@ -6,7 +6,7 @@ package: source: url: https://bitbucket.org/biobakery/kneaddata/get/{{ version }}.tar.gz - sha256: ec097857b3354e0e03d5043905d3f95afb5b763063c8bf27dda529d1dbf9bdee + sha256: 87f74c5f94a28d61384a11544f23bd6bdbca0fb4477ac29727929024e140bacb build: number: 0 From 3820b41008ea6ae62ca4edc5927f5b8dc20f417f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 8 Dec 2018 14:45:10 +0100 Subject: [PATCH 537/546] snakemake 5.3.1 (#12500) * snakemake 5.3.1 * fix jinja variables * only warn if git not present in tests * use explicit jinja for version again. Conda seems to have lost the ability to use PKG_VERSION in meta.yaml. * try masking env var * try defining env var before command --- recipes/snakemake-minimal/meta.yaml | 11 ++++++----- recipes/snakemake/meta.yaml | 9 +++++---- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/recipes/snakemake-minimal/meta.yaml b/recipes/snakemake-minimal/meta.yaml index 0d72f355a726a..9d4f61e555959 100644 --- a/recipes/snakemake-minimal/meta.yaml +++ b/recipes/snakemake-minimal/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "5.3.0" %} +{% set version = "5.3.1" %} package: name: snakemake-minimal - version: "5.3.0" + version: {{ version }} source: - url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ PKG_VERSION }}.tar.gz - sha256: 612a16f2bba580c47183e4f752ed40b034852541ca3e96e480d01fb30ad9570c + url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz + sha256: a43d66d80d7bf83b0429cf03ab5500b2775bbe78a53eee9622c1a2cb802eac5f build: - number: 2 + number: 0 noarch: python script: python -m pip install --no-deps --ignore-installed . entry_points: @@ -41,6 +41,7 @@ test: imports: - snakemake commands: + - export GIT\_PYTHON_REFRESH=warn - snakemake --version - snakemake --version | grep "{{ version }}" diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 3f38f91fbf699..c03010d193ab7 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "5.3.0" %} +{% set version = "5.3.1" %} package: name: snakemake - version: "5.3.0" + version: {{ version }} build: - number: 2 + number: 0 noarch: generic requirements: run: - - snakemake-minimal ={{ PKG_VERSION }} + - snakemake-minimal ={{ version }} # optional dependencies needed for the full experience # require this dropbox version to ensure that a conda doesn't pick up the # outdated version available @@ -34,6 +34,7 @@ test: imports: - snakemake commands: + - export GIT\_PYTHON_REFRESH=warn - snakemake --version - snakemake --version | grep "{{ version }}" From b8baefc78b0b2da5c7dc92b75bc52c5810b7cefb Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Sat, 8 Dec 2018 10:02:09 -0800 Subject: [PATCH 538/546] nextflow: pin openjdk=8 to solve java version parsing issue (#12493) * Pin openjdk=8 * Alllow openjdk 8 or 9 --- recipes/nextflow/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml index 1a86ab4e5865f..6bff6d7912a22 100644 --- a/recipes/nextflow/meta.yaml +++ b/recipes/nextflow/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 noarch: generic source: @@ -14,11 +14,11 @@ source: requirements: host: - - openjdk >=8,<=11 + - openjdk >=8,<=9 - coreutils - curl run: - - openjdk >=8,<=11 + - openjdk >=8,<=9 - coreutils - curl From 5dda32a4ea5597c738239bcbea1041a9c435c32e Mon Sep 17 00:00:00 2001 From: Elmar Pruesse Date: Sat, 8 Dec 2018 11:47:10 -0700 Subject: [PATCH 539/546] Update bioconda-utils to 0.15.3 (#12546) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 1b05d619627aa..03186fa281bac 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.2" %} -{% set sha256 = "a51b1b8e872be08c5f69aaeb55c36379ef4f08039ce51abcabc8167b8577dda2" %} +{% set version = "0.15.3" %} +{% set sha256 = "68c23754259fe7102edcc6c89ad55cf5a7ecfd453a2ea0f4e82a290129e4603c" %} package: name: bioconda-utils From 4d9c418102ea123876db0250ced6d5a55246b978 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 8 Dec 2018 21:27:03 +0100 Subject: [PATCH 540/546] Test with bioconductor-roc --- .circleci/config.yml | 21 +++++++++++++++++---- config.yml | 3 ++- recipes/bioconductor-roc/build.sh | 9 ++++++++- recipes/bioconductor-roc/meta.yaml | 16 +++++++++++----- 4 files changed, 38 insertions(+), 11 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 69f53be366c6f..f7a479bb05eff 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -28,6 +28,17 @@ variables: LANG: en_US.UTF-8 linux: &linux machine: true + macos_bulk: &macos_bulk + macos: + xcode: "8.3.3" + environment: + LC_ALL: en_US.UTF-8 + LANG: en_US.UTF-8 + BIOCONDA_LABEL: gcc7 + linux_bulk: &linux_bulk + machine: true + environment: + BIOCONDA_LABEL: gcc7 skip_fork: &skip_fork run: name: Check for fork @@ -163,7 +174,7 @@ jobs: # build, test and upload for bulk branch on linux bulk-linux: - <<: *linux + <<: *linux_bulk steps: - *fail_fork - checkout @@ -175,11 +186,12 @@ jobs: name: Building, testing, and uploading of all unpublished recipes command: | bioconda-utils build recipes config.yml \ - --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers + --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ + --check-channels conda-forge/label/gcc7 bioconda/label/gcc7 bioconda # build, test and upload for bulk branch on macos bulk-macos: - <<: *macos + <<: *macos_bulk steps: - *fail_fork - checkout @@ -191,7 +203,8 @@ jobs: name: Building, testing and uploading of all unpublished recipes command: | bioconda-utils build recipes config.yml \ - --anaconda-upload + --anaconda-upload \ + --check-channels conda-forge/label/gcc7 bioconda/label/gcc7 bioconda # nightly build, test and upload of unpublished recipes on linux nightly-upload-linux: diff --git a/config.yml b/config.yml index 25821886db1d7..b531ad6c3b781 100644 --- a/config.yml +++ b/config.yml @@ -7,6 +7,7 @@ blacklists: # of .condarc, but when adding channels using conda config --add, they should # be added in reverse (from low to high priority). channels: - - conda-forge + - conda-forge/label/gcc7 + - bioconda/label/gcc7 - bioconda - defaults diff --git a/recipes/bioconductor-roc/build.sh b/recipes/bioconductor-roc/build.sh index da43ce2168312..5ea71a1203cac 100644 --- a/recipes/bioconductor-roc/build.sh +++ b/recipes/bioconductor-roc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-roc/meta.yaml b/recipes/bioconductor-roc/meta.yaml index 219b9660b1772..fae3c6739c3a3 100644 --- a/recipes/bioconductor-roc/meta.yaml +++ b/recipes/bioconductor-roc/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "ROC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2814ca229c7dbb74479fbf7b76b20f816a70856beb9146a66346dc82061490a1 + md5: d7a7d3f092af4fbba537c070c6f0efc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Biobase requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'utilities for ROC, with uarray focus' extra: identifiers: - biotools:roc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-roc + path: recipes/bioconductor-roc + version: 1.56.0 + From 3a30880a3501f373a3ba81b2ff7ccf630247ba90 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 8 Dec 2018 21:42:20 +0100 Subject: [PATCH 541/546] add a noarch test case --- recipes/bioconductor-a4base/meta.yaml | 49 +++++++++++++++------------ 1 file changed, 28 insertions(+), 21 deletions(-) diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index fff4e6e9d30ae..6056bbc7ad27c 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,44 +1,46 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "a4Base" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520 + md5: a8238f64848e4f0974867b0a5f3dc920 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Cairo, ALL requirements: host: - - 'bioconductor-a4core >=1.28.0,<1.30.0' - - 'bioconductor-a4preproc >=1.28.0,<1.30.0' - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.28.0,<1.30.0' - - 'bioconductor-a4preproc >=1.28.0,<1.30.0' - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-glmnet - r-gplots @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Automated Affymetrix Array Analysis' extra: identifiers: - biotools:a4base - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4base + path: recipes/bioconductor-a4base + version: 1.28.0 + From 0af6cd92f097f5811151dd8484b126a3793c5c69 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 8 Dec 2018 21:54:05 +0100 Subject: [PATCH 542/546] biocgenerics should work --- recipes/bioconductor-biocgenerics/build.sh | 15 +++++++++++---- recipes/bioconductor-biocgenerics/meta.yaml | 10 +++++++--- 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/recipes/bioconductor-biocgenerics/build.sh b/recipes/bioconductor-biocgenerics/build.sh index da43ce2168312..4a709afbd7ab4 100644 --- a/recipes/bioconductor-biocgenerics/build.sh +++ b/recipes/bioconductor-biocgenerics/build.sh @@ -1,4 +1,11 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file + #!/bin/bash + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + mkdir -p ~/.R + echo -e "CC=$CC +FC=$FC +$CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars + $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index b0c0c2081048d..09b90292a59f3 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 39b4dfb1f9526c64ddcb9b994130a7c0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -30,7 +30,11 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'S4 generic functions needed by many Bioconductor packages.' - extra: identifiers: - - biotools:biocgenerics \ No newline at end of file + - biotools:biocgenerics + parent_recipe: + name: bioconductor-biocgenerics + path: recipes/bioconductor-biocgenerics + version: 0.28.0 + From be718c9db69f77a470fdb588f286200a4ae32f75 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 8 Dec 2018 22:15:51 +0100 Subject: [PATCH 543/546] CXXFLAGS --- recipes/bioconductor-roc/build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bioconductor-roc/build.sh b/recipes/bioconductor-roc/build.sh index 5ea71a1203cac..104f961245320 100644 --- a/recipes/bioconductor-roc/build.sh +++ b/recipes/bioconductor-roc/build.sh @@ -3,6 +3,7 @@ mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R echo -e "CC=$CC +CXXFLAGS=$CXXFLAGS FC=$FC CXX=$CXX CXX98=$CXX From 3c1131a48664bd2bb341acef1d9967931098e9a5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 8 Dec 2018 22:19:03 +0100 Subject: [PATCH 544/546] revert a4base bump --- recipes/bioconductor-a4base/meta.yaml | 46 ++++++++++++--------------- 1 file changed, 20 insertions(+), 26 deletions(-) diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index 6056bbc7ad27c..00603a15919f9 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.28.0" %} {% set name = "a4Base" %} -{% set bioc = "3.8" %} +{% set bioc = "3.7" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,37 +10,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8238f64848e4f0974867b0a5f3dc920 + sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520 build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic # Suggests: Cairo, ALL requirements: host: - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-a4core >=1.28.0,<1.30.0' + - 'bioconductor-a4preproc >=1.28.0,<1.30.0' + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.30.0,<1.31.0' - - 'bioconductor-a4preproc >=1.30.0,<1.31.0' - - 'bioconductor-annaffy >=1.54.0,<1.55.0' - - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.42.0,<2.43.0' - - 'bioconductor-genefilter >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.38.0,<3.39.0' - - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-a4core >=1.28.0,<1.30.0' + - 'bioconductor-a4preproc >=1.28.0,<1.30.0' + - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-multtest >=2.36.0,<2.38.0' - r-base - r-glmnet - r-gplots @@ -49,15 +48,10 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Automated Affymetrix Array Analysis' extra: identifiers: - biotools:a4base - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-a4base - path: recipes/bioconductor-a4base - version: 1.28.0 - From ef8391e5058b7d8c3a4735cef4e3eb21908f8ca5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 8 Dec 2018 22:24:46 +0100 Subject: [PATCH 545/546] remove tab --- recipes/bioconductor-a4base/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index 00603a15919f9..c833fa4cefc4a 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -10,7 +10,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520 + sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520 build: number: 0 rpaths: From 39dd094049e7fd1f027dd63fcf8d91f4094d2f40 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 8 Dec 2018 23:08:10 +0100 Subject: [PATCH 546/546] try src/Makevars --- recipes/bioconductor-roc/build.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/bioconductor-roc/build.sh b/recipes/bioconductor-roc/build.sh index 104f961245320..248d10a0bcfc4 100644 --- a/recipes/bioconductor-roc/build.sh +++ b/recipes/bioconductor-roc/build.sh @@ -1,12 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -mkdir -p ~/.R echo -e "CC=$CC CXXFLAGS=$CXXFLAGS FC=$FC CXX=$CXX CXX98=$CXX CXX11=$CXX -CXX14=$CXX" > ~/.R/Makevars +CXX14=$CXX" > src/Makevars $R CMD INSTALL --build .