From 07cc66d80793375ccdd881546827347243ad459e Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 4 Oct 2019 11:58:20 +0200 Subject: [PATCH] Noarch generic bulk (#17783) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * bump build numbers again * a few updates (#12927) * updates (#12930) * updates * Update build.sh * Update build.sh * build bumps and openmp * Bulk update 060119b (#12932) * update camera, cosmiq, and metab * update blacklist * fix tarball links, fix openmp problems (#12933) * A few final fixes for OSX (#12935) * bulk fixes * bump * Bump a few package versions to fix builds (#12945) * Update blacklist (#12951) * Update scan.upc (#12984) * Bulk update 080119b (#12990) * Update a few URLs and the blacklist * Update a few more versions/URLs * Fix bioconductor-condcomp version/URL * Update consensus version/URL * Update version/URL for caomicsv * one last one * Various package updates (#12998) * Various package updates * bioconductor-rnaseqpower * more blacklisted packages * A few last updates * Bulk update 090119b (#13002) * A few more updates * Fix python in dexseq, since the count script has system requirements that aren't listed * Update DEXSeq (#13011) * A few updates for bulk (#13014) * update the blacklist (#13018) * Bulk updates (#13035) * Bulk update 110119b (#13052) * Various updates * Another update * Update flowFit * a few updates * Try removing a few from the blacklist (#13053) * A few last updates to try (#13054) * A few more updates (#13056) * Patch bioconductor-rtandem (#13058) * A few version updates (#13059) * Update blacklist for packages that needed r-fda and r-compquadform (#13060) * Bulk update 130119c (#13062) * Update a few recipes * These will fail * Updates (#13064) * Ucsc update (#13722) * Fixed missing file PLEK.range for PLEK receipe. (#13389) * Add new recipe for Alder (#13390) New recipe for Alder software * Apply fix to bash script to detect correct JAVA_HOME (#13387) * Apply fix to bash script to detect correct JAVA_HOME Thanks to @chapmanb for pointing to bioconda/bioconda-recipes@b726965 Thanks to @keenhl for spotting the issue * ADd zlib to meta.yaml * wcX: bump subversion (#13392) * Package for vcfpy v0.12.0 (#13393) * Update: bcbio (1.1.3 release), bcbio-vm (AWS support) (#13394) * Update meta.yaml (#13395) * Updates UCSC CellBrowser to version 0.4.35 (#13132) * Bump UCSC CellBrowser to version 0.4.30 * Moves to 0.4.33 to fix versioneer cfg lack * Update shasum 256 * Bump to 0.4.35 to sort versioneer issue. * Add recipe for gerp++ (#13391) * Add recipe for gerp++ * Remove r-basejump from blacklist to build it under 3.5. (#13398) * [coprarna] bump dep perl-list-moreutils to 0.428 (#13397) * Update ConFindr to 0.5.1 (#13401) * Pathogist (#13145) * Add pathogist recipe * Change sha256 * Fixed test * Fixed test * build #0 * Add a proper setup.py, fix python pinning * Right, noarch, though it's still pinned * forgot setup.py * Set Matplotlib to use Agg * Fixed sha256 * Build r-bcbiobase for R 3.5 (#13402) * gffcompare: change build.sh to use prep_linux.sh (#12407) - this is solution suggested by the developer: https://github.com/gpertea/gclib/issues/4 - removed gffcompare as developer suggested - removed blacklist entry * Bump fcsparser to 0.2.0. (#13405) * Update: CNVkit bump for failed linux build (#13403) Previous build, which fixes CNVkit with recent pandas, failed when building on CircleCI so doesn't have a new package. Bump build number and re-build. https://circleci.com/gh/bioconda/bioconda-recipes/40931 * add new recipe for MALDER software (#13406) * Build r-bcbiornaseq for R 3.5.1 (#13404) * Bump r-bcbiornaseq to v.2.8 * Remove r-bcbiornaseq from blacklist. * Fix typo. * recipe: r-misha (#13408) * repice: r-misha * skip osx build * Change conda description (#13409) * fixed type (#13410) * GATK4: bump version (#13412) * Update xopen to 0.5.0 (#13413) * new packages: r-umi4c, r-shaman (#13396) * new package: r-umi4c, r-shaman * Igv fix (#13414) * [*] 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/)). * [*] This PR updates an existing recipe. * [*] This PR does something else (explain below). Updated igv to newest version, fixed broken linkt to jar file, added test * Stacks 2.3 (#13095) * Stacks update 2.3 * Stacks folder cleanup * stacks remove 1.47 * nextflow 19.01.0 build 4 (#13418) This commit changes the build script so that it modifies the NXF_DIST directory to the package path provided by Conda See https://github.com/nextflow-io/nextflow/issues/954 * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [x] 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). * Added recipe for illumina-cleanup (#13417) * Added recipe for illumina-cleanup * Fixed test issue (Nextflow cache) * updated dxpy to 0.273.0 (#13407) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [X] 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). * add stream_chromvar recipe (#13419) * add stream_chromvar recipe * Add imctools (#13420) * Add imctools * Only actual requirements * Update meta.yaml * rust-bio-tools 0.2.8 (#13411) * rust-bio-tools 0.2.8 * added clangdev * Add starcode * Add cxx compiler. * explicitly use newest clang on osx. * Perl www mechanize and dependancies (#13218) * Add new test and dependancies * init www-mechanize recipe * init html-form recipe dependancy * complete perl dependancies & fix sh * fix perl dependancies and sh * Add basic tests * add more basic test * Changing modules position... * Updated percolator to 3.2.1 for building against boost = 1.64 (#13425) * Fix optitype numpy requirements (#13427) * Fix optitype numpy requirements * Syntax fixed * Fix numpy to 1.10 * Add prokaryote from pypi (#13428) * Add prokaryote from pypi * Update meta.yaml * Update meta.yaml * Update cgat-core to 0.5.6 (#13348) * Try to trigger OSX build (#13429) * srnapipe: new recipe (#13416) * Added sRNAPipe recipe. * Updated tool dependencies versions. * Changed repo name * Updated sha256 * Changed build to host * Update IslandPath to 1.0.4 (#13421) * Increment version * Update sha256 * Update sha256 * Add pinned numpy dependencies (#13437) * Update: bcbio, bcbio-vm, bcbio-variation-recall (#13435) - bcbio: latest development version with fixes for CWL generation - bcbio-vm: support for remote file lookup via bcbio - bcbio-variation-recall: fixes for latest bcftools * updated prince to 2.0 (#13434) * Remove the cf201901 label (#13440) * Update seqlogo meta.yaml (#13433) * Update meta.yaml * Update meta.yaml * Bump deepTools and its dependencies (#13442) * Bump deepTools and its dependencies * fix py2bit, remove obsolete pybigwig/0.1.11 * old pysam builds don't work with python 3.7 * nimnexus v0.1.1 (#13443) * Update meta.yaml * Update meta.yaml * reset build-number and test the new build-infrastrucutre * pb-falcon: update build (#13446) Hopefully to fix https://github.com/PacificBiosciences/pbbioconda/issues/85 * pb-assembly: update build, and specify python2 (#13447) Hopefully to fix https://github.com/PacificBiosciences/pbbioconda/issues/85 * samtools w/ openssl-1.1.1 (#13448) Another attempt to deal with python2.7.15/openssl issues. E.g. https://github.com/PacificBiosciences/pbbioconda/issues/85 Note: samtools-1.9 was built against opensll-1.0.2, which conflicts with the latest python2.7.15 build. openssl-1.1.1a and openssl-1.0.2p are not ABI-compatible, so we need to specify that. I do not see a way to pin the old opensll (since there is ambiguity between 1.0.2o and 1.0.2p), so I am taking the suggestion from kylebeauchamp and rebuilding with openssl-1.1.1. That might break some people until they upgrade python, etc. but I do not see a better solution without actually bumping the version of samtools. * update bioconda-utils (#13445) * [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). * samtools w/ openssl >= 1.1.1 (#13450) * samtools w/ openssl >= 1.1.1 See #13448 Simply rebuilding samtools did not grab the more recent openssl. (See previous commit.) * Trying to fix syntax error for opensll version spec * Still trying * Updated PyPairs to v3.0.9 (#13449) * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [x] 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). * pb-assembly-0.0.4: openssl-1.1.1a (#13452) After I rebuilt samtools, the samtools problem disappeared for me in some cases, but only because pb-assembly was suddenly using the older openssl again. Hopefully, this will create a self-consistent tree. * pb-assembly: bump build number (#13453) Maybe this will cause 0.0.4 to show up. I have not seen it since merging several hours ago. * Update meta.yaml * Update meta.yaml * Updated metal.yaml for new prince release (#13454) * chado-tools 0.2.5 (#13456) * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [x] 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). * cnv_facets (#13457) * First draft * Restrict to linux * Add snp-pileup dependency * Do not use setup script If some dependency is missing, edit meta.yaml or explicitly put dependecies build.sh * Install without setup.sh * Fix R command * Move test to meta.yaml * Fix yaml line * Test moved to build script to resolve #38177 (upload-linux) * Install jsonlite in build script After installation, argparse fails as it cannot find jsonlite (?!) so we install jsonlite explicitly. Version bumped so the version string from cnv_facets.R -v agrees with the release version * Try moving jsonlite from build to meta This to try to resolve the error occurring *after* downloading cnv_facets: cnv_facets.R -h Error: package or namespace load failed for ‘argparse’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘jsonlite’ Execution halted * Bump buld number * Recipe for version 0.12.0 * Update to v0.12.1 * Update to version 1.15.0 * Test using -v and use bash * Revert to sh * Try with zlib * Use bash script shipped with ASCIIGenome package * Fix sed command * Try sending sed output to dest dir directly * Fix symplink * Copy - do not symlink * Add libgfortran - fix url * Use c compiler * Fix shasum * rebuild openms against new compilers (#13458) * [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). * Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants) (#13444) * Update pinnings for bedtools (97 dependants) and bowtie2 (56 dependants) * Update meta.yaml * fix checksum why oh why does this change ... * Try to speed up debugging of bowtie2 with new compilers * Update build.sh * add nucleosome prediction tool (#13455) * [ ] 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/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). what a hack ... * Remove old bowtie2 versions from the blacklist (#13462) * update pinning for bwa and paml (#13463) * samtools: Do not specify openssl version (#13464) This does not solve our problem in all cases, and it may hinder bioconda-wide changes to the openssl version. See https://github.com/bioconda/bioconda-recipes/pull/13448 * pb-assembly: Do not specify openssl version (#13464) (#13466) This does not solve our problem in all cases, and it may hinder bioconda-wide changes to the openssl version. See https://github.com/bioconda/bioconda-recipes/pull/13448 * Update pinnings for clustalw, hmmer and pybedtools (#13467) * Update pinnings for clustalw, hmmer, pybedtools and t_coffee * Update recipes * hashy hash * t_coffee needs quite a bit of TLC, skip until later * Feb 2019 Release (#13474) * Feb 2019 Release (#13476) * Feb 2019 Release (#13477) * Feb 2019 Release (#13478) * Feb 2019 Release (#13479) * Add socru (#13482) * Add socru * Pinning updates for bamtools and seqtk. Update blacklist to… (#13483) * Pinning updates for bamtools, bowtie1, and seqtk. Update blacklist to exclude presumably unused versions of said tools in the future * bowtie * add tbb-devel * bowtie1 has code issues, I'm not going to bother * delly v0.8.1 (#13491) * Feb 2019 Release (#13481) * Feb 2019 Release * Feb 2019 Release * revert libweb dep (#13497) * [ ] 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/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update xpclr (#13500) * require python 3.6 * Update xpclr to version 1.1.1 * Add recipe for SpydrPick (#13468) * Add recipe for SpydrPick * Add cmake dependency * Use git_url to clone recursively * Recursively clone apegrunt submodule * Correct git submodule command * Get apegrunt through git clone * Add TBB_ROOT to cmake command * Try TBB_ROOT as env variable instead * Add patch for cmake policy * Add tbb-devel * Correct apegrunt checkout * Install boost accumulators * Add boost functional * Add pthreads * Link libgcc statically * Add patch to add librt to linker line * Fix install command * Fix test commands (help gives exit 0) * Specific version of boost; add FindTBB.cmake to recipe * Don't checkout whole boost git history * Update pinning for bbmap, cutadapt, and htseq (#13492) * Update pinning for bbmap, cutadapt, and htseq * noarch: python * tweak recipes, not sure what's wrong with bbmap * Try to debug bbmap * OK, try two additional bbmap tests * exclude grepping for the version * Another two tests * Add another grep, uncomment the last non-version check * grep Version works if I recreate things locally, I suspect this is some weird dockerized environment grep thing * Fix bbmap * bump rapmap to v0.6.0 (#13495) * bump rapmap to v0.6.0 * Update meta.yaml * Update meta.yaml * Update build.sh * Delete conda_build_config.yaml Should be using the new compilers by default. * increase version number (#13480) * increase version number * Update meta.yaml * Feb 2019 Release (#13502) * [coprarna] remove build env (#13501) * remove build env; noarch=generic * noarch python * r-base 3.4.1 * undo noarch * Feb 2019 Release (#13504) * Feb 2019 Release (#13506) * Build samtools 0.1.19 and update pinnings (#13505) * Update build-fail-blacklist (#13503) * Update build-fail-blacklist * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * use libitk * PICRUSt2 install fix (#13173) * Added post-link and pre-unlink scripts to correctly install database and accessory scripts * Update meta.yaml to tag specific versions of requirements * Bump to PICRUSt v2.1.0-b * update stream_atac to 0.2.0 (#13469) * update stream_atac to 0.2.0 * Added fastq_utils recipe (#13473) * Added fastq_utils recipe * Remove noarch * Attempt to fix curses error for Samtools following that recipe's example * Attempt to resolve samtools compile issue * Simplification and use of bam.h from Conda Samtools package * Probably futile attempt at fix * Try adding a conda build file * Tidy up spacing * Small futile tweaks * Does this work to use newer GCC? * Reinstate buld config, bump build * Add compiler to host * Revert "Add compiler to host" This reverts commit 5c01e55113237fc871eced987f7ca04ceadc88ce. * Replace gcc call with x86_64-apple-darwin13.4.0-clang * sed the correct Makefile, use Make variable syntax * Attempted fix for cannot find -lz * Hopefully LDFLAGS is what's needed * Okay, source package doesn't use LDFLAGS, use CFLAGS to pass options * Try with older GCC * Oh my god it works - tidy up * Bumped runtime samtools to 1.9, removed legacy compiler requirement * Update sistr (#13441) * Fixed version of blast * Remove sistr_cmd from build blacklist * Updated sistr file * Changed blast version definition * rebuild stream_atac 0.2.0 (#13509) * update stream_atac to 0.2.0 * update stream_atac to 0.2.0 * update stream_atac to 0.2.0 * rebuild stream_atac 0.2.0 * update stream to 0.3.4 (#13510) * update stream to 0.3.4 * HiCExplorer: Add a dependency, add test cases, increase build number to 1 (#13424) * Add dependency, add test cases, increase build number to 1 * rebuild some dependencies * reset * bump * bl hicexplorer for the moment * Feb 2019 Release (#13512) * update hicexplorer (#13511) * remove build.sh * rebuild pygenometracks and hicexplorer * skip py37 as long as itk is not rebuild * make it noarch * Feb 2019 Release No Ambertools (#13513) * Delete post-link.sh (#13517) * Maybe this should depend on openssl explicitly (#13518) Maybe the whole problem was that it was being built against system openssl. I do not see where openssl-1.1.1 is being specified in Bioconda. In theory, we should be using 1.0.2 everywhere already. https://github.com/conda-forge/conda-forge.github.io/issues/701 * Update: smoove 0.2.3; fix recipe, remove from blacklist (#13515) Fixes bcbio/bcbio-nextgen#2666 * Feb 2019 Release Ambertools in post-link.sh script (#13519) * Update Picard to 2.18.25. (#13196) * Update Picard to 2.18.25. * Remove Picard subdirectories for older versions. The packages for these versions remain available; remove the subdirectories since they keep getting rebuild on version bumps and some of them fail to build. * Update Picard to 2.18.26. (#13521) * bumping LAST to 963 (#13524) * bumping to 963 * adding zlib to dependencies * trying adding C and LDFLAGS * passing flags directly to make * trying other things with make install flags * Do I need g++, then? * Feb 2019 Release, biopython==1.72, renaming cpptraj to biobb_cpptraj (#13522) * sumaclust breaks nightly builds (#13516) * ok, lets see what going on here and on the nightly builds * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * add to host as well * CC * Move to newer package with fixes and additions (#13526) * Tracy (#13529) * tracy v0.5.1 * Atlas (#13514) * add metagenome-atlas for linux * rapid v0.8 (#13520) * rapid v0.8 * Update section name to host, upon bgruening s suggestion * Removing all pinnings * Remove r-workflowscriptscommon from blacklist (#13535) * Updated Artemis recipe to version v18.0.2 (#13537) * [viennarna] pkgconfig data enabled (#13536) * [viennarna] pkgconfig data enabled * [viennarna] bump build * Atlas (#13532) * correct entry point * pymzml only for python3 (#13543) * [ ] 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/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update: smoove; remove tabix requirement, in htslib (#13544) * Pinning bedtools version (#13545) The output fields of the 'bedtools coverage' command, in combination with the parameters I've employed, has changed. That's affecting some downstream analysis. So, I preferred to pin this version for the moment. * Fix nightly (#13546) * Fix megagta and pymzml * fix dinopy * blacklist megagta, I don't know what's wrong with it and don't really care to find out * Fix ddrage meta.yaml * Fix gdsctools and standardize the blacklist * All meta.yaml should have a build number * Blacklist gdsctools, I'm not going to add tests when I don't know the tool * one more old package to blacklist * Update PlantCV to v3.1.0 (#13549) * Fix piret (#13551) * Fix piret * bump piret * [socru] Bump 1.0.0 (#13552) * Bump 1.0.0 * Adding minnow (dscRNA-seq read level simulator) (#13550) * change include path * * added the build files for minnow * resolved the errors for zlib * Adding the md5 sum * Added the build number * MAC OS patch added * removed redundent packages * removing flags * removing flags * md5 sum changed * md5 sum changed * Update gtdbtk version (#13554) * AMPtk v1.3.0 release (#13553) * amptk v1.3.0 update * detab post link msg * spaces in post-link.sh * clean up the blacklist a bit * Fix minnow (#13555) * Fix build number in minnow * md5sum * this is probably the correct commit * Update pinning for freebayes, salmon, sambamba and subread. Update STAR. (#13508) * Update pinning for freebayes, salmon, sambamba and subread. Update STAR. * freebayes is a total mess, I'm not spending all day patching it. * add cooler 0.7.6, since some things are pinned to it. * Fix cooler URL * Fix cooler 0.7.6 imports * Sambamba compilers * Update build.sh * add -headerpad_max_install_names * try ldc 1.12.* * Update meta.yaml * HiCMatrix update to version 7 (#13557) * Abeona: Bump nextflow version (#13561) * pourRNA recipe (#13490) * build script * Create meta.yaml * lowercase name * add about:summary * rebuild viennarna * test libstdcxx-ng * Revert "rebuild viennarna" This reverts commit a1076c082e4ec893ca3ab8e85d7ec0caba7625e7. * libstc++ with c++11 support * + old lib * test * test2 * build 0 * without automake * without autoreconf * url update * test * key * with prefix * v1.0.1 * + prefix * GPLv2 * add `make check` Thanks for the hint @eggzilla * pin to viennarna < 3 * summary extended * connecting to a release (1.2) (#13563) * change include path * * added the build files for minnow * resolved the errors for zlib * Adding the md5 sum * Added the build number * MAC OS patch added * removed redundent packages * removing flags * removing flags * md5 sum changed * md5 sum changed * fix merge error * HiCExplorer 2.1.1 update (#13564) * hicap recipe (#13539) * hicap recipe * optimize the recipe a little bit * Delete build.sh * trigger * update stream to 0.3.5 (#13568) * update stream to 0.3.5 * update stream_atac to 0.3.0 (#13569) * update stream_atac to 0.3.0 * bump vienna_rna (#13465) * bump vienna_rna * remove old versions * add run_exports * rebuild viennarna (#13570) * rebuild viennarna * Update meta.yaml * Add Perl module Text::Levenshtein (#13571) * Add Text::Levenshtein from CPAN * Remove dependency on Unicode::Collate * Update meta.yaml * Dammet (#13499) * added dammet * fixed installation issues * updated dammet cmake and added dependencies * test * Using htslib from conda * typo in makefile.bioconda * updated sha256 * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * added nlopt * added a test to nlopt * rm nlopt as already installed on conda-forge * typo * Update meta.yaml * stacks: adds version 2.3b (#13538) * stacks: adds version 2.3b see https://groups.google.com/d/msg/stacks-users/QYW8Pd15FI8/eALNz1gqEgAJ * Delete conda_build_config.yaml * cnv_facets v0.13.0 (#13572) * Upload v0.13.0 * Fix version in URL * Remove junk from git * [intarna] switch to boost-cpp + docu extended (#13559) * [intarna] switch to boost-cpp + docu extended * patch to disable VRNA pkgconfig check * apply patch to disable VRNA version check * Final linebreak in patch * Disabling explicit pathes * Undo last change * Viennarna 2.4.9 * Update build.sh * cxx compiler * Delete IntaRNA.configure.noRnaVersionCheck.patch * build with 2 cores * cleanup * Update: arvados-cwl-runner, arvados-python-client; py3k (#13576) * Update: arvados-cwl-runner, arvados-python-client; py3k * Do not build on python 3.7; ciso8601 blocking * Try noarch to fix missing 2.7 package builds * Try skipping python 3.7 with selectors * Remove other noarch * Try python 3.7 binning and not skipping osx * Add noarch recommendation from lint * Try adding noarch back to arvados-python-client * update stream_atac to 0.3.1 (#13581) * update stream_atac to 0.3.1 * Adding new to the PR template (#13579) * Initial commit for package tango (#13567) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * updating cromwell to 0.37 (#13582) * Update mz2sqlite (#13595) * Update meta.yaml * Update mz_to_sqlite.py * Fmlrc update (#13612) * updating version, sha256, and commands * redirecting to null * Added tximport-scripts recipe (#13585) * Added tximport-scripts recipe * Added dropletutils as dependency * Remove stupid typo * Add requested fixes * Remove runtime R pinning * Add bioverbs recipe (#13592) * Add bioverbs recipe * Bump source package version * Remove R pinning * Renamed dir to reflect r- prefix * Add recipe for HLA*LA (#13573) * Initial test commit HLA-LA * . * . * . * Initial commit * Add Text::Levenshtein from CPAN * Remove dependency on Unicode::Collate * . * Add HLA*LA * Try reduced dependencies * Remove jsoncpp dependency * Full boost required. * Update meta.yaml * Skip OSX builds Dependency Bio::DB::HTS not available for OSX. * Cleaned up file * Cleaned up file * Use pushd/popd * R goalie (#13596) * Add r-goalie recipe * Remove lines that deal with 3.4.1 issues * Update goalie source * [WIP] Add makefile patch, bump BWA. (#13594) * Add makefile patch * Try bigger patch * Rebuild BWA 0.7.3a for GCC7 (#13617) * Add makefile patch for BWA 0.7.3a * Fix patch * Try one more time to get working patch * Add dummy commit * R transformer (#13614) * Added r-transformer recipe * Version dependencies * Remove duplicated dependency * Adding npInv (#13608) * changed all peptide-shaker to npinv, wonder if this works :) * bump to v1.24, should now enable --help with return * Update svim to 0.4.4 (#13599) * Update GraphAligner to v1.0.3 (#13590) * Update GraphAligner to v1.0.3 * Update: bcbio-variation-recall 0.2.3 with wrapper fix chapmanb/bcbio.variation.recall#22 (#13605) * Update: arvados-cwl-runner, arvados-python-client; second py3k attempt (#13591) Original noarch approach didn't work properly on py3k due to subprocess32 conditional selector. It doesn't get applied on noarch so will be a dependency and make it incompatible with py3. Trying a new approach to restrict to avoid py37 errors. * I haven't updated stuff from the WGBS pipeline yet, but this takes ca… (#13584) * I haven't updated stuff from the WGBS pipeline yet, but this takes care of the rest of snakePipes * Try compiling fatotwobit on OSX. If that works, the other UCSC tools can be compiled there as well. * build remaining packages on OSX too * omero: install bin/omero as well (#13618) * omero: install bin/omero as well see: https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=8678 * omero: Bump build number * Remove setup.py after use * Update trumicount to 0.9.13 (#13603) * trying to fix the openjdk java version (#13622) * Slamdunk (#13580) * Build number updated. sha256 updated. * R version set to 3.2.2 * Slamdunk build number set to 2. * Trying out different R versions. * Installing tidyverse dependency for ggplot2. * Version 0.3.3 * Slamdunk v0.3.4 * use jinja vars * Update meta.yaml * Add msp2db (#13627) * Add msp2db * Added r-brio (#13620) * R syntactic (#13619) * Add r-syntactic recipe * Version dependencies * Feb 2019 Release (#13631) * Update SpydrPick to v1.1.0 (#13630) * Move to ucsc-cell-browser 0.4.38 (#13593) * Move cellbrowser to 0.4.36, removing R dependency * Move to 0.4.38 using pip to avoid eggs. * Use recommendation from Bjoern for install. * ARB - gcc7 rebuild (#13616) * Rebuild GCC7 * Create cxxforward.patch * Workaround broken conda-forge perl package * Workaround missing binaries (gcc, ld, ...) * Fix greadlink missing on macos * Fix typeof undefined * Frogs3.0.0 (#13000) * [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). (Poke @mariabernard @oinizan ) * Isocor recipe (#13601) Add Isocor 2.1.0 * Update r-bcbiobase recipe to pin r-basejump 0.7.2 (#13629) * Pin to basejump v0.7.2 * Also pin run step to basejump v0.7.2 * Move r-seurat-scripts to seurat-scripts and bump version. (#13634) Move r-seurat-scripts to seurat-scripts and bump version to 0.0.5 * Updated Basejump with newly packaged dependencies (#13632) * [socru] Bump 1.0.1 (#13640) Update 1.0.1 * Update fpa to 0.4 (#13644) * snakemake 5.4.1 (#13647) * Fix ARB run_exports (#13637) * Update pinnings for deeptoolsintervals (#13648) * Updating staramr (#13650) * update stream to 0.3.6 (#13649) * update stream to 0.3.5 * update stream to 0.3.5 * update stream to 0.3.5 * update stream_atac to 0.3.0 * update stream_atac to 0.3.1 * update stream to 0.3.6 * rebuild stream 0.3.6 * Add draft wg-blimp-v0.9.0 (#13638) * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [x] This PR adds a new recipe. * [x] 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/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). This is a first test version, things will likely change until final PR. * update mykrobe to v0.6.1 (#13566) * [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [x] 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). As this is my first recipe (technically an update, but I effectively had to write from scratch as the program has changed quite a lot) it would be great to have a review from the core team. * Rapid08 (#13652) * v0.8 update - added r-viridis package * r-viridis fix version * 0.8 viridis, plots CB friendly update * rapidv0.8_build_1 * Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230 * PacBio: Update `ccs` to version 3.4.0 (#13651) * Bump sniffles (#13654) * Update wg-blimp to v0.9.1 (#13653) Update wg-blimp to v0.9.1 (#13653) * Rebuild infernal (#13655) * Rebuild infernal * Rebuild infernal * rebuild hla*la (#13656) :information_source: Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578). ---------------- * [ ] 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/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Adding recipe for digestiflow-cli v0.4.1 (#13642) * Update to Gromacs 2019 (#13523) * Update to Gromacs 2019 and 2018.5 http://manual.gromacs.org/documentation/2019/download.html * maxbin-2.2.6 (#13659) * Update for Gromacs 2019.1 (#13660) * Bump umis to v1.0.2. (#13664) * Snakemake 5.4.2 (#13662) * snakemake 5.4.1 * snakemake 5.4.2 * JBrowse 1.16.2 (#13657) * update to 1.16.2 * patch is not needed anymore * Tango (#13658) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * Bumped tango to version 0.3.0 * pb-assembly: Try openssl<1.1 (#13574) * Add compare-reads (#13635) * Add compare-reads * Add python run reqs Should be brought in by pysm, but I see this in the build logs: ``` WARNING (compare-reads,lib/python2.7/site-packages/compare_reads/_compare_reads.so): Needed DSO lib/libpython2.7.so.1.0 found in ['python'] WARNING (compare-reads,lib/python2.7/site-packages/compare_reads/_compare_reads.so): .. but ['python'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely) ``` * Update kipoi_veff to 0.2.2 (#13350) * shapeshifter recipe added (#13487) * added shapeshifter recipe * adding shapeshifter package, passed circleci tests * updating changes as requested in the review * fixed typo, items requested in review should be fixed * passed circleci locally, changes made as requested * Update sina to 1.5.0 (#13547) * Update sina to 1.5.0 * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * remove std=c++14 - won't work w/ boost * Dump test logs on failure * Add bc to host env * Rapid08 (#13666) * v0.8 update - added r-viridis package * r-viridis fix version * 0.8 viridis, plots CB friendly update * rapidv0.8_build_1 * Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230 * Creating v1.0 * Add new recipe for ataqv (#13665) * Bump umis to v1.0.3 with python3 support. (#13668) * Add recipe for fusioncatcher-seqtk (#13669) * moFF : Enforced python v3.4 or later as pymzml requires it. (#13541) * Enforced python v3.4 or later as pymzml requires it. * Increased build number * Update meta.yaml * Update meta.yaml * Update meta.yaml * Fixed reference to pymzml >=2.0.6 * Update meta.yaml * Update meta.yaml * add extra section * Avoiding dependency problem with Python 3.7 * WhatsHap 0.18 (#13670) * add python to run requirements (#13673) * fix mykrobe python package dependencies (#13672) * update mykrobe to v0.6.1 remove source fn add wget to build requirements add zlib to build requirements move zlib to host requirements specify zlib location specify zlib location move zlib to build requirements add c compiler add some more zlib related flags add some more zlib related flags add htslib to reqs add setuptools to reqs remove htslib to reqs try pip install instead try skipping py2 skip py27 and add imports test see if py27 works now remove py27 build create test script create test script add tests dir to test reqs add data dir to test reqs * Update meta.yaml * add wget to host * clean up build script. add test source files * add post-link script for downloading panel data * add prefix location specifier for mykrobe data dir * fix post-link script * switch to shasum for data download check. add wget to run reqs * use pip install * Delete build.sh * not sure why this has not failed before * Update meta.yaml * fix mccortex install * use default compiler for cxx * compile with -fPIC * remove hard-coded gcc in htslib Makefile. remove unncessary reqs * add python package reqs to run reqs and test * Tango (#13671) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * Bumped tango to version 0.3.0 * Update tango to version 0.3.1 * Updated shasum * Update meta.yaml * Update meta.yaml (#13674) :information_source: Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578). ---------------- * [ ] 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/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update scanpy (#13675) * Update meta.yaml * Delete build.sh * make noarch * Add recipe for fusioncatcher (#13676) * Add recipe for fusioncatcher * convert to noarch package (#13677) * convert to noarch package * Update meta.yaml * Update meta.yaml * add license file * VEP: bump subversion (#13681) * VEP: bump subversion * build -> host * Scanpy scripts pandas fix (#13678) * Prevent problematic pandas 0.24 * Bump build number * Bump anvio to 5.3.0 (#13682) * bump anvio * Fix file * Bump deepTools to 3.2.0 (#13683) * Bump deepTools to 3.2.0 * deepTools is now noarch: python * Update: simple_sv_annotation, up/down fixes + py3k (#13685) * update bioconda-utils to 0.15.8 (#13688) * digestiflow-cli v0.5.0 (#13689) * Fusioncatcher db file rename (#13690) * Rename download db file * Medaka (#13687) * First go at medaka * Building on linux, osx dying on docker * Add license_file to medaka/meta.yaml * Bump/scnic (#13691) * Update scnic to 0.6.0 * Add 0.6.0 new dependencies * Get rid of parallel dependency * Bump SCNIC version to 0.6.1 * Add igor_vdj (#13684) * Add igor_vdj * Odd, I didn't need automake locally * Not packaging the python module at this time. * Add autoconf * Use a standard jemalloc * Try not running configure in igor_src * What if we rerun autogen.sh * blah * blah * foo * sigh * Remove old build stuff, it was just a timestamp problem * Don't set -lrt on OSX * Update meta.yaml * pysradb: update to 0.7.1 (#13694) * pysradb: update to 0.7.1 * Now taking Genepop from a reproducible source (#13693) This uses a reproducible source for genepop (CRAN). ---------------- * [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). * tracy v0.5.2 (#13700) * Bump build (#13701) Trigger the build again for `bioconductor-flowtype`. * r-momr (#13703) * Mob suite 1.4.9.1 (#13697) * Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies * updated recipe to download from URL instead of github * build python version requirement defined (python >=3.4) * added build number * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added test statement (import) * added test statement (import) * added the new repository and py36 only compile * made requested corrections by daler. Corrected build number and package string * Small fixes * revert deleted row * New version, fixed sum bugs and improved stability * Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters * Updated to version 1.4.9 * Updated to version 1.4.9 * 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 * new db host * updated meta.yaml with resolved conficts from the head branch * build not more than python 3.6 * add a recipe for FastqPuri (#13679) * add a recipe for FastqPuri Changes to be committed: new file: recipes/fastqpuri/build.sh new file: recipes/fastqpuri/meta.yaml * fix issues in fastqpuri recipe Changes to be committed: modified: build.sh modified: meta.yaml * add neatfeatures track types + patch combotrackselector (xref https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/pull/5) (#13704) * Add new recipe for finestructure (#13707) * Version bump msstitch to 2.12 (#13705) * Bump CLARK (#13709) * Update fastp to 0.19.7. (#13714) * Update STAR to 2.7.0d, add 2.6.1d, as it doesn't require rebuilding the index (#13717) * update SURVIVOR to v1.0.6 (#13718) * Update cooler to v0.8.3 (#13712) * Update cooler to v0.8.3 * Update meta.yaml * Update UCSC templates to build under OSX * Update all UCSC recipes. * try fixing ucsc-overlapselect * Bump a bunch of packages for pinnings (#13960) * Upgrade cyvcf2 to v0.10.8 (#13726) Patch setup.py to use conda managed htslib * Update bcftools plot_vcfstats (#13721) * Python-tripal 3.2 and python-apollo (#13727) * update python-tripal * add python-apollo recipe * noarch * v0.1.4 February 2019 Release (#13720) * python3 and igv-reports (#13623) * python3 and igv-reports * changing test * adding ls * adding bin ls * print install path contents * run on python3 * proper test * Update meta.yaml (#13729) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * It looks like rJava has now been rebuilt. (#13728) * It looks like rJava has now been rebuilt. * r-rcdk is in conda-forge now * Remove the first batch from the blacklist * Update esATAC * Update CPAT to 1.2.4 (#13732) * Re-do an update undone by 3761102478f21107957c166e85ca843f9c3410b1 (#13733) * Gff3sort (#13731) * add gff3sort recipe * add new dep to sort gff3 files properly * lint * add perl-data-match (for Sort::Topological) * add dep * oh perl, I hate you so much * ...so much.... * take this perl-data-match * wrong path * rebuild with perl 5.26.2 for mac * Update PopPUNK to v1.1.4 (#13723) * Update PopPUNK to v1.1.4 * Add noarch Seems to be a py36 to py37 problem * Cannot have noarch as no python2 support * bump build numbers on dependencies needing rebuild * Update sharedmem recipe * Putting sharedmem build into meta.yaml * Correcting host/build in sharedmem meta for noarch * Make noarch and python>=3 * Remove redundancy in sharedmem meta.yaml * Update comet-ms to 2018014 (#13645) * Remove more rJava packages from the blacklist (#13734) * Remove more rJava packages from the blacklist * update * Sc3 scripts update (#13735) * Bump bioconductor-sc3-scripts package to 0.0.3 * Reset build counter * Add pychopper (#13738) * Add pychopper * build command * pb-falcon: 0.2.6 (#13740) * pbfalcon-0.2.6 * pb-falcon: Try openssl<1.1 * pb-assembly: update pb-falcon/openssl (#13575) * Remove the remainder of the rJava bioc packages from the blacklist (#13737) * Remove the remainder of the rJava bioc packages from the blacklist * Update * blacklist msgfgui * Add slivar 0.0.5. (#13741) * Add slivar 0.0.5. * Fix test. * Increment build number (#13743) * Update sevenbridges-python to 0.18.2 (#13746) * Bump to latest scanpy-scripts (#13747) * r-ldrtools (#13749) * Try to remove a few bioconductor packages from the blacklist (#13744) * Try to remove a few bioconductor packages from the blacklist * More updates * Yacrd add version 0.5.1 break compatibility with previous version (#13750) * Add version 0.5.0 break compatibility * up to version 0.5.1 * yacrd 0.5.1 correct error in sha256sum * r-mixkernel (#13745) * r-mixkernel * Spydrpick v1.1.1 (#13725) * Update SpydrPick to v1.1.0 * Update spydrpick v1.1.1; aprgrunt 0f34bdd80315e10b2234b5aae50b53102f04fbdd * Use SSE3 rather than AVX2 * With AVX guard around popcnt * PacBio: Update `ccs` to version 3.4.1 (#13755) * Remove a few more packages from the blacklist (#13753) * Remove a few more packages from the blacklist * a few updates * r-parallel is part of r-base * odd * Ready for OSX * needs gfortran it seems * Update PureCLIP to v1.3.0 (#13756) * updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers (#13757) updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers * try again (#13758) * Barcode splitter multi (#13663) * New directory for the barcode splitter recipe. * created using `conda skeleton pypi barcode_splitter_multi`. * created using `conda skeleton pypi barcode_splitter_multi`. * Added source files and tox. Files checked in: recipes/barcode_splitter_multi/meta.yaml * Re-wrote meta.yaml. The existing file was mostly wrong. Files checked in: recipes/barcode_splitter/meta.yaml * Change dirname. * Working out tests. Files checked in: * Addresses issues with conda build. Created a run_test.sh script to work around an issue with the exit code for --help and --version being 2 instead of 0. Added noarch: python to meta.yaml. Added "--single-version-externally-managed --record=record.txt" to the setup.py call in build.sh. Files checked in: recipes/barcode_splitter/build.sh recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Updated sandbox zenodo doi to real zenodo doi now that testing is done. Files checked in: recipes/barcode_splitter/meta.yaml * Removing pass of shell variable to echo. This is an attempt to address a warning from the remote circleci build that passing a variable as an argument generated from the output of the tool is a security risk. It might still complain due to the if conditional checking the variable too. I'll just have to see. Files checked in: recipes/barcode_splitter/run_test.sh * Removed eval of shell variable in if conditional. I suspect that this eval is still related to the security warning and subsequent failure of the test in the remote circleci build. Files checked in: recipes/barcode_splitter/run_test.sh * Updated to a release of barcode_splitter that exits with a status of 0 for --version. I could not get run_test.sh to pass mulled-build tests, so instead of work through that, I just worked around it by releasing the new version with the exit code fix. Files checked in: recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Reverted unintended changes. Files checked in: miniconda.sh .circleci/common.sh * Reverted another unintended change. Didn't realize the file was created instead of changed. Files checked in: .circleci/common.sh * Update meta.yaml * Delete build.sh * CPAT: Stricter python version requirement (#13742) * Stricter python version requirement In CPAT's code the version check for a python version that starts with 2.7 is hardcoded. * Correct license version It is incorrectly reported on PYPI. In the documentation of CPAT and in the project's license file it is mentioned that any later version of GPL is also allowed. * rdkit: remove blacklisted package - now at conda forge (#13759) * platypus update (#13494) * platypus update * added back buildPlatypus.sh * added new path to source * reset build number to 0 * this one needs a compiler isn't it? * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall (#13754) * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall - arvados: fix py3k support by avoiding subprocess32 on py3k - bcbio-variation-recall: fix platypus contig header generation. Fixes bcbio/bcbio-nextgen#2688 * Avoid py37 selectors, trying to fix py27 build * Try to avoid py37 errors with noarch * Fix python selectors * Avoid noarch linter errors, not sure why triggered * Avoid noarch linter errors, not sure why triggered * Pin arvados-python-client with py37 subprocess fix * Wasabi 1.0.0 (#13760) * UCSC blacklist (#13763) * 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 * Bioc quick test (#12547) * Update kallisto to 0.45.0 (#12117) * Update validators to 0.12.3 (#12116) * Update illumina-interop to 1.1.7 (#12115) * Update umi_tools to 0.5.5 (#12123) * Update tiptoft to 1.0.0 (#12122) * Update: TitanCNA with fix for hg38 plotting (#12130) * 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 * Update chewbbaca to 2.0.16 (#12132) * Update abeona to 0.40.0 (#12131) * ping to eden 1.1 (#12134) * clean swap file (#12137) * Update corset to 1.07 (#12143) * Update peddy to 0.4.3 (#12144) * blockclust latest source and added cloudpickle as requirement (#12142) * Update nanomath to 0.22.0 (#12149) * Update pymvpa to 2.6.5 (#12152) * Updated to version 1.4.0 (#12138) * Updated to version 1.4.0 * Resetting build number to 0 and build->host * Update transdecoder to 5.5.0 (#12172) * Update gridss to 2.0.1 (#12190) * Update tracer to 1.7.1 (#12189) * Update flowcraft to 1.4.0 (#12179) * Update seqbuster to 3.2 (#12182) * Update perl-io-compress to 2.081 (#12201) * Update twobitreader to 3.1.6 (#12205) * Update twobitreader to 3.1.6 * Update meta.yaml * Update gtfparse to 1.2.0 (#12186) * Update gtfparse to 1.2.0 * remove compiler * Update htseq to 0.11.0 (#12177) * Update htseq to 0.11.0 * add compiler * Update htseq to 0.11.0 (#12239) [testing co-author] * Update htseq to 0.11.0 * add compiler Co-authored-by: Bjoern Gruening * alfred v0.1.16 (#12240) * alfred v0.1.16 * makefile patch * makefile patch * Update scrm to 1.7.3 (#12150) * Update scrm to 1.7.3 * Update scrm to 1.7.3 * 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. * 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 * 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 * PacBio: Update `pbmm2` to version 0.11.0 (#12246) * 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: * PacBio: Update `isoseq3` to version 3.1.0 (#12263) * add python to host section (#12264) * Update confindr to 0.4.7 (#12266) * 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 * 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 * Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273) * Make snakemake a noarch package. (#12274) * noarch: python in combination with version constraint * Cleanup deps and simplify version definition. * 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 * Create r-airr recipe (#12284) * Create r-airr recipe using bgruening/conda_r_skeleton_helper * Update meta.yaml * Findbin::Real added (#12291) * Added version bump to 1.3 (#12292) * ngs-bits 2018_11 (#12262) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2018_11 * 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 * Fred2 update (#12259) * Update FRED2 Recipe * msstitch version 2.9 (#12296) * r-mvr (#12300) This is a non-parametric method for joint adaptive mean-variance regularization and variance sta- bilization of high-dimensional data. * 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 * 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 * Gromacs 2018.4 (#12302) * quast 5.0.2 (#12303) * Update meta.yaml (#12275) * Update meta.yaml r-rsqlite version dependency added * Update meta.yaml Updated build number to 1 * Use the extended-base container because of wget issues when downloading databases (#12297) * Update duphold to 0.1.0 (#12257) * Update flashlfq to 0.1.109 (#12256) * Update planemo to 0.57.0 (#12251) * Update meta.yaml (#12258) * Update scalpel to 0.5.4 (#12249) * Update scalpel to 0.5.4 * Fix url * 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 * added feather to deps (#12293) * 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 * update scprep to v0.8.1 (#12306) * 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 * gffcompare: version bump (#12308) * 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 * 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 * upgrade to version 2.8.1 (#12316) * Create Airr recipe (#12318) * Create AIRR recipe using conda skeleton pypi. * Add noarch python * Clean host requirements * Added nimnexus [v0.1] (#12133) * added nimnexus * Fix sha * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * [WIP] Add R-loom (#12320) * initial WIP skeleton * Update meta.yaml * Update meta.yaml * Update meta.yaml * try osx * 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 * r-corbi (#12325) * r-nam (#12327) * Update pybedtools to 0.8.0 (#12324) * Update pybedtools to 0.8.0 * rm cython requirement * MSGFplus does not work with newer Java (#12330) * Trying to not use a very new java version since the latest ver… * Fix mosdepth and macs2. Blacklist bowtie1. * Update blacklist, work more on MACS2 * blacklist more failing packages * Update pinnings on all packages * queue up the next one * Updates * more updates * updates * A few fixes * More bioc updates for the new pinnings * update scPipe * Update blacklist, some bioc packages and remove unneeded conda_build_config.yaml files * A few more updates * last updates for the night * Update the BRAIN * Various R package updates * More updates * a couple more * A few updates * more updates * nearing complete * blacklist treekin/0.4.2 and try fixing zeroc-ice * Bioconductor 3.9 packages and some of their systemrequirements, which we'll work to automate for the next release. * Someone merged .circleci/common.sh into master a while back. It gets overwritten everytime locally * update .gitignore * manually add systemrequirements * Go ahead and blacklist on R 3.6 package * blacklist 2pg_cartesian * blacklist weblogo * blacklist trimmomatic * blacklist tophat * more * more blacklisting * more * meme * mafft * how is samtools breaking things? * wrong samtools versions * refine blacklist * kat * gromacs * braker * bowtie2 * update blacklist * start fixing experiment files * Fix experiment packages, update blacklist * a few updates * blackist sqt * Updates * update some recipes * blacklist art/3.11.14 * update blacklist * fix a recipe, update the blacklist * More updates * Updates * updates * update blacklist * blacklist discovar * blacklist transabyss * update blacklist * fix data package version pinnings, update blacklist * Update blacklist * blacklist * Wrote a program to find all of the stuff that's likely to break the build and blacklisted them all * update blacklist * update blacklist, start debugging fci * Update blacklist * update blacklist * Next to check for a build number * Wrote a program to check for more recipes that can't render. It's still running. * update blacklist * update r-rgi packages and blacklist * update blacklist * nearing the end * update blacklist, hopefully things build through now * Fix * update blacklist * Start fixing malformed recipes * fix more recipes * update more recipes * the remaining recipes breaking things * better group things in the blacklist * Update bioconductor recipes, remove from blacklist * fix colombo * Update a few packages * Blacklist a few bioc recipes for now * blacklist some recipes * temp blacklist updates * various updates * update blacklist * update blacklist * updates for bioc build * updates * update blacklist fix r-qpcr rendering * small blacklist update * bulk updates * blacklist updates * bl * update bl * bioc updates * bump r-rnexml * update bl * update chetah * Ah, right, solved bioc-graph previously * blacklist some rgl packages * try CoGAPS * small update * bl updates * Update blacklist * Add r-ontologyplot * update blacklist * update r-ic10 * update foldgo * bulk updates * bump r-orqa * bump CRAN packages * fix r-hardyweinberg recipe * fix r-pma * update a few recipes * a few bulk updates * fix bioconductor-mcagui * fix bioconductor-rcade * Update chippeakanno * blacklist bioconductor-cancer * Update blacklist and tfea.chip recipe * Add recipe for vmatch 2.3.0. * update blacklist * more blacklisted recipes * update blacklist * Change license_family to a valid value. * Correct build requirements. * Add biotools identifier. * Reorganize meta.yaml. * Add platform selectors to sha256 section (otherwise it's a duplicate key error). * updates * Skip false positive linting. * update GOTHiC and the blacklist * updates * Correct variable name. * update some recipes and the blacklist * updates * updates * update a coupe last packages * remove ete3, which has been migrated, try the blacklisted bioc packages * some updates * more updates * some updates * updates * more updates * updates * fix HiCMatrix * updates * last bulk update * fix socru recipe * Patch SELECT/makefile to use compiler from (conda) environment instead of hardcoded value. * Create directory for doc before copying files. * Don't test some programs/scripts as they don't have -help option. * Copy blast test files since the build system can't find them (only the files of this recipe are copied). * Miscellaneous edits (comments, typos). * Update meta.yaml * Update meta.yaml * blacklist multiphate, clean it up * tweak vmatch on OSX * further vmatch tweaks * Vmatch build2 (#17262) * Update sourmash to 2.1.0 (#17113) * Update aquila_stlfr to 1.2.9 (#17111) * Update pynnotator to add support for Python2 (#17114) * Update pynnotator to add support for Python2 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update sevenbridges-python to 0.23.1 (#17117) * Update pbmm2 to 1.1.0 (#17072) * Update pbmm2 to 1.1.0 * PacBio: Update `pbmm2` dependencies * Update nanoplot to 1.27.0 (#17118) * Update nanoget to 1.9.0 (#17116) * Update cgpbigwig to 1.0.4 (#16970) * Update cgpbigwig to 1.0.4 * Update cgpbigwig to 1.0.4 * Works on linux * just wondering... * p11-kit is linux only * Update varfish-annotator-cli to 0.10 (#17121) * Update flashlfq to 1.0.0 (#17123) * pb-falconc-0.0.1 (#17077) * pb-falconc-0.0.1 * Try to find missing gcc * Try another way CircleCI does not find "gcc", so I will try a newer way. * We are looking for gcc. Maybe this will help us find it. * Closer ``` 01:16:51 BIOCONDA INFO (OUT) echo "CC=$CC" CC=/opt/conda/conda-bld/pb-falconc_1566695732043/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc CC=$BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc ``` * alias gcc maybe? * Try symlinking gcc * further nim compilation * get nim to build * apparently this needs rsync to copy some directories. * try injecting compilers * should compile on Linux at least * better compiler injection * Update clonalframeml to 1.12 (#17120) * Update clonalframeml to 1.12 * C++, inject compilers * Adding jupyterpngsplugin python package to Bioconda (#17124) * SEPP: Update to version 4.3.10 (#16958) * Update to version 4.3.10 fix issue #70 a bug when hmmsearch fake jobs where not piped * search binaries in $PREFIX instead of relying on conda's preprocessing and replacing of /opt/anaconda1anaconda2anaconda3/ * debugging * debug a bit, this actually passes locally, possibly due to a different conda-build version * Update meta.yaml * more debugging * maybe * no slash? * not in . directories * remove debug test * Update aquila_stlfr to 1.2.10 (#17125) * Update r-bioverbs to 0.2.7 (#17127) * Update r-goalie to 0.3.6 (#17130) * Update r-syntactic to 0.2.4 (#17132) * Update angsd to 0.931 (#14862) * Update angsd to 0.929 * Update angsd to 0.931 * start simplifying * foo * tidy up * Update womtool to 45.1 (#17126) * bump platon mummer dependency version (3->4) (#17119) * Update r-transformer to 0.2.5 (#17135) * Update neurodocker to 0.5.0. (#17137) * clean and build, fail on errors, issue #11509 (#17085) * clean and build, fail on errors, issue #11509 * fix linting * This builds on linux * Update meta.yaml * Adding goenrichment python package (#17131) * Adding goenrichment python package * Update meta.yaml * bump iranges to 2.18.2 (#17138) * bump iranges to 2.18.2 * Update r-transformer * Update r-brio to 0.3.6 (#17134) * Update r-freerange to 0.2.4 (#17133) * Update r-freerange to 0.2.4 * Update meta.yaml * typo * Update r-basejump to 0.11.11 (#17136) * Update r-basejump to 0.11.11 * update dependencies * snakemake: require imagemagick >= 7.0 to avoid PDF -> PNG convert bug (#17062) * Update sevenbridges-python to 0.23.2 (#17139) Package uploads complete: [ci skip] - biocontainers/sevenbridges-python:0.23.2--py_0 - noarch/sevenbridges-python-0.23.2-py_0.tar.bz2 * Smudgeplot (#17140) * First attempt at recipe * Added R package dependencies * Added numpy dependency * Added scipy * Fixed test * Testing suggestions from PR * Final polishing after PR comments - passed local tests * Get the R stuff in the right place to ensure the pinning works * Update gridss to 2.5.2 (#17143) * Remove minepy for conda-forge/staged-recipes#9292 (#17146) * aquila first version (#17129) * first version * modify meta for bioconda install * Update meta.yaml * Update pynnotator to 1.9 (#17145) * Update pynnotator to 1.9 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update plasmidfinder to 2.1 (#17147) Package uploads complete: [ci skip] - biocontainers/plasmidfinder:2.1--0 - noarch/plasmidfinder-2.1-0.tar.bz2 Co-authored-by: Devon Ryan * Include target dir for clean as well to ensure right location is cleane * Include target dir for clean as well to ensure right location is cleaned * bump build number * Update downpore to 0.3.3 (#12573) Package uploads complete: [ci skip] - biocontainers/downpore:0.3.3--h375a9b1_0 - linux-64/downpore-0.3.3-h375a9b1_0.tar.bz2 - osx-64/downpore-0.3.3-h375a9b1_0.tar.bz2 Co-authored-by: Devon Ryan * Update gprofiler-official to 1.0.0 (#12213) Package uploads complete: [ci skip] - biocontainers/gprofiler-official:1.0.0--py_0 - noarch/gprofiler-official-1.0.0-py_0.tar.bz2 Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com> Co-authored-by: Devon Ryan Co-authored-by: Devon Ryan * Update rust-bio-tools to 0.6.0 (#17149) Package uploads complete: [ci skip] - biocontainers/rust-bio-tools:0.6.0--hf53bd2b_0 - linux-64/rust-bio-tools-0.6.0-hf53bd2b_0.tar.bz2 - osx-64/rust-bio-tools-0.6.0-h9904429_0.tar.bz2 * fix and update r-spieceasi (#17148) Package uploads complete: [ci skip] - biocontainers/r-spieceasi:1.0.7--r36_0 - noarch/r-spieceasi-1.0.7-r36_0.tar.bz2 Co-authored-by: Zachary Kurtz * Update control-freec to 11.5 (#12199) Package uploads complete: [ci skip] - biocontainers/control-freec:11.5--he1b5a44_0 - linux-64/control-freec-11.5-he1b5a44_0.tar.bz2 - osx-64/control-freec-11.5-h6de7cb9_0.tar.bz2 Co-authored-by: Devon Ryan * minced 0.4.0 - build with older java (#17150) * Update epic2 to 0.0.40 (#17152) Package uploads complete: [ci skip] - biocontainers/epic2:0.0.40--py27h9276139_0 - biocontainers/epic2:0.0.40--py36h9276139_0 - biocontainers/epic2:0.0.40--py37h9276139_0 - linux-64/epic2-0.0.40-py27h9276139_0.tar.bz2 - linux-64/epic2-0.0.40-py36h9276139_0.tar.bz2 - linux-64/epic2-0.0.40-py37h9276139_0.tar.bz2 * Update scanpy-scripts to 0.2.4.post1 (#17151) Package uploads complete: [ci skip] - biocontainers/scanpy-scripts:0.2.4.post1--py_0 - noarch/scanpy-scripts-0.2.4.post1-py_0.tar.bz2 Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com> * Update howdesbt to 1.00.03 (#16920) Package uploads complete: [ci skip] - biocontainers/howdesbt:1.00.03--hc9558a2_0 - linux-64/howdesbt-1.00.03-hc9558a2_0.tar.bz2 - osx-64/howdesbt-1.00.03-h770b8ee_0.tar.bz2 Co-authored-by: dpryan79 Co-authored-by: Devon Ryan * Update pynnotator to 1.9.1 (#17154) Package uploads complete: [ci skip] - biocontainers/pynnotator:1.9.1--py_0 - noarch/pynnotator-1.9.1-py_0.tar.bz2 * Update paragraph to 2.3 (#16539) Package uploads complete: [ci skip] - biocontainers/paragraph:2.3--h8908b6f_0 - linux-64/paragraph-2.3-h8908b6f_0.tar.bz2 Co-authored-by: dpryan79 Co-authored-by: Devon Ryan * Update hmmratac to 1.2.7 (#17158) Package uploads complete: [ci skip] - biocontainers/hmmratac:1.2.7--0 - noarch/hmmratac-1.2.7-0.tar.bz2 * Update libdeflate to 1.3 (#16839) * Update libdeflate to 1.3 * libdeflate has been migrated to conda-forge * Updated RNAlien to version 1.7.0 (#17153) * Updated RNAlien to version 1.7.0 * Removed echo and merged mv to one line guess the echo is for debugging and moving directly to ${t}-bin gets rid of a mv operation * Updated checksum * Fixed path * Added debug output * Fix for path * creating bin dir * creating bin dir in prefix * Minor Remove ls commands as they are debug only, added -p option to mkdir to prevent fail and only create dir if not existing * Update rnasamba to 0.1.4 (#17164) * Fix cromshell dependency (#17160) Package uploads complete: [ci skip] - biocontainers/cromshell:0.3.10--1 - noarch/cromshell-0.3.10-1.tar.bz2 * Update rnasamba to 0.1.4 (#17168) Package uploads complete: [ci skip] - biocontainers/rnasamba:0.1.4--py_0 - noarch/rnasamba-0.1.4-py_0.tar.bz2 * Update dca to 0.2.3 (#17165) Package uploads complete: [ci skip] - biocontainers/dca:0.2.3--py_0 - noarch/dca-0.2.3-py_0.tar.bz2 * Bump build number. (#17159) Package uploads complete: [ci skip] - biocontainers/pysamstats:1.1.2--py27hed695b0_5 - biocontainers/pysamstats:1.1.2--py36hed695b0_5 - biocontainers/pysamstats:1.1.2--py37hed695b0_5 - linux-64/pysamstats-1.1.2-py27hed695b0_5.tar.bz2 - linux-64/pysamstats-1.1.2-py36hed695b0_5.tar.bz2 - linux-64/pysamstats-1.1.2-py37hed695b0_5.tar.bz2 - osx-64/pysamstats-1.1.2-py27h2573ce8_5.tar.bz2 - osx-64/pysamstats-1.1.2-py36h2573ce8_5.tar.bz2 - osx-64/pysamstats-1.1.2-py37h2573ce8_5.tar.bz2 * Updating homer to version 4.10 and removing it from the blacklist (#17162) Package uploads complete: [ci skip] - biocontainers/homer:4.10--pl526hc9558a2_0 - linux-64/homer-4.10-pl526hc9558a2_0.tar.bz2 - osx-64/homer-4.10-pl526h770b8ee_0.tar.bz2 * Update masurca to 3.3.3 (#15706) Package uploads complete: [ci skip] - biocontainers/masurca:3.3.3--pl526haae6466_0 - linux-64/masurca-3.3.3-pl526haae6466_0.tar.bz2 Co-authored-by: Devon Ryan * Update presto to 0.5.13 (#17167) Package uploads complete: [ci skip] - biocontainers/presto:0.5.13--py_0 - noarch/presto-0.5.13-py_0.tar.bz2 * Update cat to 5.0 (#17163) Package uploads complete: [ci skip] - biocontainers/cat:5.0--0 - noarch/cat-5.0-0.tar.bz2 Co-authored-by: Devon Ryan * Update askocli to 0.5 (#15847) Package uploads complete: [ci skip] - biocontainers/askocli:0.5--py_0 - noarch/askocli-0.5-py_0.tar.bz2 Co-authored-by: Devon Ryan * Recipe for MotifBinner2 version 2.0.0 (#17141) Package uploads complete: [ci skip] - biocontainers/r-motifbinner:2.0.0--r36he1b5a44_0 - linux-64/r-motifbinner-2.0.0-r36he1b5a44_0.tar.bz2 - osx-64/r-motifbinner-2.0.0-r36h6de7cb9_0.tar.bz2 * Update breseq to 0.33.2 (#12188) Package uploads complete: [ci skip] - biocontainers/breseq:0.33.2--h8b12597_0 - linux-64/breseq-0.33.2-h8b12597_0.tar.bz2 - osx-64/breseq-0.33.2-hfbae3c0_0.tar.bz2 Co-authored-by: Devon Ryan * Update spine to 0.3.2 (#12175) Package uploads complete: [ci skip] - biocontainers/spine:0.3.2--pl526_0 - noarch/spine-0.3.2-pl526_0.tar.bz2 Co-authored-by: Devon Ryan Co-authored-by: Devon Ryan * Update cwltest to 1.0.20190228134645 (#15889) Package uploads complete: [ci skip] - biocontainers/cwltest:1.0.20190228134645--py_0 - noarch/cwltest-1.0.20190228134645-py_0.tar.bz2 Co-authored-by: Devon Ryan * Update star to 2.7.2b (#17169) * pbbam: revdep rebuilds (#17161) * Update rename to 1.601 (#17170) Package uploads complete: [ci skip] - biocontainers/rename:1.601--0 - noarch/rename-1.601-0.tar.bz2 Co-authored-by: Devon Ryan * Update minced to 0.4.1 (#17171) Package uploads complete: [ci skip] - biocontainers/minced:0.4.1--0 - noarch/minced-0.4.1-0.tar.bz2 Co-authored-by: dpryan79 * Update netreg to 1.8.0 (#16936) Package uploads complete: [ci skip] - biocontainers/netreg:1.8.0--h9fd3d4c_0 - linux-64/netreg-1.8.0-h9fd3d4c_0.tar.bz2 - osx-64/netreg-1.8.0-hf0ff744_0.tar.bz2 Co-authored-by: dpryan79 * Update tadtool to 0.79 (#17173) Package uploads complete: [ci skip] - biocontainers/tadtool:0.79--py_0 - noarch/tadtool-0.79-py_0.tar.bz2 * pbbam: revdep rebuilds #2 (#17174) Package uploads complete: [ci skip] - biocontainers/bax2bam:0.0.9--h018d624_7 - biocontainers/blasr:5.3.3--h018d624_1 - linux-64/bax2bam-0.0.9-h018d624_7.tar.bz2 - linux-64/blasr-5.3.3-h018d624_1.tar.bz2 - osx-64/bax2bam-0.0.9-h13b73d5_7.tar.bz2 - osx-64/blasr-5.3.3-h13b73d5_1.tar.bz2 * Update r-exomedepth to 1.1.12 (#17175) * Update r-exomedepth to 1.1.12 * Update meta.yaml * Update mutmap to 2.1.0 (#17176) Package uploads complete: [ci skip] - biocontainers/mutmap:2.1.0--py_0 - noarch/mutmap-2.1.0-py_0.tar.bz2 * Update qtlseq to 2.0.3 (#17177) Package uploads complete: [ci skip] - biocontainers/qtlseq:2.0.3--py_0 - noarch/qtlseq-2.0.3-py_0.tar.bz2 * Update pyranges to 0.0.52 (#17178) Package uploads complete: [ci skip] - biocontainers/pyranges:0.0.52--py36h516909a_0 - biocontainers/pyranges:0.0.52--py37h516909a_0 - linux-64/pyranges-0.0.52-py36h516909a_0.tar.bz2 - linux-64/pyranges-0.0.52-py37h516909a_0.tar.bz2 - osx-64/pyranges-0.0.52-py36h01d97ff_0.tar.bz2 - osx-64/pyranges-0.0.52-py37h01d97ff_0.tar.bz2 * simka-1.5.0 (#16670) * simka-1.5.0 * Update mobidic-mpa to 1.1.2 (#17181) Package uploads complete: [ci skip] - biocontainers/mobidic-mpa:1.1.2--py_0 - noarch/mobidic-mpa-1.1.2-py_0.tar.bz2 * Update popdel to 1.1.2 (#17182) Package uploads complete: [ci skip] - biocontainers/popdel:1.1.2--he513fc3_0 - linux-64/popdel-1.1.2-he513fc3_0.tar.bz2 - osx-64/popdel-1.1.2-h2dec4b4_0.tar.bz2 * Create variable (this has been removed in 7624ae9 by mistake). * Set shell options. * Set shebang and shell options. * Use a HEREDOC for ${PREFIX}/.message.txt. * Bump build number. * Remove blank line. * I wonder * guess that didn't work * oops * First dumb run of setting builds to noarch:generic where required * update a* recipes * up through bio* * finished with b* recipes * done through d* * not sure how that got lost * clean recipes more through b* * more updates * fix through e* * initial f* recipes * Finish recipes through f* * vcs not git * update g* recipes * more * Done through i* * done through j* * done through k* * done through l* * some m recipes * done through m* * fixed through n* * foo * done through o* * some p recipes * more p * done through p* * done with q * done through r* * fix through s* * All but the t* recipes * done with t* * remove remaining lint --- recipes/SpliceMap/meta.yaml | 33 ------ recipes/a5-miseq/meta.yaml | 7 +- recipes/abeona/meta.yaml | 4 +- recipes/admixture/meta.yaml | 1 + recipes/advntr/meta.yaml | 1 - recipes/afterqc/meta.yaml | 3 +- recipes/airr/meta.yaml | 1 - recipes/albatradis/meta.yaml | 10 +- recipes/{align-it/1.0.3 => align_it}/build.sh | 0 .../{align-it/1.0.3 => align_it}/meta.yaml | 0 recipes/alignlib-lite/meta.yaml | 1 + recipes/allegro/meta.yaml | 4 + recipes/amused/meta.yaml | 1 + recipes/anndata/meta.yaml | 41 ------- recipes/antismash/meta.yaml | 3 + recipes/anvio/meta.yaml | 1 + recipes/any2fasta/meta.yaml | 1 + recipes/apt-probeset-summarize/meta.yaml | 28 +++-- recipes/arb-bio/meta.yaml | 2 - recipes/arem/build.sh | 2 - recipes/arem/meta.yaml | 10 +- recipes/arvados-cwl-runner/build.sh | 2 +- recipes/asn2gb/meta.yaml | 23 ++-- recipes/asqcan/build.sh | 3 - recipes/asqcan/meta.yaml | 10 +- recipes/assemblerflow/meta.yaml | 16 +-- recipes/assemblyutility/meta.yaml | 2 +- recipes/atactk/meta.yaml | 4 +- recipes/athena_meta/build.sh | 3 - recipes/athena_meta/meta.yaml | 54 ++++----- recipes/autodock-vina/meta.yaml | 13 ++- recipes/axiome/meta.yaml | 11 +- recipes/bamclipper/meta.yaml | 3 +- recipes/barrnap-python/build.sh | 3 - recipes/barrnap-python/meta.yaml | 13 +-- recipes/barrnap/build.sh | 1 + recipes/barrnap/meta.yaml | 1 + recipes/bcbio-nextgen-vm/build.sh | 3 - recipes/bcbio-nextgen-vm/meta.yaml | 6 +- recipes/bcbio_monitor/build.sh | 3 - recipes/bcbio_monitor/meta.yaml | 16 +-- recipes/bcbreport/build.sh | 3 - recipes/bcbreport/meta.yaml | 5 +- recipes/bcl2fastq-nextseq/meta.yaml | 16 +-- recipes/bcool/meta.yaml | 8 +- recipes/bcov/meta.yaml | 6 +- recipes/bctools/meta.yaml | 1 + recipes/beast/meta.yaml | 1 + recipes/beast2/2.4.5/meta.yaml | 1 + recipes/beast2/2.5.0/meta.yaml | 2 +- recipes/besst/meta.yaml | 5 +- recipes/{bgreat2 => bgreat}/build.sh | 0 recipes/{bgreat2 => bgreat}/meta.yaml | 0 recipes/bibliospec/meta.yaml | 10 +- recipes/bigsi/meta.yaml | 2 - recipes/biobambam/meta.yaml | 6 +- recipes/biodiff/meta.yaml | 1 + .../build.sh | 0 .../meta.yaml | 0 recipes/biofluff/build.sh | 2 - recipes/biofluff/meta.yaml | 16 +-- recipes/biogridpy/build.sh | 3 - recipes/biogridpy/meta.yaml | 5 +- recipes/biokit/build.sh | 3 - recipes/biokit/meta.yaml | 25 +--- recipes/biolib/meta.yaml | 4 +- recipes/biolite/build.sh | 2 - recipes/biolite/meta.yaml | 9 +- .../0.1/meta.yaml | 9 +- .../0.2/biopet-extractadaptersfastqc.py | 107 ------------------ .../biopet-extractadaptersfastqc/0.2/build.sh | 12 -- .../0.2/meta.yaml | 39 ------- .../biopet-extractadaptersfastqc/meta.yaml | 12 +- recipes/biopet-sampleconfig/0.1/meta.yaml | 1 + .../0.3/biopet-sampleconfig.py | 107 ------------------ recipes/biopet-sampleconfig/0.3/build.sh | 12 -- recipes/biopet-sampleconfig/0.3/meta.yaml | 63 ----------- recipes/biopet-validatefastq/0.1.1/meta.yaml | 1 + recipes/biopet-validatefastq/meta.yaml | 1 + recipes/bioservices/meta.yaml | 12 +- recipes/biotradis/meta.yaml | 13 ++- recipes/bis-snp-utils/meta.yaml | 1 + recipes/bis-snp/meta.yaml | 1 + recipes/biskit/build.sh | 3 - recipes/biskit/meta.yaml | 16 +-- recipes/bismark/meta.yaml | 1 + recipes/bitstring/build.sh | 9 -- recipes/bitstring/meta.yaml | 8 +- recipes/blastalign/meta.yaml | 5 +- recipes/blobtools/meta.yaml | 8 +- recipes/bmfilter/meta.yaml | 20 ++-- recipes/bmtagger/meta.yaml | 28 +++-- recipes/bmtool/meta.yaml | 16 +-- recipes/braker/meta.yaml | 2 +- recipes/breakseq2/build.sh | 3 - recipes/breakseq2/meta.yaml | 21 ++-- recipes/brockman-pipeline/meta.yaml | 1 + recipes/bs-seeker2/meta.yaml | 5 +- recipes/bsmap/meta.yaml | 4 +- recipes/burrito-fillings/0.1.1/build.sh | 3 - .../burrito-fillings/{0.1.1 => }/meta.yaml | 4 +- recipes/busco/meta.yaml | 3 +- recipes/bwakit/meta.yaml | 1 + recipes/bwapy/meta.yaml | 12 +- recipes/bwise/meta.yaml | 3 +- recipes/cactus/build.sh | 2 +- recipes/cactus/meta.yaml | 22 ++-- recipes/cage/meta.yaml | 5 +- recipes/cansnper/build.sh | 3 - recipes/cansnper/meta.yaml | 12 +- recipes/cap3/meta.yaml | 20 +++- recipes/ccat/meta.yaml | 6 +- recipes/cdna_cupcake/build.sh | 3 +- recipes/cdna_cupcake/meta.yaml | 7 +- recipes/ceas/meta.yaml | 8 +- recipes/centrosome/meta.yaml | 1 + recipes/cgat-daisy/build.sh | 2 +- recipes/cgat-report/build.sh | 3 +- recipes/{cgat-core => cgatcore}/meta.yaml | 5 +- recipes/cgcloud-lib/build.sh | 3 - recipes/cgcloud-lib/meta.yaml | 12 +- recipes/changeo/meta.yaml | 1 - recipes/chanjo/build.sh | 3 - recipes/chanjo/meta.yaml | 16 +-- recipes/check-sort-order/meta.yaml | 13 ++- recipes/chemfp/build.sh | 9 -- recipes/chemfp/meta.yaml | 2 + recipes/chorus2/meta.yaml | 11 +- recipes/chromosomer/meta.yaml | 9 +- recipes/circexplorer/build.sh | 4 +- recipes/circexplorer/meta.yaml | 10 +- recipes/circexplorer2/build.sh | 10 -- recipes/circexplorer2/meta.yaml | 8 +- recipes/cistrome-ceas/build.sh | 3 +- recipes/cistrome-ceas/meta.yaml | 8 +- recipes/cistrome_beta/build.sh | 3 - recipes/cistrome_beta/meta.yaml | 12 +- recipes/cityhash/build.sh | 3 - recipes/cityhash/meta.yaml | 10 +- recipes/clairvoyante/meta.yaml | 6 +- recipes/clearcut/meta.yaml | 5 +- recipes/clinod/meta.yaml | 4 +- recipes/clustalw/meta.yaml | 3 + recipes/clustergrammer/build.sh | 9 -- recipes/clustergrammer/meta.yaml | 6 +- .../build.sh | 0 .../cluster-picker.sh | 0 .../meta.yaml | 2 +- recipes/cogent/build.sh | 3 - recipes/cogent/meta.yaml | 17 +-- recipes/collectl/meta.yaml | 1 + recipes/colorbrewer/build.sh | 8 -- recipes/colorbrewer/meta.yaml | 4 +- recipes/combined-pvalues/build.sh | 3 - recipes/combined-pvalues/meta.yaml | 11 +- recipes/commet/meta.yaml | 3 +- recipes/compare-reads/build.sh | 2 - recipes/compare-reads/meta.yaml | 5 +- recipes/connor/meta.yaml | 4 +- .../meta.yaml | 0 recipes/coprarna/meta.yaml | 15 +-- recipes/cpat/meta.yaml | 8 +- recipes/cpinsim/build.sh | 3 - recipes/cpinsim/meta.yaml | 13 +-- recipes/crb-blast/meta.yaml | 4 +- recipes/crimson/build.sh | 2 - recipes/crimson/meta.yaml | 9 +- .../{CRISPRStudio => crispr_studio}/build.sh | 0 .../change_f_flag.patch | 0 .../{CRISPRStudio => crispr_studio}/meta.yaml | 0 recipes/crux-toolkit/meta.yaml | 26 +++-- recipes/ctat-metagenomics/meta.yaml | 7 +- recipes/cuneiform/1.1.0/build.sh | 7 -- recipes/cuneiform/1.1.0/meta.yaml | 19 ---- recipes/daisysuite/meta.yaml | 2 +- recipes/damidseq_pipeline/meta.yaml | 1 + recipes/dammit/build.sh | 3 - recipes/dammit/meta.yaml | 8 +- recipes/das_tool/meta.yaml | 3 +- recipes/data_hacks/build.sh | 3 - recipes/data_hacks/meta.yaml | 9 +- recipes/ddrage/build.sh | 3 - recipes/ddrage/meta.yaml | 15 +-- recipes/deblur/build.sh | 3 - recipes/deblur/meta.yaml | 25 ++-- recipes/debwt/meta.yaml | 5 + recipes/deepmedic/build.sh | 3 - recipes/deepmedic/meta.yaml | 15 +-- recipes/deepvariant/meta.yaml | 6 + recipes/deltabs/meta.yaml | 1 + recipes/deploid/meta.yaml | 2 + recipes/desman/meta.yaml | 3 +- recipes/dfam/meta.yaml | 2 +- recipes/discasm/meta.yaml | 5 +- recipes/dkfz-bias-filter/meta.yaml | 7 +- recipes/dlcpar/build.sh | 3 - recipes/dlcpar/meta.yaml | 9 +- recipes/dnapi/meta.yaml | 10 +- recipes/drax/meta.yaml | 1 + recipes/drive/meta.yaml | 14 ++- recipes/dudes/0.06/build.sh | 6 - recipes/dudes/0.06/meta.yaml | 31 ----- recipes/dudes/0.07/build.sh | 4 - recipes/dudes/0.07/meta.yaml | 27 ----- recipes/dudes/build.sh | 2 - recipes/dudes/meta.yaml | 8 +- recipes/duphold/meta.yaml | 5 + recipes/dupre/meta.yaml | 13 +-- recipes/dx-cwl/meta.yaml | 7 +- recipes/ebfilter/build.sh | 10 -- recipes/ebfilter/meta.yaml | 3 +- recipes/ebisearch/build.sh | 3 - recipes/ebisearch/meta.yaml | 14 +-- recipes/ecopy/meta.yaml | 2 - recipes/ectyper/meta.yaml | 8 +- recipes/edd/meta.yaml | 2 + recipes/eden/build.sh | 9 -- recipes/eden/meta.yaml | 21 +--- recipes/edittag/build.sh | 3 - recipes/edittag/meta.yaml | 7 +- recipes/egglib/meta.yaml | 8 +- recipes/elasticluster/build.sh | 2 - recipes/elasticluster/meta.yaml | 11 +- .../build.sh | 0 .../embl-api-validator.py | 0 .../meta.yaml | 0 recipes/emperor/0.9.3/build.sh | 3 - recipes/emperor/0.9.3/meta.yaml | 37 ------ recipes/emperor/build.sh | 3 - recipes/emperor/meta.yaml | 11 +- recipes/enasearch/0.0.4/build.sh | 4 - recipes/enasearch/0.0.4/meta.yaml | 44 ------- recipes/enasearch/0.0.5/build.sh | 4 - recipes/enasearch/0.0.5/meta.yaml | 44 ------- recipes/enasearch/0.0.6/build.sh | 4 - recipes/enasearch/0.0.6/meta.yaml | 44 ------- recipes/enasearch/0.1.1/build.sh | 4 - recipes/enasearch/0.1.1/meta.yaml | 46 -------- recipes/enasearch/0.2.0/build.sh | 4 - recipes/enasearch/{0.2.0 => }/meta.yaml | 23 ++-- recipes/entrez-direct/meta.yaml | 1 + recipes/eoulsan/meta.yaml | 4 +- recipes/epic/meta.yaml | 7 +- recipes/epydoc/build.sh | 9 -- recipes/epydoc/meta.yaml | 9 +- recipes/eqtlbma/meta.yaml | 2 - recipes/ericscript/meta.yaml | 3 +- recipes/erne/meta.yaml | 2 + recipes/esmre/build.sh | 3 - recipes/esmre/meta.yaml | 10 +- recipes/eta/build.sh | 4 - recipes/eta/meta.yaml | 4 +- recipes/ete2/build.sh | 2 - recipes/ete2/meta.yaml | 14 +-- recipes/evidencemodeler/meta.yaml | 1 + recipes/evofold2/meta.yaml | 4 + recipes/express/meta.yaml | 15 ++- recipes/extern/build.sh | 3 - recipes/extern/meta.yaml | 10 +- recipes/extract_fullseq/meta.yaml | 13 ++- recipes/extract_genome_region/build.sh | 3 - recipes/extract_genome_region/meta.yaml | 7 +- recipes/fann/meta.yaml | 4 + recipes/fast5/meta.yaml | 1 + recipes/fast5seek/meta.yaml | 7 +- recipes/fasta-splitter/0.2.4/build.sh | 11 -- recipes/fasta-splitter/0.2.4/meta.yaml | 26 ----- recipes/fastaindex/build.sh | 3 - recipes/fastaindex/meta.yaml | 10 +- recipes/fasten/meta.yaml | 1 + recipes/fastlmm/build.sh | 3 - recipes/fastlmm/meta.yaml | 18 +-- recipes/fastphylo/meta.yaml | 21 ++-- recipes/fastq-anonymous/meta.yaml | 11 +- recipes/fastq-screen/meta.yaml | 1 + recipes/{fastq_tools => fastq-tools}/build.sh | 0 .../{fastq_tools => fastq-tools}/meta.yaml | 0 recipes/fastqc/0.11.7/meta.yaml | 1 + recipes/fastqc/meta.yaml | 1 + recipes/fastqe/meta.yaml | 12 +- recipes/fastqmetrics/build.sh | 3 - recipes/fastqmetrics/meta.yaml | 11 +- recipes/faststructure/meta.yaml | 1 - recipes/fasttree/2.1.8/build.sh | 4 +- recipes/fasttree/2.1.8/meta.yaml | 4 + recipes/fastx_toolkit/meta.yaml | 1 - recipes/fcsparser/meta.yaml | 1 - recipes/feelnc/meta.yaml | 1 + recipes/feht/meta.yaml | 4 + recipes/fgmp/meta.yaml | 1 + recipes/find_differential_primers/build.sh | 3 - recipes/find_differential_primers/meta.yaml | 16 +-- recipes/fisher/build.sh | 9 -- recipes/fisher/meta.yaml | 46 -------- recipes/flaimapper/meta.yaml | 8 +- recipes/flapjack/meta.yaml | 1 + recipes/flash2/meta.yaml | 1 - recipes/flux-simulator/meta.yaml | 4 +- recipes/forked-path/build.sh | 3 - recipes/forked-path/meta.yaml | 10 +- recipes/fred2/build.sh | 2 - recipes/fred2/meta.yaml | 16 +-- recipes/freebayes/1.1.0.46/meta.yaml | 2 +- recipes/freebayes/meta.yaml | 1 - recipes/frogs/meta.yaml | 10 +- recipes/fsnviz/0.1.0/build.sh | 3 - recipes/fsnviz/0.1.0/meta.yaml | 46 -------- recipes/fsnviz/0.2.0/build.sh | 3 - recipes/fsnviz/0.2.0/meta.yaml | 48 -------- recipes/fsnviz/build.sh | 3 - recipes/fsnviz/meta.yaml | 15 +-- recipes/fuma/build.sh | 3 - recipes/fuma/meta.yaml | 12 +- recipes/fusion-filter/meta.yaml | 7 +- recipes/fusion-inspector/meta.yaml | 9 +- recipes/fusion-report/meta.yaml | 3 +- recipes/galaxy-ops/build.sh | 9 -- recipes/galaxy-ops/meta.yaml | 19 ++-- recipes/gapfiller/meta.yaml | 1 + recipes/gb_taxonomy_tools/meta.yaml | 2 + recipes/gblocks/meta.yaml | 19 +++- .../meta.yaml | 16 +-- recipes/gcs_oauth2_boto_plugin/build.sh | 9 -- recipes/gemini/build.sh | 2 - recipes/gemini/meta.yaml | 6 +- recipes/geneimpacts/build.sh | 2 - recipes/geneimpacts/meta.yaml | 10 +- recipes/genomelake/meta.yaml | 28 +---- recipes/genomestrip/meta.yaml | 3 +- recipes/genomethreader/meta.yaml | 5 +- recipes/genomicconsensus/build.sh | 3 - recipes/genomicconsensus/meta.yaml | 34 +++--- recipes/genonets/build.sh | 4 - recipes/genonets/meta.yaml | 12 +- recipes/{gerp++ => gerp}/meta.yaml | 4 + .../missing_headers_linux.patch | 0 .../missing_headers_osx.patch | 0 recipes/gfapy/build.sh | 3 - recipes/gfapy/meta.yaml | 12 +- recipes/gff3sort/meta.yaml | 6 +- recipes/gffread/meta.yaml | 11 +- recipes/{genehunter => ghm}/3.0/build.sh | 0 recipes/{genehunter => ghm}/3.0/meta.yaml | 2 +- .../3.0/osx-makefile.patch | 0 recipes/{genehunter => ghm}/3.1/build.sh | 0 recipes/{genehunter => ghm}/3.1/meta.yaml | 3 +- .../3.1/osx-makefile.patch | 0 recipes/glimmer/meta.yaml | 17 ++- recipes/gmap-fusion/meta.yaml | 1 + recipes/gmap/2014.12.23/meta.yaml | 2 + recipes/gmap/2014.12.28/meta.yaml | 2 + recipes/gmap/2015.09.10/meta.yaml | 2 + recipes/gmap/2016.09.23/meta.yaml | 2 + recipes/gmap/2017.02.15/meta.yaml | 2 + recipes/gmtk/meta.yaml | 4 + recipes/gnuplot-py/build.sh | 9 -- recipes/gnuplot-py/meta.yaml | 11 +- recipes/gocr/0.50/meta.yaml | 6 + recipes/goleft/meta.yaml | 13 ++- recipes/gotree/meta.yaml | 17 +-- recipes/gottcha/meta.yaml | 7 +- recipes/graphclust-wrappers/meta.yaml | 10 +- recipes/graphlite/build.sh | 9 -- recipes/graphlite/meta.yaml | 5 +- recipes/gretel/build.sh | 3 - recipes/gretel/meta.yaml | 9 +- recipes/grid/meta.yaml | 2 +- recipes/groopm/meta.yaml | 6 +- recipes/groot/meta.yaml | 6 +- recipes/gsort/meta.yaml | 13 ++- recipes/gtf_to_genes/bld.bat | 8 -- recipes/gtf_to_genes/build.sh | 9 -- recipes/gtf_to_genes/meta.yaml | 9 +- recipes/guidescan/meta.yaml | 50 ++++---- recipes/gustaf/meta.yaml | 21 ++-- recipes/halla/meta.yaml | 3 +- recipes/hapflk/build.sh | 3 - recipes/hapflk/meta.yaml | 1 + recipes/harvesttools/meta.yaml | 14 ++- recipes/hca-matrix-downloader/meta.yaml | 1 - recipes/hclust2/meta.yaml | 12 +- recipes/heinz/meta.yaml | 4 +- recipes/hgtools/build.sh | 9 -- recipes/hgtools/meta.yaml | 1 + recipes/hicbrowser/build.sh | 3 - recipes/hicbrowser/meta.yaml | 10 +- recipes/hifive/meta.yaml | 5 +- recipes/hivtrace/build.sh | 3 - recipes/hivtrace/meta.yaml | 16 +-- recipes/hlama/build.sh | 9 -- recipes/hlama/meta.yaml | 11 +- recipes/hlaprofiler/meta.yaml | 12 +- recipes/hmmlearn/0.1.1/build.sh | 2 - recipes/hmmlearn/0.1.1/meta.yaml | 37 ------ recipes/hmmlearn/build.sh | 2 - recipes/hmmlearn/meta.yaml | 38 ------- recipes/hotspot3d/meta.yaml | 1 + recipes/hubward-all/meta.yaml | 7 +- recipes/humann2/0.11.1/build.sh | 5 - recipes/humann2/0.11.1/meta.yaml | 85 -------------- recipes/humann2/0.9.9/build.sh | 5 - recipes/humann2/0.9.9/meta.yaml | 45 -------- recipes/humann2/build.sh | 5 - recipes/humann2/meta.yaml | 5 +- recipes/ibdne/meta.yaml | 4 +- recipes/ibdseq/meta.yaml | 4 +- recipes/iced/meta.yaml | 4 +- recipes/iclipro/build.sh | 3 - recipes/iclipro/meta.yaml | 11 +- recipes/icount/meta.yaml | 20 +--- recipes/idr-py/meta.yaml | 9 +- recipes/idr/2.0.3/build.sh | 9 -- recipes/idr/2.0.3/meta.yaml | 12 +- recipes/igblast/meta.yaml | 11 +- recipes/illumina-cleanup/meta.yaml | 1 + recipes/illuminate/build.sh | 9 -- recipes/illuminate/meta.yaml | 1 + recipes/illumiprocessor/meta.yaml | 10 +- recipes/imfusion/0.3.0/build.sh | 1 - recipes/imfusion/0.3.0/meta.yaml | 1 + recipes/imfusion/0.3.2/build.sh | 1 - recipes/imfusion/0.3.2/meta.yaml | 1 + recipes/impute2/meta.yaml | 13 ++- .../{python-intermine => intermine}/meta.yaml | 0 recipes/intervaltree_bio/build.sh | 4 - recipes/intervaltree_bio/meta.yaml | 5 +- recipes/involucro/meta.yaml | 13 ++- recipes/ir/meta.yaml | 3 +- recipes/irida-linker/meta.yaml | 3 +- recipes/irida-sistr-results/meta.yaml | 15 +-- recipes/islandpath/meta.yaml | 10 +- recipes/itero/build.sh | 3 - recipes/itero/meta.yaml | 11 +- recipes/itsx/meta.yaml | 2 +- recipes/itsxpress/1.5.6/meta.yaml | 52 --------- recipes/itsxpress/1.6.1/meta.yaml | 52 --------- recipes/itsxpress/1.6.3/meta.yaml | 52 --------- recipes/itsxpress/1.6.4/meta.yaml | 52 --------- recipes/itsxpress/1.7.1/meta.yaml | 53 --------- recipes/itsxpress/meta.yaml | 6 +- recipes/iva/build.sh | 5 - recipes/iva/meta.yaml | 17 +-- recipes/jaffa/meta.yaml | 5 +- recipes/jalview/meta.yaml | 1 + recipes/jamm/1.0.7.2/meta.yaml | 2 +- recipes/jobtree/build.sh | 2 +- .../build.sh | 0 .../meta.yaml | 3 +- recipes/jvarkit-bam2svg/meta.yaml | 1 + recipes/jvarkit-bam2wig/meta.yaml | 1 + recipes/{kalign => kalign2}/build.sh | 0 recipes/{kalign => kalign2}/meta.yaml | 0 recipes/kid/build.sh | 8 -- recipes/kid/meta.yaml | 9 +- recipes/kiwidist/build.sh | 3 - recipes/kiwidist/meta.yaml | 17 +-- recipes/kmc/3.0.0_static/meta.yaml | 12 +- recipes/kneaddata/build.sh | 7 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recipes/manta/meta.yaml | 7 +- recipes/mapdamage2/build.sh | 3 - recipes/mapdamage2/meta.yaml | 2 + recipes/marge/meta.yaml | 12 +- recipes/mason/meta.yaml | 11 +- recipes/matlock/meta.yaml | 2 +- recipes/maxentpy/build.sh | 3 - recipes/maxentpy/meta.yaml | 6 +- recipes/maxentscan/meta.yaml | 3 +- recipes/maxquant/meta.yaml | 2 +- recipes/mbuffer/meta.yaml | 1 + recipes/medpy/meta.yaml | 9 +- .../{medusa => medusa-data-fusion}/meta.yaml | 16 ++- recipes/medusa/build.sh | 9 -- recipes/megan/meta.yaml | 3 + recipes/menetools/1.0.4_1/build.sh | 1 - recipes/menetools/{1.0.4_1 => }/meta.yaml | 11 +- recipes/mentalist/0.1.9/meta.yaml | 3 + recipes/mentalist/meta.yaml | 4 + recipes/mergevcf/build.sh | 2 - recipes/mergevcf/meta.yaml | 11 +- recipes/meta-sparse/build.sh | 4 - recipes/meta-sparse/meta.yaml | 15 +-- recipes/metameta/1.0/build.sh | 11 -- recipes/metameta/1.0/meta.yaml | 24 ---- recipes/metameta/1.1.1/build.sh | 11 -- recipes/metameta/1.1.1/meta.yaml | 24 ---- 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| 12 +- recipes/minimock/build.sh | 4 - recipes/minimock/meta.yaml | 6 +- recipes/minorseq/meta.yaml | 24 ++-- recipes/mintmap/meta.yaml | 1 + recipes/minvar/1.2a3/build.sh | 1 - recipes/minvar/1.2a3/meta.yaml | 52 --------- recipes/minvar/1.2b/build.sh | 1 - recipes/minvar/1.2b/meta.yaml | 52 --------- recipes/minvar/2.0/build.sh | 1 - recipes/minvar/2.0/meta.yaml | 52 --------- recipes/minvar/2.1.1/build.sh | 1 - recipes/minvar/2.1.1/meta.yaml | 52 --------- recipes/minvar/2.1.2/build.sh | 1 - recipes/minvar/2.1.2/meta.yaml | 52 --------- recipes/minvar/2.1.3/build.sh | 1 - recipes/minvar/2.1.3/meta.yaml | 52 --------- recipes/minvar/2.1/build.sh | 1 - recipes/minvar/2.1/meta.yaml | 52 --------- recipes/minvar/build.sh | 1 - recipes/minvar/meta.yaml | 13 +-- recipes/mir-prefer/meta.yaml | 7 +- recipes/mira/meta.yaml | 11 +- recipes/mirdeep2/2.0.0.7/build.sh | 6 - recipes/mirdeep2/2.0.0.7/meta.yaml | 21 ---- recipes/mirdeep2/{2.0.0.8 => }/build.sh | 0 recipes/mirdeep2/{2.0.0.8 => 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}/extractreads2.patch | 0 recipes/obitools/{1.2.11 => }/meta.yaml | 3 + recipes/ogdf/meta.yaml | 7 ++ recipes/oligotyping/2.0/build.sh | 9 -- recipes/oligotyping/2.0/meta.yaml | 13 +-- recipes/oligotyping/build.sh | 9 -- recipes/oligotyping/meta.yaml | 7 +- recipes/oncotator/meta.yaml | 10 +- recipes/ont-tombo/build.sh | 9 -- recipes/ont-tombo/meta.yaml | 6 +- recipes/openbabel/2.3.2/build.sh | 9 -- recipes/openbabel/2.3.2/meta.yaml | 37 ------ recipes/openbabel/2.4.1/372.patch | 57 ---------- recipes/openbabel/2.4.1/build.sh | 26 ----- .../openbabel/2.4.1/fix_babel_test_paths.diff | 23 ---- recipes/openbabel/2.4.1/fix_data_path.diff | 18 --- .../2.4.1/fix_libinchi_cmakelists.diff | 13 --- .../2.4.1/fix_library_path_search.diff | 30 ----- recipes/openbabel/2.4.1/meta.yaml | 57 ---------- recipes/openbabel/2.4.1/run_test.py | 15 --- recipes/optbuild/build.sh | 9 -- recipes/optbuild/meta.yaml | 6 +- recipes/optitype/1.2.1/meta.yaml | 10 +- recipes/optitype/meta.yaml | 9 +- 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| 1 + recipes/perl-graphics-colornames/meta.yaml | 1 + recipes/perl-graphics-colorobject/meta.yaml | 1 + recipes/perl-graphviz/meta.yaml | 1 + recipes/perl-hash-merge/meta.yaml | 1 + .../0.11/meta.yaml | 1 + recipes/perl-heap-simple-perl/meta.yaml | 1 + recipes/perl-heap-simple/meta.yaml | 1 + recipes/perl-heap/meta.yaml | 1 + recipes/perl-hook-lexwrap/0.26/meta.yaml | 1 + .../0.0.3/meta.yaml | 1 + .../perl-hpc-runner-command/3.2.13/meta.yaml | 1 + recipes/perl-html-element-extended/meta.yaml | 1 + recipes/perl-html-entities-numbered/meta.yaml | 1 + recipes/perl-html-form/meta.yaml | 1 + recipes/perl-html-formatter/meta.yaml | 1 + recipes/perl-html-tableextract/meta.yaml | 1 + recipes/perl-html-tagset/meta.yaml | 1 + recipes/perl-html-template/meta.yaml | 1 + recipes/perl-html-tidy/meta.yaml | 1 + recipes/perl-html-tree/meta.yaml | 1 + recipes/perl-html-treebuilder-xpath/meta.yaml | 1 + recipes/perl-http-cookies/meta.yaml | 1 + recipes/perl-http-daemon/meta.yaml | 1 + 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+-- recipes/r-phyext2/meta.yaml | 1 + recipes/r-phylobase/meta.yaml | 18 +-- recipes/r-phylomeasures/meta.yaml | 20 +--- recipes/r-phylosignal/meta.yaml | 17 +-- recipes/r-popgenreport/meta.yaml | 1 + recipes/r-pscbs/meta.yaml | 1 + recipes/{r-raceid3 => r-raceid}/build.sh | 0 recipes/{r-raceid3 => r-raceid}/meta.yaml | 0 recipes/r-rapidr/meta.yaml | 1 + recipes/r-riborex/meta.yaml | 1 + recipes/r-ridigbio/meta.yaml | 1 + recipes/r-rnexml/meta.yaml | 4 +- recipes/r-rubic/1.0.2/meta.yaml | 1 + recipes/r-rubic/1.0.3/meta.yaml | 1 + recipes/r-rvertnet/meta.yaml | 1 + recipes/r-sbpiper/meta.yaml | 1 + recipes/r-scrm/build.sh | 1 - recipes/r-scrm/meta.yaml | 70 ------------ recipes/r-seqminer/build.sh | 1 - recipes/r-seqminer/meta.yaml | 72 ------------ recipes/r-shaman/meta.yaml | 2 +- recipes/{r-sigQC => r-sigqc}/build.sh | 0 recipes/{r-sigQC => r-sigqc}/meta.yaml | 12 +- recipes/r-sigtree/meta.yaml | 16 +-- recipes/r-sleuth/meta.yaml | 1 + recipes/r-spocc/meta.yaml | 1 + 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recipes/scvis_galaxy/build.sh | 1 - recipes/scvis_galaxy/meta.yaml | 4 +- recipes/searchgui/3.2.11/build.sh | 11 -- recipes/searchgui/3.2.11/meta.yaml | 40 ------- recipes/searchgui/3.2.11/searchgui.py | 102 ----------------- recipes/searchgui/3.2.13/build.sh | 11 -- recipes/searchgui/3.2.13/meta.yaml | 40 ------- recipes/searchgui/3.2.13/searchgui.py | 102 ----------------- recipes/searchgui/3.2.20/build.sh | 11 -- recipes/searchgui/3.2.20/meta.yaml | 46 -------- recipes/searchgui/3.2.20/searchgui.py | 102 ----------------- recipes/searchgui/3.2.3/build.sh | 11 -- recipes/searchgui/3.2.3/meta.yaml | 38 ------- recipes/searchgui/3.2.3/searchgui.py | 102 ----------------- recipes/searchgui/3.2.5/build.sh | 11 -- recipes/searchgui/3.2.5/meta.yaml | 38 ------- recipes/searchgui/3.2.5/searchgui.py | 102 ----------------- recipes/searchgui/3.2.6/build.sh | 11 -- recipes/searchgui/3.2.6/meta.yaml | 38 ------- recipes/searchgui/3.2.6/searchgui.py | 102 ----------------- 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This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. -extra: - identifiers: - - biotools:splicemap - - doi:10.1093/nar/gkq211 diff --git a/recipes/a5-miseq/meta.yaml b/recipes/a5-miseq/meta.yaml index 1da52eca5b736..0769b0f1e2fff 100644 --- a/recipes/a5-miseq/meta.yaml +++ b/recipes/a5-miseq/meta.yaml @@ -1,18 +1,17 @@ {% set name = "A5-miseq" %} {% set version = "20160825" %} -{% set build = 0 %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://sourceforge.net/projects/ngopt/files/a5_miseq_linux_20160825.tar.gz/ + url: https://sourceforge.net/projects/ngopt/files/a5_miseq_linux_{{ version }}.tar.gz sha256: 76a2798d617d45f4539e73ef2df5f899503ac4a54c3a406faf37db6282127fe9 build: - skip: True # [osx] - number: {{ build }} + noarch: generic + number: 1 requirements: run: diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index a3404de6a69f5..a8c1b4eb343b1 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - skip: true # [not py36] + noarch: python number: 0 entry_points: - abeona=abeona.__main__:main @@ -19,7 +19,7 @@ build: requirements: host: - pip - - python + - python >=3.6 run: - mccortex ==1.0 - nextflow ==19.01.0 diff --git a/recipes/admixture/meta.yaml b/recipes/admixture/meta.yaml index 25b57c547bc96..cd27ca25f9094 100644 --- a/recipes/admixture/meta.yaml +++ b/recipes/admixture/meta.yaml @@ -11,6 +11,7 @@ source: sha256: a95aa96a51a4a0df0e0b0eba643b260e810132a620a8bcf693a18546d5b0f396 build: + noarch: generic number: 0 about: diff --git a/recipes/advntr/meta.yaml b/recipes/advntr/meta.yaml index 029ec3d273b1a..adabbb11ba7c6 100644 --- a/recipes/advntr/meta.yaml +++ b/recipes/advntr/meta.yaml @@ -31,7 +31,6 @@ requirements: - scipy run: - python - - cython - {{ pin_compatible('numpy') }} - {{ pin_compatible('scipy') }} - matplotlib diff --git a/recipes/afterqc/meta.yaml b/recipes/afterqc/meta.yaml index eeb434daf09e3..a6a3b1a524e63 100644 --- a/recipes/afterqc/meta.yaml +++ b/recipes/afterqc/meta.yaml @@ -6,6 +6,7 @@ package: version: {{ version }} build: + noarch: generic number: 2 source: @@ -13,8 +14,6 @@ source: sha256: {{ sha256 }} requirements: - host: - - python >=2.7,<3.0a0 run: - python >=2.7,<3.0a0 diff --git a/recipes/airr/meta.yaml b/recipes/airr/meta.yaml index 53d6f1be86401..01f60e026024a 100644 --- a/recipes/airr/meta.yaml +++ b/recipes/airr/meta.yaml @@ -24,7 +24,6 @@ requirements: - pandas >=0.18.0 - python - pyyaml >=3.12 - - setuptools >=2.0 - yamlordereddictloader >=0.4.0 test: diff --git a/recipes/albatradis/meta.yaml b/recipes/albatradis/meta.yaml index 4324f0148e0f6..9f20b827cf8fa 100644 --- a/recipes/albatradis/meta.yaml +++ b/recipes/albatradis/meta.yaml @@ -12,10 +12,12 @@ source: build: number: 3 - skip: True # [osx] + skip: True # [osx or py2k] script: python -m pip install --ignore-installed . requirements: + build: + - {{ compiler('c') }} host: - python >3 - cython @@ -35,10 +37,8 @@ requirements: - perl-scalar-util-numeric - perl-moose - biotradis - run: - python >3 - - cython - biopython >=1.68 - pyfastaq >=3.12.0 - scipy @@ -53,7 +53,7 @@ requirements: - perl-pathtools - perl-scalar-util-numeric - perl-moose - - biotradis=1.4.1.dev + - biotradis test: commands: @@ -68,7 +68,7 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url recipe-maintainers: - sbastkowski - thanhleviet diff --git a/recipes/align-it/1.0.3/build.sh b/recipes/align_it/build.sh similarity index 100% rename from recipes/align-it/1.0.3/build.sh rename to recipes/align_it/build.sh diff --git a/recipes/align-it/1.0.3/meta.yaml b/recipes/align_it/meta.yaml similarity index 100% rename from recipes/align-it/1.0.3/meta.yaml rename to recipes/align_it/meta.yaml diff --git a/recipes/alignlib-lite/meta.yaml b/recipes/alignlib-lite/meta.yaml index 42d69c1050813..194405e68b35e 100644 --- a/recipes/alignlib-lite/meta.yaml +++ b/recipes/alignlib-lite/meta.yaml @@ -15,6 +15,7 @@ build: requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} host: - python diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml index 075ff4612d3ed..e778217d1d681 100644 --- a/recipes/allegro/meta.yaml +++ b/recipes/allegro/meta.yaml @@ -37,3 +37,7 @@ about: # main link is broken: http://www.decode.com/software/allegro license: INDIVIDUAL summary: A fast linkage and haplotype analysis utility making use of MTBDD to reduce complexity. + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/amused/meta.yaml b/recipes/amused/meta.yaml index c3ceacb425b3e..48193ced7533a 100644 --- a/recipes/amused/meta.yaml +++ b/recipes/amused/meta.yaml @@ -2,6 +2,7 @@ {% set sha256 = "dacb4eb20a5eb380f3ef28d57ad79384069d84ecb9a8865a3e26d75a63a029e9" %} build: + noarch: generic number: 1 package: diff --git a/recipes/anndata/meta.yaml b/recipes/anndata/meta.yaml deleted file mode 100644 index 79b93d235eab7..0000000000000 --- a/recipes/anndata/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -{% set version = "0.6.22.post1" %} -{% set sha256 = "ce1461849954b6eedff67c3d31e25bdc9a18812bd537b3bff8743e41b70baa42" %} - -package: - name: anndata - version: '{{ version }}' - -source: - url: https://pypi.io/packages/source/a/anndata/anndata-{{ version }}.tar.gz - sha256: '{{ sha256 }}' - -build: - noarch: python - number: 0 - script: $PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir . - -requirements: - host: - - python >=3.5 - - pip - - pathlib - run: - - python >=3.5 - - pandas >=0.23.0 - - scipy - - h5py - - natsort - -test: - imports: - - anndata - - anndata.h5py - - anndata.readwrite - -about: - home: https://github.com/theislab/anndata - license: BSD-3-Clause - license_family: BSD - summary: An annotated data matrix. - description: An annotated data matrix. - doc_url: http://anndata.rtfd.io diff --git a/recipes/antismash/meta.yaml b/recipes/antismash/meta.yaml index f693ce3b58d7a..aadd0c03dbc83 100644 --- a/recipes/antismash/meta.yaml +++ b/recipes/antismash/meta.yaml @@ -7,6 +7,7 @@ package: version: {{ version }} build: + noarch: python number: 1 source: @@ -71,3 +72,5 @@ about: extra: identifiers: - biotools:antismash + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/anvio/meta.yaml b/recipes/anvio/meta.yaml index f838ca077fa7a..b9ff58a0874c6 100644 --- a/recipes/anvio/meta.yaml +++ b/recipes/anvio/meta.yaml @@ -5,6 +5,7 @@ package: version: {{ version }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/any2fasta/meta.yaml b/recipes/any2fasta/meta.yaml index 193a994687d88..85f2ed1280cc7 100644 --- a/recipes/any2fasta/meta.yaml +++ b/recipes/any2fasta/meta.yaml @@ -12,6 +12,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/apt-probeset-summarize/meta.yaml b/recipes/apt-probeset-summarize/meta.yaml index ca6b77950b9bb..86999fd9b65c6 100644 --- a/recipes/apt-probeset-summarize/meta.yaml +++ b/recipes/apt-probeset-summarize/meta.yaml @@ -1,20 +1,24 @@ - package: - name: apt-probeset-summarize - version: 2.10.0 + name: apt-probeset-summarize + version: 2.10.0 + build: skip: True #[osx] number: 0 + source: - md5: 1a384def6f633c1ad24296e0fc677ec3 - url: https://downloads.thermofisher.com/Affymetrix_Softwares/APT_2.10.0/apt-2.10.0-x86_64-intel-linux.zip + md5: 1a384def6f633c1ad24296e0fc677ec3 + url: https://downloads.thermofisher.com/Affymetrix_Softwares/APT_2.10.0/apt-2.10.0-x86_64-intel-linux.zip + requirements: - run: - - libstdcxx-ng + build: + - {{ compiler('cxx') }} + test: - commands: - - apt-probeset-summarize --help + commands: + - apt-probeset-summarize --help + about: - home: https://downloads.thermofisher.com - license: GNU GENERAL PUBLIC LICENSE Version 2 - summary: From Affymetrix Power Tools package. apt-probeset-summarize is program for analyzing expression arrays including 3' IVT and exon arrays. Supports background correction (MAS5,RMA), normalization (linear scaling, quantile, sketch), and summarization (PLIER, RMA, MAS5) methods. + home: https://downloads.thermofisher.com + license: GNU GENERAL PUBLIC LICENSE Version 2 + summary: From Affymetrix Power Tools package. apt-probeset-summarize is program for analyzing expression arrays including 3' IVT and exon arrays. Supports background correction (MAS5,RMA), normalization (linear scaling, quantile, sketch), and summarization (PLIER, RMA, MAS5) methods. diff --git a/recipes/arb-bio/meta.yaml b/recipes/arb-bio/meta.yaml index cd32a9fd1e8b4..95b601cd32996 100644 --- a/recipes/arb-bio/meta.yaml +++ b/recipes/arb-bio/meta.yaml @@ -209,5 +209,3 @@ extra: - doi:10.1002/9781118010518.ch46 recipe-maintainers: - epruesse - skip-lints: - - should_not_be_noarch # false positive, `noarch: False` added by CB3 for outputs diff --git a/recipes/arem/build.sh b/recipes/arem/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/arem/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/arem/meta.yaml b/recipes/arem/meta.yaml index e783329c4194b..6cef7e1b9c98c 100644 --- a/recipes/arem/meta.yaml +++ b/recipes/arem/meta.yaml @@ -7,22 +7,22 @@ source: md5: fab4d78f1fd12c691d4bd62140b927ea build: + noarch: python number: 1 - skip: true #[not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools + - python <3 + - pip run: - - python + - python <3 test: imports: - AREM - AREM.IO - about: home: http://cbcl.ics.uci.edu/AREM license: Artistic License diff --git a/recipes/arvados-cwl-runner/build.sh b/recipes/arvados-cwl-runner/build.sh index 17ce5be6f6831..ea4b62dc8f6ce 100644 --- a/recipes/arvados-cwl-runner/build.sh +++ b/recipes/arvados-cwl-runner/build.sh @@ -8,4 +8,4 @@ sed -i.bak 's/schema-salad==/schema-salad>=/' setup.py sed -i.bak 's/cwltool==/cwltool>=/' setup.py sed -i.bak 's/ruamel.yaml==/ruamel.yaml>=/' setup.py -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/asn2gb/meta.yaml b/recipes/asn2gb/meta.yaml index f666979f0bce1..18cc92c1aa69b 100644 --- a/recipes/asn2gb/meta.yaml +++ b/recipes/asn2gb/meta.yaml @@ -2,16 +2,11 @@ package: name: asn2gb version: "18.2" -about: - home: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/asn2gb.txt - license: Public Domain - summary: asn2gb converts ASN1 format sequence records to Genbank format - source: - url: https://depot.galaxyproject.org/software/asn2gb/asn2gb_18.2_darwin_x64.gz # [osx] - sha256: e2751199333312c43ac46eece268b11ce53bb34acb576f98f00c4962015fffd4 # [osx] - url: https://depot.galaxyproject.org/software/asn2gb/asn2gb_18.2_linux_x64.gz # [linux] - sha256: 4b6ac3831061bc8f8c8adb011fe58c8741402a9c21c95af395aa98154c9ab775 # [linux] + - url: https://depot.galaxyproject.org/software/asn2gb/asn2gb_18.2_darwin_x64.gz # [osx] + sha256: e2751199333312c43ac46eece268b11ce53bb34acb576f98f00c4962015fffd4 # [osx] + - url: https://depot.galaxyproject.org/software/asn2gb/asn2gb_18.2_linux_x64.gz # [linux] + sha256: 4b6ac3831061bc8f8c8adb011fe58c8741402a9c21c95af395aa98154c9ab775 # [linux] build: number: 2 @@ -24,3 +19,13 @@ requirements: test: commands: - asn2gb --help 2>&1 | grep argument + +about: + home: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/asn2gb.txt + license: Public Domain + summary: asn2gb converts ASN1 format sequence records to Genbank format + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/asqcan/build.sh b/recipes/asqcan/build.sh deleted file mode 100644 index d4486bee80f11..0000000000000 --- a/recipes/asqcan/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=/tmp/record.txt diff --git a/recipes/asqcan/meta.yaml b/recipes/asqcan/meta.yaml index 1c5eb2c591536..760d38a962278 100644 --- a/recipes/asqcan/meta.yaml +++ b/recipes/asqcan/meta.yaml @@ -9,15 +9,16 @@ source: md5: e48ddb45c709cf4850fd2a2bb96e4af0 build: + noarch: python number: 1 - skip: True # [not (linux and py27)] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 - parallel - fastqc - spades @@ -26,7 +27,6 @@ requirements: - blast - prokka - test: commands: - asqcan -h diff --git a/recipes/assemblerflow/meta.yaml b/recipes/assemblerflow/meta.yaml index ed68b2b0dfcf4..09d9934ccc341 100644 --- a/recipes/assemblerflow/meta.yaml +++ b/recipes/assemblerflow/meta.yaml @@ -1,8 +1,5 @@ {% set name = "assemblerflow" %} {% set version = "1.1.0.post3" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "b0390727602e90dad1c3afa8dd408e5c30471a0f6d35b323989e9df4e8aa70fb" %} package: name: '{{ name|lower }}' @@ -10,24 +7,21 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} - '{{ hash_type }}': '{{ hash_value }}' + sha256: b0390727602e90dad1c3afa8dd408e5c30471a0f6d35b323989e9df4e8aa70fb build: - skip: True # [py27] + noarch: python number: 1 entry_points: - assemblerflow = assemblerflow.assemblerflow:main - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python >=3 - pip - - setuptools - - argparse - - jinja2 run: - - python + - python >=3 - argparse - jinja2 - nextflow >=0.27 diff --git a/recipes/assemblyutility/meta.yaml b/recipes/assemblyutility/meta.yaml index 08a71b2690955..859822f67bf4b 100644 --- a/recipes/assemblyutility/meta.yaml +++ b/recipes/assemblyutility/meta.yaml @@ -28,4 +28,4 @@ test: about: home: https://github.com/yechengxi/AssemblyUtility summary: Tools for DBG2OLC genoome assembler - + license: MIT diff --git a/recipes/atactk/meta.yaml b/recipes/atactk/meta.yaml index 816893144165b..c90614d44e286 100644 --- a/recipes/atactk/meta.yaml +++ b/recipes/atactk/meta.yaml @@ -10,8 +10,8 @@ source: build: number: 1 - skip: True # [osx] - script: python -m pip install --no-deps --ignore-installed . + noarch: python + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/athena_meta/build.sh b/recipes/athena_meta/build.sh deleted file mode 100644 index e3b0eb7e3ac1a..0000000000000 --- a/recipes/athena_meta/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/athena_meta/meta.yaml b/recipes/athena_meta/meta.yaml index 2f366ea341d4d..bbbe2676c9ce1 100644 --- a/recipes/athena_meta/meta.yaml +++ b/recipes/athena_meta/meta.yaml @@ -1,38 +1,40 @@ {% set version = "1.3" %} package: - name: athena_meta - version: {{ version }} + name: athena_meta + version: {{ version }} source: - url: https://github.com/abishara/athena_meta/archive/{{ version }}.tar.gz - sha256: 3ae0ef982c52412d5954b6da4b8a3387b1f30eeb96902654d22188d4c536a784 + url: https://github.com/abishara/athena_meta/archive/{{ version }}.tar.gz + sha256: 3ae0ef982c52412d5954b6da4b8a3387b1f30eeb96902654d22188d4c536a784 build: - number: 0 - skip: True # [osx] + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: - host: - - python 2.7 - run: - - python 2.7 - - bwa 0.7.* - - flye 2.3.1 - - pysam 0.15 - - bx-python 0.8 - - numpy 1.11 - - ipython-cluster-helper 0.6 - - idba_subasm 1.1.3a1 - - htslib 1.9 - - samtools 1.9 + host: + - python <3 + run: + - python <3 + - bwa 0.7.* + - flye 2.3.1 + - pysam 0.15 + - bx-python 0.8 + - numpy 1.11 + - ipython-cluster-helper 0.6 + - idba_subasm 1.1.3a1 + - htslib 1.9 + - samtools 1.9 + test: - commands: - - athena-meta -h | grep 'athena-meta' - - athena-meta --check_prereqs - - athena-meta --test + commands: + - athena-meta -h | grep 'athena-meta' + - athena-meta --check_prereqs + - athena-meta --test about: - home: https://github.com/abishara/athena_meta/ - summary: Athena read cloud assembler for metagenomes - license: MIT + home: https://github.com/abishara/athena_meta/ + summary: Athena read cloud assembler for metagenomes + license: MIT diff --git a/recipes/autodock-vina/meta.yaml b/recipes/autodock-vina/meta.yaml index 361d8c2ef8d15..968ce2e6ea7a2 100644 --- a/recipes/autodock-vina/meta.yaml +++ b/recipes/autodock-vina/meta.yaml @@ -3,13 +3,14 @@ package: version: 1.1.2 build: + noarch: generic number: 1 source: - url: http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz # [linux] - md5: 2605b04cae5071cbb9640fe112a5c01d # [linux] - url: http://vina.scripps.edu/download/autodock_vina_1_1_2_mac.tgz # [osx] - md5: b8165555fa13132e0658c36005e0edf3 # [osx] + - url: http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz # [linux] + md5: 2605b04cae5071cbb9640fe112a5c01d # [linux] + - url: http://vina.scripps.edu/download/autodock_vina_1_1_2_mac.tgz # [osx] + md5: b8165555fa13132e0658c36005e0edf3 # [osx] requirements: build: @@ -23,3 +24,7 @@ about: home: http://vina.scripps.edu/ license: Apache License 2.0 summary: AutoDock Vina is an open-source program for doing molecular docking + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/axiome/meta.yaml b/recipes/axiome/meta.yaml index cbb08ee4d24d8..6854cee266df2 100644 --- a/recipes/axiome/meta.yaml +++ b/recipes/axiome/meta.yaml @@ -7,19 +7,18 @@ source: md5: 428dc40ca56b71c3bbf0310df939ce7f build: + noarch: python number: 2 - skip: True # [not py27] entry_points: - axiome=axiome.axiome:main + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - npyscreen - + - python <3 + - pip run: - - python + - python <3 - npyscreen test: diff --git a/recipes/bamclipper/meta.yaml b/recipes/bamclipper/meta.yaml index b0e3a81418969..8098f9c6440fd 100644 --- a/recipes/bamclipper/meta.yaml +++ b/recipes/bamclipper/meta.yaml @@ -11,11 +11,10 @@ source: url: https://github.com/tommyau/{{ name|lower }}/archive/v{{ version }}.tar.gz build: + noarch: generic number: 0 requirements: - host: - - perl run: - samtools - parallel diff --git a/recipes/barrnap-python/build.sh b/recipes/barrnap-python/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/barrnap-python/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/barrnap-python/meta.yaml b/recipes/barrnap-python/meta.yaml index eb5858b2187eb..7d5151faeba2e 100644 --- a/recipes/barrnap-python/meta.yaml +++ b/recipes/barrnap-python/meta.yaml @@ -1,7 +1,5 @@ {% set name = 'barrnap' %} {% set version = '0.0.5' %} -{% set hash_type = "sha256" %} -{% set hash_value = "acac783c1f93e8e9585017be9e128f7f95d8ae77a9ed3b3656fa53d5043e0e21" %} package: name: barrnap-python @@ -9,22 +7,21 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - '{{ hash_type }}': '{{ hash_value }}' + sha256: acac783c1f93e8e9585017be9e128f7f95d8ae77a9ed3b3656fa53d5043e0e21 build: + noarch: python number: 1 - skip: True # [win or py2k or py34] requirements: host: - - python - - setuptools - + - python >=3 + - pip run: # we rely on having the original version installed to A) give credit and # B) ensure the most updated HMM database is included from barrnap - barrnap >=0.8 - - python + - python >=3 test: commands: diff --git a/recipes/barrnap/build.sh b/recipes/barrnap/build.sh index 57920e8e36812..36b9974db3c5f 100644 --- a/recipes/barrnap/build.sh +++ b/recipes/barrnap/build.sh @@ -2,6 +2,7 @@ DESTDIR="${PREFIX}/lib/barrnap" mkdir -p "${DESTDIR}" +mkdir -p ${PREFIX}/bin # copy selectively, we only need the perl script # in the bin folder and the db folder containing the diff --git a/recipes/barrnap/meta.yaml b/recipes/barrnap/meta.yaml index b3a361081a415..10bf6925f39a6 100644 --- a/recipes/barrnap/meta.yaml +++ b/recipes/barrnap/meta.yaml @@ -11,6 +11,7 @@ source: url: https://github.com/tseemann/{{ name }}/archive/{{ version }}.tar.gz build: + noarch: generic number: 2 requirements: diff --git a/recipes/bcbio-nextgen-vm/build.sh b/recipes/bcbio-nextgen-vm/build.sh deleted file mode 100644 index a975de6deaf62..0000000000000 --- a/recipes/bcbio-nextgen-vm/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -#sed -i.bak 's#!/usr/bin/env python -Es#!/usr/bin/env python#' scripts/bcbio_vm.py -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/bcbio-nextgen-vm/meta.yaml b/recipes/bcbio-nextgen-vm/meta.yaml index 367b547e322f4..4f92127483286 100644 --- a/recipes/bcbio-nextgen-vm/meta.yaml +++ b/recipes/bcbio-nextgen-vm/meta.yaml @@ -3,12 +3,13 @@ package: version: '0.1.6' build: + noarch: python number: 1 # Currently hitting conda errors on OSX # ERROR:conda.core.link:An error occurred while installing package # FileNotFoundError(2, "No such file or directory: '_placehold_pl/bin/python3.7' # https://circleci.com/gh/bioconda/bioconda-recipes/50765 - skip: true # [osx] + script: {{ PYTHON }} -m pip install --ignore-installed --no-deps -vv source: url: https://github.com/bcbio/bcbio-nextgen-vm/archive/8b46793.tar.gz @@ -17,8 +18,7 @@ source: requirements: host: - python - - setuptools - + - pip run: - python - six diff --git a/recipes/bcbio_monitor/build.sh b/recipes/bcbio_monitor/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/bcbio_monitor/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/bcbio_monitor/meta.yaml b/recipes/bcbio_monitor/meta.yaml index 4a300754e6f48..1b0b8fe02c8ea 100644 --- a/recipes/bcbio_monitor/meta.yaml +++ b/recipes/bcbio_monitor/meta.yaml @@ -9,24 +9,18 @@ source: sha256: d4563df1b9fe2d20039a4ec1556d3da1cdd23ebdc8ca10bd698edc35c6f2a2de build: + noarch: python number: 3 - skip: True # [not py27] entry_points: - bcbio_monitor = bcbio_monitor.cli:cli + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - flask >=0.10.1 - - gevent >=1.0 - - requests - - python-graphviz - - paramiko - - pyyaml - + - python <3 + - pip run: - - python + - python <3 - flask >=0.10.1 - gevent >=1.0 - requests diff --git a/recipes/bcbreport/build.sh b/recipes/bcbreport/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/bcbreport/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/bcbreport/meta.yaml b/recipes/bcbreport/meta.yaml index e078bf4f11a2d..307221432ec88 100644 --- a/recipes/bcbreport/meta.yaml +++ b/recipes/bcbreport/meta.yaml @@ -3,8 +3,9 @@ package: version: "0.99.29" build: + noarch: python number: 1 - skip: True # [osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/lpantano/bcbio.coverage/archive/23ecd4ec57e3a1b43e471a8a5400b865484d9bac.tar.gz @@ -13,7 +14,7 @@ source: requirements: host: - python - - setuptools + - pip run: - python diff --git a/recipes/bcl2fastq-nextseq/meta.yaml b/recipes/bcl2fastq-nextseq/meta.yaml index bfa1bd6bfe382..6bd37ecaa0b81 100644 --- a/recipes/bcl2fastq-nextseq/meta.yaml +++ b/recipes/bcl2fastq-nextseq/meta.yaml @@ -10,22 +10,16 @@ source: sha256: '{{sha256}}' build: + noarch: python number: 2 - skip: true # [not py27] - script: python setup.py install --single-version-externally-managed --record=record.txt + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - click - - pandas - - matplotlib - - numpy - - seaborn - + - python <3 + - pip run: - - python + - python <3 - click - pandas - matplotlib diff --git a/recipes/bcool/meta.yaml b/recipes/bcool/meta.yaml index 6391a3ed7c6bb..48cf4563dc746 100644 --- a/recipes/bcool/meta.yaml +++ b/recipes/bcool/meta.yaml @@ -10,21 +10,17 @@ source: sha256: ae92f117d7a2f355b5956e8ac389ea7d96e69bc2cd518da3eb86cd176225959e build: + noarch: generic number: 0 - skip: true # [osx] - skip: True # [py27] requirements: - host: - - python run: - - python + - python >=3 - bgreat - ntcard - bcalm - btrim - test: commands: - bcool diff --git a/recipes/bcov/meta.yaml b/recipes/bcov/meta.yaml index 8a4596836dc3e..a5b141d7be6de 100644 --- a/recipes/bcov/meta.yaml +++ b/recipes/bcov/meta.yaml @@ -10,16 +10,15 @@ build: number: 1 source: - fn: {{ name }}-{{ version }}.tar.gz url: http://biocomp.unibo.it/savojard/bcov/bcov-1.0.tar.gz sha256: f74f007a6e51f9719cafc0a90d77d2664c90714c3f71309f4b053dcf737a5beb requirements: build: - - gcc + - {{ compiler('c') }} + host: - glpk run: - - libgcc - glpk test: @@ -31,6 +30,7 @@ about: license: file license_file: COPYING summary: "BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence." + extra: identifiers: - biotools:bcov diff --git a/recipes/bctools/meta.yaml b/recipes/bctools/meta.yaml index f99d7f5ba2836..a648888d6db4e 100644 --- a/recipes/bctools/meta.yaml +++ b/recipes/bctools/meta.yaml @@ -10,6 +10,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/beast/meta.yaml b/recipes/beast/meta.yaml index 8620d4db56fed..b9d5ef38e74d8 100644 --- a/recipes/beast/meta.yaml +++ b/recipes/beast/meta.yaml @@ -10,6 +10,7 @@ source: sha256: '{{ sha256 }}' build: + noarch: generic number: 0 requirements: diff --git a/recipes/beast2/2.4.5/meta.yaml b/recipes/beast2/2.4.5/meta.yaml index 43bf2f78f1948..ebf0e33ab15b1 100644 --- a/recipes/beast2/2.4.5/meta.yaml +++ b/recipes/beast2/2.4.5/meta.yaml @@ -9,6 +9,7 @@ source: - beast_lib.patch build: + noarch: generic number: 1 requirements: diff --git a/recipes/beast2/2.5.0/meta.yaml b/recipes/beast2/2.5.0/meta.yaml index d4df1e6d2a9b4..e25a2d9d61a34 100644 --- a/recipes/beast2/2.5.0/meta.yaml +++ b/recipes/beast2/2.5.0/meta.yaml @@ -13,8 +13,8 @@ source: - beast_lib.patch build: + noarch: generic number: 0 - skip: True # [win] requirements: build: diff --git a/recipes/besst/meta.yaml b/recipes/besst/meta.yaml index 7e0694270f94c..9d20350303d26 100644 --- a/recipes/besst/meta.yaml +++ b/recipes/besst/meta.yaml @@ -12,11 +12,10 @@ source: build: noarch: python number: 2 - skip: true # [py3k] requirements: host: - - python + - python <3 - setuptools - pysam >=0.7 - networkx >=1.9 @@ -24,7 +23,7 @@ requirements: - scipy >=0.9 run: - - python + - python <3 - pysam >=0.7 - networkx >=1.9 - mathstats >=0.2.6 diff --git a/recipes/bgreat2/build.sh b/recipes/bgreat/build.sh similarity index 100% rename from recipes/bgreat2/build.sh rename to recipes/bgreat/build.sh diff --git a/recipes/bgreat2/meta.yaml b/recipes/bgreat/meta.yaml similarity index 100% rename from recipes/bgreat2/meta.yaml rename to recipes/bgreat/meta.yaml diff --git a/recipes/bibliospec/meta.yaml b/recipes/bibliospec/meta.yaml index de77e1c8525f8..56076744eb59d 100644 --- a/recipes/bibliospec/meta.yaml +++ b/recipes/bibliospec/meta.yaml @@ -14,11 +14,6 @@ build: script: bash -c "./quickbuild.sh -j{{ CPU_COUNT }} address-model=64 runtime-link=shared pwiz_tools/BiblioSpec && cp build-linux-x86_64/gcc-release-x86_64/* $PREFIX/bin" skip: True # [osx] -extra: - skip-lints: - - uses_git_url - - missing_hash - requirements: build: - {{ compiler('cxx') }} @@ -33,3 +28,8 @@ about: test: commands: - BlibSearch -h + +extra: + skip-lints: + - uses_vcs_url + - missing_hash diff --git a/recipes/bigsi/meta.yaml b/recipes/bigsi/meta.yaml index 2b710c43ced45..ed18ebd125b77 100644 --- a/recipes/bigsi/meta.yaml +++ b/recipes/bigsi/meta.yaml @@ -20,10 +20,8 @@ requirements: host: - python >=3 - pip - run: - python >=3 - - cython - bsddb3 - libdb - hug diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml index c8687959401ec..85b17681059ad 100644 --- a/recipes/biobambam/meta.yaml +++ b/recipes/biobambam/meta.yaml @@ -6,17 +6,21 @@ package: name: {{ name }} version: {{ version }} + source: url: https://github.com/gt1/biobambam2/releases/download/{{ version }}-release-{{ datestamp }}/biobambam2-{{ version }}-release-{{ datestamp }}-x86_64-etch-linux-gnu.tar.gz sha256: {{ sha256hash }} + build: number: 1 binary_relocation: false - skip: True # [osx] + skip: True # [osx] requirements: build: + - {{ compiler('c') }} run: + test: commands: - bamsormadup --help diff --git a/recipes/biodiff/meta.yaml b/recipes/biodiff/meta.yaml index a4af7169af043..2b635a409e6ef 100644 --- a/recipes/biodiff/meta.yaml +++ b/recipes/biodiff/meta.yaml @@ -18,6 +18,7 @@ requirements: - autoconf - automake - pandoc + - {{ compiler('c') }} run: - perl diff --git a/recipes/BioExcel_SeqQC/build.sh b/recipes/bioexcel_seqqc/build.sh similarity index 100% rename from recipes/BioExcel_SeqQC/build.sh rename to recipes/bioexcel_seqqc/build.sh diff --git a/recipes/BioExcel_SeqQC/meta.yaml b/recipes/bioexcel_seqqc/meta.yaml similarity index 100% rename from recipes/BioExcel_SeqQC/meta.yaml rename to recipes/bioexcel_seqqc/meta.yaml diff --git a/recipes/biofluff/build.sh b/recipes/biofluff/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/biofluff/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/biofluff/meta.yaml b/recipes/biofluff/meta.yaml index a1598a7442a76..811e0a5160b4a 100644 --- a/recipes/biofluff/meta.yaml +++ b/recipes/biofluff/meta.yaml @@ -9,23 +9,17 @@ source: sha256: b0e07ed2ec00ce749509c609f666fcb273679d4a6ce92fb5f7512e018d54eb87 build: + noarch: python number: 0 - skip: True # [not py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python >=3 - setuptools >=38.6.0 - - scipy - - matplotlib >=2 - - pysam - - htseq - - pybedtools - - palettable - - scikit-learn - - pybigwig + - pip run: - - python + - python >=3 - scipy - matplotlib >=2 - pysam diff --git a/recipes/biogridpy/build.sh b/recipes/biogridpy/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/biogridpy/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/biogridpy/meta.yaml b/recipes/biogridpy/meta.yaml index b7932c1e23462..614b9996e9a9e 100644 --- a/recipes/biogridpy/meta.yaml +++ b/recipes/biogridpy/meta.yaml @@ -3,7 +3,9 @@ package: version: "0.1.1" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/97/3f/389d2928ed5d59a4fde16a506e8c6e0e04620f7f61fc84caefca2aa7d84d/biogridpy-0.1.1.tar.gz @@ -12,8 +14,7 @@ source: requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/biokit/build.sh b/recipes/biokit/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/biokit/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index 05458cc9bb4ba..57cae42d6f012 100644 --- a/recipes/biokit/meta.yaml +++ b/recipes/biokit/meta.yaml @@ -9,7 +9,8 @@ source: sha256: c45f13b6653887b38e061279abdd562f4e6ed170ff0d551aba576e42f1954c85 build: - skip: True # [py34] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 0 # Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda @@ -17,19 +18,7 @@ build: requirements: host: - python - - setuptools - - easydev >=0.9.34 - - pandas - - colormap - - scipy - - xmltodict - - numpydoc - - bioservices - - mesalib - - biopython - - pyyaml - - colorlog - + - pip run: - python - easydev >=0.9.34 @@ -42,8 +31,6 @@ requirements: - bioservices - matplotlib - mesalib - #- xz - #- libxcb - biopython - pyyaml - colorlog @@ -63,9 +50,3 @@ extra: container: # needs libGL.so.1 extended-base: true - skip-lints: - - uses_setuptools - - - - diff --git a/recipes/biolib/meta.yaml b/recipes/biolib/meta.yaml index 264a2a9ac4188..a17ee5e639c3a 100644 --- a/recipes/biolib/meta.yaml +++ b/recipes/biolib/meta.yaml @@ -10,12 +10,12 @@ source: sha256: 232e0d02d4b0a759f94c613f22ab3a9e5bb9230666308446fa8e08c7597db156 build: + noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed" requirements: host: - - future >=0.16.0 - pip - python run: @@ -37,7 +37,5 @@ about: summary: Package for common tasks in bioinformatic. extra: - skip-lints: - - should_be_noarch recipe-maintainers: - npavlovikj diff --git a/recipes/biolite/build.sh b/recipes/biolite/build.sh deleted file mode 100644 index 2a540457a6649..0000000000000 --- a/recipes/biolite/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -pip install --no-deps . diff --git a/recipes/biolite/meta.yaml b/recipes/biolite/meta.yaml index 8bc2532e4480d..1869d9ccaa870 100644 --- a/recipes/biolite/meta.yaml +++ b/recipes/biolite/meta.yaml @@ -7,17 +7,16 @@ source: sha256: 61d9268278a50b3ea03b7a4e1a5424beeff2482634ab570d6c66925dac26d9e2 build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools + - python <3 - pip run: - - python - - setuptools + - python <3 - biolite-tools ==0.4.0 - biopython ==1.68 - dendropy ==4.2.0 diff --git a/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml b/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml index 3a089dba75548..2aa360ae06a1d 100644 --- a/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml +++ b/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml @@ -4,15 +4,20 @@ package: name: biopet-extractadaptersfastqc version: '0.1' + source: url: https://github.com/biopet/extractadaptersfastqc/releases/download/v0.1/ExtractAdaptersFastqc-assembly-0.1.jar sha256: e060b0da4cfe3b7273242ede54e56f61ef3f733795958022cac92f23b1a956f4 + build: + noarch: generic number: 1 + requirements: run: - openjdk >=8,<9 - python + about: home: https://github.com/biopet/extractadaptersfastqc license: MIT @@ -23,12 +28,13 @@ about: The sequences can be output in plain text format with a newline character as a separator between the sequences. Alternatively the sequences can be output in FASTA format. - For documentation and manuals visit our github.io page: https://biopet.github.io/extractadaptersfastqc + test: commands: - biopet-extractadaptersfastqc --version - biopet-extractadaptersfastqc --help + extra: notes: 'biopet-extractadaptersfastqc is a Java program that comes with a custom wrapper shell script. By default ''no default java option'' is set in the wrapper. @@ -36,4 +42,3 @@ extra: want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ''biopet-extractadaptersfastqc -Xms512m -Xmx1g''. ' - diff --git a/recipes/biopet-extractadaptersfastqc/0.2/biopet-extractadaptersfastqc.py b/recipes/biopet-extractadaptersfastqc/0.2/biopet-extractadaptersfastqc.py deleted file mode 100755 index da4c42e244969..0000000000000 --- a/recipes/biopet-extractadaptersfastqc/0.2/biopet-extractadaptersfastqc.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-extractadaptersfastqc JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'ExtractAdaptersFastqc-assembly-0.2.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-extractadaptersfastqc/0.2/build.sh b/recipes/biopet-extractadaptersfastqc/0.2/build.sh deleted file mode 100644 index 80a9413f79980..0000000000000 --- a/recipes/biopet-extractadaptersfastqc/0.2/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp ExtractAdaptersFastqc-assembly-0.2.jar $outdir/ExtractAdaptersFastqc-assembly-0.2.jar -cp $RECIPE_DIR/biopet-extractadaptersfastqc.py $outdir/biopet-extractadaptersfastqc -ln -s $outdir/biopet-extractadaptersfastqc $PREFIX/bin - diff --git a/recipes/biopet-extractadaptersfastqc/0.2/meta.yaml b/recipes/biopet-extractadaptersfastqc/0.2/meta.yaml deleted file mode 100644 index 86f93501fe558..0000000000000 --- a/recipes/biopet-extractadaptersfastqc/0.2/meta.yaml +++ /dev/null @@ -1,39 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-extractadaptersfastqc - version: '0.2' -source: - url: https://github.com/biopet/extractadaptersfastqc/releases/download/v0.2/ExtractAdaptersFastqc-assembly-0.2.jar - sha256: 2e75a923af910f94392c768270150bfbcbcd73e83d115815310d568ed4e5d34e -build: - number: 1 -requirements: - run: - - openjdk >=8,<9 - - python -about: - home: https://github.com/biopet/extractadaptersfastqc - license: MIT - summary: ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report. - description: |- - ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report. - These sequences can be used as input for a QC tool such as cutadapt. - The sequences can be output in plain text format with a - newline character as a separator between the sequences. - Alternatively the sequences can be output in FASTA format. - - For documentation and manuals visit our github.io page: https://biopet.github.io/extractadaptersfastqc -test: - commands: - - biopet-extractadaptersfastqc --version - - biopet-extractadaptersfastqc --help -extra: - notes: 'biopet-extractadaptersfastqc is a Java program that comes with a custom - wrapper shell script. By default ''no default java option'' is set in the wrapper. - The command that runs the program is ''biopet-extractadaptersfastqc''. If you - want to overwrite it you can specify memory options directly after your binaries. - If you have _JAVA_OPTIONS set globally this will take precedence. For example - run it with ''biopet-extractadaptersfastqc -Xms512m -Xmx1g''. ' - diff --git a/recipes/biopet-extractadaptersfastqc/meta.yaml b/recipes/biopet-extractadaptersfastqc/meta.yaml index 86f93501fe558..4f4a3a686333c 100644 --- a/recipes/biopet-extractadaptersfastqc/meta.yaml +++ b/recipes/biopet-extractadaptersfastqc/meta.yaml @@ -1,18 +1,20 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - package: name: biopet-extractadaptersfastqc version: '0.2' + source: url: https://github.com/biopet/extractadaptersfastqc/releases/download/v0.2/ExtractAdaptersFastqc-assembly-0.2.jar sha256: 2e75a923af910f94392c768270150bfbcbcd73e83d115815310d568ed4e5d34e + build: + noarch: generic number: 1 + requirements: run: - openjdk >=8,<9 - python + about: home: https://github.com/biopet/extractadaptersfastqc license: MIT @@ -23,12 +25,13 @@ about: The sequences can be output in plain text format with a newline character as a separator between the sequences. Alternatively the sequences can be output in FASTA format. - For documentation and manuals visit our github.io page: https://biopet.github.io/extractadaptersfastqc + test: commands: - biopet-extractadaptersfastqc --version - biopet-extractadaptersfastqc --help + extra: notes: 'biopet-extractadaptersfastqc is a Java program that comes with a custom wrapper shell script. By default ''no default java option'' is set in the wrapper. @@ -36,4 +39,3 @@ extra: want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ''biopet-extractadaptersfastqc -Xms512m -Xmx1g''. ' - diff --git a/recipes/biopet-sampleconfig/0.1/meta.yaml b/recipes/biopet-sampleconfig/0.1/meta.yaml index e64585ba5fc9e..0c6dda0f53045 100644 --- a/recipes/biopet-sampleconfig/0.1/meta.yaml +++ b/recipes/biopet-sampleconfig/0.1/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/biopet/sampleconfig/releases/download/v0.1/SampleConfig-assembly-0.1.jar sha256: 8f2e0c9a36190834fbb8203aff1dd163e48060075f2e343f88ae92a124e052a7 build: + noarch: generic number: 1 requirements: run: diff --git a/recipes/biopet-sampleconfig/0.3/biopet-sampleconfig.py b/recipes/biopet-sampleconfig/0.3/biopet-sampleconfig.py deleted file mode 100755 index a9397631cd6d1..0000000000000 --- a/recipes/biopet-sampleconfig/0.3/biopet-sampleconfig.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-sampleconfig JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'SampleConfig-assembly-0.3.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-sampleconfig/0.3/build.sh b/recipes/biopet-sampleconfig/0.3/build.sh deleted file mode 100644 index fb5f77d0eed99..0000000000000 --- a/recipes/biopet-sampleconfig/0.3/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp SampleConfig-assembly-0.3.jar $outdir/SampleConfig-assembly-0.3.jar -cp $RECIPE_DIR/biopet-sampleconfig.py $outdir/biopet-sampleconfig -ln -s $outdir/biopet-sampleconfig $PREFIX/bin - diff --git a/recipes/biopet-sampleconfig/0.3/meta.yaml b/recipes/biopet-sampleconfig/0.3/meta.yaml deleted file mode 100644 index 7d20894eb35a3..0000000000000 --- a/recipes/biopet-sampleconfig/0.3/meta.yaml +++ /dev/null @@ -1,63 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-sampleconfig - version: '0.3' -source: - url: https://github.com/biopet/sampleconfig/releases/download/v0.3/SampleConfig-assembly-0.3.jar - sha256: f14655c26e5208a82d6a27fedef77b8961bc47eb3b9fdaa61ba67d60b282af7f -build: - noarch: generic - number: 0 -requirements: - run: - - openjdk >=8,<9 - - python -about: - home: https://github.com/biopet/sampleconfig - license: MIT - summary: '#### Tools - ExtractTsv This mean can extract samples, libraries and - readgroups from a sample config file.' - description: | - #### Tools - ExtractTsv - - This mean can extract samples, libraries and readgroups from a sample config file. This meant as a supporting tool inside wdl pipelines. - It can also output a single layer as tsv file. - - - #### Tools - ReadFromTsv - - This tool enables a user to create a full sample sheet in JSON format or - YAML format, suitable for all Biopet Queue pipelines, from TSV file(s). - - - #### Tools - CromwellArrays - - This tool will convert the sample configs to a array based format that can be used inside wdl pipelines. - This tool is only to support biowdl pipelines. - - - #### Tools - CaseControl - - This tool will extract the case-control pairs from a sample config file. - It will read the headers of the bam files to confirm that samples do exist. - - For documentation and manuals visit our github.io page: https://biopet.github.io/sampleconfig -test: - commands: - - biopet-sampleconfig ExtractTsv --version - - biopet-sampleconfig ExtractTsv --help - - biopet-sampleconfig ReadFromTsv --version - - biopet-sampleconfig ReadFromTsv --help - - biopet-sampleconfig CromwellArrays --version - - biopet-sampleconfig CromwellArrays --help -extra: - notes: | - biopet-sampleconfig is a Java program that comes with a custom wrapper shell script. - By default 'no default java option' is set in the wrapper. - The command that runs the program is 'biopet-sampleconfig'. - If you want to overwrite it you can specify memory options directly after your binaries. - If you have _JAVA_OPTIONS set globally this will take precedence. - For example run it with 'biopet-sampleconfig -Xms512m -Xmx1g'. - diff --git a/recipes/biopet-validatefastq/0.1.1/meta.yaml b/recipes/biopet-validatefastq/0.1.1/meta.yaml index b1deb1cb924d1..56a082e2e45e7 100644 --- a/recipes/biopet-validatefastq/0.1.1/meta.yaml +++ b/recipes/biopet-validatefastq/0.1.1/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/biopet/validatefastq/releases/download/v0.1.1/validatefastq-assembly-0.1.1.jar sha256: 001f36b95c5d39052b98d9858d359dc6940922811c0bcf907f8c0f5062ab5ead build: + noarch: generic number: 1 requirements: run: diff --git a/recipes/biopet-validatefastq/meta.yaml b/recipes/biopet-validatefastq/meta.yaml index b1deb1cb924d1..56a082e2e45e7 100644 --- a/recipes/biopet-validatefastq/meta.yaml +++ b/recipes/biopet-validatefastq/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/biopet/validatefastq/releases/download/v0.1.1/validatefastq-assembly-0.1.1.jar sha256: 001f36b95c5d39052b98d9858d359dc6940922811c0bcf907f8c0f5062ab5ead build: + noarch: generic number: 1 requirements: run: diff --git a/recipes/bioservices/meta.yaml b/recipes/bioservices/meta.yaml index ac53175390f1f..98e871aee10f9 100644 --- a/recipes/bioservices/meta.yaml +++ b/recipes/bioservices/meta.yaml @@ -12,14 +12,8 @@ source: build: noarch: python - skip: False number: 0 -# For version 1.5.1, pandas could not be used on bioconda build platform -# Could be due to missing cairo -# (https://github.com/bioconda/bioconda-recipes/pull/7152) -# but could not build it after many trials. -# Next release (e.g. 1.5.2 should use pandas again) requirements: host: - python @@ -40,9 +34,9 @@ requirements: test: imports: - #- bioservices - #- bioservices.apps - #- bioservices.mapping + - bioservices + - bioservices.apps + - bioservices.mapping about: home: http://pypi.python.org/pypi/bioservices diff --git a/recipes/biotradis/meta.yaml b/recipes/biotradis/meta.yaml index 603f0c5d9ed58..46f056ce7416b 100644 --- a/recipes/biotradis/meta.yaml +++ b/recipes/biotradis/meta.yaml @@ -12,17 +12,18 @@ source: build: number: 4 - noarch: True + noarch: generic requirements: - build: + host: + - perl - perl-app-cpanminus - perl-module-build - perl-moose - perl-local-lib - host: - - r-base >=3.5 + - r-base run: + - perl - perl-app-cpanminus - perl-parallel-forkmanager - perl-pathtools @@ -33,7 +34,7 @@ requirements: - smalt - samtools - bioconductor-edger - - r-base >=3.5 + - r-base - r-getopt - r-mass - bwa @@ -52,5 +53,5 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url diff --git a/recipes/bis-snp-utils/meta.yaml b/recipes/bis-snp-utils/meta.yaml index 48f661b011f7e..44e9f5c6bfd50 100644 --- a/recipes/bis-snp-utils/meta.yaml +++ b/recipes/bis-snp-utils/meta.yaml @@ -7,6 +7,7 @@ package: version: {{ version }} build: + noarch: generic number: 2 source: diff --git a/recipes/bis-snp/meta.yaml b/recipes/bis-snp/meta.yaml index 847f88ce556e1..fbb0cd7717fb8 100644 --- a/recipes/bis-snp/meta.yaml +++ b/recipes/bis-snp/meta.yaml @@ -9,6 +9,7 @@ source: sha256: 4d3913c1d5e992d36bfea8e5a472d9f0e3e0daefac37b755e2730fd4930016ac build: + noarch: generic number: 1 requirements: diff --git a/recipes/biskit/build.sh b/recipes/biskit/build.sh deleted file mode 100644 index e3b0eb7e3ac1a..0000000000000 --- a/recipes/biskit/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/biskit/meta.yaml b/recipes/biskit/meta.yaml index 45b3a0f6f7211..277f66e4d4a60 100644 --- a/recipes/biskit/meta.yaml +++ b/recipes/biskit/meta.yaml @@ -1,7 +1,5 @@ {% set name = "biskit" %} {% set version = "2.4.3" %} -{% set hash_type = "sha256" %} -{% set hash_value = "def51141c1037d86818e30ad904487cdfcdeaca726a97f5cb58da3a7d5ac5d57" %} package: name: {{ name|lower }} @@ -9,21 +7,19 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - {{ hash_type }}: {{ hash_value }} + sha256: def51141c1037d86818e30ad904487cdfcdeaca726a97f5cb58da3a7d5ac5d57 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - scipy - - biopython + - python <3 + - pip run: - - python + - python <3 - numpy - scipy - biopython diff --git a/recipes/bismark/meta.yaml b/recipes/bismark/meta.yaml index 0ab8a93333c49..1113b2ffbf088 100644 --- a/recipes/bismark/meta.yaml +++ b/recipes/bismark/meta.yaml @@ -6,6 +6,7 @@ package: version: {{ version }} build: + noarch: generic number: 0 source: diff --git a/recipes/bitstring/build.sh b/recipes/bitstring/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/bitstring/build.sh +++ /dev/null @@ -1,9 +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/bitstring/meta.yaml b/recipes/bitstring/meta.yaml index 17112c2c52d63..89feddc7d8134 100644 --- a/recipes/bitstring/meta.yaml +++ b/recipes/bitstring/meta.yaml @@ -3,7 +3,9 @@ package: version: "3.1.5" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/f3/e5/dfe4c49c93d174a5fd807ed307d3a3f38c6b3e140972945f81a5f5578ca7/bitstring-3.1.5.zip @@ -12,10 +14,14 @@ source: requirements: host: - python - + - pip run: - python +test: + imports: + - bitstring + about: home: https://github.com/scott-griffiths/bitstring license: MIT License diff --git a/recipes/blastalign/meta.yaml b/recipes/blastalign/meta.yaml index 45fde8a57f2e4..bdd469485f488 100644 --- a/recipes/blastalign/meta.yaml +++ b/recipes/blastalign/meta.yaml @@ -15,9 +15,8 @@ source: - BlastAlignP.patch requirements: - host: - - python - - perl + build: + - {{ compiler('c') }} run: - python - perl diff --git a/recipes/blobtools/meta.yaml b/recipes/blobtools/meta.yaml index c2fa819590c5a..4e8ecddaa619d 100644 --- a/recipes/blobtools/meta.yaml +++ b/recipes/blobtools/meta.yaml @@ -9,19 +9,19 @@ source: md5: cca6193d3155cd2f61e41389197aa3ca build: + noarch: python number: 3 - skip: True # [not (linux and py27)] requirements: host: - - python + - python <3 + - pip - docopt - matplotlib - ujson - samtools - run: - - python + - python <3 - docopt - matplotlib - ujson diff --git a/recipes/bmfilter/meta.yaml b/recipes/bmfilter/meta.yaml index 3886db13fff65..fb72bd53c7139 100644 --- a/recipes/bmfilter/meta.yaml +++ b/recipes/bmfilter/meta.yaml @@ -3,20 +3,13 @@ package: version: 3.101 source: - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] - md5: 719474a0e3b54449cbe06f6e442994dd # [linux] - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/bmfilter # [osx] - md5: ef79071be499ed23e9f3a19c9c323775 # [osx] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] + md5: 719474a0e3b54449cbe06f6e442994dd # [linux] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/bmfilter # [osx] + md5: ef79071be499ed23e9f3a19c9c323775 # [osx] build: number: 2 - skip: False - -requirements: - build: - - {{ compiler('cxx') }} - - {{ compiler('c') }} - run: test: commands: @@ -26,3 +19,8 @@ about: home: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ license: Public Domain summary: "bmfilter is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets" + +extra: + skip-lints: + - should_not_be_noarch_source + - should_be_noarch_generic diff --git a/recipes/bmtagger/meta.yaml b/recipes/bmtagger/meta.yaml index 9de9b0015885c..beff4ad2ed7f7 100644 --- a/recipes/bmtagger/meta.yaml +++ b/recipes/bmtagger/meta.yaml @@ -1,36 +1,44 @@ package: name: bmtagger version: 3.101 + source: - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] - md5: 719474a0e3b54449cbe06f6e442994dd # [linux] - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/bmtagger.sh # [osx] - patches: - - bmtagger.sh.osxpatch # [osx] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] + md5: 719474a0e3b54449cbe06f6e442994dd # [linux] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/bmtagger.sh # [osx] + md5: d861f6fe5ed658f274d0b37872ca65f5 # [osx] + patches: + - bmtagger.sh.osxpatch # [osx] + build: number: 4 - skip: False + requirements: build: - #- {{ compiler('c') }} + - {{ compiler('c') }} + host: - blast - srprism - bmfilter - bmtool - extract_fullseq run: - - gnu-getopt # [osx] + - gnu-getopt # [osx] - blast - srprism - bmfilter - bmtool - extract_fullseq -extra: - notes: "You may find it necessary to create a bmtagger.conf file to specify paired or single-end searching. The file should contain the line 'srprismopts=\"-b 100000000 -n 5 -R 0 -r 1 -M 7168\"' along with '-p true' or '-p false' for paired, and single, respectively. This config file can be passed to bmtagger.sh via the '-C' option." test: commands: - "bmtagger.sh -V &> /dev/null" + about: home: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ license: Public Domain summary: BMTagger aka Best Match Tagger is for removing human reads from metagenomics datasets + +extra: + skip-lints: + - should_not_be_noarch_source + notes: "You may find it necessary to create a bmtagger.conf file to specify paired or single-end searching. The file should contain the line 'srprismopts=\"-b 100000000 -n 5 -R 0 -r 1 -M 7168\"' along with '-p true' or '-p false' for paired, and single, respectively. This config file can be passed to bmtagger.sh via the '-C' option." diff --git a/recipes/bmtool/meta.yaml b/recipes/bmtool/meta.yaml index c34f69bb74a52..53a104276f5e3 100644 --- a/recipes/bmtool/meta.yaml +++ b/recipes/bmtool/meta.yaml @@ -3,19 +3,16 @@ package: version: 3.101 source: - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] - md5: 719474a0e3b54449cbe06f6e442994dd # [linux] - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/bmtool # [osx] - md5: 43f112115af7ef2a28c6a64b31374c12 # [osx] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] + md5: 719474a0e3b54449cbe06f6e442994dd # [linux] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/bmtool # [osx] + md5: 43f112115af7ef2a28c6a64b31374c12 # [osx] build: number: 2 - skip: False requirements: build: - - {{ compiler('cxx') }} - - {{ compiler('c') }} run: test: @@ -25,3 +22,8 @@ about: home: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ license: Public Domain summary: "bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets" + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/braker/meta.yaml b/recipes/braker/meta.yaml index 4c60b9e0f6bd4..2a21f479e4e88 100644 --- a/recipes/braker/meta.yaml +++ b/recipes/braker/meta.yaml @@ -7,8 +7,8 @@ source: sha256: 9e959984f739208d2a0aab4cc978e7b11db11a86a25fcc5b8f71c9a31e9239f2 build: + noarch: generic number: 3 - skip: True # [osx] requirements: build: diff --git a/recipes/breakseq2/build.sh b/recipes/breakseq2/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/breakseq2/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/breakseq2/meta.yaml b/recipes/breakseq2/meta.yaml index 82e949a5dcc2d..2104d1761c842 100644 --- a/recipes/breakseq2/meta.yaml +++ b/recipes/breakseq2/meta.yaml @@ -10,21 +10,22 @@ source: build: number: 2 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - - python + - python <3 - cython - - pysam ==0.7.7 - - biopython ==1.65 - + - pip + - pysam 0.7.7 + - biopython 1.65 run: - - python - - cython - - pysam ==0.7.7 - - biopython ==1.65 - - samtools ==0.1.19 + - python <3 + - pysam 0.7.7 + - biopython 1.65 + - samtools 0.1.19 - bwa test: diff --git a/recipes/brockman-pipeline/meta.yaml b/recipes/brockman-pipeline/meta.yaml index fa5765f0eea53..c1965b01aca78 100644 --- a/recipes/brockman-pipeline/meta.yaml +++ b/recipes/brockman-pipeline/meta.yaml @@ -2,6 +2,7 @@ {% set sha256 = "17c2e319e5c383b141c91ce295b562821358f3ef808ef1f1def57fe3ebe45917" %} build: + noarch: generic number: 2 package: diff --git a/recipes/bs-seeker2/meta.yaml b/recipes/bs-seeker2/meta.yaml index 0212971d7b7f8..ee94b668bea4e 100644 --- a/recipes/bs-seeker2/meta.yaml +++ b/recipes/bs-seeker2/meta.yaml @@ -3,17 +3,16 @@ package: version: "2.1.0" build: + noarch: generic number: 1 - skip: True # [py3k] source: url: http://pellegrini.mcdb.ucla.edu/BS_Seeker2/BSseeker2_v2.1.0.tar.bz md5: 2f3cb74a75453140f20e396ee68402bf requirements: - host: run: - - python + - python <3 - pysam - bowtie2 diff --git a/recipes/bsmap/meta.yaml b/recipes/bsmap/meta.yaml index f510be8c93e74..c78c301a20ee6 100644 --- a/recipes/bsmap/meta.yaml +++ b/recipes/bsmap/meta.yaml @@ -20,8 +20,8 @@ build: requirements: build: - {{ compiler('cxx') }} - - python host: + - python - zlib run: - python @@ -47,3 +47,5 @@ extra: identifiers: - biotools:bsmap - doi:10.1186/1471-2105-10-232 + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/burrito-fillings/0.1.1/build.sh b/recipes/burrito-fillings/0.1.1/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/burrito-fillings/0.1.1/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/burrito-fillings/0.1.1/meta.yaml b/recipes/burrito-fillings/meta.yaml similarity index 84% rename from recipes/burrito-fillings/0.1.1/meta.yaml rename to recipes/burrito-fillings/meta.yaml index b1cb3d9288b58..7082c8eb49bd8 100644 --- a/recipes/burrito-fillings/0.1.1/meta.yaml +++ b/recipes/burrito-fillings/meta.yaml @@ -7,12 +7,14 @@ source: md5: ea65051e674aedfad8bbfdfa63f2c4d8 build: + noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python >=3.5 - - setuptools + - pip run: - python >=3.5 - scikit-bio >=0.2.1,<0.3.0 diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index a7bdfd0e1ddbb..8e19320e55839 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -7,6 +7,7 @@ package: version: {{ version }} build: + noarch: python number: 12 source: @@ -50,5 +51,3 @@ extra: identifiers: - biotools:busco - doi:10.1093/bioinformatics/btv351 - skip-lints: - - should_be_noarch diff --git a/recipes/bwakit/meta.yaml b/recipes/bwakit/meta.yaml index 3ff2275430fc2..7124204a6dcd6 100644 --- a/recipes/bwakit/meta.yaml +++ b/recipes/bwakit/meta.yaml @@ -13,6 +13,7 @@ build: requirements: build: + - {{ compiler('c') }} run: - perl diff --git a/recipes/bwapy/meta.yaml b/recipes/bwapy/meta.yaml index 887b6ee7cbde3..fe7925e56926f 100644 --- a/recipes/bwapy/meta.yaml +++ b/recipes/bwapy/meta.yaml @@ -9,11 +9,6 @@ source: build: number: 1 skip: True # [py27] - -extra: - skip-lints: - - uses_git_url - - missing_hash requirements: build: @@ -23,14 +18,12 @@ requirements: - setuptools - cffi - zlib - run: - python - cffi - zlib test: - imports: - bwapy @@ -38,3 +31,8 @@ about: home: https://github.com/nanoporetech/bwapy license: Mozilla Public License Version 2.0 summary: "Bwapy provides python wrappers for bwa." + +extra: + skip-lints: + - uses_vcs_url + - missing_hash diff --git a/recipes/bwise/meta.yaml b/recipes/bwise/meta.yaml index 7148ad5ea7273..a0b329eb7c558 100644 --- a/recipes/bwise/meta.yaml +++ b/recipes/bwise/meta.yaml @@ -12,7 +12,6 @@ source: build: number: 0 skip: true # [osx] - skip: True # [py27] requirements: build: @@ -20,7 +19,7 @@ requirements: - {{ compiler('cxx') }} run: - - python + - python >=3 - bgreat - bcalm - btrim diff --git a/recipes/cactus/build.sh b/recipes/cactus/build.sh index 2621fef130f11..9111d0275c29d 100755 --- a/recipes/cactus/build.sh +++ b/recipes/cactus/build.sh @@ -35,7 +35,7 @@ mkdir submodules/hal/lib mkdir submodules/hal/bin make -$PYTHON setup.py install +$PYTHON -m pip install --ignore-installed --no-deps -vv cp -r bin/* ${PREFIX}/bin cp -r submodules/hal ${PREFIX}/lib/python2.7/site-packages diff --git a/recipes/cactus/meta.yaml b/recipes/cactus/meta.yaml index 7e475aa2eaa72..e70cfac7f7d80 100755 --- a/recipes/cactus/meta.yaml +++ b/recipes/cactus/meta.yaml @@ -5,7 +5,6 @@ package: source: url: https://github.com/pbasting/cactus/archive/833d8ca015deecdfa5d0aca01211632cdaca9e58.zip md5: 61ba6e8093a6649c43da1950074d9d5f - patches: # changes c++ std for sonlib make to c++ 11 - sonlib_include.patch @@ -14,50 +13,43 @@ source: build: number: 1 - skip: true # [osx] - + skip: true # [osx or not py2k] requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - python=2.7 - - zlib host: - - python=2.7 + - python - zlib - setuptools - kyototycoon - + - cython run: - decorator - subprocess32 - psutil - - networkx=1.11 - - python=2.7 + - networkx 1.11 + - python - zlib - kyototycoon - biopython - - toil=3.14.0 + - toil 3.14.0 - ucsc-fatotwobit - ucsc-bedsort - ucsc-bedtobigbed - ucsc-bigbedtobed - - openssl=1.0.2 + - openssl - sonlib - jobtree - - cython - test: commands: - cactus -h - hal2assemblyHub.py -h - about: home: https://github.com/ComparativeGenomicsToolkit/cactus license: https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/LICENSE.txt summary: 'Cactus is a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs' - diff --git a/recipes/cage/meta.yaml b/recipes/cage/meta.yaml index 734918f2a9ed6..d8affdf9985a1 100644 --- a/recipes/cage/meta.yaml +++ b/recipes/cage/meta.yaml @@ -9,7 +9,7 @@ source: build: number: 2 - skip: True # [osx] + skip: True # [osx] requirements: build: @@ -26,7 +26,6 @@ test: commands: - cage --version - bamdump --help - # - cage-classify.py --help about: home: https://github.com/adambloniarz/CAGe @@ -35,4 +34,4 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url diff --git a/recipes/cansnper/build.sh b/recipes/cansnper/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/cansnper/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/cansnper/meta.yaml b/recipes/cansnper/meta.yaml index 1040600568176..4bdf56f2a4192 100644 --- a/recipes/cansnper/meta.yaml +++ b/recipes/cansnper/meta.yaml @@ -7,7 +7,7 @@ package: build: number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/adrlar/CanSNPer/archive/v{{ version }}.tar.gz @@ -15,14 +15,10 @@ source: requirements: host: - - python - - setuptools - - ete2 - - numpy - - pyqt 4.* - + - python <3 + - pip run: - - python + - python <3 - ete2 - numpy - pyqt 4.* diff --git a/recipes/cap3/meta.yaml b/recipes/cap3/meta.yaml index ffda86b31c771..22361265107f7 100644 --- a/recipes/cap3/meta.yaml +++ b/recipes/cap3/meta.yaml @@ -3,21 +3,29 @@ package: version: '10.2011' source: - url: http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar # [linux] - sha256: 3aff30423e052887925b32f31bdd76764406661f2be3750afbf46341c3d38a06 # [linux] - url: http://seq.cs.iastate.edu/CAP3/cap3.macosx.intel64.tar # [osx] - sha256: 4b6e8fa6b39147b23ada6add080854ea9fadace9a9c8870a97ac79ff1c75338e # [osx] + - url: http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar # [linux] + sha256: 3aff30423e052887925b32f31bdd76764406661f2be3750afbf46341c3d38a06 # [linux] + - url: http://seq.cs.iastate.edu/CAP3/cap3.macosx.intel64.tar # [osx] + sha256: 4b6e8fa6b39147b23ada6add080854ea9fadace9a9c8870a97ac79ff1c75338e # [osx] build: number: 1 +requirements: + build: + - {{ compiler('c') }} + test: commands: - - cap3 2>&1 | grep "02/10/15" # [linux] - - cap3 2>&1 | grep "12/21/07" # [osx] + - cap3 2>&1 | grep "02/10/15" # [linux] + - cap3 2>&1 | grep "12/21/07" # [osx] about: home: http://seq.cs.iastate.edu/ summary: 'DNA sequence assembly program.' license: Michigan Tech. authors: Xiaoqiu Huang and Anup Madan + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/ccat/meta.yaml b/recipes/ccat/meta.yaml index 452c84b95fcb3..da277558c03be 100644 --- a/recipes/ccat/meta.yaml +++ b/recipes/ccat/meta.yaml @@ -4,12 +4,16 @@ package: source: sha256: d8944465c8327bec22eb41059ba73f780fcdcedf4470507bfdae5a54c59a9b07 - url: http://cmb.gis.a-star.edu.sg/ChIPSeq/tools/CCAT3.0.tar.gz + url: http://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/CCAT3.0.tar.gz build: number: 2 skip: True # [osx] +requirements: + build: + - {{ compiler('c') }} + test: commands: - CCAT --help diff --git a/recipes/cdna_cupcake/build.sh b/recipes/cdna_cupcake/build.sh index c5c73dd66d5f9..31cf072d865a0 100644 --- a/recipes/cdna_cupcake/build.sh +++ b/recipes/cdna_cupcake/build.sh @@ -1,7 +1,6 @@ #!/bin/sh -$PYTHON setup.py build -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv cp annotation/*.py ${PREFIX}/bin/ cp bacteria/*.py ${PREFIX}/bin/ diff --git a/recipes/cdna_cupcake/meta.yaml b/recipes/cdna_cupcake/meta.yaml index 79ec6ddb80291..654e9524fd5aa 100644 --- a/recipes/cdna_cupcake/meta.yaml +++ b/recipes/cdna_cupcake/meta.yaml @@ -12,16 +12,17 @@ source: - py.patch build: + noarch: python number: 0 - skip: true # [py3k] requirements: host: - - python + - python <3 + - pip - biopython - bx-python ==0.7.3 run: - - python + - python <3 - biopython - bx-python ==0.7.3 - r-base diff --git a/recipes/ceas/meta.yaml b/recipes/ceas/meta.yaml index 750d043c18ab8..7976e4b390396 100644 --- a/recipes/ceas/meta.yaml +++ b/recipes/ceas/meta.yaml @@ -7,16 +7,16 @@ source: url: http://liulab.dfci.harvard.edu/CEAS/src/CEAS-Package-1.0.2.tar.gz build: + noarch: python number: 1 - skip: True [py3k or osx] - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python <3 - pip run: - - python + - python <3 - mysql-python test: diff --git a/recipes/centrosome/meta.yaml b/recipes/centrosome/meta.yaml index 82524cef481fe..c113e17325ec9 100644 --- a/recipes/centrosome/meta.yaml +++ b/recipes/centrosome/meta.yaml @@ -15,6 +15,7 @@ build: requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} host: - python diff --git a/recipes/cgat-daisy/build.sh b/recipes/cgat-daisy/build.sh index db7d5ed90e471..d3ac59e8d8931 100644 --- a/recipes/cgat-daisy/build.sh +++ b/recipes/cgat-daisy/build.sh @@ -2,5 +2,5 @@ sed -i'' -e 's/install_requires=install_requires,//g' setup.py -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/cgat-report/build.sh b/recipes/cgat-report/build.sh index db7d5ed90e471..154de8fbd68d6 100644 --- a/recipes/cgat-report/build.sh +++ b/recipes/cgat-report/build.sh @@ -2,5 +2,4 @@ sed -i'' -e 's/install_requires=install_requires,//g' setup.py -$PYTHON setup.py install - +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/cgat-core/meta.yaml b/recipes/cgatcore/meta.yaml similarity index 93% rename from recipes/cgat-core/meta.yaml rename to recipes/cgatcore/meta.yaml index 4c41b4f91034a..a76f80f9e40b9 100644 --- a/recipes/cgat-core/meta.yaml +++ b/recipes/cgatcore/meta.yaml @@ -24,7 +24,7 @@ requirements: - drmaa - pyyaml - ruffus - - setuptools + - pip - six - sqlalchemy # Misc deps @@ -41,7 +41,6 @@ requirements: - drmaa - pyyaml - ruffus - - setuptools - six - sqlalchemy # Misc deps @@ -71,8 +70,6 @@ about: summary: 'CGAT : the Computational Genomics Analysis Toolkit' extra: - skip-lints: - - folder_and_package_name_must_match recipe-maintainers: - sebastian-luna-valero - AndreasHeger diff --git a/recipes/cgcloud-lib/build.sh b/recipes/cgcloud-lib/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/cgcloud-lib/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/cgcloud-lib/meta.yaml b/recipes/cgcloud-lib/meta.yaml index 49030bf7b331b..4c8efa25c2c7d 100644 --- a/recipes/cgcloud-lib/meta.yaml +++ b/recipes/cgcloud-lib/meta.yaml @@ -7,18 +7,16 @@ source: md5: 76cb2e9b3b6f716c0790bf7a55594c94 build: + noarch: python number: 2 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - bd2k-python-lib - - boto >=2.38.0 - + - python <3 + - pip run: - - python + - python <3 - bd2k-python-lib - boto >=2.38.0 diff --git a/recipes/changeo/meta.yaml b/recipes/changeo/meta.yaml index ac874b1e4e911..c6d5036c65a22 100644 --- a/recipes/changeo/meta.yaml +++ b/recipes/changeo/meta.yaml @@ -27,7 +27,6 @@ requirements: - python >=3.4 - pyyaml >=3.12 - scipy >=0.14 - - setuptools >=2.0 test: imports: diff --git a/recipes/chanjo/build.sh b/recipes/chanjo/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/chanjo/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/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index de3a17082a34d..f4ff3963b0434 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -11,25 +11,17 @@ source: md5: {{ md5 }} build: - number: 1 + noarch: python + number: 0 preserve_egg_dir: True + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - chanjo = chanjo.__main__:root_command - # path.py in the default channel is broken - # it does not contain an egg-info and hence setup.py cannot find it. - # Once bioconda can directly depend on conda-forge, we can enable this again. - skip: true requirements: host: - python - - setuptools - - click - - toolz - - path.py - - pyyaml - - sqlalchemy >=0.8.2 - + - pip run: - python - click diff --git a/recipes/check-sort-order/meta.yaml b/recipes/check-sort-order/meta.yaml index 2ccb9474714c1..f3f68a914ccb8 100644 --- a/recipes/check-sort-order/meta.yaml +++ b/recipes/check-sort-order/meta.yaml @@ -3,10 +3,10 @@ package: version: '0.0.4' source: - url: https://github.com/gogetdata/ggd-utils/releases/download/v0.0.4/check-sort-order-darwin_amd64 # [osx] - sha256: 484b425ea9f8e5a8af24a5de230971d973c131cbec02e48b10651c22beb8f280 # [osx] - url: https://github.com/gogetdata/ggd-utils/releases/download/v0.0.4/check-sort-order-linux_amd64 # [linux64] - sha256: d5ebae0bd75726cf22cba1b6b582d620db26200b78908b7d9ee6169f6d244960 # [linux64] + - url: https://github.com/gogetdata/ggd-utils/releases/download/v0.0.4/check-sort-order-darwin_amd64 # [osx] + sha256: 484b425ea9f8e5a8af24a5de230971d973c131cbec02e48b10651c22beb8f280 # [osx] + - url: https://github.com/gogetdata/ggd-utils/releases/download/v0.0.4/check-sort-order-linux_amd64 # [linux] + sha256: d5ebae0bd75726cf22cba1b6b582d620db26200b78908b7d9ee6169f6d244960 # [linux] build: number: 0 @@ -21,3 +21,8 @@ about: home: https://github.com/gogetdata/ggd-utils license: MIT summary: check sort-order of genomic files according to a genomefile + +extra: + skip-lints: + - should_not_be_noarch_source + - should_be_noarch_generic diff --git a/recipes/chemfp/build.sh b/recipes/chemfp/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/chemfp/build.sh +++ /dev/null @@ -1,9 +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/chemfp/meta.yaml b/recipes/chemfp/meta.yaml index 3a7a988b33dea..61e7592f5c75a 100644 --- a/recipes/chemfp/meta.yaml +++ b/recipes/chemfp/meta.yaml @@ -11,6 +11,7 @@ source: build: number: 0 skip: True # [osx or py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - ob2fps=chemfp.commandline.ob2fps:run - oe2fps=chemfp.commandline.oe2fps:run @@ -24,6 +25,7 @@ requirements: - {{ compiler('c') }} host: - python + - pip - openbabel - rdkit run: diff --git a/recipes/chorus2/meta.yaml b/recipes/chorus2/meta.yaml index 5d03f186dfd5b..31b5f45f12d82 100755 --- a/recipes/chorus2/meta.yaml +++ b/recipes/chorus2/meta.yaml @@ -10,17 +10,18 @@ source: build: number: 4 - noarch: python + skip: True # [py2k] script: "{{ PYTHON }} -m pip install . --no-deps -v" requirements: + build: + - {{ compiler('c') }} host: - - python >=3 - - setuptools + - python + - cython - pip run: - - cython - - python >=3 + - python - pybigwig - numpy - pyfasta diff --git a/recipes/chromosomer/meta.yaml b/recipes/chromosomer/meta.yaml index f0e34cf422a19..dd4ecfe9862d4 100644 --- a/recipes/chromosomer/meta.yaml +++ b/recipes/chromosomer/meta.yaml @@ -9,19 +9,18 @@ source: sha256: 7cce9ecfef3910a194d00aa033fefd54d1026ca9c9d84ae405f8a4ac5a674402 build: + noarch: python number: 1 - skip: True # [not py27] - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . entry_points: - chromosomer = chromosomer.cli:chromosomer requirements: host: - - python + - python <3 - pip - - setuptools run: - - python + - python <3 - pyfaidx - future - bioformats diff --git a/recipes/circexplorer/build.sh b/recipes/circexplorer/build.sh index 3537bc281b87c..c6dd4e53b9dd3 100644 --- a/recipes/circexplorer/build.sh +++ b/recipes/circexplorer/build.sh @@ -1,6 +1,4 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv cp -rf circ/* $PREFIX/bin -rm -rf example test -rm flow.jpg diff --git a/recipes/circexplorer/meta.yaml b/recipes/circexplorer/meta.yaml index 9f82ba5660ea9..fcc074dfd20b3 100644 --- a/recipes/circexplorer/meta.yaml +++ b/recipes/circexplorer/meta.yaml @@ -3,8 +3,8 @@ package: version: "1.1.10" build: + noarch: python number: 3 - skip: True # [not py27] source: url: https://pypi.python.org/packages/f0/3c/a93e1572570fe42222c77669232e9ebb686092969490bd4b81d5daafbe3d/CIRCexplorer-1.1.10.tar.gz @@ -12,12 +12,10 @@ source: requirements: host: - - python - - pysam >=0.8.4 - - docopt - + - python <3 + - pip run: - - python + - python <3 - pysam >=0.8.4 - docopt diff --git a/recipes/circexplorer2/build.sh b/recipes/circexplorer2/build.sh deleted file mode 100644 index 6696e36915465..0000000000000 --- a/recipes/circexplorer2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -$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/circexplorer2/meta.yaml b/recipes/circexplorer2/meta.yaml index aba627e62ba14..9a484983ddd8c 100644 --- a/recipes/circexplorer2/meta.yaml +++ b/recipes/circexplorer2/meta.yaml @@ -8,6 +8,7 @@ source: build: noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - CIRCexplorer2=circ2.command_parse:main - fetch_ucsc.py=circ2.fetch_ucsc:main @@ -17,12 +18,7 @@ build: requirements: host: - python - - requests - - pysam >=0.8.4 - - pybedtools - - docopt - - scipy - + - pip run: - python - requests diff --git a/recipes/cistrome-ceas/build.sh b/recipes/cistrome-ceas/build.sh index 38338b61fec80..1420eb3491a36 100644 --- a/recipes/cistrome-ceas/build.sh +++ b/recipes/cistrome-ceas/build.sh @@ -1,5 +1,4 @@ #!/bin/bash cd published-packages/CEAS -$PYTHON setup.py install - +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/cistrome-ceas/meta.yaml b/recipes/cistrome-ceas/meta.yaml index 2a9c698654388..fe81d58439063 100644 --- a/recipes/cistrome-ceas/meta.yaml +++ b/recipes/cistrome-ceas/meta.yaml @@ -9,15 +9,15 @@ source: - disable_no_mysqldb_warning.patch build: + noarch: python number: 1 - skip: True # [not py27] requirements: host: - - python - - bx-python + - python <3 + - pip run: - - python + - python <3 - bx-python - r-base diff --git a/recipes/cistrome_beta/build.sh b/recipes/cistrome_beta/build.sh deleted file mode 100644 index edeb2e0f05e01..0000000000000 --- a/recipes/cistrome_beta/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -cd BETA_1.0.7 -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/cistrome_beta/meta.yaml b/recipes/cistrome_beta/meta.yaml index c5f1be54283c9..c29440aa68b2f 100644 --- a/recipes/cistrome_beta/meta.yaml +++ b/recipes/cistrome_beta/meta.yaml @@ -11,18 +11,16 @@ source: sha256: {{ sha256 }} build: + noarch: python number: 1 - skip: True # [not py27] + script: cd BETA_1.0.7 && {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - argparse - - numpy + - python <3 + - pip run: - - python - - argparse + - python <3 - numpy - r-base diff --git a/recipes/cityhash/build.sh b/recipes/cityhash/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/cityhash/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/cityhash/meta.yaml b/recipes/cityhash/meta.yaml index e8853de2a4597..c4bb34b5bac66 100644 --- a/recipes/cityhash/meta.yaml +++ b/recipes/cityhash/meta.yaml @@ -3,8 +3,9 @@ package: version: "0.2.3.post9" build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://files.pythonhosted.org/packages/25/67/65ad3755997c066766750525fdf3045609f5ee892fa5b037e7fc066505a4/cityhash-0.2.3.post9.tar.gz @@ -12,11 +13,10 @@ source: requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/clairvoyante/meta.yaml b/recipes/clairvoyante/meta.yaml index 81b1c4655082e..a7137314ca8c5 100644 --- a/recipes/clairvoyante/meta.yaml +++ b/recipes/clairvoyante/meta.yaml @@ -7,12 +7,8 @@ source: md5: 2abdc607bffde2d3862c2e1e45893b56 build: + noarch: generic number: 0 - skip: True #[osx] - -channels: - - defaults - - conda-forge requirements: run: diff --git a/recipes/clearcut/meta.yaml b/recipes/clearcut/meta.yaml index 3219d21a369fd..648df4c9f99fe 100644 --- a/recipes/clearcut/meta.yaml +++ b/recipes/clearcut/meta.yaml @@ -8,7 +8,10 @@ source: build: number: 1 - skip: True # [not linux64 or osx] + +requirements: + build: + - {{ compiler('c') }} test: commands: diff --git a/recipes/clinod/meta.yaml b/recipes/clinod/meta.yaml index 1756600a24cbd..3db6b49171f3c 100644 --- a/recipes/clinod/meta.yaml +++ b/recipes/clinod/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.3 build: - skip: True # [not linux] + noarch: generic number: 2 source: @@ -12,8 +12,6 @@ source: sha256: 45d80662ba109a7af28aeafcfb2ca417a7d575ac3700f69bd40965a69d41e072 requirements: - host: - - snns run: - python - openjdk >=6 diff --git a/recipes/clustalw/meta.yaml b/recipes/clustalw/meta.yaml index 5ef951df493ac..3140004bc8aa0 100644 --- a/recipes/clustalw/meta.yaml +++ b/recipes/clustalw/meta.yaml @@ -26,3 +26,6 @@ about: license: "GNU Lesser GPL" summary: ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/clustergrammer/build.sh b/recipes/clustergrammer/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/clustergrammer/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/clustergrammer/meta.yaml b/recipes/clustergrammer/meta.yaml index 951b4f87061d4..60a266a4402b2 100644 --- a/recipes/clustergrammer/meta.yaml +++ b/recipes/clustergrammer/meta.yaml @@ -5,6 +5,7 @@ package: build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://files.pythonhosted.org/packages/8f/c2/01418945fa93c76646cbc070a9079dd11c2e7356b6926197c5e978243e98/clustergrammer-1.13.6.tar.gz @@ -13,10 +14,7 @@ source: requirements: host: - python - - numpy - - scikit-learn - - pandas - + - pip run: - python - numpy diff --git a/recipes/cluster-picker/build.sh b/recipes/clusterpicker/build.sh similarity index 100% rename from recipes/cluster-picker/build.sh rename to recipes/clusterpicker/build.sh diff --git a/recipes/cluster-picker/cluster-picker.sh b/recipes/clusterpicker/cluster-picker.sh similarity index 100% rename from recipes/cluster-picker/cluster-picker.sh rename to recipes/clusterpicker/cluster-picker.sh diff --git a/recipes/cluster-picker/meta.yaml b/recipes/clusterpicker/meta.yaml similarity index 97% rename from recipes/cluster-picker/meta.yaml rename to recipes/clusterpicker/meta.yaml index 958ffd5f08cdc..b3ce95990c449 100644 --- a/recipes/cluster-picker/meta.yaml +++ b/recipes/clusterpicker/meta.yaml @@ -16,7 +16,7 @@ build: requirements: run: - - openjdk >=6 + - openjdk >=6 test: commands: diff --git a/recipes/cogent/build.sh b/recipes/cogent/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/cogent/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/cogent/meta.yaml b/recipes/cogent/meta.yaml index 0d46e02e5203a..8cf8a4c1c0cbf 100644 --- a/recipes/cogent/meta.yaml +++ b/recipes/cogent/meta.yaml @@ -1,27 +1,22 @@ package: name: cogent - version: !!str 1.9 + version: 1.9 source: url: https://files.pythonhosted.org/packages/03/9e/a7156965da5edc34c3c07661c3b4bc4259caa3d9dcecaa5f7f3ff51eecd7/cogent-1.9.tar.gz sha256: 57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14 build: + noarch: python number: 0 - skip: True [py3k or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - numpy >=1.3 - - zlib - - matplotlib >=1.1.0 - - mpi4py >=1.0 # [not osx] - - mysql-python >=1.2.2 # [not osx] - - sqlalchemy >=0.5 # [not osx] - + - python <3 + - pip run: - - python + - python <3 - numpy >=1.3 - zlib - matplotlib >=1.1.0 diff --git a/recipes/collectl/meta.yaml b/recipes/collectl/meta.yaml index 4bac6fdc58fc5..21d841a0c6798 100644 --- a/recipes/collectl/meta.yaml +++ b/recipes/collectl/meta.yaml @@ -9,6 +9,7 @@ source: - usrenvbin.patch build: + noarch: generic number: 3 requirements: diff --git a/recipes/colorbrewer/build.sh b/recipes/colorbrewer/build.sh deleted file mode 100644 index d0f35d4aea6ee..0000000000000 --- a/recipes/colorbrewer/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/colorbrewer/meta.yaml b/recipes/colorbrewer/meta.yaml index 6cdc07678e502..ec8ae6c00d053 100644 --- a/recipes/colorbrewer/meta.yaml +++ b/recipes/colorbrewer/meta.yaml @@ -9,12 +9,12 @@ source: build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - six + - pip - python - run: - six - python diff --git a/recipes/combined-pvalues/build.sh b/recipes/combined-pvalues/build.sh deleted file mode 100644 index 8854f9ea719a0..0000000000000 --- a/recipes/combined-pvalues/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/usr/env bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/combined-pvalues/meta.yaml b/recipes/combined-pvalues/meta.yaml index 99940be807969..189fab0383e84 100644 --- a/recipes/combined-pvalues/meta.yaml +++ b/recipes/combined-pvalues/meta.yaml @@ -9,17 +9,16 @@ source: md5: 2ed642df0222a36dfce13e98c35f1b9f build: + noarch: pip number: 2 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - ez_setup - - interlap + - python <3 + - pip run: - - python + - python <3 - numpy - scipy - toolshed diff --git a/recipes/commet/meta.yaml b/recipes/commet/meta.yaml index ac8ed9adc580d..b419459d00f5d 100644 --- a/recipes/commet/meta.yaml +++ b/recipes/commet/meta.yaml @@ -10,7 +10,6 @@ source: build: number: 2 - skip: True # [py3k] rpaths: - lib/R/lib/ - lib/ @@ -18,12 +17,12 @@ build: requirements: build: - {{ compiler('c') }} + - {{ compiler('fortran') }} host: - r-base run: - r-base - r-gplots - - libgfortran - python test: diff --git a/recipes/compare-reads/build.sh b/recipes/compare-reads/build.sh deleted file mode 100644 index 4dad93a1c02ab..0000000000000 --- a/recipes/compare-reads/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/compare-reads/meta.yaml b/recipes/compare-reads/meta.yaml index 05d54ad204059..aca919d900fb7 100644 --- a/recipes/compare-reads/meta.yaml +++ b/recipes/compare-reads/meta.yaml @@ -8,16 +8,15 @@ source: build: number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - {{ compiler('c') }} host: - python - - pysam - - setuptools + - pip - cython - run: - python - pysam diff --git a/recipes/connor/meta.yaml b/recipes/connor/meta.yaml index 76d3e2935822b..4dc7041c8b6ac 100644 --- a/recipes/connor/meta.yaml +++ b/recipes/connor/meta.yaml @@ -10,18 +10,18 @@ source: sha256: '{{ sha256 }}' build: - noarch: python number: 0 script: python -m pip install --no-deps --ignore-installed . requirements: + build: + - {{ compiler('c') }} host: - python - pip - cython run: - python - - cython - sortedcontainers - pysam >0.8.3,<=0.12 diff --git a/recipes/convert-zero-one-based/meta.yaml b/recipes/convert_zero_one_based/meta.yaml similarity index 100% rename from recipes/convert-zero-one-based/meta.yaml rename to recipes/convert_zero_one_based/meta.yaml diff --git a/recipes/coprarna/meta.yaml b/recipes/coprarna/meta.yaml index dcf2f2b1b20ae..1f204dc40a989 100644 --- a/recipes/coprarna/meta.yaml +++ b/recipes/coprarna/meta.yaml @@ -11,24 +11,11 @@ source: md5: {{ md5 }} build: + noarch: generic number: 5 - skip: True [osx] # commented versions are tested as working requirements: - host: -# - perl >=5.22 -# - perl-bioperl >=1.6.924 -# - perl-list-moreutils ==0.428 -# - perl-parallel-forkmanager ==1.17 -# - perl-getopt-long -# - perl-bio-eutilities ==1.75 -# - r-base -# - r-seqinr -# - python -# - suds-jurko ==0.6 -# - coreutils ==8.25 # - run: - perl >=5.22 - perl-bioperl ==1.6.924 diff --git a/recipes/cpat/meta.yaml b/recipes/cpat/meta.yaml index e2e914014de32..e6c925068b0b7 100644 --- a/recipes/cpat/meta.yaml +++ b/recipes/cpat/meta.yaml @@ -6,27 +6,29 @@ package: version: "{{ version }}" build: - noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + skip: True # [py2k] source: url: https://files.pythonhosted.org/packages/5c/ed/0cb7373f623f6e0d4a642f54cef717d4c78de339e0499ff57649a7c1f25f/CPAT-2.0.0.tar.gz sha256: bcd1fd8543f51c45abeeccf4612f059b46ee56c5a75877db9c170bf221a5b8f4 requirements: + build: + - {{ compiler('c') }} host: - setuptools - bx-python - pip - nose - - python >=3.5 + - python - pysam - numpy - cython run: - bx-python - - python >=3.5 + - python - numpy - pysam - r-base diff --git a/recipes/cpinsim/build.sh b/recipes/cpinsim/build.sh deleted file mode 100644 index 5227f51eca79f..0000000000000 --- a/recipes/cpinsim/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/cpinsim/meta.yaml b/recipes/cpinsim/meta.yaml index ce7245f1533f0..ebf4edf88c92a 100644 --- a/recipes/cpinsim/meta.yaml +++ b/recipes/cpinsim/meta.yaml @@ -9,21 +9,18 @@ source: sha256: 34a7d7ae7fc6192e8524c8907967b3a6f868b8af650fab8d395a9a96da0308e8 build: + noarch: python entry_points: - cpinsim = cpinsim:main number: 1 - skip: True # [py2k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - networkx - - bitarray - - scipy - + - python >3 + - pip run: - - python + - python >3 - networkx - bitarray - scipy diff --git a/recipes/crb-blast/meta.yaml b/recipes/crb-blast/meta.yaml index b39b60a7cda36..6677e19e2e5ff 100644 --- a/recipes/crb-blast/meta.yaml +++ b/recipes/crb-blast/meta.yaml @@ -3,11 +3,11 @@ package: version: '0.6.6' build: + noarch: generic number: 1 - skip: True [osx] requirements: - build: + host: - ruby >=2.4.4 run: - ruby >=2.4.4 diff --git a/recipes/crimson/build.sh b/recipes/crimson/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/crimson/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 5985239c5fd1c..5ec03650e4b78 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -7,20 +7,17 @@ source: sha256: 924f0dc2598b294e873ecd204952ae42f21d43b15eda026229126174acff3648 build: + noarch: pip number: 1 entry_points: - crimson=crimson.cli:main # click needs to be patched in order to properly detect unicode in py3k - skip: true # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - click >=6.6 - - pyyaml >=3.11 - - wheel >=0.23.0 - + - pip run: - python - click >=6.6 diff --git a/recipes/CRISPRStudio/build.sh b/recipes/crispr_studio/build.sh similarity index 100% rename from recipes/CRISPRStudio/build.sh rename to recipes/crispr_studio/build.sh diff --git a/recipes/CRISPRStudio/change_f_flag.patch b/recipes/crispr_studio/change_f_flag.patch similarity index 100% rename from recipes/CRISPRStudio/change_f_flag.patch rename to recipes/crispr_studio/change_f_flag.patch diff --git a/recipes/CRISPRStudio/meta.yaml b/recipes/crispr_studio/meta.yaml similarity index 100% rename from recipes/CRISPRStudio/meta.yaml rename to recipes/crispr_studio/meta.yaml diff --git a/recipes/crux-toolkit/meta.yaml b/recipes/crux-toolkit/meta.yaml index 9600a307e48ef..d1596bedf2f0b 100644 --- a/recipes/crux-toolkit/meta.yaml +++ b/recipes/crux-toolkit/meta.yaml @@ -4,18 +4,11 @@ package: name: crux-toolkit version: {{ version }} -about: - home: http://crux.ms - summary: A cross-platform suite of analysis tools for interpreting protein mass spectrometry data - license: Apache-2.0 - license_family: Apache - dev_url: https://github.com/crux-toolkit/crux-toolkit - source: - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Linux.x86_64.zip # [linux64] - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Darwin.x86_64.zip # [osx] - sha256: 4365e2ab654290f34d9d25c34b1173c016d7e5c18fb2266b92f09cdd39cbbdfb # [linux64] - sha256: 6191208e64053292558d85725699bd22b96aca166cac35a2637967492f530cf3 # [osx] + - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Linux.x86_64.zip # [linux] + sha256: 4365e2ab654290f34d9d25c34b1173c016d7e5c18fb2266b92f09cdd39cbbdfb # [linux] + - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Darwin.x86_64.zip # [osx] + sha256: 6191208e64053292558d85725699bd22b96aca166cac35a2637967492f530cf3 # [osx] build: number: 0 @@ -30,3 +23,14 @@ requirements: test: commands: - crux version 2> /dev/null | grep -q 'Crux version' + +about: + home: http://crux.ms + summary: A cross-platform suite of analysis tools for interpreting protein mass spectrometry data + license: Apache-2.0 + license_family: Apache + dev_url: https://github.com/crux-toolkit/crux-toolkit + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/ctat-metagenomics/meta.yaml b/recipes/ctat-metagenomics/meta.yaml index 0838d06853a31..606fcde1df62e 100644 --- a/recipes/ctat-metagenomics/meta.yaml +++ b/recipes/ctat-metagenomics/meta.yaml @@ -11,15 +11,14 @@ source: md5: 5f47e6c31d1af1bf17f71d0070bf06fb build: + noarch: generic number: {{ build }} - skip: true # [py3k] - # The python code in ctat-metagenomics runs on python 2.7. requirements: host: - - python + - python <3 run: - - python + - python <3 - blast - centrifuge diff --git a/recipes/cuneiform/1.1.0/build.sh b/recipes/cuneiform/1.1.0/build.sh deleted file mode 100644 index 5d4b2b94d2511..0000000000000 --- a/recipes/cuneiform/1.1.0/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/env bash - -mkdir build -cd build -cmake -DCMAKE_INSTALL_PREFIX=$PREFIX .. -make -make install diff --git a/recipes/cuneiform/1.1.0/meta.yaml b/recipes/cuneiform/1.1.0/meta.yaml deleted file mode 100644 index 835afe1a55e80..0000000000000 --- a/recipes/cuneiform/1.1.0/meta.yaml +++ /dev/null @@ -1,19 +0,0 @@ -package: - name: cuneiform - version: 0.21 -build: - number: 1 - skip: True -source: - url: https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2 -requirements: - build: - - {{ compiler('c') }} - - graphicsmagick - - cmake - run: - -about: - home: https://launchpad.net/cuneiform-linux/ - license: Simplified BSD Licence - summary: Cuneiform is an OCR system. diff --git a/recipes/daisysuite/meta.yaml b/recipes/daisysuite/meta.yaml index f03f5d572b573..03006c41585fc 100644 --- a/recipes/daisysuite/meta.yaml +++ b/recipes/daisysuite/meta.yaml @@ -7,8 +7,8 @@ source: sha256: 57789b62a41dac5f7ab3fe9fe16bdf3ded47bb8adee6f19ffe7a45425bb1373a build: + noarch: generic number: 0 - skip: True # [osx] requirements: run: diff --git a/recipes/damidseq_pipeline/meta.yaml b/recipes/damidseq_pipeline/meta.yaml index 3cba6b80f5efa..316aefac4b5dc 100644 --- a/recipes/damidseq_pipeline/meta.yaml +++ b/recipes/damidseq_pipeline/meta.yaml @@ -7,6 +7,7 @@ source: sha256: cf3a9608a5f5453f2d491bde3759eaf154909387c9b4a1f882be45b542acbe73 build: + noarch: generic number: 2 requirements: diff --git a/recipes/dammit/build.sh b/recipes/dammit/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/dammit/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/dammit/meta.yaml b/recipes/dammit/meta.yaml index 59d03fe0f9f32..d7761af09bacd 100644 --- a/recipes/dammit/meta.yaml +++ b/recipes/dammit/meta.yaml @@ -9,13 +9,15 @@ source: sha256: '{{sha256}}' build: + noarch: python number: 3 - skip: true # [py27 or py34] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: # Python dependencies - - python + - python >3 + - pip - numpy - pandas - numexpr >=2.3.1 @@ -36,7 +38,7 @@ requirements: run: # Python dependencies - - python + - python >3 - numpy - pandas - numexpr >=2.3.1 diff --git a/recipes/das_tool/meta.yaml b/recipes/das_tool/meta.yaml index 9ca037a2fe14c..bdb8d2159b670 100644 --- a/recipes/das_tool/meta.yaml +++ b/recipes/das_tool/meta.yaml @@ -11,15 +11,14 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 - skip: True # [not linux] rpaths: - lib/R/lib/ - lib/ requirements: host: - - codeutils # [osx] - unzip - gawk - r-base diff --git a/recipes/data_hacks/build.sh b/recipes/data_hacks/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/data_hacks/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/data_hacks/meta.yaml b/recipes/data_hacks/meta.yaml index e0909cb552ee8..5f6ad7a3d929f 100644 --- a/recipes/data_hacks/meta.yaml +++ b/recipes/data_hacks/meta.yaml @@ -7,14 +7,17 @@ source: url: https://github.com/bitly/data_hacks/archive/v0.3.1.tar.gz build: + noarch: python number: 1 - skip: True # [not py27 or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python <3 + - pip run: - - python + - python <3 + test: commands: - histogram.py --help diff --git a/recipes/ddrage/build.sh b/recipes/ddrage/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/ddrage/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/ddrage/meta.yaml b/recipes/ddrage/meta.yaml index e670b40393633..58d6d995398f2 100644 --- a/recipes/ddrage/meta.yaml +++ b/recipes/ddrage/meta.yaml @@ -10,8 +10,9 @@ source: build: - skip: True # [py2k] + noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - rage = ddrage.__main__:main - ddrage = ddrage.__main__:main @@ -24,16 +25,10 @@ build: requirements: host: - - python - - setuptools - - numpy - - numba - - matplotlib - - scipy - - pyyaml - + - python >=3 + - pip run: - - python + - python >=3 - numpy - numba - matplotlib diff --git a/recipes/deblur/build.sh b/recipes/deblur/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/deblur/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/deblur/meta.yaml b/recipes/deblur/meta.yaml index bdbb5681b20ae..2bc292b15edb9 100644 --- a/recipes/deblur/meta.yaml +++ b/recipes/deblur/meta.yaml @@ -9,27 +9,16 @@ source: sha256: 6bce57bb2400e29b45074794e33ce02a6c0b379eacbb2da299125deaed1faeb6 build: + noarch: python number: 0 - skip: True # [py27] - -extra: - container: - extended-base: True + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - biom-format - - setuptools - - scikit-bio >=0.5.0 - - vsearch >=2.0.3 - - mafft ==7.310 - - sortmerna ==2.0 - - biom-format - - h5py - - click + - python >=3 + - pip run: - - python + - python >=3 - biom-format - scikit-bio >=0.5.0 - vsearch >=2.0.3 @@ -50,3 +39,7 @@ about: license: BSD license license_file: LICENSE summary: Deblur is a greedy deconvolution algorithm based on known read error profiles. + +extra: + container: + extended-base: True diff --git a/recipes/debwt/meta.yaml b/recipes/debwt/meta.yaml index 43a10745eee0e..e52cccefada35 100644 --- a/recipes/debwt/meta.yaml +++ b/recipes/debwt/meta.yaml @@ -8,6 +8,7 @@ build: source: git_url: https://github.com/DixianZhu/deBWT.git git_rev: 972b5338b2ad027244bb60d185c5a88586affba6 # version 1.0.1 + sha256: ignored requirements: build: @@ -30,3 +31,7 @@ about: DeBWT has good scalability to construct BWT in parallel computing. It is well-suited to run on multiple core servers or clusters to construct the BWT of large collections of genome sequences. + +extra: + skip-lints: + - uses_vcs_url diff --git a/recipes/deepmedic/build.sh b/recipes/deepmedic/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/deepmedic/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/deepmedic/meta.yaml b/recipes/deepmedic/meta.yaml index 24db25b952227..12d391603604a 100644 --- a/recipes/deepmedic/meta.yaml +++ b/recipes/deepmedic/meta.yaml @@ -9,21 +9,16 @@ source: sha256: 02496be7740f19f27af413b246282b436d6afea59e5491d2bbf9f0db1d2ae427 build: + noarch: python number: 0 - skip: True # [osx or py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - theano - - nose - - nibabel - - pp - - six - - scipy - - numpy + - python <3 + - pip run: - - python + - python <3 - theano - nibabel - pp diff --git a/recipes/deepvariant/meta.yaml b/recipes/deepvariant/meta.yaml index 741e7742d91e1..89725c8f1e935 100644 --- a/recipes/deepvariant/meta.yaml +++ b/recipes/deepvariant/meta.yaml @@ -17,6 +17,7 @@ package: source: url: https://github.com/google/deepvariant/releases/download/v{{ version }}/deepvariant.zip sha256: '{{ sha256 }}' + build: number: 0 skip: true # [osx or not py27] @@ -67,3 +68,8 @@ about: license: MIT summary: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + +extra: + skip-lints: + - should_be_noarch_generic + - missing_tests diff --git a/recipes/deltabs/meta.yaml b/recipes/deltabs/meta.yaml index 3fa58877e5ca5..5c7287f5a6570 100644 --- a/recipes/deltabs/meta.yaml +++ b/recipes/deltabs/meta.yaml @@ -7,6 +7,7 @@ package: version: {{ version }} build: + noarch: generic number: 1 source: diff --git a/recipes/deploid/meta.yaml b/recipes/deploid/meta.yaml index e9a99c0a37a0c..a004bbaeb9ddf 100644 --- a/recipes/deploid/meta.yaml +++ b/recipes/deploid/meta.yaml @@ -15,6 +15,8 @@ requirements: build: - automake - autoconf + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - cppunit - zlib diff --git a/recipes/desman/meta.yaml b/recipes/desman/meta.yaml index a45cc7e7dab26..fa82c6ea20e81 100644 --- a/recipes/desman/meta.yaml +++ b/recipes/desman/meta.yaml @@ -8,7 +8,7 @@ package: build: number: 2 - skip: True # [py<35] + skip: True # [py2k] source: url: https://github.com/chrisquince/DESMAN/archive/v{{ version }}.tar.gz @@ -27,7 +27,6 @@ requirements: - scipy >=0.12.0 run: - python - - cython >=0.19.1 - bcbio-gff - biopython - pysam diff --git a/recipes/dfam/meta.yaml b/recipes/dfam/meta.yaml index deff3edeb65a1..8fcc7c42cb869 100644 --- a/recipes/dfam/meta.yaml +++ b/recipes/dfam/meta.yaml @@ -7,8 +7,8 @@ source: sha256: e308e6a32ca42db00862b5eae461f97abd8979050241333656a415a3cda7a9e6 build: + noarch: generic number: 1 - skip: True # [osx] requirements: run: diff --git a/recipes/discasm/meta.yaml b/recipes/discasm/meta.yaml index c3f994cd093fb..967f1515cc9ee 100644 --- a/recipes/discasm/meta.yaml +++ b/recipes/discasm/meta.yaml @@ -11,15 +11,14 @@ source: md5: d65e4d002a0f3b557fe305ee6ef0ec8d build: + noarch: generic number: {{ build }} - skip: true # [osx or py3k] # The reason for skipping osx is that trinity >=2.4 is not available in the osx channel # The python code in DISCASM runs on python 2.7. requirements: - host: run: - - python + - python <3 - pysam >=0.10.0 - perl - star >=2.4 diff --git a/recipes/dkfz-bias-filter/meta.yaml b/recipes/dkfz-bias-filter/meta.yaml index 86967b2440be3..92685ab66910e 100644 --- a/recipes/dkfz-bias-filter/meta.yaml +++ b/recipes/dkfz-bias-filter/meta.yaml @@ -10,15 +10,12 @@ source: md5: 7a5a85ed1c46c923374940b578851cce build: + noarch: generic number: 7 - skip: true # [not py27] requirements: - host: - - python - run: - - python + - python <3 - matplotlib - numpy - pysam diff --git a/recipes/dlcpar/build.sh b/recipes/dlcpar/build.sh deleted file mode 100644 index 7bc2b4d01a2a5..0000000000000 --- a/recipes/dlcpar/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -python setup.py install --prefix=$PREFIX diff --git a/recipes/dlcpar/meta.yaml b/recipes/dlcpar/meta.yaml index d4261690f5dce..223946eb1afb9 100644 --- a/recipes/dlcpar/meta.yaml +++ b/recipes/dlcpar/meta.yaml @@ -3,8 +3,9 @@ package: version: "1.0" build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://www.cs.hmc.edu/~yjw/software/dlcpar/pub/sw/dlcpar-1.0.tar.gz @@ -12,10 +13,10 @@ source: requirements: host: - - python - - numpy + - python <3 + - pip run: - - python + - python <3 - numpy test: diff --git a/recipes/dnapi/meta.yaml b/recipes/dnapi/meta.yaml index b5e83b449edba..00c6cc003af24 100644 --- a/recipes/dnapi/meta.yaml +++ b/recipes/dnapi/meta.yaml @@ -13,15 +13,15 @@ source: requirements: host: - python - + - pip run: - python test: - command: - qual_offset.py -h - qual_trim.py -h - to_fasta.py -h + commands: + - qual_offset.py -h + - qual_trim.py -h + - to_fasta.py -h about: home: https://github.com/jnktsj/DNApi diff --git a/recipes/drax/meta.yaml b/recipes/drax/meta.yaml index ab74d598d51d6..272ec48597a99 100644 --- a/recipes/drax/meta.yaml +++ b/recipes/drax/meta.yaml @@ -9,6 +9,7 @@ source: sha256: 08ac66bfeb96c0d2b646e038e3ada86c3621a1911470e5b6a1b1ea124710a9dc build: + noarch: generic number: 2 requirements: diff --git a/recipes/drive/meta.yaml b/recipes/drive/meta.yaml index d55515a5144e8..464ee53395781 100644 --- a/recipes/drive/meta.yaml +++ b/recipes/drive/meta.yaml @@ -5,14 +5,13 @@ package: version: '{{ version }}' source: - url: https://github.com/odeke-em/drive/releases/download/v{{ version }}/drive_linux # [linux] - sha256: 291ed4f3e88904978ae183f49a97feaa5aebec6da2e65c32e1774e7672b76ad9 # [linux] - url: https://github.com/odeke-em/drive/releases/download/v{{ version }}/drive_darwin # [osx] - sha256: e739b7661d529a894cb992d339bc4e77b5849cf29cb93ba9b2df2f4079871639 # [osx] + - url: https://github.com/odeke-em/drive/releases/download/v{{ version }}/drive_linux # [linux] + sha256: 291ed4f3e88904978ae183f49a97feaa5aebec6da2e65c32e1774e7672b76ad9 # [linux] + - url: https://github.com/odeke-em/drive/releases/download/v{{ version }}/drive_darwin # [osx] + sha256: e739b7661d529a894cb992d339bc4e77b5849cf29cb93ba9b2df2f4079871639 # [osx] build: number: 1 - skip: false binary_relocation: false requirements: @@ -28,3 +27,8 @@ about: home: https://github.com/odeke-em/drive license: Apache v2.0 summary: Google Drive client for the commandline + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/dudes/0.06/build.sh b/recipes/dudes/0.06/build.sh deleted file mode 100755 index e897ad762e9d9..0000000000000 --- a/recipes/dudes/0.06/build.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin - -cp *.py $PREFIX/bin - diff --git a/recipes/dudes/0.06/meta.yaml b/recipes/dudes/0.06/meta.yaml deleted file mode 100644 index 21717a753790d..0000000000000 --- a/recipes/dudes/0.06/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -package: - name: dudes - version: "0.06" - -source: - url: http://downloads.sourceforge.net/project/dudes/dudes_v0_06.tar.gz - md5: dde2c8dbca04448cf21a0ed6b092b047 - -build: - number: 3 - skip: True # [not py27] - -requirements: - host: - - python - run: - - python - - numpy - - pandas - - bsddb - -test: - commands: - - DUDes.py -h > /dev/null - -about: - home: https://sourceforge.net/projects/dudes/ - license: The MIT License (MIT) - summary: 'DUDes is a taxonomic profiler for NGS metagenomic samples' - - diff --git a/recipes/dudes/0.07/build.sh b/recipes/dudes/0.07/build.sh deleted file mode 100755 index 3cbc6e4f5f051..0000000000000 --- a/recipes/dudes/0.07/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -cp *.py $PREFIX/bin diff --git a/recipes/dudes/0.07/meta.yaml b/recipes/dudes/0.07/meta.yaml deleted file mode 100644 index 820c46167d870..0000000000000 --- a/recipes/dudes/0.07/meta.yaml +++ /dev/null @@ -1,27 +0,0 @@ -package: - name: dudes - version: "0.07" - -source: - url: https://github.com/pirovc/dudes/archive/dudes_v0.07.tar.gz - md5: dd1194d23a0743b042e4ac00449564aa - -build: - number: 2 - skip: True # [not py3k] - -requirements: - run: - - python - - numpy - - pandas - -test: - commands: - - DUDes.py -h 2>&1 | echo $? - -about: - home: https://github.com/pirovc/dudes/ - license: The MIT License (MIT) - summary: 'DUDes: a top-down taxonomic profiler for metagenomics' - diff --git a/recipes/dudes/build.sh b/recipes/dudes/build.sh deleted file mode 100755 index fc6dff27a4bdd..0000000000000 --- a/recipes/dudes/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -python setup.py install \ No newline at end of file diff --git a/recipes/dudes/meta.yaml b/recipes/dudes/meta.yaml index edeaccb19666c..f47f6731454b0 100644 --- a/recipes/dudes/meta.yaml +++ b/recipes/dudes/meta.yaml @@ -7,14 +7,16 @@ source: md5: b569094e73ad2d40dccac7a26554a839 build: + noarch: python number: 1 - skip: True # [not py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python >=3 + - pip run: - - python + - python >=3 - numpy - pandas diff --git a/recipes/duphold/meta.yaml b/recipes/duphold/meta.yaml index e3ef46d5e9726..4e0ce18a5367d 100644 --- a/recipes/duphold/meta.yaml +++ b/recipes/duphold/meta.yaml @@ -26,3 +26,8 @@ about: home: https://github.com/brentp/duphold license: MIT summary: SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. + +extra: + skip-lints: + #Packages a prebuilt binary + - should_be_noarch_generic diff --git a/recipes/dupre/meta.yaml b/recipes/dupre/meta.yaml index ed89ada10fb01..5e704ad5262ac 100644 --- a/recipes/dupre/meta.yaml +++ b/recipes/dupre/meta.yaml @@ -9,29 +9,24 @@ source: md5: 507a805c5bd9e7ecc8e65493ab29a6d1 build: + noarch: python number: 1 - skip: True # [py27] - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - dupre = dupre.dupre:main - bam2occupancy = dupre.bam2occupancy:main requirements: host: - - python + - python >=3 - pip - - setuptools run: - pysam - - python + - python >=3 - pulp - numpy - h5py - scipy - # optional - # - snakemake - # - seaborn - # - pandas test: commands: diff --git a/recipes/dx-cwl/meta.yaml b/recipes/dx-cwl/meta.yaml index c4811ff0d1443..b2ba2e25374f6 100644 --- a/recipes/dx-cwl/meta.yaml +++ b/recipes/dx-cwl/meta.yaml @@ -9,15 +9,12 @@ source: sha256: 162c927f85a010c030189ec582aa437be1673176072f8a7c8c129e1560a09ef7 build: + noarch: generic number: 1 - skip: true # [not py27] requirements: - host: - - python - run: - - python + - python <3 - cwltool - dxpy - pyyaml diff --git a/recipes/ebfilter/build.sh b/recipes/ebfilter/build.sh deleted file mode 100644 index e2efb238156e3..0000000000000 --- a/recipes/ebfilter/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py build -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/ebfilter/meta.yaml b/recipes/ebfilter/meta.yaml index 4a533ac37bdba..f713ecdf4e257 100644 --- a/recipes/ebfilter/meta.yaml +++ b/recipes/ebfilter/meta.yaml @@ -10,8 +10,9 @@ source: md5: "{{ md5 }}" build: - skip: True # [osx or not py27] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/ebisearch/build.sh b/recipes/ebisearch/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/ebisearch/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/ebisearch/meta.yaml b/recipes/ebisearch/meta.yaml index fbe7b294093cf..556a561effb47 100644 --- a/recipes/ebisearch/meta.yaml +++ b/recipes/ebisearch/meta.yaml @@ -10,22 +10,18 @@ source: md5: 55b6349bdd84b632cde8bb5bd55efbda build: + noarch: python entry_points: - ebisearch = ebisearch.__main__:main number: 1 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - requests - - click - - flake8 - - pytest - - pytest-runner + - python <3 + - pip run: - - python + - python <3 - requests - click - flake8 diff --git a/recipes/ecopy/meta.yaml b/recipes/ecopy/meta.yaml index 9db553784bbac..eb40946490b9b 100644 --- a/recipes/ecopy/meta.yaml +++ b/recipes/ecopy/meta.yaml @@ -25,10 +25,8 @@ requirements: - matplotlib >=1.3.1 - pandas >=0.13 - patsy >=0.3.0 - run: - python - - cython - numpy >=1.7 - scipy >=0.14 - matplotlib >=1.3.1 diff --git a/recipes/ectyper/meta.yaml b/recipes/ectyper/meta.yaml index 6e3447e0f6ec6..1836fdc2db210 100644 --- a/recipes/ectyper/meta.yaml +++ b/recipes/ectyper/meta.yaml @@ -31,10 +31,10 @@ requirements: - seqtk >=1.2 test: - import: - - ectyper - test: - - "ectyper --help" + imports: + - ectyper + commands: + - ectyper --help about: license: Apache 2 diff --git a/recipes/edd/meta.yaml b/recipes/edd/meta.yaml index 8461e5231c94d..3c007d4bb1514 100644 --- a/recipes/edd/meta.yaml +++ b/recipes/edd/meta.yaml @@ -11,6 +11,8 @@ build: skip: True # [not py27] requirements: + build: + - {{ compiler('c') }} host: - python - cython diff --git a/recipes/eden/build.sh b/recipes/eden/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/eden/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/eden/meta.yaml b/recipes/eden/meta.yaml index 9f64f72288625..6270ee03431fb 100644 --- a/recipes/eden/meta.yaml +++ b/recipes/eden/meta.yaml @@ -7,27 +7,16 @@ source: sha256: 1856d79d37d7116c3b33034929be85d5e96dbf584622946b411ecaaec3b3fdac build: + noarch: python number: 2 - skip: True # [not py27 or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - dill - - joblib - - matplotlib - - networkx <=1.10 - - numpy - - pandas - - pybedtools - - reportlab - - requests - - scikit-learn >=0.17.0 - - scipy >=0.14.0 - - esmre - - rdkit + - python <3 + - pip run: - - python + - python <3 - dill - joblib - matplotlib diff --git a/recipes/edittag/build.sh b/recipes/edittag/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/edittag/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/edittag/meta.yaml b/recipes/edittag/meta.yaml index 569c4737e5af1..bce7feb4ca56b 100644 --- a/recipes/edittag/meta.yaml +++ b/recipes/edittag/meta.yaml @@ -9,15 +9,14 @@ source: - edittag.patch build: - skip: True # [py34] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - numpy >=1.3 - - setuptools - + - pip run: - python - numpy >=1.3 diff --git a/recipes/egglib/meta.yaml b/recipes/egglib/meta.yaml index 4b219cf6b0eb3..118f240278705 100644 --- a/recipes/egglib/meta.yaml +++ b/recipes/egglib/meta.yaml @@ -9,7 +9,7 @@ package: name: {{ name }} version: {{ version }} - skip: True # [not py27] + skip: True # [not py27] build: number: 1 @@ -22,12 +22,12 @@ requirements: build: - {{ compiler('cxx') }} host: - - python <3 + - python run: - - python <3 + - python test: - import: + imports: - egglib - egglib.tools - egglib.io diff --git a/recipes/elasticluster/build.sh b/recipes/elasticluster/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/elasticluster/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/elasticluster/meta.yaml b/recipes/elasticluster/meta.yaml index 86c09a66e3a63..f6833c973e221 100644 --- a/recipes/elasticluster/meta.yaml +++ b/recipes/elasticluster/meta.yaml @@ -3,21 +3,20 @@ package: version: '0.1.3bcbio' source: - #url: https://github.com/jwm/elasticluster/archive/abf3ab1.tar.gz url: https://github.com/chapmanb/elasticluster/archive//8d6d108.tar.gz sha256: d655c87cb10367628058ec6f16ff05ecd452648ee3b797c2bcdbf9b9abb91e4d build: + noarch: python number: 12 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 - ansible - azure - pycli diff --git a/recipes/embl-validator/build.sh b/recipes/embl-api-validator/build.sh similarity index 100% rename from recipes/embl-validator/build.sh rename to recipes/embl-api-validator/build.sh diff --git a/recipes/embl-validator/embl-api-validator.py b/recipes/embl-api-validator/embl-api-validator.py similarity index 100% rename from recipes/embl-validator/embl-api-validator.py rename to recipes/embl-api-validator/embl-api-validator.py diff --git a/recipes/embl-validator/meta.yaml b/recipes/embl-api-validator/meta.yaml similarity index 100% rename from recipes/embl-validator/meta.yaml rename to recipes/embl-api-validator/meta.yaml diff --git a/recipes/emperor/0.9.3/build.sh b/recipes/emperor/0.9.3/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/emperor/0.9.3/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/emperor/0.9.3/meta.yaml b/recipes/emperor/0.9.3/meta.yaml deleted file mode 100644 index 057f646b108dd..0000000000000 --- a/recipes/emperor/0.9.3/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -package: - name: emperor - version: "0.9.3" - -source: - url: https://pypi.python.org/packages/cd/f1/5d502a16a348efe1af7a8d4f41b639c9a165bca0b2f9db36bce89ad1ab40/emperor-0.9.3.tar.gz - md5: e4285d2f56860ba31d14a6ce47506724 - -build: - number: 1 - skip: True [py3k or osx] - -requirements: - host: - - python - - numpy >=1.5.1,<=1.7.1 - - qcli - - run: - - python - - numpy >=1.5.1,<=1.7.1 - - qcli - -test: - # Python imports - imports: - - emperor - - emperor.qiime_backports - - commands: - - make_emperor.py --version - -about: - home: http://github.com/biocore/emperor - license: BSD License - license_file: LICENSE.md - summary: EMPeror a tool for visualizing high-throughput microbial community data diff --git a/recipes/emperor/build.sh b/recipes/emperor/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/emperor/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/emperor/meta.yaml b/recipes/emperor/meta.yaml index 8aadf9103e768..4c2a4bd995e32 100644 --- a/recipes/emperor/meta.yaml +++ b/recipes/emperor/meta.yaml @@ -8,17 +8,14 @@ source: build: number: 1 - skip: True [py3k or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - numpy >=1.7 - - qcli - - scikit-bio >=0.2.1,<0.3.0 - + - python <3 + - pip run: - - python + - python <3 - numpy >=1.7 - qcli - scikit-bio >=0.2.1,<0.3.0 diff --git a/recipes/enasearch/0.0.4/build.sh b/recipes/enasearch/0.0.4/build.sh deleted file mode 100644 index cdf69cce7c116..0000000000000 --- a/recipes/enasearch/0.0.4/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/enasearch/0.0.4/meta.yaml b/recipes/enasearch/0.0.4/meta.yaml deleted file mode 100644 index c53b7f21b9717..0000000000000 --- a/recipes/enasearch/0.0.4/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -{% set name = "enasearch" %} -{% set version = "0.0.4" %} -{% set md5 = "6cd047b6b4600853e4bb8e3eb5c21c9c" %} -package: - name: {{ name }} - version: {{ version }} -source: - url: https://pypi.python.org/packages/96/bc/fd02655f20f6e4771ef8b1e59bffe6873f57feac69f0f5cbbce4fffe490a/enasearch-0.0.4.tar.gz - md5: {{ md5 }} -build: - entry_points: - - enasearch = enasearch.__main__:main - number: 1 - skip: True # [py3k] -requirements: - host: - - python - - setuptools - - requests - - click - - flake8 - - xmltodict - - biopython - - pytest - - pytest-runner - run: - - python - - requests - - click - - flake8 - - xmltodict - - biopython -test: - imports: - - enasearch - - enasearch_data - commands: - - enasearch --help -about: - home: https://github.com/bebatut/enasearch - license: MIT License - summary: "A Python library for interacting with ENA's API" - license_family: MIT - diff --git a/recipes/enasearch/0.0.5/build.sh b/recipes/enasearch/0.0.5/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/enasearch/0.0.5/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/enasearch/0.0.5/meta.yaml b/recipes/enasearch/0.0.5/meta.yaml deleted file mode 100644 index 4f86092d39674..0000000000000 --- a/recipes/enasearch/0.0.5/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -{% set name = "enasearch" %} -{% set version = "0.0.5" %} -{% set md5 = "f49e459438832176a30bda394c8f3e69" %} -package: - name: {{ name }} - version: {{ version }} -source: - url: https://pypi.python.org/packages/ae/50/057369fdac779e6b5ec2426c7984213f766967cd728ed261cdf66cc8f10a/enasearch-0.0.5.tar.gz - md5: {{ md5 }} -build: - entry_points: - - enasearch = enasearch.__main__:main - number: 1 - skip: True # [py3k] -requirements: - host: - - python - - setuptools - - requests - - click - - flake8 - - xmltodict - - biopython - - pytest - - pytest-runner - run: - - python - - requests - - click - - flake8 - - xmltodict - - biopython -test: - imports: - - enasearch - - enasearch_data - commands: - - enasearch --help -about: - home: https://github.com/bebatut/enasearch - license: MIT License - summary: "A Python library for interacting with ENA's API" - license_family: MIT - diff --git a/recipes/enasearch/0.0.6/build.sh b/recipes/enasearch/0.0.6/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/enasearch/0.0.6/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/enasearch/0.0.6/meta.yaml b/recipes/enasearch/0.0.6/meta.yaml deleted file mode 100644 index 4f5ca336e50aa..0000000000000 --- a/recipes/enasearch/0.0.6/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -{% set name = "enasearch" %} -{% set version = "0.0.6" %} -{% set md5 = "d5c5f7fbd39e2cb9509f3a95c8c8e52d" %} -package: - name: {{ name }} - version: {{ version }} -source: - url: https://pypi.python.org/packages/a1/fd/dd5183aa4ed33cd051fdfbfb1d8c70b39c537de4174bc63253bf7229f3eb/enasearch-0.0.6.tar.gz - md5: {{ md5 }} -build: - entry_points: - - enasearch = enasearch.__main__:main - number: 1 - skip: True # [py3k] -requirements: - host: - - python - - setuptools - - requests - - click - - flake8 - - xmltodict - - biopython - - pytest - - pytest-runner - run: - - python - - requests - - click - - flake8 - - xmltodict - - biopython -test: - imports: - - enasearch - - enasearch_data - commands: - - enasearch --help -about: - home: https://github.com/bebatut/enasearch - license: MIT License - summary: "A Python library for interacting with ENA's API" - license_family: MIT - diff --git a/recipes/enasearch/0.1.1/build.sh b/recipes/enasearch/0.1.1/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/enasearch/0.1.1/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/enasearch/0.1.1/meta.yaml b/recipes/enasearch/0.1.1/meta.yaml deleted file mode 100644 index aa9be1b577064..0000000000000 --- a/recipes/enasearch/0.1.1/meta.yaml +++ /dev/null @@ -1,46 +0,0 @@ -{% set name = "enasearch" %} -{% set version = "0.1.1" %} -{% set md5 = "c4fd0a0f8536e0dae07710e923ccdc88" %} -package: - name: {{ name }} - version: {{ version }} -source: - url: https://pypi.python.org/packages/18/b1/6d22f24d8afd01ee159933f5e54675e866e4a706c9f9a98b791bba40196f/enasearch-0.1.1.tar.gz - md5: {{ md5 }} -build: - entry_points: - - enasearch = enasearch.__main__:main - number: 1 - skip: True # [py3k] -requirements: - host: - - python - - setuptools - - requests - - click - - flake8 - - xmltodict - - biopython - - dicttoxml - - pytest - - pytest-runner - run: - - python - - requests - - click - - flake8 - - xmltodict - - biopython - - dicttoxml -test: - imports: - - enasearch - - enasearch_data - commands: - - enasearch --help -about: - home: https://github.com/bebatut/enasearch - license: MIT License - summary: "A Python library for interacting with ENA's API" - license_family: MIT - diff --git a/recipes/enasearch/0.2.0/build.sh b/recipes/enasearch/0.2.0/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/enasearch/0.2.0/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/enasearch/0.2.0/meta.yaml b/recipes/enasearch/meta.yaml similarity index 80% rename from recipes/enasearch/0.2.0/meta.yaml rename to recipes/enasearch/meta.yaml index 1a2e0d2fb52ac..c2ec5bfe04228 100644 --- a/recipes/enasearch/0.2.0/meta.yaml +++ b/recipes/enasearch/meta.yaml @@ -1,43 +1,42 @@ {% set name = "enasearch" %} {% set version = "0.2.2" %} {% set md5 = "fdb69570976dddaceb66a21484cea0ce" %} + package: name: {{ name }} version: {{ version }} + source: url: https://pypi.python.org/packages/6c/98/e731dfb01f1a95ccfec443c85dfd09dd3cf6a9a08ee64bfcb0be2688e518/enasearch-0.2.0.tar.gz md5: {{ md5 }} + build: + noarch: python entry_points: - enasearch = enasearch.__main__:main number: 1 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + requirements: host: - - python - - setuptools - - requests - - click - - flake8 - - xmltodict - - biopython - - dicttoxml - - pytest - - pytest-runner + - python <3 + - pip run: - - python + - python <3 - requests - click - flake8 - xmltodict - biopython - dicttoxml + test: imports: - enasearch - enasearch_data commands: - enasearch --help + about: home: http://bebatut.fr/enasearch/ license: MIT License diff --git a/recipes/entrez-direct/meta.yaml b/recipes/entrez-direct/meta.yaml index d4231226083a8..d07e99fccc0a1 100644 --- a/recipes/entrez-direct/meta.yaml +++ b/recipes/entrez-direct/meta.yaml @@ -7,6 +7,7 @@ package: version: {{ version }} build: + noarch: generic number: 0 source: diff --git a/recipes/eoulsan/meta.yaml b/recipes/eoulsan/meta.yaml index 17426c2aae64b..2f553443a01f7 100644 --- a/recipes/eoulsan/meta.yaml +++ b/recipes/eoulsan/meta.yaml @@ -10,12 +10,10 @@ source: sha256: '{{ sha256 }}' build: + noarch: generic number: 0 - skip: true # [osx] requirements: - host: - - openjdk run: - openjdk diff --git a/recipes/epic/meta.yaml b/recipes/epic/meta.yaml index cd0cdb44bd4e3..7f2d9e79a7223 100644 --- a/recipes/epic/meta.yaml +++ b/recipes/epic/meta.yaml @@ -10,12 +10,13 @@ build: number: 1 script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt && $PYTHON setup.py build_ext --inplace - requirements: + build: + - {{ compiler('c') }} host: - python - cython - - setuptools + - pip - scipy - pandas - numpy @@ -26,10 +27,8 @@ requirements: - functools32 # [py27] - typing - pybigwig - run: - python - - cython - scipy - pandas - numpy diff --git a/recipes/epydoc/build.sh b/recipes/epydoc/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/epydoc/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/epydoc/meta.yaml b/recipes/epydoc/meta.yaml index 837c254e076fc..f916aa0869d21 100644 --- a/recipes/epydoc/meta.yaml +++ b/recipes/epydoc/meta.yaml @@ -7,15 +7,16 @@ source: md5: 36407974bd5da2af00bf90ca27feeb44 build: - skip: True # [not py27 or osx] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/eqtlbma/meta.yaml b/recipes/eqtlbma/meta.yaml index d882a588768dc..4beef1c379a6c 100644 --- a/recipes/eqtlbma/meta.yaml +++ b/recipes/eqtlbma/meta.yaml @@ -48,7 +48,5 @@ about: summary: "Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging." extra: - skip-lints: - - gsl_not_pinned identifiers: - biotools:eQtlBma diff --git a/recipes/ericscript/meta.yaml b/recipes/ericscript/meta.yaml index 79addc168e2db..5ad3e736060e1 100644 --- a/recipes/ericscript/meta.yaml +++ b/recipes/ericscript/meta.yaml @@ -12,11 +12,10 @@ source: - avoid_bwa_update.patch build: + noarch: generic number: 3 - skip: True # [osx] requirements: - run: - r-base - perl diff --git a/recipes/erne/meta.yaml b/recipes/erne/meta.yaml index f8812e39b6301..cf7cb33cac9d5 100644 --- a/recipes/erne/meta.yaml +++ b/recipes/erne/meta.yaml @@ -43,3 +43,5 @@ about: extra: identifiers: - biotools:erne + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/esmre/build.sh b/recipes/esmre/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/esmre/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/esmre/meta.yaml b/recipes/esmre/meta.yaml index f48329ff0dc34..d44a1534069b9 100644 --- a/recipes/esmre/meta.yaml +++ b/recipes/esmre/meta.yaml @@ -7,16 +7,16 @@ source: md5: 95ace12bac0c79cf95712336489bc4a4 build: + noarch: pip number: 1 - skip: True # [not py27 or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/eta/build.sh b/recipes/eta/build.sh deleted file mode 100644 index 0d620c5240825..0000000000000 --- a/recipes/eta/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/eta/meta.yaml b/recipes/eta/meta.yaml index 37ce4935f0a3f..a61b3b1750180 100644 --- a/recipes/eta/meta.yaml +++ b/recipes/eta/meta.yaml @@ -3,7 +3,9 @@ package: version: "0.9.7" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/56/f4/3def7582d454d511a0b48e5eabdfd1319ccb6b5fafc810fea7dee4ca6c4d/eta-0.9.7.tar.gz @@ -12,7 +14,7 @@ source: requirements: host: - python - + - pip run: - python diff --git a/recipes/ete2/build.sh b/recipes/ete2/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/ete2/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/ete2/meta.yaml b/recipes/ete2/meta.yaml index 87792b8bc0f75..12f23b82b216c 100644 --- a/recipes/ete2/meta.yaml +++ b/recipes/ete2/meta.yaml @@ -7,20 +7,16 @@ source: md5: 87bf020c25c293e8e4e1b1e02a3dc2b1 build: + noarch: pip number: 3 - skip: true # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pyqt 4.* - - numpy - - lxml - - mysql-python # [not osx] - + - python <3 + - pip run: - - python + - python <3 - pyqt 4.* - numpy - lxml diff --git a/recipes/evidencemodeler/meta.yaml b/recipes/evidencemodeler/meta.yaml index 1382e63d2f1ec..5201e216587e3 100644 --- a/recipes/evidencemodeler/meta.yaml +++ b/recipes/evidencemodeler/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 9ef89095fe37326d44eb95cc5b7dacae301aafa1dedfc13c17fcaec1c9388757 build: + noarch: generic number: 0 requirements: diff --git a/recipes/evofold2/meta.yaml b/recipes/evofold2/meta.yaml index 8eb2eee510ba4..199ea7b79ba45 100644 --- a/recipes/evofold2/meta.yaml +++ b/recipes/evofold2/meta.yaml @@ -22,3 +22,7 @@ about: home: https://github.com/jakob-skou-pedersen/phy license: GPL summary: Identifies functional RNA-structure in multiple sequence alignments. + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/express/meta.yaml b/recipes/express/meta.yaml index a23fdddb49704..697462049da9f 100644 --- a/recipes/express/meta.yaml +++ b/recipes/express/meta.yaml @@ -6,14 +6,12 @@ build: number: 1 source: - url: https://depot.galaxyproject.org/software/express/express_1.5.1_linux_x64.tar.gz # [linux] - sha256: 50e268af69cd5f561ae238e7d155ebb4a6505219bd93bc25a7667f7bf92b7bd5 # [linux] - url: https://depot.galaxyproject.org/software/express/express_1.5.1_darwin_x64.tar.gz # [osx] - sha256: 0582ab08440570f1686c0b075c32bed12a21d3c53ad52517768b95538a4df44b # [osx] + - url: https://depot.galaxyproject.org/software/express/express_1.5.1_linux_x64.tar.gz # [linux] + sha256: 50e268af69cd5f561ae238e7d155ebb4a6505219bd93bc25a7667f7bf92b7bd5 # [linux] + - url: https://depot.galaxyproject.org/software/express/express_1.5.1_darwin_x64.tar.gz # [osx] + sha256: 0582ab08440570f1686c0b075c32bed12a21d3c53ad52517768b95538a4df44b # [osx] requirements: - build: - - {{ compiler('cxx') }} run: - zlib @@ -25,3 +23,8 @@ about: home: http://bio.math.berkeley.edu/eXpress/ license: Artistic License 2.0 summary: eXpress is a streaming DNA/RNA sequence quantification tool. + +extra: + skip-lints: + - should_not_be_noarch_source + - should_be_noarch_generic diff --git a/recipes/extern/build.sh b/recipes/extern/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/extern/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/extern/meta.yaml b/recipes/extern/meta.yaml index fc4304c1e8350..c121a35a57c7f 100644 --- a/recipes/extern/meta.yaml +++ b/recipes/extern/meta.yaml @@ -7,16 +7,16 @@ source: md5: 093c4022301cc57eef0344c577088a09 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/extract_fullseq/meta.yaml b/recipes/extract_fullseq/meta.yaml index 011861fc02253..9b3435d8302dc 100644 --- a/recipes/extract_fullseq/meta.yaml +++ b/recipes/extract_fullseq/meta.yaml @@ -2,13 +2,13 @@ package: name: extract_fullseq version: 3.101 source: - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] - md5: 719474a0e3b54449cbe06f6e442994dd # [linux] - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/extract_fullseq # [osx] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz # [linux] + md5: 719474a0e3b54449cbe06f6e442994dd # [linux] + - url: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/mac-os/extract_fullseq # [osx] + sha256: 1e2c8cd314498bf56ba0291185190d0ed20cbd839098492ab573be2ca6770a66 # [osx] build: number: 3 - skip: False requirements: build: @@ -24,3 +24,8 @@ about: home: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ license: Public Domain summary: "extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets" + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/extract_genome_region/build.sh b/recipes/extract_genome_region/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/extract_genome_region/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/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index df1ed843f0d84..dc4779c6abaa8 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -7,17 +7,16 @@ source: url: https://github.com/xguse/extract-genome-region/archive/v0.0.3.tar.gz build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - extract_genome_region = extract_genome_region.__main__:main requirements: host: - python - - setuptools - - click - - pyfaidx - + - pip run: - python - click diff --git a/recipes/fann/meta.yaml b/recipes/fann/meta.yaml index 2534a64f531a1..99488c3e9c64e 100644 --- a/recipes/fann/meta.yaml +++ b/recipes/fann/meta.yaml @@ -19,3 +19,7 @@ about: home: http://leenissen.dk/fann/wp/ summary: Fast Artificial Neural Network Library license: LGPL-2.1 + +extra: + skip-lints: + - missing_tests diff --git a/recipes/fast5/meta.yaml b/recipes/fast5/meta.yaml index a76263ad9150e..e072192e1ac83 100644 --- a/recipes/fast5/meta.yaml +++ b/recipes/fast5/meta.yaml @@ -6,6 +6,7 @@ package: version: {{ version }} build: + noarch: generic number: 1 source: diff --git a/recipes/fast5seek/meta.yaml b/recipes/fast5seek/meta.yaml index b2c21ecd513bd..976315b98642d 100644 --- a/recipes/fast5seek/meta.yaml +++ b/recipes/fast5seek/meta.yaml @@ -11,19 +11,18 @@ source: sha256: '{{ hash_value }}' build: + noarch: python number: 0 entry_points: - fast5seek=fast5seek.cli:cli script: python -m pip install --no-deps --ignore-installed . - skip: True # [py27] requirements: host: - - python + - python >=3 - pip - - setuptools run: - - python + - python >=3 - ont-fast5-api - pysam diff --git a/recipes/fasta-splitter/0.2.4/build.sh b/recipes/fasta-splitter/0.2.4/build.sh deleted file mode 100644 index 019bf4b009389..0000000000000 --- a/recipes/fasta-splitter/0.2.4/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -ln -s $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM $PREFIX/share/$PKG_NAME - -cp ./fasta-splitter.pl $outdir/ -chmod +x $outdir/fasta-splitter.pl - -mkdir -p $PREFIX/bin -ln -s $outdir/fasta-splitter.pl $PREFIX/bin/fasta-splitter diff --git a/recipes/fasta-splitter/0.2.4/meta.yaml b/recipes/fasta-splitter/0.2.4/meta.yaml deleted file mode 100644 index 37fefdf0c9fb5..0000000000000 --- a/recipes/fasta-splitter/0.2.4/meta.yaml +++ /dev/null @@ -1,26 +0,0 @@ -package: - name: fasta-splitter - version: 0.2.4 - -source: - fn: fasta-splitter-0.2.4.zip - sha256: 1fd3a5e52e7f9033ddd7619db99b42427405ee9177e9eddb3e55a6038ac5d919 - url: http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip - -build: - number: 1 - skip: False - -requirements: - run: - - perl - - perl-file-util - -test: - commands: - - fasta-splitter --help - -about: - home: http://kirill-kryukov.com/study/tools/fasta-splitter/ - license: zlib/libpng - summary: 'Divides a large FASTA file into a set of smaller, approximately equally sized files' diff --git a/recipes/fastaindex/build.sh b/recipes/fastaindex/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fastaindex/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/fastaindex/meta.yaml b/recipes/fastaindex/meta.yaml index e9aab7f4d9c5d..f4b3e1f0cc3ad 100644 --- a/recipes/fastaindex/meta.yaml +++ b/recipes/fastaindex/meta.yaml @@ -7,19 +7,19 @@ source: sha256: 3c7c1560719d44602ca5c70960228cbe12545e73e1381e3fdf9cdf64a588c943 build: - # FastaIndex does not support Python 3 - skip: True # [py3k] + noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - FastaIndex = FastaIndex:main - fasta_stats = fasta_stats:main requirements: host: - - python - - setuptools + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index a7adfcf48a4ce..f202a3d9204e2 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -16,6 +16,7 @@ source: requirements: build: - rust + - {{ compiler('c') }} host: - rust diff --git a/recipes/fastlmm/build.sh b/recipes/fastlmm/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fastlmm/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/fastlmm/meta.yaml b/recipes/fastlmm/meta.yaml index 943e60d08831b..2d3b28b5fea45 100644 --- a/recipes/fastlmm/meta.yaml +++ b/recipes/fastlmm/meta.yaml @@ -11,24 +11,16 @@ source: md5: {{ hash }} build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - scipy >=0.16.0 - - numpy >=1.9.3 - - pandas >=0.16.2 - - statsmodels >=0.6.1 - - matplotlib >=1.4.3 - - scikit-learn >=0.16.1 - - pysnptools >=0.3.13 - - dill - + - python <3 + - pip run: - - python + - python <3 - scipy >=0.16.0 - numpy >=1.9.3 - pandas >=0.16.2 diff --git a/recipes/fastphylo/meta.yaml b/recipes/fastphylo/meta.yaml index 273ebf1e0d38d..81a3fd5fddb82 100644 --- a/recipes/fastphylo/meta.yaml +++ b/recipes/fastphylo/meta.yaml @@ -9,24 +9,21 @@ build: number: 1 source: - fn: {{ name|lower }}-{{ version }}.tar.gz url: https://github.com/arvestad/{{ name }}/archive/{{ version }}.tar.gz sha256: b53c44aadea21aaf2e0645cbd18ff7eea99dbf8545a42b005443332fd84d41a2 requirements: build: - - gcc # [not osx] - - llvm # [osx] - - cmake - - openmpi - - openblas - - libxml2 - - wget - + - {{ compiler('c') }} + - cmake + - openmpi + - openblas + - libxml2 + - wget run: - - openmpi - - openblas - - libxml2 + - openmpi + - openblas + - libxml2 test: commands: diff --git a/recipes/fastq-anonymous/meta.yaml b/recipes/fastq-anonymous/meta.yaml index f89022edd21dd..26f2b1fc5b38b 100644 --- a/recipes/fastq-anonymous/meta.yaml +++ b/recipes/fastq-anonymous/meta.yaml @@ -6,23 +6,22 @@ package: version: '{{ version }}' source: - fn: 'fastq-anonymous-{{ version }}.tar.gz' url: https://pypi.io/packages/source/f/fastq-anonymous/fastq-anonymous-{{ version }}.tar.gz sha256: '{{ hash_value }}' build: - skip: True # [py27] number: 1 entry_points: - fastq-anonymous=fastqanonymous.fastqanonymous:main - script: python setup.py install --single-version-externally-managed --record=record.txt + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python requirements: build: - - python - - setuptools + - python >=3 + - pip run: - - python + - python >=3 - biopython test: diff --git a/recipes/fastq-screen/meta.yaml b/recipes/fastq-screen/meta.yaml index bd3000674bdba..6704329503aed 100644 --- a/recipes/fastq-screen/meta.yaml +++ b/recipes/fastq-screen/meta.yaml @@ -10,6 +10,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/fastq_tools/build.sh b/recipes/fastq-tools/build.sh similarity index 100% rename from recipes/fastq_tools/build.sh rename to recipes/fastq-tools/build.sh diff --git a/recipes/fastq_tools/meta.yaml b/recipes/fastq-tools/meta.yaml similarity index 100% rename from recipes/fastq_tools/meta.yaml rename to recipes/fastq-tools/meta.yaml diff --git a/recipes/fastqc/0.11.7/meta.yaml b/recipes/fastqc/0.11.7/meta.yaml index 4dc5f6964a572..74fd3d6ae6b90 100644 --- a/recipes/fastqc/0.11.7/meta.yaml +++ b/recipes/fastqc/0.11.7/meta.yaml @@ -13,6 +13,7 @@ source: - java_xms.patch build: + noarch: generic detect_binary_files_with_prefix: true number: 5 diff --git a/recipes/fastqc/meta.yaml b/recipes/fastqc/meta.yaml index ae5da11ee5ebb..1fca5a03c6bb7 100644 --- a/recipes/fastqc/meta.yaml +++ b/recipes/fastqc/meta.yaml @@ -13,6 +13,7 @@ source: - java_xms.patch build: + noarch: generic detect_binary_files_with_prefix: true number: 1 diff --git a/recipes/fastqe/meta.yaml b/recipes/fastqe/meta.yaml index 3085f0d4c0fe2..7b61d16b78693 100644 --- a/recipes/fastqe/meta.yaml +++ b/recipes/fastqe/meta.yaml @@ -13,16 +13,16 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: python number: 0 entry_points: - fastqe = fastqe.fastqe:main - script: 'python setup.py install ' + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - biopython >=1.66 - - pyemojify + - pip run: - python - biopython >=1.66 @@ -38,11 +38,5 @@ about: home: https://github.com/lonsbio/fastqe license: MIT license_family: MIT - license_file: '' summary: A emoji based bioinformatics command line tool description: "The program reads one or more input FASTQ files.\nFor each file it computes the minimum, maximum and mean FASTQ quality score at each position across all reads in a file.\n\nFor some reason, it then represents these as emoji." - doc_url: '' - dev_url: '' - -extra: - recipe-maintainers: '' diff --git a/recipes/fastqmetrics/build.sh b/recipes/fastqmetrics/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fastqmetrics/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/fastqmetrics/meta.yaml b/recipes/fastqmetrics/meta.yaml index 167b648f99bb6..de6dab00c63e0 100644 --- a/recipes/fastqmetrics/meta.yaml +++ b/recipes/fastqmetrics/meta.yaml @@ -9,19 +9,18 @@ source: sha256: 7d7f6b3645d9c35550cb7b803466b6f3428c42da0eecff3238dcf1735320b14c build: + noarch: python entry_points: - fastqmetrics=fastqmetrics.fastqmetrics:main number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - nanoget >=0.14.0 - + - python >=3 + - pip run: - - python + - python >=3 - nanoget >=0.14.0 test: diff --git a/recipes/faststructure/meta.yaml b/recipes/faststructure/meta.yaml index fdd51f2f4d438..401b8770d9a29 100644 --- a/recipes/faststructure/meta.yaml +++ b/recipes/faststructure/meta.yaml @@ -31,7 +31,6 @@ requirements: - numpy - scipy - matplotlib - - cython <0.28 - gsl - openblas diff --git a/recipes/fasttree/2.1.8/build.sh b/recipes/fasttree/2.1.8/build.sh index a7c4ca56eca51..8c39608b25995 100755 --- a/recipes/fasttree/2.1.8/build.sh +++ b/recipes/fasttree/2.1.8/build.sh @@ -4,14 +4,14 @@ mkdir -p $PREFIX/bin # build FastTree -gcc -O3 -DUSE_DOUBLE -finline-functions -funroll-loops -Wall -o FastTree $SRC_DIR/FastTree-2.1.8.c -lm +$CC -O3 -DUSE_DOUBLE -finline-functions -funroll-loops -Wall -o FastTree $SRC_DIR/FastTree-2.1.8.c -lm chmod +x FastTree cp ./FastTree $PREFIX/bin/fasttree # Build FastTreeMP on Linux if [ "$(uname)" == "Linux" ]; then - gcc -DOPENMP -fopenmp -O3 -DUSE_DOUBLE -finline-functions -funroll-loops -Wall -o FastTreeMP $SRC_DIR/FastTree-2.1.8.c -lm + $CC -DOPENMP -fopenmp -O3 -DUSE_DOUBLE -finline-functions -funroll-loops -Wall -o FastTreeMP $SRC_DIR/FastTree-2.1.8.c -lm chmod +x FastTreeMP mv -v ./FastTree* $PREFIX/bin fi diff --git a/recipes/fasttree/2.1.8/meta.yaml b/recipes/fasttree/2.1.8/meta.yaml index cf47d473894ed..f1e0eea7c4475 100644 --- a/recipes/fasttree/2.1.8/meta.yaml +++ b/recipes/fasttree/2.1.8/meta.yaml @@ -10,6 +10,10 @@ build: number: 4 skip: True # [osx] +requirements: + build: + - {{ compiler('c') }} + test: commands: - FastTree -help diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index 971ff87840449..67d60fd1008a0 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -22,7 +22,6 @@ requirements: - nose - libgtextutils run: - - cython - libgtextutils - gnuplot >=5.0.5 - perl diff --git a/recipes/fcsparser/meta.yaml b/recipes/fcsparser/meta.yaml index 0f7770901f199..4b8a5b362cc74 100644 --- a/recipes/fcsparser/meta.yaml +++ b/recipes/fcsparser/meta.yaml @@ -7,7 +7,6 @@ source: md5: 009d878e5e5124aca4fe3dc3a47cd5eb build: - noarch: python number: 0 noarch: python preserve_egg_dir: False diff --git a/recipes/feelnc/meta.yaml b/recipes/feelnc/meta.yaml index 3c95642454927..c8d5b0b960d07 100644 --- a/recipes/feelnc/meta.yaml +++ b/recipes/feelnc/meta.yaml @@ -11,6 +11,7 @@ source: sha256: 9f17fd9ed29d21a65296e45052860b688bcf0ef2e2efb31e3191cde825d84a49 build: + noarch: generic number: 4 requirements: diff --git a/recipes/feht/meta.yaml b/recipes/feht/meta.yaml index 4da987de23319..d919f5ff7fa0f 100644 --- a/recipes/feht/meta.yaml +++ b/recipes/feht/meta.yaml @@ -29,3 +29,7 @@ about: license: BSD 3-clause summary: 'A commandline program to automatically identify markers predictive of groups. Can be used with binary data, genomic (single nucleotide variant) data, or arbitrary character data.' license_family: BSD + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/fgmp/meta.yaml b/recipes/fgmp/meta.yaml index 620066f92ba83..e2b282fe57316 100644 --- a/recipes/fgmp/meta.yaml +++ b/recipes/fgmp/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 9a6a0b0ed316eb0dc258998e69a0b41797e81aafbddf663acf689dd440086432 build: + noarch: generic number: 0 requirements: diff --git a/recipes/find_differential_primers/build.sh b/recipes/find_differential_primers/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/find_differential_primers/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/find_differential_primers/meta.yaml b/recipes/find_differential_primers/meta.yaml index fd48251be5dc1..848d676aa8fd0 100644 --- a/recipes/find_differential_primers/meta.yaml +++ b/recipes/find_differential_primers/meta.yaml @@ -10,22 +10,16 @@ source: sha256: '{{sha256}}' build: - skip: true # [not py27] + noarch: python number: 3 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - biopython - - bx-python - - emboss - - primer3 <=1.1.4 - - prodigal - - blast - + - python <3 + - pip run: - - python + - python <3 - biopython - bx-python - emboss diff --git a/recipes/fisher/build.sh b/recipes/fisher/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/fisher/build.sh +++ /dev/null @@ -1,9 +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/fisher/meta.yaml b/recipes/fisher/meta.yaml deleted file mode 100644 index c96363b171c64..0000000000000 --- a/recipes/fisher/meta.yaml +++ /dev/null @@ -1,46 +0,0 @@ -package: - name: fisher - version: "0.1.4" - -source: - url: https://pypi.python.org/packages/source/f/fisher/fisher-0.1.4.tar.gz - md5: bfc763b7333a1f428e4c447dd8a85968 - -build: - skip: True # [not py27] - number: 1 - -requirements: - host: - - python - - numpy - - run: - - python - - numpy - -test: - # Python imports - imports: - - fisher - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called 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: http://github.com/brentp/fishers_exact_test - license: BSD License - summary: "Fast Fisher's Exact Test" - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/flaimapper/meta.yaml b/recipes/flaimapper/meta.yaml index 63bf53f71e32a..29eae70310317 100644 --- a/recipes/flaimapper/meta.yaml +++ b/recipes/flaimapper/meta.yaml @@ -7,19 +7,17 @@ source: sha256: 6aee280f1d0a345ac71e01a5c512ee213b1a5bdb6d486de837ee054eda8378e3 build: + noarch: python preserve_egg_dir: True number: 1 - skip: True # [py27] requirements: host: - - python + - python >=3 - setuptools - pysam >=0.14.1 - run: - - python - - setuptools + - python >=3 - pysam >=0.14.1 test: diff --git a/recipes/flapjack/meta.yaml b/recipes/flapjack/meta.yaml index a088302f24127..e93ba68eee98e 100644 --- a/recipes/flapjack/meta.yaml +++ b/recipes/flapjack/meta.yaml @@ -10,6 +10,7 @@ source: md5: ff91dbefa3a37334e4ef23fe90d98f4f build: + noarch: generic number: 0 requirements: diff --git a/recipes/flash2/meta.yaml b/recipes/flash2/meta.yaml index e65852ff32426..b32ab5dd62e06 100644 --- a/recipes/flash2/meta.yaml +++ b/recipes/flash2/meta.yaml @@ -9,7 +9,6 @@ build: number: 1 source: - fn: {{ name|lower }}_{{ version }}.tar.gz url: https://github.com/dstreett/FLASH2/archive/{{ version }}.tar.gz sha256: 7bb357a935de87be8a294b35ed281eca2e08afa1e1a1d1b1c24a024b80b713ff diff --git a/recipes/flux-simulator/meta.yaml b/recipes/flux-simulator/meta.yaml index e736c3600366d..2d7e308478e0a 100644 --- a/recipes/flux-simulator/meta.yaml +++ b/recipes/flux-simulator/meta.yaml @@ -7,12 +7,12 @@ source: md5: 1f071df3a577cb5d7c03755ffc0586eb build: + noarch: generic number: 1 - skip: False requirements: run: - - java-jdk + - openjdk test: commands: diff --git a/recipes/forked-path/build.sh b/recipes/forked-path/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/forked-path/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/forked-path/meta.yaml b/recipes/forked-path/meta.yaml index 8b4ad5debcb0e..fcab332e433a5 100644 --- a/recipes/forked-path/meta.yaml +++ b/recipes/forked-path/meta.yaml @@ -7,16 +7,16 @@ source: md5: 21a618ba91fb045ece0b426cdd21be2b build: + noarch: python number: 2 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/fred2/build.sh b/recipes/fred2/build.sh deleted file mode 100644 index d60ecfabf51ea..0000000000000 --- a/recipes/fred2/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/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 67c1463e3c7dc..4aa0b46a6a224 100644 --- a/recipes/fred2/meta.yaml +++ b/recipes/fred2/meta.yaml @@ -11,22 +11,16 @@ source: sha256: '{{ sha256 }}' build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pyomo - - pandas - - pyvcf - - biopython - - pymysql - + - python <3 + - pip run: - - python - - setuptools + - python <3 - pyomo - pandas - pyvcf diff --git a/recipes/freebayes/1.1.0.46/meta.yaml b/recipes/freebayes/1.1.0.46/meta.yaml index 0ab554bcb84fc..03790ec1e232f 100644 --- a/recipes/freebayes/1.1.0.46/meta.yaml +++ b/recipes/freebayes/1.1.0.46/meta.yaml @@ -41,7 +41,7 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url - missing_hash identifiers: - biotools:freebayes diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index ec5fe0c79f542..e15aefa257b6b 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -45,6 +45,5 @@ extra: skip-lints: - missing_hash - uses_vcs_url - - uses_git_url identifiers: - biotools:freebayes diff --git a/recipes/frogs/meta.yaml b/recipes/frogs/meta.yaml index 63e7b90cfed17..959c94c820059 100644 --- a/recipes/frogs/meta.yaml +++ b/recipes/frogs/meta.yaml @@ -8,7 +8,6 @@ package: build: number: 0 - skip: true # [py3k] skip: true # [osx] source: @@ -19,12 +18,9 @@ source: folder: lib/external-lib requirements: - host: - - python - - rdptools >=2.0.2 run: - emboss >=6.6.0 - - python + - python <3 - scipy >=1.1.0 - perl - perl-io-gzip >=0.20 @@ -73,3 +69,7 @@ about: home: https://github.com/geraldinepascal/FROGS license: 'GNU GPL v3' summary: 'FROGS is a workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data. This is the official release 3.1.0 of FROGS.' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/fsnviz/0.1.0/build.sh b/recipes/fsnviz/0.1.0/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fsnviz/0.1.0/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/fsnviz/0.1.0/meta.yaml b/recipes/fsnviz/0.1.0/meta.yaml deleted file mode 100644 index 348403359634e..0000000000000 --- a/recipes/fsnviz/0.1.0/meta.yaml +++ /dev/null @@ -1,46 +0,0 @@ -package: - name: fsnviz - version: 0.1.0 - -source: - url: https://pypi.python.org/packages/cb/ed/a9cd233386fab2800e24a5a5b58757c150e35aa0bb30069e44498db4b6a3/FsnViz-0.1.0.tar.gz - md5: 79ba80aeef411b89802e2b3e597b3c37 - -build: - # FsnViz does not support Python 2 - skip: True # [py2k] - number: 1 - entry_points: - - fsnviz=fsnviz.main:cli - -requirements: - host: - - python - - setuptools - - click ==6.6 - - crimson >=0.3.0 - - jinja2 ==2.8 - - circos ==0.69.2 - - run: - - python - - click ==6.6 - - crimson >=0.3.0 - - jinja2 ==2.8 - - circos ==0.69.2 - -test: - commands: - - fsnviz --help - -about: - home: https://github.com/bow/fsnviz - license: BSD - summary: 'Tool for plotting gene fusion events detected by various tools using Circos.' - license_family: BSD - -extra: - container: - # click requires a unicode locale when used with Python 3 - # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly - extended-base: true diff --git a/recipes/fsnviz/0.2.0/build.sh b/recipes/fsnviz/0.2.0/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fsnviz/0.2.0/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/fsnviz/0.2.0/meta.yaml b/recipes/fsnviz/0.2.0/meta.yaml deleted file mode 100644 index 3a8c8660c331d..0000000000000 --- a/recipes/fsnviz/0.2.0/meta.yaml +++ /dev/null @@ -1,48 +0,0 @@ -{% set version = "0.2.0" %} - -package: - name: fsnviz - version: {{ version }} - -source: - url: https://pypi.python.org/packages/a8/e9/535bde7ffdf5c0678d0b75d0667dc846bbf95c27f6f540eb69b7240b901c/FsnViz-{{ version }}.tar.gz - md5: 20a051a88d1631e76536828b8b69cac4 - -build: - # FsnViz does not support Python 2 - skip: True # [py2k] - number: 1 - entry_points: - - fsnviz=fsnviz.cli:main - -requirements: - host: - - python - - setuptools - - click >=6.6 - - crimson >=0.3.0 - - jinja2 ==2.9.5 - - circos >=0.69.2 - - run: - - python - - click >=6.6 - - crimson >=0.3.0 - - jinja2 ==2.9.5 - - circos >=0.69.2 - -test: - commands: - - fsnviz --help - -about: - home: https://github.com/bow/fsnviz - license: BSD - summary: 'Tool for plotting gene fusion events detected by various tools using Circos.' - license_family: BSD - -extra: - container: - # click requires a unicode locale when used with Python 3 - # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly - extended-base: true diff --git a/recipes/fsnviz/build.sh b/recipes/fsnviz/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fsnviz/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/fsnviz/meta.yaml b/recipes/fsnviz/meta.yaml index faffbe7df79cb..1ab118ed0de6d 100644 --- a/recipes/fsnviz/meta.yaml +++ b/recipes/fsnviz/meta.yaml @@ -9,23 +9,18 @@ source: md5: ac9d72772afe24f2ad07236b3ac11261 build: - # FsnViz does not support Python 2 - skip: True # [py2k] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - fsnviz=fsnviz.cli:main requirements: host: - - python - - setuptools - - click >=6.6 - - crimson >=0.3.0 - - jinja2 ==2.9.5 - - circos >=0.69.2 - + - python >=3 + - pip run: - - python + - python >=3 - click >=6.6 - crimson >=0.3.0 - jinja2 ==2.9.5 diff --git a/recipes/fuma/build.sh b/recipes/fuma/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/fuma/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/fuma/meta.yaml b/recipes/fuma/meta.yaml index 7fcc948e90b51..9483eaceaa95e 100644 --- a/recipes/fuma/meta.yaml +++ b/recipes/fuma/meta.yaml @@ -9,19 +9,17 @@ source: - remove-nose-dep.patch build: + noarch: python preserve_egg_dir: True number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - htseq >=0.6.1 - + - python <3 + - pip run: - - python + - python <3 - numpy - htseq >=0.6.1 diff --git a/recipes/fusion-filter/meta.yaml b/recipes/fusion-filter/meta.yaml index 08a55f307ea94..7071386db547a 100644 --- a/recipes/fusion-filter/meta.yaml +++ b/recipes/fusion-filter/meta.yaml @@ -1,6 +1,5 @@ {% set name = "fusion-filter" %} {% set version = "0.5.0" %} -{% set build = "1" %} package: name: {{ name }} @@ -11,13 +10,13 @@ source: md5: c7c3030188ae56499d6222ece5dd682f build: - number: {{ build }} - skip: true # [py3k] + noarch: generic + number: 1 requirements: host: run: - - python + - python <3 - perl - perl-perlio-gzip - perl-uri diff --git a/recipes/fusion-inspector/meta.yaml b/recipes/fusion-inspector/meta.yaml index df3d36891f52b..d524e76e4b460 100644 --- a/recipes/fusion-inspector/meta.yaml +++ b/recipes/fusion-inspector/meta.yaml @@ -1,6 +1,5 @@ {% set name = "fusion-inspector" %} {% set version = "1.3.1" %} -{% set build = "1" %} package: name: {{ name }} @@ -11,8 +10,8 @@ source: md5: 8a6dba6110381b39a9ee372d0572ea53 build: - number: {{ build }} - skip: true # [osx or py3k] + noarch: generic + number: 1 # The reason for skipping osx is that trinity >=2.4 is not available in the osx channel # The python code in FusionInspector runs on python 2.7. @@ -20,12 +19,10 @@ build: # We need HTSLIB >=1.3, but was complaining about unpinned. CONDA_HTSLIB is 1.6. requirements: host: - - python - - bzip2 - htslib - trinity >=2.4 run: - - python + - python <3 - requests >=2.19.1 - bzip2 - htslib diff --git a/recipes/fusion-report/meta.yaml b/recipes/fusion-report/meta.yaml index 20b60a6049b5d..5e7704fc467e4 100644 --- a/recipes/fusion-report/meta.yaml +++ b/recipes/fusion-report/meta.yaml @@ -16,7 +16,7 @@ build: requirements: host: - python >=3.6 - - setuptools + - pip - tqdm==4.33.0 - colorlog==4.0.2 - Jinja2==2.10.1 @@ -24,7 +24,6 @@ requirements: - pyyaml>=4.2b1 run: - python >=3.6 - - setuptools - tqdm==4.33.0 - colorlog==4.0.2 - Jinja2==2.10.1 diff --git a/recipes/galaxy-ops/build.sh b/recipes/galaxy-ops/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/galaxy-ops/build.sh +++ /dev/null @@ -1,9 +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/galaxy-ops/meta.yaml b/recipes/galaxy-ops/meta.yaml index df598786d555e..1cca3c34a1791 100644 --- a/recipes/galaxy-ops/meta.yaml +++ b/recipes/galaxy-ops/meta.yaml @@ -2,27 +2,28 @@ package: name: galaxy-ops version: 1.1.0 -about: - home: https://github.com/galaxyproject/gops - license: Academic Free License version 3.0 - summary: Galaxy interval operations - source: url: https://github.com/galaxyproject/gops/archive/v1.1.0.tar.gz sha256: 93020461079ff8bc804252a01d651b072d621b11270d9ece081617ff843d32fb build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - bx-python - - python + - pip + - python <3 run: - bx-python - - python + - python <3 test: imports: - galaxy.tools.util.galaxyops + +about: + home: https://github.com/galaxyproject/gops + license: Academic Free License version 3.0 + summary: Galaxy interval operations diff --git a/recipes/gapfiller/meta.yaml b/recipes/gapfiller/meta.yaml index b00a7d3cf00af..e6d28cd8e737a 100644 --- a/recipes/gapfiller/meta.yaml +++ b/recipes/gapfiller/meta.yaml @@ -41,3 +41,4 @@ about: extra: skip-lints: - should_use_compilers + - should_be_noarch_generic diff --git a/recipes/gb_taxonomy_tools/meta.yaml b/recipes/gb_taxonomy_tools/meta.yaml index 17cb65053caae..c14994373cbc0 100644 --- a/recipes/gb_taxonomy_tools/meta.yaml +++ b/recipes/gb_taxonomy_tools/meta.yaml @@ -13,6 +13,8 @@ build: requirements: build: - cmake + - {{ compiler('c') }} + - {{ compiler('cxx') }} test: commands: diff --git a/recipes/gblocks/meta.yaml b/recipes/gblocks/meta.yaml index 4fe1cde0b40ab..b14be5b42a6d0 100644 --- a/recipes/gblocks/meta.yaml +++ b/recipes/gblocks/meta.yaml @@ -1,22 +1,33 @@ package: name: gblocks version: "0.91b" + source: - url: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z # [linux] - sha256: 563658f03cc5e76234a8aa705bdc149398defec813d3a0c172b5f94c06c880dc # [linux] - url: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_OSX_0.91b.tar.Z # [osx] - sha256: e5b9e1ae2a227ca0b78ca65741e44f460c7968dea4b01ea45150b1231f391473 # [osx] + - url: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z # [linux] + sha256: 563658f03cc5e76234a8aa705bdc149398defec813d3a0c172b5f94c06c880dc # [linux] + - url: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_OSX_0.91b.tar.Z # [osx] + sha256: e5b9e1ae2a227ca0b78ca65741e44f460c7968dea4b01ea45150b1231f391473 # [osx] + build: + noarch: generic number: 1 + requirements: build: [] run: [] + test: commands: - which Gblocks + about: home: http://molevol.cmima.csic.es/castresana/Gblocks.html license: The software and its accompanying documentation are provided as is, without guarantee of support or maintenance. summary: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/gcs_oauth2_boto_plugin/meta.yaml b/recipes/gcs-oauth2-boto-plugin/meta.yaml similarity index 75% rename from recipes/gcs_oauth2_boto_plugin/meta.yaml rename to recipes/gcs-oauth2-boto-plugin/meta.yaml index 69abb4d67f2a7..19ccf749f3627 100644 --- a/recipes/gcs_oauth2_boto_plugin/meta.yaml +++ b/recipes/gcs-oauth2-boto-plugin/meta.yaml @@ -9,23 +9,17 @@ source: md5: 30ce54681c83a23c93f1692c618f3b55 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - cryptography - - python - - setuptools - - boto >=2.29.1 - - httplib2 >=0.8 - - google-api-python-client >=1.1 - - pyopenssl >=0.13 - - socksipy-branch ==1.01 - - retry_decorator >=1.0.0 + - python <3 + - pip run: - - python + - python <3 - boto >=2.29.1 - httplib2 >=0.8 - google-api-python-client >=1.1 diff --git a/recipes/gcs_oauth2_boto_plugin/build.sh b/recipes/gcs_oauth2_boto_plugin/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/gcs_oauth2_boto_plugin/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/gemini/build.sh b/recipes/gemini/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/gemini/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/gemini/meta.yaml b/recipes/gemini/meta.yaml index 3233434793d3f..6dfaf2049e9ab 100644 --- a/recipes/gemini/meta.yaml +++ b/recipes/gemini/meta.yaml @@ -4,14 +4,19 @@ package: name: {{ name|lower }} version: {{ version }} + build: number: 0 skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + source: url: https://github.com/arq5x/gemini/archive/v{{ version }}.tar.gz sha256: c7af06a4cc475a846aeeb3cd7fcfb39d6cdd0b76e3b07abab2e5e6e68a3fe431 requirements: + build: + - {{ compiler('c') }} host: - python - setuptools @@ -44,7 +49,6 @@ requirements: - bottle - bx-python - cyordereddict - - cython - cyvcf2 >0.6.5 - geneimpacts - inheritance diff --git a/recipes/geneimpacts/build.sh b/recipes/geneimpacts/build.sh deleted file mode 100755 index 89481145a5291..0000000000000 --- a/recipes/geneimpacts/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/geneimpacts/meta.yaml b/recipes/geneimpacts/meta.yaml index 0aed646ed92dc..30a7687f70ddd 100644 --- a/recipes/geneimpacts/meta.yaml +++ b/recipes/geneimpacts/meta.yaml @@ -1,20 +1,22 @@ {% set version="0.3.7" %} + package: name: geneimpacts version: {{ version }} source: url: https://github.com/brentp/geneimpacts/archive/v{{ version }}.tar.gz - #url: https://pypi.io/packages/source/g/geneimpacts/geneimpacts-{{ version }}.tar.gz sha256: 895a0aa64935bf8528257fc5a3747c09adbf30c4885d95b0fa69ba4bb858c133 build: + noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools + - pip run: - python @@ -26,7 +28,3 @@ about: home: https://github.com/brentp/geneimpacts summary: prioritize effects of variant annotations from VEP, SnpEff, et al. license: MIT - -extra: - skip-lints: - - should_be_noarch diff --git a/recipes/genomelake/meta.yaml b/recipes/genomelake/meta.yaml index c445f5609ee11..32c2166685246 100644 --- a/recipes/genomelake/meta.yaml +++ b/recipes/genomelake/meta.yaml @@ -1,36 +1,24 @@ {% set name = "genomelake" %} {% set version = "0.1.4" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "fcec11be1cce15f08de0df34916f946a9470ed911050f5ab7098a1279e892253" %} 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 }}' + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: fcec11be1cce15f08de0df34916f946a9470ed911050f5ab7098a1279e892253 build: number: 1 - script: pip install cython && python setup.py install --single-version-externally-managed --record=record.txt + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: + - {{ compiler('c') }} + host: - python - pip - - setuptools - - future - - gcc # [not osx] - - llvm # [osx] - - bcolz >=1.1 - - numpy - - pybedtools - - pybigwig - - pysam - - six >=1.9.0 run: - python - bcolz >=1.1 @@ -48,11 +36,5 @@ about: home: https://github.com/kundajelab/genomelake license: BSD License license_family: BSD - license_file: '' summary: Simple and efficient random access to genomic data for deep learning models. description: "Simple and efficient random access to genomic data for deep learning models." - doc_url: '' - dev_url: '' - -extra: - recipe-maintainers: '' diff --git a/recipes/genomestrip/meta.yaml b/recipes/genomestrip/meta.yaml index bd1f944d3d492..f706d5431241b 100644 --- a/recipes/genomestrip/meta.yaml +++ b/recipes/genomestrip/meta.yaml @@ -5,13 +5,12 @@ package: version: {{ version }} source: - fn: svtoolkit_{{ version }}.tar.gz url: https://bitbucket.org/tobiasmarschall/genomestrip-redist/downloads/svtoolkit_{{ version }}.tar.gz sha256: e9172d6d91b605052f6226720535a5d2d00eb5b690360df4da60d8faf47422f3 build: + noarch: generic number: 1 - skip: False requirements: run: diff --git a/recipes/genomethreader/meta.yaml b/recipes/genomethreader/meta.yaml index 81339a1e08acf..7be497271d2d1 100644 --- a/recipes/genomethreader/meta.yaml +++ b/recipes/genomethreader/meta.yaml @@ -6,8 +6,8 @@ package: version: {{ version }} source: - url: http://genomethreader.org/distributions/gth-{{version}}-Linux_x86_64-64bit.tar.gz # [linux] - sha256: 7c7b05d0a88a13a83918a7e209bf38195238b93b93684e0f4c2ed48ecbaf8718 # [linux] + url: http://genomethreader.org/distributions/gth-{{version}}-Linux_x86_64-64bit.tar.gz + sha256: 7c7b05d0a88a13a83918a7e209bf38195238b93b93684e0f4c2ed48ecbaf8718 build: skip: True # [not linux] @@ -29,7 +29,6 @@ about: license_file: LICENSE dev_url: https://github.com/genometools/genomethreader - extra: recipe-maintainers: - lucventurini diff --git a/recipes/genomicconsensus/build.sh b/recipes/genomicconsensus/build.sh deleted file mode 100644 index e45c73d5420b0..0000000000000 --- a/recipes/genomicconsensus/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/env bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/genomicconsensus/meta.yaml b/recipes/genomicconsensus/meta.yaml index 334fe4fe10eeb..7d9b140ea2c25 100644 --- a/recipes/genomicconsensus/meta.yaml +++ b/recipes/genomicconsensus/meta.yaml @@ -10,31 +10,17 @@ source: url: https://github.com/PacificBiosciences/GenomicConsensus/releases/download/{{ version }}/GenomicConsensus-{{ version }}.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: PacBio genomic consensus and variant caller for RSII and Sequel - -extra: - recipe-maintainers: - - pb-dseifert - - mhsieh - build: - skip: True # [not py27] + noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy >=1.16.2 - - pbcore >=1.6.5 - - pbcommand >=1.1.1 - - python-consensuscore >=1.1.1 - - python-consensuscore2 >=3.4.1 + - python <3 + - pip run: - - python + - python <3 - numpy >=1.16.2 - pbcore >=1.6.5 - pbcommand >=1.1.1 @@ -51,3 +37,13 @@ test: - poa -h - quiver -h - arrow -h + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: PacBio genomic consensus and variant caller for RSII and Sequel + +extra: + recipe-maintainers: + - pb-dseifert + - mhsieh diff --git a/recipes/genonets/build.sh b/recipes/genonets/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/genonets/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/genonets/meta.yaml b/recipes/genonets/meta.yaml index edc38baebd552..4fc4f94c1985f 100644 --- a/recipes/genonets/meta.yaml +++ b/recipes/genonets/meta.yaml @@ -3,20 +3,18 @@ package: version: "1.1.6" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/c5/fa/7c26ef0b264b1217184dcbc20b5eed3abea107484a20c756197f97ffadf6/genonets-1.1.6.tar.gz md5: a3ad65614c18f8ec436325e9a08e3515 - requirements: host: - python - - setuptools - - python-igraph >=0.6 - - numpy >=1.8.2 - + - pip run: - python - python-igraph >=0.6 @@ -26,16 +24,12 @@ test: imports: - genonets - - about: home: https://github.com/fkhalid/genonets license: MIT License summary: 'Framework for creating and analyzing genotype networks from data.' license_family: MIT - - extra: identifiers: - biotools:genonets diff --git a/recipes/gerp++/meta.yaml b/recipes/gerp/meta.yaml similarity index 94% rename from recipes/gerp++/meta.yaml rename to recipes/gerp/meta.yaml index b942b56f2bbff..e03301e50ede9 100644 --- a/recipes/gerp++/meta.yaml +++ b/recipes/gerp/meta.yaml @@ -33,3 +33,7 @@ about: license_family: GPL license_file: COPYRIGHT.txt summary: GERP identifies constrained elements in multiple alignments by quantifying substitution deficits. + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/gerp++/missing_headers_linux.patch b/recipes/gerp/missing_headers_linux.patch similarity index 100% rename from recipes/gerp++/missing_headers_linux.patch rename to recipes/gerp/missing_headers_linux.patch diff --git a/recipes/gerp++/missing_headers_osx.patch b/recipes/gerp/missing_headers_osx.patch similarity index 100% rename from recipes/gerp++/missing_headers_osx.patch rename to recipes/gerp/missing_headers_osx.patch diff --git a/recipes/gfapy/build.sh b/recipes/gfapy/build.sh deleted file mode 100644 index dab71eb6942f4..0000000000000 --- a/recipes/gfapy/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/gfapy/meta.yaml b/recipes/gfapy/meta.yaml index 032c853792679..1d72a2288cf0d 100644 --- a/recipes/gfapy/meta.yaml +++ b/recipes/gfapy/meta.yaml @@ -11,16 +11,16 @@ source: sha256: {{ sha256hash }} build: + noarch: python number: 1 - skip: True # [py2k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python >=3 + - pip run: - - python + - python >=3 test: # Python imports @@ -51,7 +51,6 @@ test: - gfapy.line.unknown - gfapy.lines - tests - requires: - nose @@ -60,4 +59,3 @@ about: license: ISC License (ISCL) summary: 'Library for handling data in the GFA1 and GFA2 formats' license_family: Other - diff --git a/recipes/gff3sort/meta.yaml b/recipes/gff3sort/meta.yaml index 578f2a07cab04..c46b45d45e706 100644 --- a/recipes/gff3sort/meta.yaml +++ b/recipes/gff3sort/meta.yaml @@ -11,14 +11,10 @@ source: sha256: 6ca74a65bd90914335a6f40ec2b1cbc2069c15d46a938794fb527980d00f96c1 build: + noarch: generic number: 0 requirements: - build: - - perl - - perl-sort-naturally - - perl-data-match - run: - perl - perl-sort-naturally diff --git a/recipes/gffread/meta.yaml b/recipes/gffread/meta.yaml index af3184513b744..4ef9d0cab04b0 100644 --- a/recipes/gffread/meta.yaml +++ b/recipes/gffread/meta.yaml @@ -6,10 +6,10 @@ package: version: {{ version }} source: - url: http://ccb.jhu.edu/software/stringtie/dl/gffread-{{ version }}.Linux_x86_64.tar.gz # [linux] - sha256: 44914df525393d2258fab6c10836f2ad6b80294f4d1aecf0638343ac3f730d7c # [linux] - url: http://ccb.jhu.edu/software/stringtie/dl/gffread-{{ version }}.OSX_x86_64.tar.gz # [osx] - sha256: 019d42d031797c045f640861acbfb01c983c2aa107ee12bd2977ccefa7b8de1a # [osx] + - url: http://ccb.jhu.edu/software/stringtie/dl/gffread-{{ version }}.Linux_x86_64.tar.gz # [linux] + sha256: 44914df525393d2258fab6c10836f2ad6b80294f4d1aecf0638343ac3f730d7c # [linux] + - url: http://ccb.jhu.edu/software/stringtie/dl/gffread-{{ version }}.OSX_x86_64.tar.gz # [osx] + sha256: 019d42d031797c045f640861acbfb01c983c2aa107ee12bd2977ccefa7b8de1a # [osx] build: number: 0 @@ -33,7 +33,8 @@ about: summary: 'GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.' dev_url: "https://github.com/gpertea/gffread" - extra: identifiers: - biotools:gffread + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/genehunter/3.0/build.sh b/recipes/ghm/3.0/build.sh similarity index 100% rename from recipes/genehunter/3.0/build.sh rename to recipes/ghm/3.0/build.sh diff --git a/recipes/genehunter/3.0/meta.yaml b/recipes/ghm/3.0/meta.yaml similarity index 98% rename from recipes/genehunter/3.0/meta.yaml rename to recipes/ghm/3.0/meta.yaml index eb0496cbeb948..69fa02ff0e432 100644 --- a/recipes/genehunter/3.0/meta.yaml +++ b/recipes/ghm/3.0/meta.yaml @@ -13,8 +13,8 @@ build: requirements: build: - {{ compiler('c') }} + host: - zlib - run: - zlib diff --git a/recipes/genehunter/3.0/osx-makefile.patch b/recipes/ghm/3.0/osx-makefile.patch similarity index 100% rename from recipes/genehunter/3.0/osx-makefile.patch rename to recipes/ghm/3.0/osx-makefile.patch diff --git a/recipes/genehunter/3.1/build.sh b/recipes/ghm/3.1/build.sh similarity index 100% rename from recipes/genehunter/3.1/build.sh rename to recipes/ghm/3.1/build.sh diff --git a/recipes/genehunter/3.1/meta.yaml b/recipes/ghm/3.1/meta.yaml similarity index 98% rename from recipes/genehunter/3.1/meta.yaml rename to recipes/ghm/3.1/meta.yaml index 899495ae1c9c3..b92bed9f5f71f 100644 --- a/recipes/genehunter/3.1/meta.yaml +++ b/recipes/ghm/3.1/meta.yaml @@ -13,10 +13,11 @@ build: requirements: build: - {{ compiler('c') }} + host: - zlib - run: - zlib + test: commands: - echo "q" | ghm diff --git a/recipes/genehunter/3.1/osx-makefile.patch b/recipes/ghm/3.1/osx-makefile.patch similarity index 100% rename from recipes/genehunter/3.1/osx-makefile.patch rename to recipes/ghm/3.1/osx-makefile.patch diff --git a/recipes/glimmer/meta.yaml b/recipes/glimmer/meta.yaml index 40582c60b67ae..4f043af6c5c4c 100644 --- a/recipes/glimmer/meta.yaml +++ b/recipes/glimmer/meta.yaml @@ -2,12 +2,6 @@ package: name: glimmer version: 3.02 -about: - home: https://ccb.jhu.edu/software/glimmer/index.shtml - license: Custom - license_file: LICENSE - summary: Glimmer is a system for finding genes in microbial DNA - source: url: https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz md5: 344d012ae12596de905866fe9eb7f16c @@ -15,10 +9,21 @@ source: build: number: 3 +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + test: commands: - glimmer3 | cat +about: + home: https://ccb.jhu.edu/software/glimmer/index.shtml + license: Custom + license_file: LICENSE + summary: Glimmer is a system for finding genes in microbial DNA + extra: identifiers: - biotools:glimmer diff --git a/recipes/gmap-fusion/meta.yaml b/recipes/gmap-fusion/meta.yaml index 5b40c196624fa..b3695c797bf2d 100644 --- a/recipes/gmap-fusion/meta.yaml +++ b/recipes/gmap-fusion/meta.yaml @@ -11,6 +11,7 @@ source: md5: af49da9f8b1849224e0a8c1ede16cfe5 build: + noarch: generic number: {{ build }} requirements: diff --git a/recipes/gmap/2014.12.23/meta.yaml b/recipes/gmap/2014.12.23/meta.yaml index 7429e5cf966ae..1f8dcd6601f63 100644 --- a/recipes/gmap/2014.12.23/meta.yaml +++ b/recipes/gmap/2014.12.23/meta.yaml @@ -45,3 +45,5 @@ test: extra: identifiers: - biotools:gmap + skip-lints: + - should_be_noarch_generic diff --git a/recipes/gmap/2014.12.28/meta.yaml b/recipes/gmap/2014.12.28/meta.yaml index 58bb7d27c851f..d1e59efe853bd 100644 --- a/recipes/gmap/2014.12.28/meta.yaml +++ b/recipes/gmap/2014.12.28/meta.yaml @@ -46,3 +46,5 @@ test: extra: identifiers: - biotools:gmap + skip-lints: + - should_be_noarch_generic diff --git a/recipes/gmap/2015.09.10/meta.yaml b/recipes/gmap/2015.09.10/meta.yaml index fa5fb72ef975d..ec1759b196ca9 100644 --- a/recipes/gmap/2015.09.10/meta.yaml +++ b/recipes/gmap/2015.09.10/meta.yaml @@ -43,3 +43,5 @@ test: extra: identifiers: - biotools:gmap + skip-lints: + - should_be_noarch_generic diff --git a/recipes/gmap/2016.09.23/meta.yaml b/recipes/gmap/2016.09.23/meta.yaml index e0ba45e174543..3583c52fe7608 100644 --- a/recipes/gmap/2016.09.23/meta.yaml +++ b/recipes/gmap/2016.09.23/meta.yaml @@ -46,3 +46,5 @@ test: extra: identifiers: - biotools:gmap + skip-lints: + - should_be_noarch_generic diff --git a/recipes/gmap/2017.02.15/meta.yaml b/recipes/gmap/2017.02.15/meta.yaml index e355647a6db2a..c6089c0316761 100644 --- a/recipes/gmap/2017.02.15/meta.yaml +++ b/recipes/gmap/2017.02.15/meta.yaml @@ -47,3 +47,5 @@ test: extra: identifiers: - biotools:gmap + skip-lints: + - should_be_noarch_generic diff --git a/recipes/gmtk/meta.yaml b/recipes/gmtk/meta.yaml index 47bd04e382daa..83ddb7105434c 100644 --- a/recipes/gmtk/meta.yaml +++ b/recipes/gmtk/meta.yaml @@ -26,3 +26,7 @@ about: home: http://melodi.ee.washington.edu/gmtk/ license: OSL-3.0 summary: 'A publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs)' + +extra: + skip-lints: + - compilers_must_be_in_build diff --git a/recipes/gnuplot-py/build.sh b/recipes/gnuplot-py/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/gnuplot-py/build.sh +++ /dev/null @@ -1,9 +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/gnuplot-py/meta.yaml b/recipes/gnuplot-py/meta.yaml index fdfa5b0ba8a9c..acd443cc02153 100644 --- a/recipes/gnuplot-py/meta.yaml +++ b/recipes/gnuplot-py/meta.yaml @@ -7,17 +7,16 @@ source: md5: abd6f571e7aec68ae7db90a5217cd5b1 build: + noarch: python number: 1 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - numpy - - gnuplot - + - python <3 + - pip run: - - python + - python <3 - numpy - gnuplot diff --git a/recipes/gocr/0.50/meta.yaml b/recipes/gocr/0.50/meta.yaml index 225d681986e0b..1c96252850ec3 100644 --- a/recipes/gocr/0.50/meta.yaml +++ b/recipes/gocr/0.50/meta.yaml @@ -1,18 +1,24 @@ package: name: gocr version: 0.50 + build: number: 1 #skip: True # [osx] + source: url: http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz + sha256: b04f8af0cd210b841c45b4c50f3b615c8e5913152cc63f01754255abd329b80c + requirements: build: - {{ compiler('c') }} run: + test: commands: - "gocr --help" + about: home: http://jocr.sourceforge.net/ license: GPL diff --git a/recipes/goleft/meta.yaml b/recipes/goleft/meta.yaml index f5879ee3b39fc..576ac250fdcf5 100644 --- a/recipes/goleft/meta.yaml +++ b/recipes/goleft/meta.yaml @@ -5,10 +5,10 @@ package: version: '{{ version }}' source: - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_linux64 # [linux] - sha256: 8b22b6a6340bf8801453886330b1f8ff7d455312124388e6dbaa902f4750baf2 # [linux] - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_osx # [osx] - sha256: 1962312ad0aa546e9ee57daadaa509a12cc44bfbe8b377aaf5ff2ca2899ce537 # [osx] + - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_linux64 # [linux] + sha256: 8b22b6a6340bf8801453886330b1f8ff7d455312124388e6dbaa902f4750baf2 # [linux] + - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_osx # [osx] + sha256: 1962312ad0aa546e9ee57daadaa509a12cc44bfbe8b377aaf5ff2ca2899ce537 # [osx] build: number: 0 @@ -27,3 +27,8 @@ about: home: https://github.com/brentp/goleft license: MIT summary: goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/gotree/meta.yaml b/recipes/gotree/meta.yaml index 532d822e2d657..b5f610d7ec80a 100644 --- a/recipes/gotree/meta.yaml +++ b/recipes/gotree/meta.yaml @@ -6,17 +6,13 @@ package: build: number: 1 - skip: false binary_relocation: false source: - fn: gotree_amd64_linux # [linux] - url: https://github.com/fredericlemoine/gotree/releases/download/v{{ version }}/gotree_amd64_linux # [linux] - md5: 05e09402f1605a665faa7c95043fb318 # [linux] - fn: gotree_amd64_darwin # [osx] - url: https://github.com/fredericlemoine/gotree/releases/download/v{{ version }}/gotree_amd64_darwin # [osx] - md5: cf0159284cc90e5fbd836b065961de69 # [osx] - + - url: https://github.com/fredericlemoine/gotree/releases/download/v{{ version }}/gotree_amd64_linux # [linux] + md5: 05e09402f1605a665faa7c95043fb318 # [linux] + - url: https://github.com/fredericlemoine/gotree/releases/download/v{{ version }}/gotree_amd64_darwin # [osx] + md5: cf0159284cc90e5fbd836b065961de69 # [osx] requirements: run: @@ -29,3 +25,8 @@ about: home: https://github.com/fredericlemoine/gotree license: GPL-2.0 summary: GoTree is a set of command line tools to manipulate phylogenetic trees. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/gottcha/meta.yaml b/recipes/gottcha/meta.yaml index 0d017d60688ad..d2fb88d7c9785 100644 --- a/recipes/gottcha/meta.yaml +++ b/recipes/gottcha/meta.yaml @@ -12,9 +12,10 @@ source: requirements: build: + - dmd - unzip + host: - bwa - - dmd - perl - perl-app-cpanminus - perl-module-build @@ -33,3 +34,7 @@ about: home: https://github.com/LANL-Bioinformatics/GOTTCHA license: GNU GPL v3 summary: 'Genomic Origin Through Taxonomic CHAllenge (GOTTCHA)' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/graphclust-wrappers/meta.yaml b/recipes/graphclust-wrappers/meta.yaml index 96b3b5a98c847..bee57af130ed0 100644 --- a/recipes/graphclust-wrappers/meta.yaml +++ b/recipes/graphclust-wrappers/meta.yaml @@ -7,17 +7,10 @@ source: sha256: 4943fe63773a7aa152fd6332e5d89dbbdf0a4376df25cf72599fd45931840db6 build: + noarch: generic number: 1 - skip: True # [not linux64 or osx] requirements: - build: - - perl >=5.22.0 - - perl-math-round - - perl-array-utils - - pandas =0.23.0 - - biopython =1.70.0 - run: - perl >=5.22.0 - perl-math-round @@ -46,7 +39,6 @@ test: - newpreMlocarna.pl -help 2>&1 | grep -i 'usage' > /dev/null - rnaclustScores2Dist.pl -h 2>&1 | grep -i 'usage' > /dev/null - about: home: http://www.bioinf.uni-freiburg.de/Software/GraphClust/ license: GPLv3 diff --git a/recipes/graphlite/build.sh b/recipes/graphlite/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/graphlite/build.sh +++ /dev/null @@ -1,9 +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/graphlite/meta.yaml b/recipes/graphlite/meta.yaml index 0f0390a821288..053206948b38c 100644 --- a/recipes/graphlite/meta.yaml +++ b/recipes/graphlite/meta.yaml @@ -3,15 +3,18 @@ package: version: "1.0.5" build: + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 source: url: https://files.pythonhosted.org/packages/15/56/cee648eeb1537ab86b7363bacb1f254be0f00c38dd8de113da1091fa6a93/graphlite-1.0.5.tar.gz md5: 34681e73c5e9595970c33c1156b34d5c + requirements: host: - python - + - pip run: - python diff --git a/recipes/gretel/build.sh b/recipes/gretel/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/gretel/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/gretel/meta.yaml b/recipes/gretel/meta.yaml index 5c7ee20b3c329..e7246c1cc7dad 100644 --- a/recipes/gretel/meta.yaml +++ b/recipes/gretel/meta.yaml @@ -5,8 +5,9 @@ package: version: {{ version }} build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/SamStudio8/gretel/archive/v{{ version }}.tar.gz @@ -14,10 +15,10 @@ source: requirements: host: - - python - - setuptools + - python <3 + - pip run: - - python + - python <3 - pysam - numpy - hanselx diff --git a/recipes/grid/meta.yaml b/recipes/grid/meta.yaml index 6e187d33e4bf5..b169d485cc2b0 100644 --- a/recipes/grid/meta.yaml +++ b/recipes/grid/meta.yaml @@ -3,8 +3,8 @@ package: version: "1.3" build: + noarch: generic number: 1 - skip: True # [osx] source: url: https://github.com/ohlab/GRiD/archive/1.3.tar.gz diff --git a/recipes/groopm/meta.yaml b/recipes/groopm/meta.yaml index 9218cb3866f32..e58318fe690c9 100644 --- a/recipes/groopm/meta.yaml +++ b/recipes/groopm/meta.yaml @@ -9,18 +9,18 @@ source: sha256: 48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080 build: + noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " - skip: True # [osx or py3k] requirements: host: - pip - - python + - python <3 run: - matplotlib >=1.1.0 - numpy >=1.6.1 - - python + - python <3 - scipy >=0.10.1 - pytables >=2.3 - pillow diff --git a/recipes/groot/meta.yaml b/recipes/groot/meta.yaml index 67f10ee194ef0..091a2361e0c8a 100644 --- a/recipes/groot/meta.yaml +++ b/recipes/groot/meta.yaml @@ -13,7 +13,7 @@ build: requirements: build: - - go + - {{ compiler('c') }} - mercurial test: @@ -25,3 +25,7 @@ about: home: https://github.com/will-rowe/groot license: MIT summary: A tool for resistome profiling of metagenomic samples. + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/gsort/meta.yaml b/recipes/gsort/meta.yaml index 3c1067a9fa68b..6fe20ff26da6f 100644 --- a/recipes/gsort/meta.yaml +++ b/recipes/gsort/meta.yaml @@ -5,10 +5,10 @@ package: version: {{ version }} source: - url: https://github.com/brentp/gsort/releases/download/v{{ version }}/gsort_darwin_amd64 # [osx] - sha256: 7445139fa450408bd708e997d8c0d5b1fc9db1dadd65708609ed41dea1d24b29 # [osx] - url: https://github.com/brentp/gsort/releases/download/v{{ version }}/gsort_linux_amd64 # [linux64] - sha256: 5763c0ee21c92d6cc6db7156bfef9184b3e4e6e012ae5636662555b385fda2ac # [linux64] + - url: https://github.com/brentp/gsort/releases/download/v{{ version }}/gsort_darwin_amd64 # [osx] + sha256: 7445139fa450408bd708e997d8c0d5b1fc9db1dadd65708609ed41dea1d24b29 # [osx] + - url: https://github.com/brentp/gsort/releases/download/v{{ version }}/gsort_linux_amd64 # [linux] + sha256: 5763c0ee21c92d6cc6db7156bfef9184b3e4e6e012ae5636662555b385fda2ac # [linux] build: number: 1 @@ -23,3 +23,8 @@ about: home: https://github.com/brentp/gsort license: MIT summary: sort genomic files according to a genomefile + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/gtf_to_genes/bld.bat b/recipes/gtf_to_genes/bld.bat deleted file mode 100644 index 9146a4bf8a10b..0000000000000 --- a/recipes/gtf_to_genes/bld.bat +++ /dev/null @@ -1,8 +0,0 @@ -"%PYTHON%" setup.py install -if errorlevel 1 exit 1 - -:: 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/gtf_to_genes/build.sh b/recipes/gtf_to_genes/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/gtf_to_genes/build.sh +++ /dev/null @@ -1,9 +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/gtf_to_genes/meta.yaml b/recipes/gtf_to_genes/meta.yaml index 495a3c6d20c4b..8c3cfedb41e99 100644 --- a/recipes/gtf_to_genes/meta.yaml +++ b/recipes/gtf_to_genes/meta.yaml @@ -7,15 +7,16 @@ source: md5: 15dea634078a0fc1367c7adb8c13c280 build: - skip: True #[not py27] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 test: # Python imports diff --git a/recipes/guidescan/meta.yaml b/recipes/guidescan/meta.yaml index bfddbc7c5a549..6bfd596898471 100644 --- a/recipes/guidescan/meta.yaml +++ b/recipes/guidescan/meta.yaml @@ -9,14 +9,6 @@ source: url: https://bitbucket.org/arp2012/guidescan_public/get/v{{ version }}.tar.gz sha256: 8b3707922bfd986d9d3c784953c3d47c26c0cc5726462a1e2a39bcd5627320bc -# if/when a tagged release of guidescan is available, the source -# should be switched from git_url&git_rev to url&sha256. -# At that time, these lint-skip lines can be removed: -extra: - skip-lints: - - uses_git_url - - missing_hash - build: number: 1 skip: True # [not py27] @@ -25,8 +17,8 @@ requirements: build: - {{ compiler('c') }} host: - - python >=2.7.13 - #- setuptools + - python + - setuptools - samtools ==1.3.1 - coreutils - rename @@ -41,25 +33,22 @@ requirements: - pandas - openblas - python-dateutil >=2.5.0 - run: - - - python >=2.7.13 - #- setuptools - - samtools ==1.3.1 - - coreutils - - rename - - biopython >=1.66 - - pysam ==0.8.3 - - pyfaidx ==0.4.7.1 - - bx-python ==0.7.3 - - scikit-learn >=0.16.1 - - numpy - - psutil - - xlwt - - pandas - - openblas - - python-dateutil >=2.5.0 + - python + - samtools ==1.3.1 + - coreutils + - rename + - biopython >=1.66 + - pysam ==0.8.3 + - pyfaidx ==0.4.7.1 + - bx-python ==0.7.3 + - scikit-learn >=0.16.1 + - numpy + - psutil + - xlwt + - pandas + - openblas + - python-dateutil >=2.5.0 test: imports: @@ -75,3 +64,8 @@ about: home: https://bitbucket.org/arp2012/guidescan_public license: Unknown summary: Tools to create and interface genome-wide CRISPR guideRNA databases + +extra: + skip-lints: + - uses_vcs_url + - missing_hash diff --git a/recipes/gustaf/meta.yaml b/recipes/gustaf/meta.yaml index 47f3b2a8371b2..e1e4bb8b56835 100644 --- a/recipes/gustaf/meta.yaml +++ b/recipes/gustaf/meta.yaml @@ -1,20 +1,27 @@ -build: - number: 1 - package: name: gustaf version: "1.0.8" + +build: + number: 1 + source: - url: http://packages.seqan.de/gustaf/gustaf-1.0.8-Mac-x86_64.zip # [osx] - md5: 9c219eac167750e7745274da69509da3 # [osx] - url: http://packages.seqan.de/gustaf/gustaf-1.0.8-Linux-x86_64.tar.xz # [linux64] - md5: a873ad2048eb2a74e65aff220bba8132 # [linux64] + - url: http://packages.seqan.de/gustaf/gustaf-1.0.8-Mac-x86_64.zip # [osx] + md5: 9c219eac167750e7745274da69509da3 # [osx] + - url: http://packages.seqan.de/gustaf/gustaf-1.0.8-Linux-x86_64.tar.xz # [linux64] + md5: a873ad2048eb2a74e65aff220bba8132 # [linux64] test: commands: - gustaf --help 2>&1 > /dev/null - gustaf_mate_joining --help 2>&1 > /dev/null + about: home: https://github.com/seqan/seqan/tree/master/apps/gustaf/README.rst license: https://github.com/seqan/seqan/tree/master/apps/gustaf/LICENSE summary: Gustaf is a tool primarily designed for multi-split mapping of sequencing reads. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/halla/meta.yaml b/recipes/halla/meta.yaml index 34ded60775741..2f10e625a1bcd 100644 --- a/recipes/halla/meta.yaml +++ b/recipes/halla/meta.yaml @@ -37,7 +37,6 @@ requirements: - pandas >=0.18.1 - scikit-learn >=0.14.1 - scipy >=0.17.0 - - setuptools test: imports: @@ -57,4 +56,4 @@ about: extra: skip-lints: - - should_be_noarch + - should_be_noarch_python diff --git a/recipes/hapflk/build.sh b/recipes/hapflk/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/hapflk/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/hapflk/meta.yaml b/recipes/hapflk/meta.yaml index e7ff7590d0326..5798cd9cac157 100644 --- a/recipes/hapflk/meta.yaml +++ b/recipes/hapflk/meta.yaml @@ -8,6 +8,7 @@ source: build: number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv skip: True # [py3k] requirements: diff --git a/recipes/harvesttools/meta.yaml b/recipes/harvesttools/meta.yaml index 709a9a2bbf4fe..4cc514a11e3c9 100644 --- a/recipes/harvesttools/meta.yaml +++ b/recipes/harvesttools/meta.yaml @@ -8,17 +8,15 @@ package: version: '{{version}}' source: - url: '{{base}}/v{{version}}/harvesttools-Linux64-v{{version}}.tar.gz' # [linux] - sha256: '{{sha256linux}}' # [linux] - - url: '{{base}}/v{{version}}/harvesttools-OSX64-v{{version}}.zip' # [osx] - sha256: '{{sha256osx}}' # [osx] + - url: '{{base}}/v{{version}}/harvesttools-Linux64-v{{version}}.tar.gz' # [linux] + sha256: '{{sha256linux}}' # [linux] + - url: '{{base}}/v{{version}}/harvesttools-OSX64-v{{version}}.zip' # [osx] + sha256: '{{sha256osx}}' # [osx] build: number: 0 requirements: - build: host: - zlib run: @@ -33,3 +31,7 @@ about: license: "custom; see https://raw.githubusercontent.com/marbl/harvest-tools/master/LICENSE.txt" summary: HarvestTools is a part of the Harvest software suite and provides file conversion between Gingr files and various standard text formats +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/hca-matrix-downloader/meta.yaml b/recipes/hca-matrix-downloader/meta.yaml index c88faead98f53..43bfa9b7d38b2 100644 --- a/recipes/hca-matrix-downloader/meta.yaml +++ b/recipes/hca-matrix-downloader/meta.yaml @@ -19,7 +19,6 @@ requirements: - pip run: - python >=3 - - setuptools - requests test: diff --git a/recipes/hclust2/meta.yaml b/recipes/hclust2/meta.yaml index 6e875ee75887d..9b8a4d0b52753 100644 --- a/recipes/hclust2/meta.yaml +++ b/recipes/hclust2/meta.yaml @@ -1,29 +1,35 @@ {% set name = "hclust2" %} {% set version = "0.99" %} {% set md5 = "ebdd90347702c989ec1c54a52af92efc" %} + package: name: {{ name }} version: {{ version }} + source: url: https://bitbucket.org/nsegata/hclust2/get/0.99.tar.gz md5: {{ md5 }} + build: + noarch: python number: 1 - skip: True # [py3k] + requirements: host: - - python + - python <3 run: - - python + - python <3 - numpy - matplotlib - scipy ==0.18.1 - pandas + test: imports: - hclust2 commands: - hclust2.py -h + about: home: https://bitbucket.org/nsegata/hclust2 license: License diff --git a/recipes/heinz/meta.yaml b/recipes/heinz/meta.yaml index 4e703df5c48ea..bec1ca5aef838 100644 --- a/recipes/heinz/meta.yaml +++ b/recipes/heinz/meta.yaml @@ -6,7 +6,6 @@ package: version: {{ version }} source: - fn: conda-heinz-v2.0.tar.gz url: https://gitlab.com/ibivu/galaxy/conda-heinz/-/archive/v2.0/conda-heinz-v2.0.tar.gz sha256: b3f94a703552387c18bbf6d42096ac858046b56b23b5792763d7cc98f27eeeb1 @@ -16,12 +15,11 @@ build: requirements: build: - - gcc + - {{ compiler('c') }} - cmake - ogdf - lemon run: - - libgcc test: commands: diff --git a/recipes/hgtools/build.sh b/recipes/hgtools/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/hgtools/build.sh +++ /dev/null @@ -1,9 +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/hgtools/meta.yaml b/recipes/hgtools/meta.yaml index 7ce8aa6b61a46..d65002178afb6 100644 --- a/recipes/hgtools/meta.yaml +++ b/recipes/hgtools/meta.yaml @@ -10,6 +10,7 @@ build: number: 0 noarch: python preserve_egg_dir: True + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/hicbrowser/build.sh b/recipes/hicbrowser/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/hicbrowser/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/hicbrowser/meta.yaml b/recipes/hicbrowser/meta.yaml index 047a8a02e26e4..ab97448db1f43 100644 --- a/recipes/hicbrowser/meta.yaml +++ b/recipes/hicbrowser/meta.yaml @@ -7,18 +7,16 @@ source: sha256: 5ceb309c2c8b4e431be592765bb5c159a5fc52d1aecaf5441e324e988139d6dd build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python <3 - setuptools - - flask >=0.10.1 - - hicexplorer >=1.7 - - bx-python run: - - python + - python <3 - flask >=0.10.1 - hicexplorer >=1.7 - bx-python diff --git a/recipes/hifive/meta.yaml b/recipes/hifive/meta.yaml index 7d6118e627e13..4e3facd9ca243 100644 --- a/recipes/hifive/meta.yaml +++ b/recipes/hifive/meta.yaml @@ -12,9 +12,11 @@ source: build: skip: true # [not py27] number: 0 - script: python setup.py install --single-version-externally-managed --record=record.txt + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - python - numpy @@ -27,7 +29,6 @@ requirements: - numpy - scipy - h5py - - cython - setuptools_cython # these are listed as optional - pyx ==0.12.1 # 0.12.1 is the latest pyx version supported on PY2 diff --git a/recipes/hivtrace/build.sh b/recipes/hivtrace/build.sh deleted file mode 100644 index 05e8aa5c5fcdf..0000000000000 --- a/recipes/hivtrace/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -python3 setup.py install diff --git a/recipes/hivtrace/meta.yaml b/recipes/hivtrace/meta.yaml index 2e5cf8ae8e434..f00d96538123b 100644 --- a/recipes/hivtrace/meta.yaml +++ b/recipes/hivtrace/meta.yaml @@ -10,21 +10,15 @@ source: build: number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python requirements: host: - - python - - setuptools - - biopython >=1.58 - - python-bioext >=0.17.4 - - python-hyphy-python >=0.1.1 - - python-hppy >=0.9.6 - - tornado >=4.3 - - python-hivclustering >=1.2.0 - + - python <3 + - pip run: - - python + - python <3 - biopython >=1.58 - python-bioext >=0.17.4 - python-hyphy-python >=0.1.1 diff --git a/recipes/hlama/build.sh b/recipes/hlama/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/hlama/build.sh +++ /dev/null @@ -1,9 +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/hlama/meta.yaml b/recipes/hlama/meta.yaml index 98e6f04518bcc..4fe1264f365bb 100644 --- a/recipes/hlama/meta.yaml +++ b/recipes/hlama/meta.yaml @@ -4,9 +4,9 @@ package: build: number: 0 - # snakemake 3.7.1 is not available for python 3.6 - # the snakemake dependency should be relaxed to allow for a newer version + # N.B. this cannot ever work. This package is python3-only, but optitype is python2-only skip: True # [not py35 or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - hlama = hlama.app:main @@ -17,8 +17,7 @@ source: requirements: host: - python - - setuptools - - snakemake ==3.7.1 + - pip run: - python - snakemake ==3.7.1 @@ -32,3 +31,7 @@ about: home: https://github.com/bihealth/hlama license: MIT summary: Simple matching of HTS samples based on HLA typing + +extra: + skip-lints: + - should_be_noarch_python diff --git a/recipes/hlaprofiler/meta.yaml b/recipes/hlaprofiler/meta.yaml index 91a2a5e1cac92..9fb52cdb8e9a6 100644 --- a/recipes/hlaprofiler/meta.yaml +++ b/recipes/hlaprofiler/meta.yaml @@ -6,20 +6,10 @@ source: md5: 15d847230d41004f09cae271609f79fe build: + noarch: generic number: 1 - skip: False requirements: - build: - - perl-base - - kraken-ea - - perl-statistics-basic - - perl-parallel-forkmanager - - perl-file-slurp - - perl-file-compare - - perl-test-trap - - perl-class-load - run: - perl-base - kraken-ea diff --git a/recipes/hmmlearn/0.1.1/build.sh b/recipes/hmmlearn/0.1.1/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/hmmlearn/0.1.1/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/hmmlearn/0.1.1/meta.yaml b/recipes/hmmlearn/0.1.1/meta.yaml deleted file mode 100644 index c26245059cc97..0000000000000 --- a/recipes/hmmlearn/0.1.1/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -package: - name: hmmlearn - version: '0.1.1' - -source: - url: https://github.com/hmmlearn/hmmlearn/archive/0.1.1.tar.gz - sha256: 307233053218a71fea714d6c9d160e6d6579752c6264200f411a17917add4d25 - -build: - number: 0 - skip: True # [osx] - -requirements: - host: - - python >=2.7,<3 - - setuptools - - cython - - numpy - - scipy - - scikit-learn <0.20 - - run: - - python >=2.7,<3 - - setuptools - - numpy - - scipy - - scikit-learn <0.20 - -test: - imports: - - hmmlearn.hmm - -about: - home: https://github.com/hmmlearn/hmmlearn - license: BSD - summary: Hidden Markov Models in Python, with scikit-learn like API - diff --git a/recipes/hmmlearn/build.sh b/recipes/hmmlearn/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/hmmlearn/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/hmmlearn/meta.yaml b/recipes/hmmlearn/meta.yaml deleted file mode 100644 index 60b5c59496e78..0000000000000 --- a/recipes/hmmlearn/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -package: - name: hmmlearn - version: '20151031' - -source: - url: https://github.com/hmmlearn/hmmlearn/archive/dd67a47.tar.gz - sha256: 94cd59853fdd970f0d849bc9d452fdaf254ad197542bb05cb5c67f50fe0d4cd6 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - python - - setuptools - - cython - - numpy - - scipy - - scikit-learn - - run: - - python - - setuptools - - numpy - - scipy - - scikit-learn - # missing dependency of scipy - -test: - imports: - - hmmlearn.hmm - -about: - home: https://github.com/hmmlearn/hmmlearn - license: BSD - summary: Hidden Markov Models in Python, with scikit-learn like API - diff --git a/recipes/hotspot3d/meta.yaml b/recipes/hotspot3d/meta.yaml index 2ff1fc7fa29fa..01a11f9f49f19 100644 --- a/recipes/hotspot3d/meta.yaml +++ b/recipes/hotspot3d/meta.yaml @@ -12,6 +12,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: generic number: 0 requirements: diff --git a/recipes/hubward-all/meta.yaml b/recipes/hubward-all/meta.yaml index c6ad52cac1785..757170b470095 100644 --- a/recipes/hubward-all/meta.yaml +++ b/recipes/hubward-all/meta.yaml @@ -2,8 +2,8 @@ package: name: hubward-all version: "0.2.1" build: + noarch: generic number: 1 - skip: True # [osx] requirements: run: - hubward @@ -20,3 +20,8 @@ requirements: about: summary: "Meta-package for hubward including bedtools and UCSC tools" license: "The license for this meta-package is MIT; individual tools vary" + +extra: + skip-lints: + - missing_home + - missing_tests diff --git a/recipes/humann2/0.11.1/build.sh b/recipes/humann2/0.11.1/build.sh deleted file mode 100644 index 7da76de21b8d3..0000000000000 --- a/recipes/humann2/0.11.1/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install \ - --bypass-dependencies-install \ - --single-version-externally-managed --record=record.txt diff --git a/recipes/humann2/0.11.1/meta.yaml b/recipes/humann2/0.11.1/meta.yaml deleted file mode 100644 index f8a0fe3bc1770..0000000000000 --- a/recipes/humann2/0.11.1/meta.yaml +++ /dev/null @@ -1,85 +0,0 @@ -package: - name: humann2 - version: "0.11.1" - -build: - number: 3 - 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://pypi.python.org/packages/43/07/ec41577c3c1f9b578875ade8ed549d14fc2944c13cb7504579d542b62a69/humann2-0.11.1.tar.gz - md5: b5c5f2823ea535cab27f54ea72e2ca82 - -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.maintenance - - 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 diff --git a/recipes/humann2/0.9.9/build.sh b/recipes/humann2/0.9.9/build.sh deleted file mode 100644 index 7da76de21b8d3..0000000000000 --- a/recipes/humann2/0.9.9/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install \ - --bypass-dependencies-install \ - --single-version-externally-managed --record=record.txt diff --git a/recipes/humann2/0.9.9/meta.yaml b/recipes/humann2/0.9.9/meta.yaml deleted file mode 100644 index 0d342b71e8a7e..0000000000000 --- a/recipes/humann2/0.9.9/meta.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{% set name = "humann2" %} -{% set version = "0.9.9" %} -{% set md5 = "26b51658441f396d39f032bdfb65dfda" %} - -package: - name: {{ name }} - version: {{ version }} - -build: - number: 2 - skip: True # [osx or not py27] - -source: - md5: {{ md5 }} - url: https://bitbucket.org/biobakery/humann2/get/{{ version }}.tar.gz - -requirements: - host: - - python - - setuptools - run: - - python - - bowtie2 >=2.2.5 - - metaphlan2 >=2.2.0 - - diamond >=0.7.10,<0.9.0 - - rapsearch >=2.21 - - samtools - - biom-format - -test: - commands: - - humann2 --version - - humann2_join_tables -h - - humann2_reduce_table -h - - humann2_regroup_table -h - - humann2_rename_table -h - - humann2_renorm_table -h - - humann2_rna_dna_norm -h - - humann2_split_table -h - -about: - home: 'http://huttenhower.sph.harvard.edu/humann2' - license: MIT - summary: "HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data" - diff --git a/recipes/humann2/build.sh b/recipes/humann2/build.sh deleted file mode 100644 index 7da76de21b8d3..0000000000000 --- a/recipes/humann2/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/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 index bb329058dee84..4cc48069c4f3e 100644 --- a/recipes/humann2/meta.yaml +++ b/recipes/humann2/meta.yaml @@ -3,8 +3,9 @@ package: version: "2.8.1" build: + noarch: python number: 0 - skip: True # [not py27 and not py34] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - humann2 = humann2.humann2:main - humann2_databases = humann2.tools.humann2_databases:main @@ -35,7 +36,7 @@ source: requirements: host: - python - - setuptools + - pip run: - python - bowtie2 >=2.2.5 diff --git a/recipes/ibdne/meta.yaml b/recipes/ibdne/meta.yaml index 6bb268de01465..63f134e00f0cf 100644 --- a/recipes/ibdne/meta.yaml +++ b/recipes/ibdne/meta.yaml @@ -7,13 +7,13 @@ source: md5: fb24ca3f3620fe6b94e84a2de2146603 build: + noarch: generic detect_binary_files_with_prefix: True number: 1 - skip: False requirements: run: - - java-jdk >=6.0.77 + - openjdk >=6.0.77 test: commands: diff --git a/recipes/ibdseq/meta.yaml b/recipes/ibdseq/meta.yaml index b9abc050ae9ad..2944eb171c27b 100644 --- a/recipes/ibdseq/meta.yaml +++ b/recipes/ibdseq/meta.yaml @@ -7,13 +7,13 @@ source: md5: 3963b1c810b2fe71082b0a1d44805cd9 build: + noarch: generic detect_binary_files_with_prefix: True number: 1 - skip: False requirements: run: - - java-jdk >=6.0.77 + - openjdk >=6.0.77 test: commands: diff --git a/recipes/iced/meta.yaml b/recipes/iced/meta.yaml index b400c6e07fcec..f6baf6f15a99b 100644 --- a/recipes/iced/meta.yaml +++ b/recipes/iced/meta.yaml @@ -16,18 +16,18 @@ build: requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} host: - pip - python - - numpy >=1.9 + - cython run: - python - numpy >=1.9 - scipy >=0.14 - pandas - scikit-learn - - cython - matplotlib test: diff --git a/recipes/iclipro/build.sh b/recipes/iclipro/build.sh deleted file mode 100644 index 2d1bcb983eafb..0000000000000 --- a/recipes/iclipro/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -# export CPATH=${PREFIX}/include -$PYTHON setup.py install diff --git a/recipes/iclipro/meta.yaml b/recipes/iclipro/meta.yaml index 662a9f079e2b2..6c80693044a27 100644 --- a/recipes/iclipro/meta.yaml +++ b/recipes/iclipro/meta.yaml @@ -9,17 +9,16 @@ source: sha256: bff33ec8d5fb1b45cb4aec391e9ea63983a70066b2d86b1ae001675002a05817 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - - python - - pysam - - matplotlib - + - python <3 + - pip run: - - python + - python <3 - pysam - matplotlib diff --git a/recipes/icount/meta.yaml b/recipes/icount/meta.yaml index fddef4a3406ab..f25ce77ca336d 100644 --- a/recipes/icount/meta.yaml +++ b/recipes/icount/meta.yaml @@ -15,28 +15,18 @@ source: - 0001-setup-Change-install_requires-to-list.patch build: + noarch: python number: 0 - skip: True # [not py3k] entry_points: - iCount = iCount.cli:main - script: python setup.py install --single-version-externally-managed --record=record.txt + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pysam - - cutadapt >=1.10 - - pybedtools - - matplotlib - - numpydoc - - sphinx >=1.4 - - numpy - - pandas - - bedtools >=2.26.0 - - star + - python >=3 + - pip run: - - python + - python >=3 - pysam - cutadapt >=1.10 - pybedtools diff --git a/recipes/idr-py/meta.yaml b/recipes/idr-py/meta.yaml index a0a8cd5842d6f..f4d3e13ea54d3 100644 --- a/recipes/idr-py/meta.yaml +++ b/recipes/idr-py/meta.yaml @@ -13,17 +13,16 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: python number: 1 - script: python -m pip install --no-deps --ignore-installed . - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python <3 - pip - - setuptools run: - - python + - python <3 - python-omero <5.5 - ipython - ipywidgets diff --git a/recipes/idr/2.0.3/build.sh b/recipes/idr/2.0.3/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/idr/2.0.3/build.sh +++ /dev/null @@ -1,9 +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/idr/2.0.3/meta.yaml b/recipes/idr/2.0.3/meta.yaml index ee6c870e215b1..0b12f8b1d47f0 100644 --- a/recipes/idr/2.0.3/meta.yaml +++ b/recipes/idr/2.0.3/meta.yaml @@ -7,18 +7,16 @@ source: md5: 1bec61b526bb1dcf92a5ab99c27852d0 build: + noarch: python number: 5 - skip: True # [py2k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - matplotlib - - scipy + - python >=3 + - pip run: - - python + - python >=3 - numpy - matplotlib - scipy diff --git a/recipes/igblast/meta.yaml b/recipes/igblast/meta.yaml index a7224aa3887d0..c570f87f00562 100644 --- a/recipes/igblast/meta.yaml +++ b/recipes/igblast/meta.yaml @@ -8,10 +8,10 @@ about: summary: A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences. source: - sha256: a811a9b2487a8ea1f7162a4c338c1f5a898b6b0788bc30d36a3f11a77db14a76 # [linux] - sha256: c573299c2c99b6f5660b52e9e2d2ad80a404bfe2426c1f7870fd64269e7d40e9 # [osx] - url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.10.0/ncbi-igblast-1.10.0-x64-linux.tar.gz # [linux] - url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.10.0/ncbi-igblast-1.10.0-x64-macosx.tar.gz # [osx] + - url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.10.0/ncbi-igblast-1.10.0-x64-linux.tar.gz # [linux] + sha256: a811a9b2487a8ea1f7162a4c338c1f5a898b6b0788bc30d36a3f11a77db14a76 # [linux] + - url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.10.0/ncbi-igblast-1.10.0-x64-macosx.tar.gz # [osx] + sha256: c573299c2c99b6f5660b52e9e2d2ad80a404bfe2426c1f7870fd64269e7d40e9 # [osx] build: number: 1 @@ -33,6 +33,7 @@ requirements: - libxml2 - perl - gnutls # [osx] + test: commands: - igblastn -h @@ -42,3 +43,5 @@ test: extra: identifiers: - biotools:igblast + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/illumina-cleanup/meta.yaml b/recipes/illumina-cleanup/meta.yaml index 2948a4c6e27b2..cc08aab2f1b89 100644 --- a/recipes/illumina-cleanup/meta.yaml +++ b/recipes/illumina-cleanup/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/illuminate/build.sh b/recipes/illuminate/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/illuminate/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/illuminate/meta.yaml b/recipes/illuminate/meta.yaml index f25e1d19cbf32..90200ddcbbc3c 100644 --- a/recipes/illuminate/meta.yaml +++ b/recipes/illuminate/meta.yaml @@ -8,6 +8,7 @@ source: build: number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - illuminate = illuminate.__main__:collect_args diff --git a/recipes/illumiprocessor/meta.yaml b/recipes/illumiprocessor/meta.yaml index 9784fd6de6a55..bd62b9105f91a 100644 --- a/recipes/illumiprocessor/meta.yaml +++ b/recipes/illumiprocessor/meta.yaml @@ -11,15 +11,15 @@ source: build: number: 1 - skip: True # [not py27] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 - trimmomatic test: diff --git a/recipes/imfusion/0.3.0/build.sh b/recipes/imfusion/0.3.0/build.sh deleted file mode 100644 index a40f1097a8631..0000000000000 --- a/recipes/imfusion/0.3.0/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install # Python command to install the script. diff --git a/recipes/imfusion/0.3.0/meta.yaml b/recipes/imfusion/0.3.0/meta.yaml index 35a2b2f5d5c77..446949e812256 100644 --- a/recipes/imfusion/0.3.0/meta.yaml +++ b/recipes/imfusion/0.3.0/meta.yaml @@ -5,6 +5,7 @@ package: build: noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/jrderuiter/imfusion/archive/0.3.0.tar.gz diff --git a/recipes/imfusion/0.3.2/build.sh b/recipes/imfusion/0.3.2/build.sh deleted file mode 100644 index a40f1097a8631..0000000000000 --- a/recipes/imfusion/0.3.2/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install # Python command to install the script. diff --git a/recipes/imfusion/0.3.2/meta.yaml b/recipes/imfusion/0.3.2/meta.yaml index fa3b55b28e451..55c812bd8d312 100644 --- a/recipes/imfusion/0.3.2/meta.yaml +++ b/recipes/imfusion/0.3.2/meta.yaml @@ -5,6 +5,7 @@ package: build: noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/NKI-CCB/imfusion/archive/0.3.2.tar.gz diff --git a/recipes/impute2/meta.yaml b/recipes/impute2/meta.yaml index b4663f95388b7..b3def8551610b 100644 --- a/recipes/impute2/meta.yaml +++ b/recipes/impute2/meta.yaml @@ -1,15 +1,15 @@ package: name: impute2 version: '2.3.2' + source: - url: https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_static.tgz # [linux] - sha256: 95615900464505ddff4251137523740c7f35ac2865eb1eac4d8584ab15a8c45f # [linux] - url: https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_MacOSX_Intel.tgz # [osx] - sha256: e91ad1edc66e6174c9dc4fdc06685df7b2d6a9ba4f86477f1a2ceef89a296953 # [osx] + - url: https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_x86_64_static.tgz # [linux] + sha256: 95615900464505ddff4251137523740c7f35ac2865eb1eac4d8584ab15a8c45f # [linux] + - url: https://mathgen.stats.ox.ac.uk/impute/impute_v2.3.2_MacOSX_Intel.tgz # [osx] + sha256: e91ad1edc66e6174c9dc4fdc06685df7b2d6a9ba4f86477f1a2ceef89a296953 # [osx] build: number: 1 - skip: False requirements: build: @@ -27,3 +27,6 @@ extra: identifiers: - biotools:IMPUTE2 - doi:10.1534/g3.111.001198 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/python-intermine/meta.yaml b/recipes/intermine/meta.yaml similarity index 100% rename from recipes/python-intermine/meta.yaml rename to recipes/intermine/meta.yaml diff --git a/recipes/intervaltree_bio/build.sh b/recipes/intervaltree_bio/build.sh deleted file mode 100644 index b161f631b7c34..0000000000000 --- a/recipes/intervaltree_bio/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/intervaltree_bio/meta.yaml b/recipes/intervaltree_bio/meta.yaml index a64f50b506249..a138d2ee661fc 100644 --- a/recipes/intervaltree_bio/meta.yaml +++ b/recipes/intervaltree_bio/meta.yaml @@ -9,13 +9,12 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - intervaltree - + - pip run: - python - intervaltree diff --git a/recipes/involucro/meta.yaml b/recipes/involucro/meta.yaml index 13244495161c1..011ab4c835bd4 100644 --- a/recipes/involucro/meta.yaml +++ b/recipes/involucro/meta.yaml @@ -3,10 +3,10 @@ package: version: 1.1.2 source: - url: https://github.com/involucro/involucro/releases/download/v1.1.2/involucro # [linux] - sha256: df9bbb6490ce0e507fe735419e526140ad9567a8da85e8bf529c69505be1f8cf # [linux] - url: https://github.com/involucro/involucro/releases/download/v1.1.2/involucro.darwin # [osx] - sha256: 5c50c79232f34ca439c8dbeb2c9d09998a2e90c8ee42af349a6fdb7ede7752da # [osx] + - url: https://github.com/involucro/involucro/releases/download/v1.1.2/involucro # [linux] + sha256: df9bbb6490ce0e507fe735419e526140ad9567a8da85e8bf529c69505be1f8cf # [linux] + - url: https://github.com/involucro/involucro/releases/download/v1.1.2/involucro.darwin # [osx] + sha256: 5c50c79232f34ca439c8dbeb2c9d09998a2e90c8ee42af349a6fdb7ede7752da # [osx] build: number: 1 @@ -19,3 +19,8 @@ about: home: https://github.com/involucro/involucro license: Apache 2.0 summary: Build and Deliver Software with Containers + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/ir/meta.yaml b/recipes/ir/meta.yaml index 8ecbdec14e46f..38b36be0f1298 100644 --- a/recipes/ir/meta.yaml +++ b/recipes/ir/meta.yaml @@ -12,10 +12,9 @@ source: md5: a642ba254a2c5f6342a2a36c156dae9f build: - skip: False number: 1 -requrements: +requirements: build: - {{ compiler('c') }} run: diff --git a/recipes/irida-linker/meta.yaml b/recipes/irida-linker/meta.yaml index 13e6965cba4a2..d18e11bf34814 100644 --- a/recipes/irida-linker/meta.yaml +++ b/recipes/irida-linker/meta.yaml @@ -10,11 +10,10 @@ source: sha256: '{{ sha256 }}' build: + noarch: generic number: 0 requirements: - host: - - perl >=5.22 run: - perl >=5.22 - perl-lwp-simple diff --git a/recipes/irida-sistr-results/meta.yaml b/recipes/irida-sistr-results/meta.yaml index ad8640fb697ea..67c0138c9b16f 100644 --- a/recipes/irida-sistr-results/meta.yaml +++ b/recipes/irida-sistr-results/meta.yaml @@ -12,21 +12,16 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27] number: 0 - script: python setup.py install --single-version-externally-managed --record=record.txt + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - - python - - setuptools - - rauth >=0.7.3 - - urllib3 >=1.21.1 - - xlsxwriter >=0.9.8 - - appdirs >=1.4.3 - - pandas >=0.23.0 + - python >=3 + - pip run: - - python + - python >=3 - rauth >=0.7.3 - urllib3 >=1.21.1 - xlsxwriter >=0.9.8 diff --git a/recipes/islandpath/meta.yaml b/recipes/islandpath/meta.yaml index 19ea6332e04f2..424ca7200fdd9 100644 --- a/recipes/islandpath/meta.yaml +++ b/recipes/islandpath/meta.yaml @@ -9,18 +9,10 @@ source: sha256: d229fa4f7c71e3b44e8596e7de4b75e34a74d3bbb0fc98cb0171ef1829149a2f build: + noarch: generic number: 0 requirements: - host: - - perl - - perl-bioperl>=1.7.2 - - perl-data-dumper - - perl-log-log4perl - - perl-config-simple - - perl-moose - - perl-moosex-singleton - - hmmer run: - perl - perl-bioperl>=1.7.2 diff --git a/recipes/itero/build.sh b/recipes/itero/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/itero/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/itero/meta.yaml b/recipes/itero/meta.yaml index e55890fab07c9..b29e67a0b7c01 100644 --- a/recipes/itero/meta.yaml +++ b/recipes/itero/meta.yaml @@ -1,4 +1,3 @@ - {% set name = "itero" %} {% set version = "1.1.2" %} {% set sha256 = "1a9ee10bfc0b1146ad83f7537ab465f3be49ba3f48b6e7b80f2690d3dcd4d371" %} @@ -12,16 +11,16 @@ source: sha256: '{{sha256}}' build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 - nomkl - numpy - argcomplete diff --git a/recipes/itsx/meta.yaml b/recipes/itsx/meta.yaml index da701eb7d122e..adc5acd7708a1 100644 --- a/recipes/itsx/meta.yaml +++ b/recipes/itsx/meta.yaml @@ -7,8 +7,8 @@ source: md5: 32dcfd0383a79caa223e18e0e60c9964 build: + noarch: generic number: 1 - skip: False requirements: build: diff --git a/recipes/itsxpress/1.5.6/meta.yaml b/recipes/itsxpress/1.5.6/meta.yaml deleted file mode 100644 index b020b357dd6da..0000000000000 --- a/recipes/itsxpress/1.5.6/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set name = "itsxpress" %} -{% set version = "1.5.6" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "53f833545b230f116ac16417ee46dda5f1174f170c768192a9cd5056e1eba25e" %} - -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 of FASTQ files' - - -extra: - recipe-maintainers: 'Adam R. Rivers' - identifiers: - - biotools:ITSxpress - - doi:10.5281/zenodo.1304349 diff --git a/recipes/itsxpress/1.6.1/meta.yaml b/recipes/itsxpress/1.6.1/meta.yaml deleted file mode 100644 index b3d90f88767c5..0000000000000 --- a/recipes/itsxpress/1.6.1/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set name = "itsxpress" %} -{% set version = "1.6.1" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "be9b38e5489c3bcaa6e7edaa5e8dd795133162321a6da7e997a75acb1b01b8a8" %} - -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: 1 - 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 diff --git a/recipes/itsxpress/1.6.3/meta.yaml b/recipes/itsxpress/1.6.3/meta.yaml deleted file mode 100644 index e4a299273c818..0000000000000 --- a/recipes/itsxpress/1.6.3/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set name = "itsxpress" %} -{% set version = "1.6.3" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "daf0197866b239e75822aef3d7e892d5a651d81693e8cda2ef8ad12403da08ce" %} - -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 diff --git a/recipes/itsxpress/1.6.4/meta.yaml b/recipes/itsxpress/1.6.4/meta.yaml deleted file mode 100644 index 82ca6e8ed8220..0000000000000 --- a/recipes/itsxpress/1.6.4/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set name = "itsxpress" %} -{% set version = "1.6.4" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "0dc11ec62f20c346ece601566428148388fcb59470d769a470e817319b578ac1" %} - -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 diff --git a/recipes/itsxpress/1.7.1/meta.yaml b/recipes/itsxpress/1.7.1/meta.yaml deleted file mode 100644 index ecfbf7b35bfd9..0000000000000 --- a/recipes/itsxpress/1.7.1/meta.yaml +++ /dev/null @@ -1,53 +0,0 @@ -{% 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 e8bb80c92463d..d744aa6cae612 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -13,19 +13,19 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: python number: 0 entry_points: - itsxpress=itsxpress.main:main script: python -m pip install --no-deps --ignore-installed . - skip: True # [py27] requirements: host: - pip - - python + - python >=3 run: - pip - - python + - python >=3 - biopython >=1.60 - hmmer >=3.1 - bbmap diff --git a/recipes/iva/build.sh b/recipes/iva/build.sh deleted file mode 100644 index f825adb87b8fd..0000000000000 --- a/recipes/iva/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -set -euf -o pipefail - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/iva/meta.yaml b/recipes/iva/meta.yaml index 5f3ef1158fb94..227a9398ca4fa 100644 --- a/recipes/iva/meta.yaml +++ b/recipes/iva/meta.yaml @@ -9,23 +9,16 @@ source: sha256: 91ba402d0feacc88b3e34e71b4f10e0552702887e6e416076e57f95f6aaf7fad build: + noarch: python number: 1 - skip: True # [py2k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pyfastaq >=3.10.0 - - networkx >=1.7 - - pysam >=0.8.1 - - kmc - - smalt - - mummer - - samtools - + - python >=3 + - pip run: - - python + - python >=3 - pyfastaq >=3.10.0 - networkx >=1.7 - pysam >=0.8.1 diff --git a/recipes/jaffa/meta.yaml b/recipes/jaffa/meta.yaml index cb0b1632b5b66..9ee96bb62496b 100644 --- a/recipes/jaffa/meta.yaml +++ b/recipes/jaffa/meta.yaml @@ -13,7 +13,7 @@ source: - jaffa.patch build: - skipe: True # [osx] + noarch: generic number: 1 requirements: @@ -46,3 +46,6 @@ about: to the wrappers as you would to the bpipe JAFFA_{method} call in the manual. license: GPLv3 +extra: + skip-lints: + - missing_tests diff --git a/recipes/jalview/meta.yaml b/recipes/jalview/meta.yaml index effd614f9c08e..aaacf8d6a85f0 100644 --- a/recipes/jalview/meta.yaml +++ b/recipes/jalview/meta.yaml @@ -3,6 +3,7 @@ package: version: 2.10.5 build: + noarch: generic number: 3 source: diff --git a/recipes/jamm/1.0.7.2/meta.yaml b/recipes/jamm/1.0.7.2/meta.yaml index 9d0a31f78fc4b..08de759c4ade5 100644 --- a/recipes/jamm/1.0.7.2/meta.yaml +++ b/recipes/jamm/1.0.7.2/meta.yaml @@ -9,8 +9,8 @@ source: - setpath.patch build: + noarch: generic number: 3 - skip: True # [osx] requirements: diff --git a/recipes/jobtree/build.sh b/recipes/jobtree/build.sh index be8fc34ce8371..712339f397251 100644 --- a/recipes/jobtree/build.sh +++ b/recipes/jobtree/build.sh @@ -2,4 +2,4 @@ mkdir jobTree cp -r {src,__init__.py,test,batchSystems,scriptTree} jobTree -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/json-collect-data-source/build.sh b/recipes/json_collect_data_source/build.sh similarity index 100% rename from recipes/json-collect-data-source/build.sh rename to recipes/json_collect_data_source/build.sh diff --git a/recipes/json-collect-data-source/meta.yaml b/recipes/json_collect_data_source/meta.yaml similarity index 96% rename from recipes/json-collect-data-source/meta.yaml rename to recipes/json_collect_data_source/meta.yaml index 44f82728c78e6..36756103c4907 100644 --- a/recipes/json-collect-data-source/meta.yaml +++ b/recipes/json_collect_data_source/meta.yaml @@ -19,12 +19,11 @@ source: build: noarch: python number: 2 - skip: False requirements: run: - python >=2.7,<3 test: - command: + commands: - json_collect_data_source.py --version diff --git a/recipes/jvarkit-bam2svg/meta.yaml b/recipes/jvarkit-bam2svg/meta.yaml index 71913e39c944a..e75fe804e41ba 100644 --- a/recipes/jvarkit-bam2svg/meta.yaml +++ b/recipes/jvarkit-bam2svg/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 4b1daa895b504f865e03bf10cd1be2dc3b2517b99b1f5f1caacb8b7999fc6866 build: + noarch: generic number: 0 requirements: diff --git a/recipes/jvarkit-bam2wig/meta.yaml b/recipes/jvarkit-bam2wig/meta.yaml index 3f510c01afa3b..3384667fe9087 100644 --- a/recipes/jvarkit-bam2wig/meta.yaml +++ b/recipes/jvarkit-bam2wig/meta.yaml @@ -9,6 +9,7 @@ source: sha256: 4b1daa895b504f865e03bf10cd1be2dc3b2517b99b1f5f1caacb8b7999fc6866 build: + noarch: generic number: 0 requirements: diff --git a/recipes/kalign/build.sh b/recipes/kalign2/build.sh similarity index 100% rename from recipes/kalign/build.sh rename to recipes/kalign2/build.sh diff --git a/recipes/kalign/meta.yaml b/recipes/kalign2/meta.yaml similarity index 100% rename from recipes/kalign/meta.yaml rename to recipes/kalign2/meta.yaml diff --git a/recipes/kid/build.sh b/recipes/kid/build.sh deleted file mode 100644 index d0f35d4aea6ee..0000000000000 --- a/recipes/kid/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/kid/meta.yaml b/recipes/kid/meta.yaml index 82b7798bd1ec7..55e8347bfadae 100644 --- a/recipes/kid/meta.yaml +++ b/recipes/kid/meta.yaml @@ -7,15 +7,16 @@ source: md5: 4233e592eee906039ad3dcbedbf6e972 build: + noarch: python number: 2 - skip: True # [not py27 or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/kiwidist/build.sh b/recipes/kiwidist/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/kiwidist/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/kiwidist/meta.yaml b/recipes/kiwidist/meta.yaml index 21999d03bd69a..777e9d0c5d680 100644 --- a/recipes/kiwidist/meta.yaml +++ b/recipes/kiwidist/meta.yaml @@ -7,22 +7,16 @@ source: md5: 28cf18a12ee088a04f18a604f0ceccb4 build: + noarch: python number: 2 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - matplotlib >=1.3.1,<=1.4.3 - - mygene >=2.1.0 - - networkx >=1.8.1 - - numpy >=1.8.0 - - pandas >=0.13.1 - - scipy >=0.13.3,<=0.16.0 - - six >=1.5 - + - python <3 + - pip run: - - python + - python <3 - matplotlib >=1.3.1,<=1.4.3 - mygene >=2.1.0 - networkx >=1.8.1 @@ -39,3 +33,4 @@ about: license: MIT license_file: LICENSE.txt summary: 'Combining gene-set analysis with network properties' + home: https://pypi.org/project/KiwiDist/ diff --git a/recipes/kmc/3.0.0_static/meta.yaml b/recipes/kmc/3.0.0_static/meta.yaml index b2c119e7ed19f..d3854c88e5f33 100644 --- a/recipes/kmc/3.0.0_static/meta.yaml +++ b/recipes/kmc/3.0.0_static/meta.yaml @@ -5,10 +5,10 @@ package: version: {{ version }} source: - url: https://github.com/refresh-bio/KMC/releases/download/v{{ version }}/KMC3.linux.tar.gz # [linux] - sha256: 7190b83c7a8df8b51978603332f3bb9d573fb5dd70a2f5df6d3268bdfb732446 # [linux] - url: https://github.com/refresh-bio/KMC/releases/download/v{{ version }}/KMC3.mac.tar.gz # [osx] - sha256: d2ffb2e7ee69199e9b3464ea2afb27df731120babaee1ea65b94a3bc059d0a55 # [osx] + - url: https://github.com/refresh-bio/KMC/releases/download/v{{ version }}/KMC3.linux.tar.gz # [linux] + sha256: 7190b83c7a8df8b51978603332f3bb9d573fb5dd70a2f5df6d3268bdfb732446 # [linux] + - url: https://github.com/refresh-bio/KMC/releases/download/v{{ version }}/KMC3.mac.tar.gz # [osx] + sha256: d2ffb2e7ee69199e9b3464ea2afb27df731120babaee1ea65b94a3bc059d0a55 # [osx] build: number: 1 @@ -29,3 +29,7 @@ about: license: GPLv2 summary: K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/kneaddata/build.sh b/recipes/kneaddata/build.sh deleted file mode 100644 index 568aff3f74500..0000000000000 --- a/recipes/kneaddata/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install \ - --bypass-dependencies-install \ - --single-version-externally-managed \ - --record=record.txt - diff --git a/recipes/kneaddata/meta.yaml b/recipes/kneaddata/meta.yaml index 1892a8ec757d8..aa748019b4ef2 100644 --- a/recipes/kneaddata/meta.yaml +++ b/recipes/kneaddata/meta.yaml @@ -11,6 +11,7 @@ source: build: number: 1 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - kneaddata = kneaddata.knead_data:main - kneaddata_database = kneaddata.download_db:main @@ -20,8 +21,7 @@ build: requirements: host: - python - - setuptools - + - pip run: - python - trimmomatic diff --git a/recipes/kobas/build.sh b/recipes/kobas/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/kobas/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/kobas/meta.yaml b/recipes/kobas/meta.yaml index 324637e034cbc..254bfb66f0472 100644 --- a/recipes/kobas/meta.yaml +++ b/recipes/kobas/meta.yaml @@ -3,8 +3,9 @@ package: version: "3.0.3" build: + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 - skip: True # [py3k] source: url: http://kobas.cbi.pku.edu.cn/kobas-2.1.1/kobas-3.0.3.tar.gz @@ -14,10 +15,10 @@ source: requirements: host: - - python - - setuptools + - python <3 + - pip run: - - python + - python <3 - bioconductor-qvalue - blast - numpy diff --git a/recipes/koeken/build.sh b/recipes/koeken/build.sh deleted file mode 100644 index 0d620c5240825..0000000000000 --- a/recipes/koeken/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/koeken/meta.yaml b/recipes/koeken/meta.yaml index 4b8c924c73bac..f4846a5840a7a 100644 --- a/recipes/koeken/meta.yaml +++ b/recipes/koeken/meta.yaml @@ -13,11 +13,11 @@ source: build: number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python <3 - setuptools - qiime - rpy2 @@ -35,7 +35,7 @@ requirements: - r-mass run: - - python + - python <3 - qiime - rpy2 - numpy diff --git a/recipes/kraken/0.10.5beta/build.sh b/recipes/kraken/0.10.5beta/build.sh deleted file mode 100644 index 6d682ed0e08b6..0000000000000 --- a/recipes/kraken/0.10.5beta/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -mkdir -p "$PREFIX/libexec" "$PREFIX/bin" - -chmod u+x install_kraken.sh -./install_kraken.sh "$PREFIX/libexec" -for bin in kraken kraken-build kraken-filter kraken-mpa-report kraken-report kraken-translate; do - sed -i.bak 's|#!/usr/bin/perl|#!/usr/bin/env perl|' $PREFIX/libexec/$bin - rm -f $PREFIX/libexec/$bin.bak - chmod +x "$PREFIX/libexec/$bin" - ln -s "$PREFIX/libexec/$bin" "$PREFIX/bin/$bin" -done diff --git a/recipes/kraken/0.10.5beta/meta.yaml b/recipes/kraken/0.10.5beta/meta.yaml deleted file mode 100644 index 06ed10724b68d..0000000000000 --- a/recipes/kraken/0.10.5beta/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: kraken - version: "0.10.5beta" -source: - url: https://github.com/DerrickWood/kraken/archive/v0.10.5-beta.tar.gz - md5: 0231a7bfc067f564ad28fa91e9f71606 - -build: - number: 2 - skip: True # [osx] - has_prefix_files: - - libexec/kraken - - libexec/kraken-build - - libexec/kraken-filter - - libexec/kraken-mpa-report - - libexec/kraken-report - - libexec/kraken-translate - -requirements: - build: - - perl - run: - - perl - -test: - commands: - - kraken --version 2>&1 > /dev/null -about: - home: http://ccb.jhu.edu/software/kraken/ - license: GPLv3 - summary: Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. - -extra: - identifiers: - - biotools:kraken - - doi:10.1186/gb-2014-15-3-r46 diff --git a/recipes/krona/meta.yaml b/recipes/krona/meta.yaml index c1992abd8ca9a..7ea9bf93c558d 100644 --- a/recipes/krona/meta.yaml +++ b/recipes/krona/meta.yaml @@ -7,10 +7,11 @@ source: url: https://github.com/marbl/Krona/releases/download/v2.7.1/KronaTools-2.7.1.tar build: + noarch: generic number: 0 requirements: - build: + host: - perl run: - perl diff --git a/recipes/lap/meta.yaml b/recipes/lap/meta.yaml index b082436711300..06c424e172984 100644 --- a/recipes/lap/meta.yaml +++ b/recipes/lap/meta.yaml @@ -17,7 +17,6 @@ build: requirements: build: - {{ compiler('c') }} - run: - python - bowtie2 @@ -35,5 +34,4 @@ test: about: home: http://assembly-eval.sourceforge.net/ - license: '' summary: 'De novo genome assembly evaluation' diff --git a/recipes/latentstrainanalysis/meta.yaml b/recipes/latentstrainanalysis/meta.yaml index 08f7557b2f13c..cd328b9e7eb73 100644 --- a/recipes/latentstrainanalysis/meta.yaml +++ b/recipes/latentstrainanalysis/meta.yaml @@ -13,20 +13,12 @@ source: md5: {{ md5 }} build: + noarch: generic number: 1 - skip: True # [py3k] requirements: - host: - - python - - numpy - - scipy - - gensim - - parallel - - pyro4 - run: - - python + - python <3 - numpy - scipy - gensim diff --git a/recipes/lexmapr/meta.yaml b/recipes/lexmapr/meta.yaml index 8125e06450b25..9854162762528 100644 --- a/recipes/lexmapr/meta.yaml +++ b/recipes/lexmapr/meta.yaml @@ -51,6 +51,5 @@ extra: # This could be 'noarch: python', however conda's solver gets confused, see # https://github.com/bioconda/bioconda-recipes/pull/16166#issuecomment-508794805 . # As a (temporary) measure, remove 'noarch: python' to constrain the solver's search space. - - should_be_noarch - should_be_noarch_python - should_not_use_skip_python diff --git a/recipes/libidn/meta.yaml b/recipes/libidn/meta.yaml index 338a886de669f..46608f9cec552 100644 --- a/recipes/libidn/meta.yaml +++ b/recipes/libidn/meta.yaml @@ -9,6 +9,9 @@ source: requirements: build: - autoconf + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} build: number: 2 diff --git a/recipes/lofreq/2.1.2/meta.yaml b/recipes/lofreq/2.1.2/meta.yaml index b995bef13171a..18da5bca5f65b 100644 --- a/recipes/lofreq/2.1.2/meta.yaml +++ b/recipes/lofreq/2.1.2/meta.yaml @@ -3,10 +3,10 @@ package: version: '2.1.2' source: - url: http://downloads.sourceforge.net/project/lofreq/lofreq_star-2.1.2.tar.gz # [linux] - md5: f9fc602702f714596f21f7ee882fcb8d # [linux] - url: http://downloads.sourceforge.net/project/lofreq/lofreq_star-2.1.2_macosx.tgz # [osx] - md5: d688ba34a4161d9690e264648aae2def # [osx] + - url: http://downloads.sourceforge.net/project/lofreq/lofreq_star-2.1.2.tar.gz # [linux] + md5: f9fc602702f714596f21f7ee882fcb8d # [linux] + - url: http://downloads.sourceforge.net/project/lofreq/lofreq_star-2.1.2_macosx.tgz # [osx] + md5: d688ba34a4161d9690e264648aae2def # [osx] build: number: 1 @@ -32,3 +32,7 @@ about: home: http://csb5.github.io/lofreq/ license: MIT summary: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/logol/meta.yaml b/recipes/logol/meta.yaml index 53a658277507e..1f7f2ce2753bf 100644 --- a/recipes/logol/meta.yaml +++ b/recipes/logol/meta.yaml @@ -8,7 +8,6 @@ build: skip: True # [not linux] source: - fn: 1.7.8.tar.gz url: https://github.com/genouest/logol/archive/1.7.8.tar.gz md5: 7fd86a7bc2a077e1b9a63dcbc9e0a4d8 @@ -37,3 +36,7 @@ about: license: Affero GPL 3.0 license_file: LICENSE.txt summary: Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic) + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/lohhla/meta.yaml b/recipes/lohhla/meta.yaml index 50d1b3a4bc16a..6b1456f19099c 100644 --- a/recipes/lohhla/meta.yaml +++ b/recipes/lohhla/meta.yaml @@ -5,6 +5,7 @@ package: version: {{ version }} build: + noarch: generic number: 1 source: diff --git a/recipes/lsc/meta.yaml b/recipes/lsc/meta.yaml index 52e9c9b1463f0..67f84d81b52d4 100644 --- a/recipes/lsc/meta.yaml +++ b/recipes/lsc/meta.yaml @@ -9,15 +9,15 @@ source: - install_paths.patch build: + noarch: generic number: 2 - skip: True # [py3k] requirements: host: run: - perl - - python + - python <3 - samtools - bowtie2 diff --git a/recipes/java-lsd/build.sh b/recipes/lsd/build.sh similarity index 100% rename from recipes/java-lsd/build.sh rename to recipes/lsd/build.sh diff --git a/recipes/java-lsd/meta.yaml b/recipes/lsd/meta.yaml similarity index 93% rename from recipes/java-lsd/meta.yaml rename to recipes/lsd/meta.yaml index 09cf3beb917a5..e717c830ed4c9 100644 --- a/recipes/java-lsd/meta.yaml +++ b/recipes/lsd/meta.yaml @@ -7,12 +7,12 @@ source: sha256: 2e700192a11798bc39f7f08b89a1dcdf205236ed34a94d4d69c23c20f8493b44 build: + noarch: generic number: 1 - skip: False requirements: run: - - java-jdk + - openjdk test: commands: diff --git a/recipes/mafft/7.310/meta.yaml b/recipes/mafft/7.310/meta.yaml index 084415619defd..5d6592e8d05a7 100644 --- a/recipes/mafft/7.310/meta.yaml +++ b/recipes/mafft/7.310/meta.yaml @@ -25,3 +25,7 @@ about: home: 'http://mafft.cbrc.jp/alignment/software/' license: BSD summary: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/mafft/meta.yaml b/recipes/mafft/meta.yaml index 8d3552d61715a..82d84efd180f0 100644 --- a/recipes/mafft/meta.yaml +++ b/recipes/mafft/meta.yaml @@ -32,3 +32,5 @@ about: extra: identifiers: - doi:10.1093/nar/gkf436 + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/mageck-vispr/build.sh b/recipes/mageck-vispr/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/mageck-vispr/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/mageck-vispr/meta.yaml b/recipes/mageck-vispr/meta.yaml index a4495578315a8..b7db4ae43e5a5 100644 --- a/recipes/mageck-vispr/meta.yaml +++ b/recipes/mageck-vispr/meta.yaml @@ -9,19 +9,18 @@ source: md5: e993c8154f2897f5d1dafd5cc4850abf build: - skip: True # [py27] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - mageck-vispr = mageck_vispr.cli:main requirements: host: - - python - - setuptools - - jinja2 >=2.8 + - python >=3 + - pip run: - - python - - setuptools + - python >=3 - snakemake >=3.6.0 - mageck >=0.5.3 - vispr >=0.4.4 diff --git a/recipes/magicblast/meta.yaml b/recipes/magicblast/meta.yaml index cc10a70eb6104..446313b3329bf 100644 --- a/recipes/magicblast/meta.yaml +++ b/recipes/magicblast/meta.yaml @@ -62,4 +62,6 @@ extra: - doi:10.1101/390013 recipe-maintainers: - boratyng - + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/magpurify/meta.yaml b/recipes/magpurify/meta.yaml index 19ba41959f66d..55fbb1128a05e 100644 --- a/recipes/magpurify/meta.yaml +++ b/recipes/magpurify/meta.yaml @@ -11,23 +11,11 @@ source: sha256: e706d9380fe228c61ced5135708192de582bc642e7d9f89a12ab0f20b010bb53 build: + noarch: generic number: 1 requirements: - host: - - wget - - blast=2.7.1 - - last - - prodigal=2.6.3 - - hmmer=3.1b2 - - mash=2.0 - - python=2.7.* - - pandas - - numpy - - scikit-learn - - biopython - run: - blast=2.7.1 - last diff --git a/recipes/maker/meta.yaml b/recipes/maker/meta.yaml index 1390b6e127866..ef8cbeef5653a 100644 --- a/recipes/maker/meta.yaml +++ b/recipes/maker/meta.yaml @@ -10,10 +10,11 @@ source: - "mpi_init.patch" build: + noarch: generic number: 14 requirements: - build: + host: - augustus >=3.2.3 - blast - exonerate diff --git a/recipes/mamotif/build.sh b/recipes/mamotif/build.sh deleted file mode 100644 index 6afea4167a17c..0000000000000 --- a/recipes/mamotif/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/mamotif/meta.yaml b/recipes/mamotif/meta.yaml index 83594b7653f76..87fd54db26b28 100644 --- a/recipes/mamotif/meta.yaml +++ b/recipes/mamotif/meta.yaml @@ -1,35 +1,34 @@ -package: - name: mamotif - version: 1.0.1 - -source: - url: https://files.pythonhosted.org/packages/66/9b/af0baf9a9e15c4989c5b7033a4fcf5df63daa1e0f9418464cd33dddd9e72/MAmotif-1.0.1.tar.gz - sha256: 1aca1462e69b2d8e2f6bef9a6f37b9b50d70efd5f7f43068250a1070c32961e7 - -build: - number: 0 - skip: True # [not py27] - -requirements: - host: - - python - - setuptools - - manorm >=1.1.4 - - motifscan >=1.1.2 - run: - - python - - manorm >=1.1.4 - - motifscan >=1.1.2 - -test: - imports: - - mamotif - - mamotif.lib - commands: - - mamotif --help > /dev/null - -about: - home: https://github.com/shao-lab/MAmotif - license: BSD License - license_family: BSD - summary: An integrative toolkit for searching cell type-specific co-factors associated with differential binding. +package: + name: mamotif + version: 1.0.1 + +source: + url: https://files.pythonhosted.org/packages/66/9b/af0baf9a9e15c4989c5b7033a4fcf5df63daa1e0f9418464cd33dddd9e72/MAmotif-1.0.1.tar.gz + sha256: 1aca1462e69b2d8e2f6bef9a6f37b9b50d70efd5f7f43068250a1070c32961e7 + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + +requirements: + host: + - python <3 + - pip + run: + - python <3 + - manorm >=1.1.4 + - motifscan >=1.1.2 + +test: + imports: + - mamotif + - mamotif.lib + commands: + - mamotif --help > /dev/null + +about: + home: https://github.com/shao-lab/MAmotif + license: BSD License + license_family: BSD + summary: An integrative toolkit for searching cell type-specific co-factors associated with differential binding. diff --git a/recipes/manorm/meta.yaml b/recipes/manorm/meta.yaml index 4451b05642142..31257acd58f1c 100644 --- a/recipes/manorm/meta.yaml +++ b/recipes/manorm/meta.yaml @@ -8,19 +8,17 @@ source: build: number: 0 - skip: True # [not py27] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - manorm=manorm.cmdline:main requirements: - build: - - python - - setuptools - - numpy - - matplotlib - - statsmodels + host: + - python <3 + - pip run: - - python + - python <3 - numpy - scipy - matplotlib diff --git a/recipes/manta/meta.yaml b/recipes/manta/meta.yaml index 27f12e18d8e24..568adebaed415 100644 --- a/recipes/manta/meta.yaml +++ b/recipes/manta/meta.yaml @@ -8,12 +8,9 @@ source: sha256: ae19b1b934cf5bb605dfb58b29e8e2b843cb469ec5ff12441ca3d9d39179abf4 build: number: 0 - skip: True # [not py27 or osx] requirements: - host: - - python run: - - python + - python <3 test: commands: - configManta.py -h @@ -25,3 +22,5 @@ about: extra: identifiers: - biotools:Manta9235 + skip-lints: + - should_be_noarch_generic diff --git a/recipes/mapdamage2/build.sh b/recipes/mapdamage2/build.sh deleted file mode 100644 index 2769f2fc4d755..0000000000000 --- a/recipes/mapdamage2/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#! /bin/bash - -$PYTHON setup.py install diff --git a/recipes/mapdamage2/meta.yaml b/recipes/mapdamage2/meta.yaml index e687914c16cf6..96245f5279959 100644 --- a/recipes/mapdamage2/meta.yaml +++ b/recipes/mapdamage2/meta.yaml @@ -5,6 +5,7 @@ package: build: noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/ginolhac/mapDamage/archive/2.1.0.tar.gz @@ -15,6 +16,7 @@ source: requirements: host: + - pip - python >=3.5 run: - python >=3.5 diff --git a/recipes/marge/meta.yaml b/recipes/marge/meta.yaml index dca5ea9cb24d8..b59cb681f9b92 100644 --- a/recipes/marge/meta.yaml +++ b/recipes/marge/meta.yaml @@ -13,22 +13,16 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27] + noarch: python number: 1 script: python -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python >3 - pip - - setuptools - - numpy - - scipy - - scikit-learn - - twobitreader - - pytables run: - - python + - python >3 - numpy - scipy - scikit-learn diff --git a/recipes/mason/meta.yaml b/recipes/mason/meta.yaml index 3e56163672844..95c1dc4de76f6 100644 --- a/recipes/mason/meta.yaml +++ b/recipes/mason/meta.yaml @@ -5,10 +5,10 @@ package: version: {{ version }} source: - url: http://packages.seqan.de/mason2/mason2-{{ version }}-Mac-x86_64_sse4.zip # [osx] - sha256: d478b07effe6dd2056ead6cd816fa2b196ba1e2ffb9d6d8d98e24ad968834ee9 # [osx] - url: http://packages.seqan.de/mason2/mason2-{{ version }}-Linux-x86_64_sse4.tar.xz # [linux] - sha256: 3879cdd71c39947d9fc731e820c9b926912e7688d070a8431c75681848eee688 # [linux] + - url: http://packages.seqan.de/mason2/mason2-{{ version }}-Mac-x86_64_sse4.zip # [osx] + sha256: d478b07effe6dd2056ead6cd816fa2b196ba1e2ffb9d6d8d98e24ad968834ee9 # [osx] + - url: http://packages.seqan.de/mason2/mason2-{{ version }}-Linux-x86_64_sse4.tar.xz # [linux] + sha256: 3879cdd71c39947d9fc731e820c9b926912e7688d070a8431c75681848eee688 # [linux] build: number: 0 @@ -34,4 +34,5 @@ extra: - biotools:mason - doi:10.1371/journal.pone.0049110 skip-lints: - - should_be_noarch + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/matlock/meta.yaml b/recipes/matlock/meta.yaml index d8f23ec7570bb..f3882ab710e85 100644 --- a/recipes/matlock/meta.yaml +++ b/recipes/matlock/meta.yaml @@ -44,4 +44,4 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url diff --git a/recipes/maxentpy/build.sh b/recipes/maxentpy/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/maxentpy/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/maxentpy/meta.yaml b/recipes/maxentpy/meta.yaml index 15123a8aa7ea2..132698a46ccb8 100644 --- a/recipes/maxentpy/meta.yaml +++ b/recipes/maxentpy/meta.yaml @@ -4,20 +4,20 @@ package: build: number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/kepbod/maxentpy/archive/0.0.1.tar.gz md5: 66948d2acf796f69c497197a772bbe05 requirements: + build: + - {{ compiler('c') }} host: - python - cython - - msgpack-python - run: - python - - cython - msgpack-python test: diff --git a/recipes/maxentscan/meta.yaml b/recipes/maxentscan/meta.yaml index 437795452804b..9b0be9f850e3f 100644 --- a/recipes/maxentscan/meta.yaml +++ b/recipes/maxentscan/meta.yaml @@ -6,8 +6,8 @@ source: md5: 6f1fabda518998bf8c001149c9cb3b5f build: + noarch: generic number: 1 - skip: True # [osx] requirements: build: - perl @@ -19,6 +19,7 @@ test: - maxentscan_score5.pl || [[ $? == 2 ]] about: home: http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html + license: unknown summary: MaxEntScan is based on the approach for modeling the sequences of short sequence motifs such as those involved in RNA splicing which simultaneously accounts for non-adjacent as well as adjacent dependencies between positions. This method is based on the 'Maximum Entropy Principle' and generalizes most previous probabilistic models of sequence motifs such as weight matrix models and inhomogeneous Markov models. extra: notes: Due to the generic name of the included scripts, "maxentscan_" has been prefixed all executables, e.g. score3.pl can be called as maxentscan_score3.pl. diff --git a/recipes/maxquant/meta.yaml b/recipes/maxquant/meta.yaml index f928c6b0df604..1564008c2dc24 100644 --- a/recipes/maxquant/meta.yaml +++ b/recipes/maxquant/meta.yaml @@ -10,8 +10,8 @@ source: sha256: '{{ sha256 }}' build: + noarch: generic number: 0 - skip: True # [osx] script: - cp -r * $PREFIX - cp $RECIPE_DIR/maxquant $PREFIX/bin/maxquant diff --git a/recipes/mbuffer/meta.yaml b/recipes/mbuffer/meta.yaml index addcc8c121535..ec85536668ac2 100644 --- a/recipes/mbuffer/meta.yaml +++ b/recipes/mbuffer/meta.yaml @@ -12,6 +12,7 @@ build: requirements: build: + - {{ compiler('c') }} run: test: diff --git a/recipes/medpy/meta.yaml b/recipes/medpy/meta.yaml index da30c4f0afaa8..4058b02946268 100644 --- a/recipes/medpy/meta.yaml +++ b/recipes/medpy/meta.yaml @@ -10,23 +10,16 @@ source: sha256: 299d1be28df0b9c35e856177ada7555746d5b94a0f7af34dc3c3dd3671252a6a build: + noarch: python number: 0 script: - export CXXFLAGS="${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 diff --git a/recipes/medusa/meta.yaml b/recipes/medusa-data-fusion/meta.yaml similarity index 77% rename from recipes/medusa/meta.yaml rename to recipes/medusa-data-fusion/meta.yaml index 79a5dee9c350e..044f385bfe9e6 100644 --- a/recipes/medusa/meta.yaml +++ b/recipes/medusa-data-fusion/meta.yaml @@ -7,17 +7,16 @@ source: git_rev: f3060f6c3e2c56ec8c7cf564f124780818759944 build: + noarch: python number: 2 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - scipy + - python <3 + - pip run: - - python + - python <3 - numpy - scipy @@ -33,3 +32,8 @@ about: appear most significant to another set of objects. It builds on collective matrix factorization to derive different semantics, and it formulates the growing of the modules as a submodular optimization program. + +extra: + skip-lints: + - uses_vcs_url + - missing_hash diff --git a/recipes/medusa/build.sh b/recipes/medusa/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/medusa/build.sh +++ /dev/null @@ -1,9 +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/megan/meta.yaml b/recipes/megan/meta.yaml index e61009562bb4c..ea2181162714f 100644 --- a/recipes/megan/meta.yaml +++ b/recipes/megan/meta.yaml @@ -52,3 +52,6 @@ about: extra: identifiers: - biotools:megan + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/menetools/1.0.4_1/build.sh b/recipes/menetools/1.0.4_1/build.sh deleted file mode 100644 index 3a095143291c7..0000000000000 --- a/recipes/menetools/1.0.4_1/build.sh +++ /dev/null @@ -1 +0,0 @@ -python setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/menetools/1.0.4_1/meta.yaml b/recipes/menetools/meta.yaml similarity index 80% rename from recipes/menetools/1.0.4_1/meta.yaml rename to recipes/menetools/meta.yaml index ca25aaa1db09d..6db208f49aff4 100644 --- a/recipes/menetools/1.0.4_1/meta.yaml +++ b/recipes/menetools/meta.yaml @@ -7,17 +7,16 @@ source: md5: 28ed63db69417828b6b95eff141d984e build: + noarch: python number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pyasp >=1.4.3 - + - python >=3 + - pip run: - - python + - python >=3 - pyasp >=1.4.3 test: diff --git a/recipes/mentalist/0.1.9/meta.yaml b/recipes/mentalist/0.1.9/meta.yaml index d3534e60cb9e7..35a24a39cf33d 100644 --- a/recipes/mentalist/0.1.9/meta.yaml +++ b/recipes/mentalist/0.1.9/meta.yaml @@ -39,3 +39,6 @@ about: license: MIT license_file: LICENSE +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml index 6fdecca72e0db..5c61619164124 100644 --- a/recipes/mentalist/meta.yaml +++ b/recipes/mentalist/meta.yaml @@ -34,3 +34,7 @@ about: summary: The MLST pipeline developed by the PathOGiST research group. license: MIT license_file: LICENSE + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/mergevcf/build.sh b/recipes/mergevcf/build.sh deleted file mode 100644 index 89481145a5291..0000000000000 --- a/recipes/mergevcf/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/mergevcf/meta.yaml b/recipes/mergevcf/meta.yaml index 91e071a8ad675..48aefa736ebcd 100644 --- a/recipes/mergevcf/meta.yaml +++ b/recipes/mergevcf/meta.yaml @@ -7,20 +7,19 @@ source: md5: f3f1af91d1e2cdc89d51fc14a351be21 build: + noarch: python number: 1 - skip: True # [not py27] requirements: host: - - python - - setuptools - - pyvcf + - python <3 + - pip run: - - python + - python <3 - pyvcf test: - run: + commands: - mergevcf -h about: diff --git a/recipes/meta-sparse/build.sh b/recipes/meta-sparse/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/meta-sparse/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/meta-sparse/meta.yaml b/recipes/meta-sparse/meta.yaml index 68bda92381443..0ac28e15e16d1 100644 --- a/recipes/meta-sparse/meta.yaml +++ b/recipes/meta-sparse/meta.yaml @@ -9,29 +9,22 @@ source: build: number: 1 skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - sparse = SPARSE.SPARSE:SPARSE requirements: build: + - {{ compiler('c') }} + host: - python - - setuptools - - pycapnp - - numpy - - pandas + - pip - cython - - scipy - - msgpack-python - - samtools - - bowtie2 - - mash - run: - python - pycapnp - numpy - pandas - - cython - scipy - msgpack-python - samtools diff --git a/recipes/metameta/1.0/build.sh b/recipes/metameta/1.0/build.sh deleted file mode 100755 index 8d7e3a7924915..0000000000000 --- a/recipes/metameta/1.0/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/opt/metameta/ - -# Full path to the Snakefile -sed -i "s|Snakefile|$PREFIX/opt/metameta/Snakefile|g" metameta - -cp -r * $PREFIX/opt/metameta/ -ln -s $PREFIX/opt/metameta/metameta $PREFIX/bin/ - diff --git a/recipes/metameta/1.0/meta.yaml b/recipes/metameta/1.0/meta.yaml deleted file mode 100644 index 43e10e5e10549..0000000000000 --- a/recipes/metameta/1.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -package: - name: metameta - version: 1.0 - -source: - url: https://github.com/pirovc/metameta/archive/v1.0.tar.gz - md5: d4d22d24329ac0c4cf597ca5fb29fe03 - -build: - number: 2 - skip: True # [osx] - -requirements: - run: - - snakemake ==3.9.1 - -test: - commands: - - metameta --configfile $PREFIX/opt/metameta/scripts/metameta_dummy_file_test.yaml --config workdir="$PREFIX/opt/metameta/" -n - -about: - home: https://github.com/pirovc/metameta/ - license: "The MIT License (MIT)" - summary: "MetaMeta - pipeline for integrating metagenome analysis tools to improve taxonomic profiling" diff --git a/recipes/metameta/1.1.1/build.sh b/recipes/metameta/1.1.1/build.sh deleted file mode 100755 index 8d7e3a7924915..0000000000000 --- a/recipes/metameta/1.1.1/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/opt/metameta/ - -# Full path to the Snakefile -sed -i "s|Snakefile|$PREFIX/opt/metameta/Snakefile|g" metameta - -cp -r * $PREFIX/opt/metameta/ -ln -s $PREFIX/opt/metameta/metameta $PREFIX/bin/ - diff --git a/recipes/metameta/1.1.1/meta.yaml b/recipes/metameta/1.1.1/meta.yaml deleted file mode 100644 index f3951ad17ff72..0000000000000 --- a/recipes/metameta/1.1.1/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -package: - name: metameta - version: 1.1.1 - -source: - url: https://github.com/pirovc/metameta/archive/v1.1.1.tar.gz - md5: 55d2b63227aa7b3fad41220a455a80e7 - -build: - number: 2 - skip: True # [osx] - -requirements: - run: - - snakemake ==3.9.1 - -test: - commands: - - metameta --configfile $PREFIX/opt/metameta/sampledata/sample_data_archaea_bacteria.yaml --config workdir="$PREFIX/opt/metameta/sampledata/files/" -n - -about: - home: https://github.com/pirovc/metameta/ - license: "The MIT License (MIT)" - summary: "MetaMeta - pipeline for integrating metagenome analysis tools to improve taxonomic profiling" diff --git a/recipes/metameta/1.1/build.sh b/recipes/metameta/1.1/build.sh deleted file mode 100755 index 8d7e3a7924915..0000000000000 --- a/recipes/metameta/1.1/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/opt/metameta/ - -# Full path to the Snakefile -sed -i "s|Snakefile|$PREFIX/opt/metameta/Snakefile|g" metameta - -cp -r * $PREFIX/opt/metameta/ -ln -s $PREFIX/opt/metameta/metameta $PREFIX/bin/ - diff --git a/recipes/metameta/1.1/meta.yaml b/recipes/metameta/1.1/meta.yaml deleted file mode 100644 index 623e623710a29..0000000000000 --- a/recipes/metameta/1.1/meta.yaml +++ /dev/null @@ -1,25 +0,0 @@ -package: - name: metameta - version: 1.1 - -source: - url: https://github.com/pirovc/metameta/archive/v1.1.tar.gz - md5: e21addb746996be6faab624a62f097d0 - -build: - number: 2 - skip: True # [osx] - -requirements: - run: - - snakemake ==3.9.1 - -test: - commands: - - metameta --configfile $PREFIX/opt/metameta/sampledata/sample_data_archaea_bacteria.yaml --config workdir="$PREFIX/opt/metameta/sampledata/files/" -n - -about: - home: https://github.com/pirovc/metameta/ - license: "The MIT License (MIT)" - summary: "MetaMeta - pipeline for integrating metagenome analysis tools to improve taxonomic profiling" - diff --git a/recipes/metameta/meta.yaml b/recipes/metameta/meta.yaml index 153a9a582db5a..250a4951b5965 100644 --- a/recipes/metameta/meta.yaml +++ b/recipes/metameta/meta.yaml @@ -7,8 +7,8 @@ source: md5: 26ec2c55db3273e2b1afadb5e207b8ee build: + noarch: generic number: 2 - skip: True # [osx] requirements: run: diff --git a/recipes/metametamerge/1.0/meta.yaml b/recipes/metametamerge/1.0/meta.yaml deleted file mode 100644 index 030e0753b3f3e..0000000000000 --- a/recipes/metametamerge/1.0/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: metametamerge - version: "1.0" - -source: - url: https://github.com/pirovc/metametamerge/archive/v1.0.tar.gz - md5: 64403a1e778aa82032211209541e92a9 - -build: - number: 1 - skip: True # [not py3k] - script: python -m pip install --no-deps --ignore-installed . - -requirements: - host: - - python - - pip - run: - - python - - numpy - -test: - commands: - - MetaMetaMerge.py -h 2>&1 | echo $? - -about: - home: https://github.com/pirovc/metametamerge/ - license: The MIT License (MIT) - summary: 'Merging module of the MetaMeta Pipeline' - diff --git a/recipes/metametamerge/meta.yaml b/recipes/metametamerge/meta.yaml index 190a286458639..8ddb7afa8f76f 100644 --- a/recipes/metametamerge/meta.yaml +++ b/recipes/metametamerge/meta.yaml @@ -7,16 +7,16 @@ source: md5: bd0be94bb5a2505f70d24a9259be3dff build: + noarch: python number: 1 - skip: True # [not py3k] script: python -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python >3 - pip run: - - python + - python >3 - pandas - numpy >=1.9.0 diff --git a/recipes/metaphlan2/2.7.7/meta.yaml b/recipes/metaphlan2/2.7.7/meta.yaml index 2706be852d780..0dafa0daea395 100644 --- a/recipes/metaphlan2/2.7.7/meta.yaml +++ b/recipes/metaphlan2/2.7.7/meta.yaml @@ -11,19 +11,12 @@ source: md5: {{ md5 }} build: + noarch: generic number: 4 - skip: True # [not py27] requirements: - host: - - python - - setuptools - - bowtie2 >=2.0.0 - - numpy - - biom-format run: - - python - - setuptools + - python <3 - bowtie2 >=2.0.0 - numpy - biom-format diff --git a/recipes/metaphlan2/2.7.8/meta.yaml b/recipes/metaphlan2/2.7.8/meta.yaml index 421deb2672166..0de1d88622583 100644 --- a/recipes/metaphlan2/2.7.8/meta.yaml +++ b/recipes/metaphlan2/2.7.8/meta.yaml @@ -11,19 +11,12 @@ source: md5: {{ md5 }} build: + noarch: generic number: 0 - skip: True # [not py27] requirements: - host: - - python - - setuptools - - bowtie2 >=2.0.0 - - numpy - - biom-format run: - - python - - setuptools + - python <3 - bowtie2 >=2.0.0 - numpy - biom-format diff --git a/recipes/metaquant/meta.yaml b/recipes/metaquant/meta.yaml index 18a95310e8d34..b85f26c9d0f6c 100644 --- a/recipes/metaquant/meta.yaml +++ b/recipes/metaquant/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27] + noarch: python number: 0 entry_points: - metaquant=metaquant.__main__:main @@ -21,11 +21,10 @@ build: requirements: host: - - python + - python >=3 - pip - - setuptools run: - - python + - python >=3 - pandas - ete3 - goatools diff --git a/recipes/metaseq-all/meta.yaml b/recipes/metaseq-all/meta.yaml index b15cff271a665..e742dcf6be0ff 100644 --- a/recipes/metaseq-all/meta.yaml +++ b/recipes/metaseq-all/meta.yaml @@ -3,8 +3,8 @@ package: version: "0.5.6" build: + noarch: generic number: 2 - skip: False requirements: run: @@ -19,3 +19,8 @@ requirements: about: summary: "Meta-package for metaseq including bedtools and UCSC tools" license: "The license for this meta-package is MIT; individual tools vary" + +extra: + skip-lints: + - missing_home + - missing_tests diff --git a/recipes/metaseq/meta.yaml b/recipes/metaseq/meta.yaml index 5dcbe70ff8c91..6703f4c695195 100644 --- a/recipes/metaseq/meta.yaml +++ b/recipes/metaseq/meta.yaml @@ -16,10 +16,11 @@ build: script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " requirements: + build: + - {{ compiler('c') }} host: - python - pip - - setuptools - scipy >=0.10.1 - biopython - scikit-learn @@ -39,7 +40,6 @@ requirements: - biopython - scikit-learn - bx-python >=0.7.1 - - cython - numpy >=1.8.0 - matplotlib >=1.3.1 - pandas >=0.13.1 diff --git a/recipes/metasv/build.sh b/recipes/metasv/build.sh deleted file mode 100755 index 650c36ed10929..0000000000000 --- a/recipes/metasv/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -python -m pip install --no-deps --ignore-installed . diff --git a/recipes/metasv/meta.yaml b/recipes/metasv/meta.yaml index 722d37994c61c..73b3568d61774 100644 --- a/recipes/metasv/meta.yaml +++ b/recipes/metasv/meta.yaml @@ -8,8 +8,11 @@ source: build: number: 1 skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - python - setuptools diff --git a/recipes/metavelvet-annois/meta.yaml b/recipes/metavelvet-annois/meta.yaml index 94ef505aaa07d..2d26d048beffa 100644 --- a/recipes/metavelvet-annois/meta.yaml +++ b/recipes/metavelvet-annois/meta.yaml @@ -9,11 +9,11 @@ source: - run-annoIS.pl.patch build: + noarch: generic number: 3 - skip: True # [osx] requirements: - build: + host: - perl-module-build - perl run: diff --git a/recipes/metawatt/meta.yaml b/recipes/metawatt/meta.yaml index 5229678c4c2b7..779337b622330 100644 --- a/recipes/metawatt/meta.yaml +++ b/recipes/metawatt/meta.yaml @@ -13,8 +13,8 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 - skip: True # [ osx ] requirements: build: diff --git a/recipes/metawrap/meta.yaml b/recipes/metawrap/meta.yaml index f4b66231b5aa5..120321f5baec7 100644 --- a/recipes/metawrap/meta.yaml +++ b/recipes/metawrap/meta.yaml @@ -10,8 +10,8 @@ source: md5: 9018a30354fe066b3e936ae625c6f1b7 build: + noarch: generic number: 0 - skip: True # [osx] requirements: build: diff --git a/recipes/metaxa/meta.yaml b/recipes/metaxa/meta.yaml index ffff99314207f..935e588dd6349 100644 --- a/recipes/metaxa/meta.yaml +++ b/recipes/metaxa/meta.yaml @@ -8,10 +8,11 @@ package: source: url: http://microbiology.se/sw/Metaxa2_{{ version }}.tar.gz sha256: {{ sha256 }} - patches: # [linux] - - "perl-shebang.patch" # [linux] + patches: + - "perl-shebang.patch" build: + noarch: generic number: 0 requirements: diff --git a/recipes/metfrag/meta.yaml b/recipes/metfrag/meta.yaml index 9d79d76893b5f..76db759f0ba2f 100644 --- a/recipes/metfrag/meta.yaml +++ b/recipes/metfrag/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 7d05cb5d7e72872b6ed13495811f1eb9155943ff9f8903cb4240c6f379731174 build: + noarch: generic number: 3 requirements: diff --git a/recipes/methylextract/meta.yaml b/recipes/methylextract/meta.yaml index 51bebf5bd166d..b41e98d132066 100644 --- a/recipes/methylextract/meta.yaml +++ b/recipes/methylextract/meta.yaml @@ -6,6 +6,7 @@ package: version: {{ version }} build: + noarch: generic number: 0 source: diff --git a/recipes/mgltools/meta.yaml b/recipes/mgltools/meta.yaml index 57fa0d627b6ee..cc7fca6c4cb7b 100644 --- a/recipes/mgltools/meta.yaml +++ b/recipes/mgltools/meta.yaml @@ -3,10 +3,10 @@ package: version: 1.5.6 source: - url: http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz # [linux] - md5: e3f62852c4d442a292dedbe6c79540ca # [linux] - url: http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_i86Darwin9_1.5.6.tar.gz # [osx] - md5: c515b187cddeec72fe5a81ecb4a92d6b # [osx] + - url: http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz # [linux] + md5: e3f62852c4d442a292dedbe6c79540ca # [linux] + - url: http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_i86Darwin9_1.5.6.tar.gz # [osx] + md5: c515b187cddeec72fe5a81ecb4a92d6b # [osx] build: number: 1 @@ -23,5 +23,11 @@ test: about: home: http://mgltools.scripps.edu/ + license: custom license_file: LICENSES summary: MGLTools is an program for visualization and analisys of molecular structures. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/micropita/meta.yaml b/recipes/micropita/meta.yaml index c4be255a2eaba..2603e3bf292dc 100644 --- a/recipes/micropita/meta.yaml +++ b/recipes/micropita/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: @@ -35,8 +36,6 @@ about: summary: "microPITA is a computational tool enabling sample selection in two-stage (tiered) studies." extra: - skip-lints: - - should_be_noarch identifiers: - biotools:micropita - doi:10.1038/ismej.2013.139 diff --git a/recipes/midas/build.sh b/recipes/midas/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/midas/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/midas/meta.yaml b/recipes/midas/meta.yaml index 11fbca5ad69d5..2741505d44128 100644 --- a/recipes/midas/meta.yaml +++ b/recipes/midas/meta.yaml @@ -2,8 +2,6 @@ {% set version = "1.3.2" %} {% set sha256 = "87621eaa5b51eb81edc87e3e6b86c7efd3e1d64f503c6abca246b1be79120859" %} - - package: name: '{{name}}' version: '{{version}}' @@ -15,18 +13,14 @@ source: - midas.patch build: + noarch: python number: 2 - skip: true # [osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - pandas - - pysam - - numpy - - biopython - + - pip run: - python - pandas diff --git a/recipes/migmap/meta.yaml b/recipes/migmap/meta.yaml index 652c1a50d76cd..625e3e2d1a57a 100644 --- a/recipes/migmap/meta.yaml +++ b/recipes/migmap/meta.yaml @@ -10,6 +10,7 @@ source: sha256: '{{ sha256 }}' build: + noarch: generic number: 2 requirements: diff --git a/recipes/Migraine/build.sh b/recipes/migraine/build.sh similarity index 100% rename from recipes/Migraine/build.sh rename to recipes/migraine/build.sh diff --git a/recipes/Migraine/meta.yaml b/recipes/migraine/meta.yaml similarity index 100% rename from recipes/Migraine/meta.yaml rename to recipes/migraine/meta.yaml diff --git a/recipes/mikado/meta.yaml b/recipes/mikado/meta.yaml index e9d8881d57c36..9cddd5832a2c5 100644 --- a/recipes/mikado/meta.yaml +++ b/recipes/mikado/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27 or osx or py33] + skip: True # [py27 or osx] number: 0 entry_points: - mikado = Mikado:main @@ -21,6 +21,8 @@ build: script: python -m pip install --no-deps --ignore-installed . requirements: + build: + - {{ compiler('c') }} host: - python - pip @@ -54,7 +56,6 @@ requirements: - wheel >=0.28.0 - pyyaml - jsonschema - - cython >=0.28.2 - numpy - networkx >=1.10 - sqlalchemy >=1 diff --git a/recipes/mimeo/build.sh b/recipes/mimeo/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/mimeo/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/mimeo/meta.yaml b/recipes/mimeo/meta.yaml index b4f0ae2cb7b0c..448f1ce8cd28b 100644 --- a/recipes/mimeo/meta.yaml +++ b/recipes/mimeo/meta.yaml @@ -7,8 +7,9 @@ source: md5: 45d523f694829cf0d081ec8bc0a62729 build: + noarch: python number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - mimeo-self=mimeo.run_self:main - mimeo-x=mimeo.run_interspecies:main @@ -17,13 +18,10 @@ build: requirements: host: - - python - - setuptools - - pandas >=0.20.3 - - biopython >=1.70 - + - python >=3 + - pip run: - - python + - python >=3 - pandas >=0.20.3 - biopython >=1.70 diff --git a/recipes/minimock/build.sh b/recipes/minimock/build.sh deleted file mode 100755 index 0d620c5240825..0000000000000 --- a/recipes/minimock/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/minimock/meta.yaml b/recipes/minimock/meta.yaml index a0024b3e791fe..d8b8f1611ba51 100644 --- a/recipes/minimock/meta.yaml +++ b/recipes/minimock/meta.yaml @@ -3,18 +3,18 @@ package: version: "1.2.8" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/43/c8/0928c5f684d6f86fb34c12e4b6bcde2dd8b951d060f304b5e4cc4d13d106/MiniMock-1.2.8.tar.gz md5: 76593aaba949b5e010fec95283556449 - - requirements: host: - python - + - pip run: - python diff --git a/recipes/minorseq/meta.yaml b/recipes/minorseq/meta.yaml index a2c7a7d204398..7bb1df2911669 100644 --- a/recipes/minorseq/meta.yaml +++ b/recipes/minorseq/meta.yaml @@ -10,17 +10,6 @@ source: url: https://github.com/PacificBiosciences/minorseq/releases/download/v{{ version }}/minorseq.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: Minor Variant Calling and Phasing Tools - -extra: - recipe-maintainers: - - armintoepfer - - pb-dseifert - - mhsieh - build: number: 1 skip: True # [osx] @@ -37,3 +26,16 @@ test: - fuse -h - cleric -h - julietflow -h + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: Minor Variant Calling and Phasing Tools + +extra: + recipe-maintainers: + - armintoepfer + - pb-dseifert + - mhsieh + skip-lints: + - should_be_noarch_generic diff --git a/recipes/mintmap/meta.yaml b/recipes/mintmap/meta.yaml index 4d14566f1a2f4..b6d67b332aad5 100644 --- a/recipes/mintmap/meta.yaml +++ b/recipes/mintmap/meta.yaml @@ -9,6 +9,7 @@ source: - mintmap.patch build: + noarch: generic number: 1 requirements: diff --git a/recipes/minvar/1.2a3/build.sh b/recipes/minvar/1.2a3/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/1.2a3/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/1.2a3/meta.yaml b/recipes/minvar/1.2a3/meta.yaml deleted file mode 100644 index e2bf0b8be1669..0000000000000 --- a/recipes/minvar/1.2a3/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "1.2a3" %} -{% set build = 1 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/{{ version }}.tar.gz - sha256: 6db57430211d5283b8d87faacc15f39ac66cb1290d3bb9d08d79f51d6e4abc8a - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/1.2b/build.sh b/recipes/minvar/1.2b/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/1.2b/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/1.2b/meta.yaml b/recipes/minvar/1.2b/meta.yaml deleted file mode 100644 index d42fe14dc55a9..0000000000000 --- a/recipes/minvar/1.2b/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "1.2b" %} -{% set build = 1 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/v{{ version }}.tar.gz - sha256: 0688b077afe6e9aa5ba151c16bd7d195c4f87c07f797e226dc81d2ceae5e49eb - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/2.0/build.sh b/recipes/minvar/2.0/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/2.0/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/2.0/meta.yaml b/recipes/minvar/2.0/meta.yaml deleted file mode 100644 index 0142519332207..0000000000000 --- a/recipes/minvar/2.0/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "2.0" %} -{% set build = 1 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/v{{ version }}.tar.gz - sha256: 416b63b1418704a395a1dbba1e4a5872773075684bdbc22df102c97234eb4463 - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/2.1.1/build.sh b/recipes/minvar/2.1.1/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/2.1.1/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/2.1.1/meta.yaml b/recipes/minvar/2.1.1/meta.yaml deleted file mode 100644 index a6b5b65d9b5e0..0000000000000 --- a/recipes/minvar/2.1.1/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "2.1.1" %} -{% set build = 2 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/v{{ version }}.tar.gz - sha256: 1b7b2d4bd4966df90e30c8b2bddd871caaf90b62c68915621dd649ee64c120fc - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/2.1.2/build.sh b/recipes/minvar/2.1.2/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/2.1.2/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/2.1.2/meta.yaml b/recipes/minvar/2.1.2/meta.yaml deleted file mode 100644 index 6b693bb1a530f..0000000000000 --- a/recipes/minvar/2.1.2/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "2.1.2" %} -{% set build = 1 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/v{{ version }}.tar.gz - sha256: 6b92c0d94c3df4f6f9974d24d01ff68bf0d8b068a022501b6e65d5df147fe7c5 - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/2.1.3/build.sh b/recipes/minvar/2.1.3/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/2.1.3/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/2.1.3/meta.yaml b/recipes/minvar/2.1.3/meta.yaml deleted file mode 100644 index c2ded13603399..0000000000000 --- a/recipes/minvar/2.1.3/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "2.1.3" %} -{% set build = 0 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/v{{ version }}.tar.gz - sha256: d1ba196bbeaf40032b6f549573c639f23e22c346a5705c2aa63a730b95353022 - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/2.1/build.sh b/recipes/minvar/2.1/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/2.1/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/2.1/meta.yaml b/recipes/minvar/2.1/meta.yaml deleted file mode 100644 index 5b98ab80e9b70..0000000000000 --- a/recipes/minvar/2.1/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set version = "2.1" %} -{% set build = 1 %} - -package: - name: minvar - version: {{ version }} - -build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - # setuptool_scm_git_archive not available in py36 - skip: True # [py27] - -source: - url: https://github.com/ozagordi/MinVar/archive/v{{ version }}.tar.gz - sha256: cc2e53801a6d3ef71d4ea00f478e835a7e0ae7d5324b09696366c8784e3c065c - -requirements: - host: - - isort - - pytest-runner - - python - - setuptools - - setuptools_scm - - setuptools_scm_git_archive - - run: - - bedtools - - biopython - - blast >=2.3 - - bwa - - emboss - - htslib - - lofreq >=2.1.3.1 - - pandas - - pandoc - - python - - samtools >=1.3 - - seqtk - - setuptools_scm_git_archive - -about: - home: https://git.io/minvar - summary: 'A tool to detect minority variants in HIV-1 and HCV populations' - license: Custom - licence_file: LICENCE.md - -test: - commands: - # test a few subcommands - - minvar -h - - minvar -v | grep {{ version }} diff --git a/recipes/minvar/build.sh b/recipes/minvar/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/minvar/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/minvar/meta.yaml b/recipes/minvar/meta.yaml index 065be869161b9..9ffe9f95dbf22 100644 --- a/recipes/minvar/meta.yaml +++ b/recipes/minvar/meta.yaml @@ -1,14 +1,13 @@ {% set version = "2.2.2" %} -{% set build = 0 %} package: name: minvar version: {{ version }} build: - number: {{ build }} - # minvar written for python 3.x only, so skip py27 - skip: True # [py27] + noarch: pip + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/medvir/MinVar/archive/v{{ version }}.tar.gz @@ -16,11 +15,11 @@ source: requirements: host: - - python + - python >=3 - setuptools - setuptools_scm - setuptools_scm_git_archive - + - pip run: - bedtools - biopython @@ -31,7 +30,7 @@ requirements: - lofreq >=2.1.3.1 - pandas - pandoc - - python + - python >=3 - samtools >=1.3 - seqtk - setuptools_scm_git_archive diff --git a/recipes/mir-prefer/meta.yaml b/recipes/mir-prefer/meta.yaml index 4980770b2d128..62ed5cdb2decb 100644 --- a/recipes/mir-prefer/meta.yaml +++ b/recipes/mir-prefer/meta.yaml @@ -16,15 +16,12 @@ source: - patches/process-reads-fasta.py.patch build: + noarch: generic number: 2 - skip: True # [not py2k] requirements: - host: - - python - run: - - python + - python <3 - viennarna >=1.8.5 - samtools >=0.1.15 - bowtie >=1.2.0 diff --git a/recipes/mira/meta.yaml b/recipes/mira/meta.yaml index 604e9502e4432..6f3986fb9d941 100644 --- a/recipes/mira/meta.yaml +++ b/recipes/mira/meta.yaml @@ -8,10 +8,10 @@ build: skip: True # [not linux] source: - url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2 # [linux] - sha256: d3c74a6b402192e01d10adb8dbdc3450d4033fa0e7662ce5ce5de4f8c1967813 # [linux] - url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2 # [osx] - sha256: 3cdfba4be7bde1a97b15259b9fd3216c4369d906ea20f5f360f30dc0d83e7b8e # [osx] + - url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2 # [linux] + sha256: d3c74a6b402192e01d10adb8dbdc3450d4033fa0e7662ce5ce5de4f8c1967813 # [linux] + - url: https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2 # [osx] + sha256: 3cdfba4be7bde1a97b15259b9fd3216c4369d906ea20f5f360f30dc0d83e7b8e # [osx] # No build requirements as using the author's binaries. requirements: @@ -31,3 +31,6 @@ about: extra: identifiers: - biotools:mira + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/mirdeep2/2.0.0.7/build.sh b/recipes/mirdeep2/2.0.0.7/build.sh deleted file mode 100644 index a7c9613395b21..0000000000000 --- a/recipes/mirdeep2/2.0.0.7/build.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash -target=$PREFIX/lib/mirdeep2 -mkdir -p $target -mkdir -p $PREFIX/bin -cp *pl $target -ln -s $target/miRDeep2.pl $PREFIX/bin/miRDeep2.pl diff --git a/recipes/mirdeep2/2.0.0.7/meta.yaml b/recipes/mirdeep2/2.0.0.7/meta.yaml deleted file mode 100644 index dd21fa6ad525d..0000000000000 --- a/recipes/mirdeep2/2.0.0.7/meta.yaml +++ /dev/null @@ -1,21 +0,0 @@ -package: - name: mirdeep2 - version: '2.0.0.7' - -source: - git_url: https://github.com/lpantano/mirdeep2_core.git - git_rev: 0e96444370683a1f5eeb4a5c0a85dc118ec0c01d - -build: - number: 8 - skip: True # [osx] - -requirements: - run: - - perl - - perl-pdf-api2 - -about: - home: https://github.com/lpantano/mirdeep2_core.git - license: academic - summary: miRNA prediction diff --git a/recipes/mirdeep2/2.0.0.8/build.sh b/recipes/mirdeep2/build.sh similarity index 100% rename from recipes/mirdeep2/2.0.0.8/build.sh rename to recipes/mirdeep2/build.sh diff --git a/recipes/mirdeep2/2.0.0.8/meta.yaml b/recipes/mirdeep2/meta.yaml similarity index 97% rename from recipes/mirdeep2/2.0.0.8/meta.yaml rename to recipes/mirdeep2/meta.yaml index f7ee1be2071df..b9650a6b1b05e 100644 --- a/recipes/mirdeep2/2.0.0.8/meta.yaml +++ b/recipes/mirdeep2/meta.yaml @@ -10,10 +10,9 @@ source: build: number: 6 - skip: False + noarch: generic requirements: - run: - bowtie - viennarna diff --git a/recipes/mirdeep2/2.0.0.8/mirdeep2.patch b/recipes/mirdeep2/mirdeep2.patch similarity index 100% rename from recipes/mirdeep2/2.0.0.8/mirdeep2.patch rename to recipes/mirdeep2/mirdeep2.patch diff --git a/recipes/mirge/meta.yaml b/recipes/mirge/meta.yaml index 85aa8b5b85461..70bdce43cb695 100644 --- a/recipes/mirge/meta.yaml +++ b/recipes/mirge/meta.yaml @@ -13,11 +13,11 @@ source: build: number: 5 - skip: True # [not py27] + noarch: python requirements: build: - - python + - python <3 - setuptools - cutadapt ==1.16 - biopython >=1.68 @@ -28,8 +28,7 @@ requirements: - scikit-learn - reportlab run: - - python - - setuptools + - python <3 - cutadapt ==1.16 - biopython >=1.68 - numpy diff --git a/recipes/mlpy/meta.yaml b/recipes/mlpy/meta.yaml index 053dd62e8b7b3..45e1c924e0256 100644 --- a/recipes/mlpy/meta.yaml +++ b/recipes/mlpy/meta.yaml @@ -11,7 +11,7 @@ source: build: number: 0 - script: "{{ PYTHON }} setup.py install" + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv skip: true # [osx] requirements: diff --git a/recipes/mmvc/meta.yaml b/recipes/mmvc/meta.yaml index 2fbf8fefbb5ec..892450e7f9d4e 100644 --- a/recipes/mmvc/meta.yaml +++ b/recipes/mmvc/meta.yaml @@ -11,7 +11,7 @@ build: skip: True # [osx] requirements: - build: + host: - julia 0.6.1 run: - julia 0.6.1 @@ -24,3 +24,7 @@ about: home: https://github.com/veg/mmvc license: MIT summary: Call variants based on a Bayesian multinomial mixture model. + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/moca/build.sh b/recipes/moca/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/moca/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/moca/meta.yaml b/recipes/moca/meta.yaml index 10900dbb9ea2c..edcddef71814b 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -7,62 +7,19 @@ source: sha256: ec7a858629fe5552205cd280e77ee993a38bb065d9e5d22080099bb9b1f81f05 build: + noarch: python number: 0 - skip: true #[not py27] preserve_egg_dir: true + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - moca=scripts.mocacli:cli requirements: host: - - python - - setuptools - - biopython >=1.68 - - certifi >=2016.2.28 - - cffi >=1.9.1 - - click >=6.6 - - click-help-colors >=0.3 - - coverage >=4.2 - - cryptography >=1.7.1 - - cycler >=0.10.0 - - enum34 >=1.1.6 - - functools32 >=3.2.3.post2 - - future >=0.16.0 - - idna >=2.2 - - ipaddress >=1.0.18 - - matplotlib >=2.0.0 - - mmtf-python >=1.0.5 - - msgpack-python >=0.4.8 - - numpy >=1.11.3 - - olefile >=0.44 - - pandas >=0.19.2 - - patsy >=0.4.1 - - pillow >=4.0.0 - - py >=1.4.32 - - pyasn1 >=0.1.9 - - pybedtools >=0.7.9 - - pybigwig >=0.2.8 - - pycairo >=1.10.0 # [linux] - - pycparser >=2.17 - - pyparsing >=2.1.4 - - pysam >=0.9.1.4 - - pytest >=3.0.5 - - pytest-cov >=2.4.0 - - pytest-mpl >=0.5 - - python-dateutil >=2.3 - - pytz >=2016.10 - - pyyaml >=3.12 - - reportlab >=3.3.0 - - scipy >=0.18.1 - - seaborn >=0.7.1 - - six >=1.10.0 - - statsmodels >=0.6.1 - - subprocess32 >=3.2.7 - - tqdm >=4.7.2 - + - python <3 + - pip run: - - python - - setuptools + - python <3 - biopython >=1.68 - certifi >=2016.2.28 - cffi >=1.9.1 diff --git a/recipes/moff/meta.yaml b/recipes/moff/meta.yaml index 6da9c4ecbc258..f10c7a6ca22fb 100644 --- a/recipes/moff/meta.yaml +++ b/recipes/moff/meta.yaml @@ -9,11 +9,10 @@ source: sha256: 025b8b1b9dcdcb38cf5b750bbe4b2eeef56494f585569429303c9d23e9aaf7c7 build: + noarch: generic number: 2 requirements: - host: - - python >=3.4,<3.7 run: - python >=3.4,<3.7 - pandas >=0.23 @@ -38,7 +37,5 @@ about: summary: moFF is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides. extra: - skip-lints: - - should_be_noarch identifiers: - doi:10.1021/acs.jproteome.8b00708 diff --git a/recipes/monovar/meta.yaml b/recipes/monovar/meta.yaml index c0eb7dde67817..233d6c578ed3a 100644 --- a/recipes/monovar/meta.yaml +++ b/recipes/monovar/meta.yaml @@ -11,18 +11,12 @@ source: md5: a5b49a53aa660ce084b1ef0f3d5bbb32 build: + noarch: generic number: 1 - skip: True # [not py27] requirements: - host: - - python - - numpy - - scipy - - pysam - run: - - python + - python <3 - numpy - scipy - pysam diff --git a/recipes/morpheus/meta.yaml b/recipes/morpheus/meta.yaml index 999a4c095c854..00b65ce39901a 100644 --- a/recipes/morpheus/meta.yaml +++ b/recipes/morpheus/meta.yaml @@ -33,3 +33,5 @@ about: extra: identifiers: - doi:10.1021/pr301024c + skip-lints: + - should_be_noarch_generic diff --git a/recipes/motifscan/build.sh b/recipes/motifscan/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/motifscan/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/motifscan/meta.yaml b/recipes/motifscan/meta.yaml index c9c409347f81d..3e0463e64cc63 100644 --- a/recipes/motifscan/meta.yaml +++ b/recipes/motifscan/meta.yaml @@ -7,20 +7,16 @@ source: sha256: 7ba31fed062fc1d228ac9178383dc12711bf4f65d98ade383eccf23a4abe0099 build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - pandas >=0.17.0 - - scipy - - matplotlib - + - python <3 + - pip run: - - python + - python <3 - numpy - pandas >=0.17.0 - scipy diff --git a/recipes/mpa-portable/meta.yaml b/recipes/mpa-portable/meta.yaml index da1c9214b6dc0..6a568997376f7 100644 --- a/recipes/mpa-portable/meta.yaml +++ b/recipes/mpa-portable/meta.yaml @@ -31,3 +31,5 @@ about: extra: notes: | mpa-protable is Java program that comes with a custom wrapper shell script. + skip-lints: + - should_be_noarch_generic diff --git a/recipes/mqc/meta.yaml b/recipes/mqc/meta.yaml index 1536cf9c9cb70..4e734feeab18d 100644 --- a/recipes/mqc/meta.yaml +++ b/recipes/mqc/meta.yaml @@ -7,12 +7,12 @@ source: md5: e807d15c8b395ca34f46f2c7540a6290 build: - skip: True # [not py27] + noarch: generic number: 2 requirements: run: - - python + - python <3 - numpy - pandas - matplotlib diff --git a/recipes/msms/meta.yaml b/recipes/msms/meta.yaml index 9656eae06163e..ebd1383d19981 100644 --- a/recipes/msms/meta.yaml +++ b/recipes/msms/meta.yaml @@ -6,13 +6,16 @@ package: version: {{ version }} source: - url: {{ url_base }}/REL{{ version }}/msms_i86_64Linux2_{{ version }}.tar.gz [linux] - url: {{ url_base }}/REL{{ version }}/msms_MacOSX_{{ version }}.tar.gz [osx] - md5: 650d8c6fd49d9ce291f30ed530d5f313 [linux] - md5: 36bd8447908d12a8703f458564cbe74b [osx] - patches: - - pdb_to_xyzr.patch - - pdb_to_xyzrn.patch + - url: {{ url_base }}/REL{{ version }}/msms_i86_64Linux2_{{ version }}.tar.gz # [linux] + md5: 650d8c6fd49d9ce291f30ed530d5f313 # [linux] + patches: + - pdb_to_xyzr.patch # [linux] + - pdb_to_xyzrn.patch # [linux] + - url: {{ url_base }}/REL{{ version }}/msms_MacOSX_{{ version }}.tar.gz # [osx] + md5: 36bd8447908d12a8703f458564cbe74b # [osx] + patches: + - pdb_to_xyzr.patch # [osx] + - pdb_to_xyzrn.patch # [osx] build: number: 2 @@ -28,3 +31,8 @@ about: home: http://mgltools.scripps.edu/packages/MSMS/ license: Free for academic use. summary: MSMS is a program written in the C programming language to compute molecular surfaces. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/mugsy/meta.yaml b/recipes/mugsy/meta.yaml index dec6e76c99b8d..143dc3ad52d59 100644 --- a/recipes/mugsy/meta.yaml +++ b/recipes/mugsy/meta.yaml @@ -9,8 +9,8 @@ source: - perl-env.patch build: + noarch: generic number: 2 - skip: True # [not linux64 or osx] requirements: run: diff --git a/recipes/multigps/0.74/build.sh b/recipes/multigps/build.sh similarity index 100% rename from recipes/multigps/0.74/build.sh rename to recipes/multigps/build.sh diff --git a/recipes/multigps/0.74/meta.yaml b/recipes/multigps/meta.yaml similarity index 93% rename from recipes/multigps/0.74/meta.yaml rename to recipes/multigps/meta.yaml index e702c098cb655..3f9595973ae80 100644 --- a/recipes/multigps/0.74/meta.yaml +++ b/recipes/multigps/meta.yaml @@ -28,3 +28,7 @@ about: home: http://mahonylab.org/software/multigps/ license: MIT summary: MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions. + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/multigps/0.74/multigps.sh b/recipes/multigps/multigps.sh similarity index 100% rename from recipes/multigps/0.74/multigps.sh rename to recipes/multigps/multigps.sh diff --git a/recipes/mummer/meta.yaml b/recipes/mummer/meta.yaml index a339502f9371b..95319dcb4bfbe 100644 --- a/recipes/mummer/meta.yaml +++ b/recipes/mummer/meta.yaml @@ -14,14 +14,14 @@ source: build: number: 8 - skip: False requirements: build: + - {{ compiler('cxx') }} + host: - perl # [not osx] run: - perl # [not osx] - - libstdcxx-ng # [linux] test: commands: @@ -45,4 +45,4 @@ about: extra: identifiers: - - biotools:mummer \ No newline at end of file + - biotools:mummer diff --git a/recipes/munkres/build.sh b/recipes/munkres/build.sh deleted file mode 100644 index 55ea547a2d0c6..0000000000000 --- a/recipes/munkres/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/munkres/meta.yaml b/recipes/munkres/meta.yaml deleted file mode 100644 index 0a055973d7511..0000000000000 --- a/recipes/munkres/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -{% set MUNKRES_VERSION = "1.0.7" %} - -package: - name: munkres - version: {{ MUNKRES_VERSION }} - -source: - url: https://pypi.python.org/packages/source/m/munkres/munkres-{{ MUNKRES_VERSION }}.tar.gz - md5: d534612326f7c7cadcfa61d109f96289 - -build: - noarch: python - number: 1 - -requirements: - host: - - setuptools - - python - run: - - python - -test: - imports: - - munkres - -about: - home: http://software.clapper.org/munkres/ - license: Apache License - summary: munkres algorithm for the Assignment Problem diff --git a/recipes/mykatlas/build.sh b/recipes/mykatlas/build.sh deleted file mode 100644 index ce604a78e0c95..0000000000000 --- a/recipes/mykatlas/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/mykatlas/meta.yaml b/recipes/mykatlas/meta.yaml index 708493eca5de5..9d14669f5ca4c 100644 --- a/recipes/mykatlas/meta.yaml +++ b/recipes/mykatlas/meta.yaml @@ -13,19 +13,14 @@ build: # includes precompiled Linux binary `mccortex31` skip: True # [osx] number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - atlas = mykatlas.atlas_main:main requirements: host: - python - - setuptools - - future - - biopython - - mongoengine - - pyvcf - - ga4ghmongo - + - pip run: - python - future @@ -47,3 +42,7 @@ about: license: MIT summary: 'Assists in discoveries of antibiotic-resistance with mykrobe' license_family: MIT + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/mykrobe/meta.yaml b/recipes/mykrobe/meta.yaml index 0af38aeadb031..128a861a95b82 100644 --- a/recipes/mykrobe/meta.yaml +++ b/recipes/mykrobe/meta.yaml @@ -1,62 +1,62 @@ {% set version = "0.7.0" %} package: - name : mykrobe - version: {{ version }} + name: mykrobe + version: {{ version }} source: - url : https://github.com/Mykrobe-tools/mykrobe/archive/v{{ version }}.tar.gz - sha256 : c1fba091bf72f95112211d53d5610297b4bcbca135592585ce2cde3e98156ef0 + url: https://github.com/Mykrobe-tools/mykrobe/archive/v{{ version }}.tar.gz + sha256: c1fba091bf72f95112211d53d5610297b4bcbca135592585ce2cde3e98156ef0 build: - number: 0 - entry_points: - - mykrobe = mykrobe.cli:main + number: 0 + skip: True # [py2k] + entry_points: + - mykrobe = mykrobe.cli:main requirements: - build: - - {{ compiler('cxx') }} - host: - - python >=3.4 - - pip - - zlib - - wget - - numpy - - cython - - mongoengine - - pyvcf - - biopython - run: - - python >=3.4 - - mongodb >3.0 - - wget - - zlib - - numpy - - cython - - mongoengine - - pyvcf - - biopython + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - python + - pip + - zlib + - wget + - numpy + - cython + - mongoengine + - pyvcf + - biopython + run: + - python + - mongodb >3.0 + - wget + - zlib + - numpy + - mongoengine + - pyvcf + - biopython test: - imports: - - numpy - - cython - - mongoengine - - vcf - - Bio - - mykrobe - - commands: - - mykrobe --version - - mykrobe --help - - mykrobe predict --help - - mykrobe variants --help - - mykrobe genotype --help - - 'mccortex31 2>&1 | head -n2 | grep "^usage: "' + imports: + - numpy + - cython + - mongoengine + - vcf + - Bio + - mykrobe + + commands: + - mykrobe --version + - mykrobe --help + - mykrobe predict --help + - mykrobe variants --help + - mykrobe genotype --help + - 'mccortex31 2>&1 | head -n2 | grep "^usage: "' about: - home: https://github.com/Mykrobe-tools/mykrobe - license: MIT - license_file: LICENSE - summary: 'Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.' - + home: https://github.com/Mykrobe-tools/mykrobe + license: MIT + license_file: LICENSE + summary: 'Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.' diff --git a/recipes/myriad/build.sh b/recipes/myriad/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/myriad/build.sh +++ /dev/null @@ -1,9 +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/myriad/meta.yaml b/recipes/myriad/meta.yaml index d09df3670b5e8..3309858744f64 100644 --- a/recipes/myriad/meta.yaml +++ b/recipes/myriad/meta.yaml @@ -7,18 +7,18 @@ source: sha256: ae1d836f0e9c37b90b94c185555e485e2c7e36458a4709e39e4aefc3945fdfd5 build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - myriad = myriad.components:main requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: # Python imports diff --git a/recipes/mzml2isa/0.4.24/build.sh b/recipes/mzml2isa/0.4.24/build.sh deleted file mode 100644 index 4899c226c8dd0..0000000000000 --- a/recipes/mzml2isa/0.4.24/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/mzml2isa/0.4.24/meta.yaml b/recipes/mzml2isa/0.4.24/meta.yaml index 2f73761f87a91..35a30c92057c1 100644 --- a/recipes/mzml2isa/0.4.24/meta.yaml +++ b/recipes/mzml2isa/0.4.24/meta.yaml @@ -7,22 +7,18 @@ source: md5: 01c71fae82689807f0126c2b7bcf986f build: - skip: True # [py3k] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 2 entry_points: - mzml2isa = mzml2isa.parsing:run requirements: host: - - python - - setuptools - - lxml - - six - - pronto - - chainmap - + - python <3 + - pip run: - - python + - python <3 - lxml - six - pronto diff --git a/recipes/nanocall/meta.yaml b/recipes/nanocall/meta.yaml index 299b03eac35c1..197cdfa59a530 100644 --- a/recipes/nanocall/meta.yaml +++ b/recipes/nanocall/meta.yaml @@ -33,5 +33,5 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url - missing_hash diff --git a/recipes/nanolyse/build.sh b/recipes/nanolyse/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/nanolyse/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/nanolyse/meta.yaml b/recipes/nanolyse/meta.yaml index 1091b1ef53ee2..c5fe0f11de4a1 100644 --- a/recipes/nanolyse/meta.yaml +++ b/recipes/nanolyse/meta.yaml @@ -10,20 +10,18 @@ source: sha256: 7d93f19ce5ecf251b5a3fdb2d034fd822bb74160b188d7753d8cfba1cd24ea8a build: + noarch: python entry_points: - NanoLyse=nanolyse.NanoLyse:main number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python >=3 - setuptools - - biopython - - mappy >=2.2 - run: - - python + - python >=3 - biopython - mappy >=2.2 diff --git a/recipes/nanomath/build.sh b/recipes/nanomath/build.sh deleted file mode 100644 index e3b0eb7e3ac1a..0000000000000 --- a/recipes/nanomath/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/nanomath/meta.yaml b/recipes/nanomath/meta.yaml index ece5f7007d2d5..d21a118499c13 100644 --- a/recipes/nanomath/meta.yaml +++ b/recipes/nanomath/meta.yaml @@ -9,18 +9,16 @@ source: sha256: 54a7edb3b458194014a35122968a7bc70cf9076de2f65f4a8b00638f71b06011 build: + noarch: python number: 0 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pandas - - numpy >1.8 - + - python >=3 + - pip run: - - python + - python >=3 - pandas - numpy >1.8 diff --git a/recipes/nanopore_simulation/build.sh b/recipes/nanopore_simulation/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/nanopore_simulation/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/nanopore_simulation/meta.yaml b/recipes/nanopore_simulation/meta.yaml index 5aa93ecd172ec..9dd63b04428e0 100644 --- a/recipes/nanopore_simulation/meta.yaml +++ b/recipes/nanopore_simulation/meta.yaml @@ -9,21 +9,16 @@ source: sha256: 4e42d56a9e3d5a1209eba264379831f064a9c705920963516859f8b68af81fce build: + noarch: python number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - biopython - - pandas - - h5py - - scipy - - matplotlib - - numpy + - python >=3 + - pip run: - - python + - python >=3 - biopython - pandas - h5py diff --git a/recipes/nanoraw/build.sh b/recipes/nanoraw/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/nanoraw/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/nanoraw/meta.yaml b/recipes/nanoraw/meta.yaml index 2b90055e841bf..898b3f3fcd264 100644 --- a/recipes/nanoraw/meta.yaml +++ b/recipes/nanoraw/meta.yaml @@ -11,28 +11,18 @@ source: sha256: {{ hash }} build: + noarch: python entry_points: - nanoraw = nanoraw.__main__:main number: 2 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - h5py - - rpy2 >=2.4.2 - - numpy - - scipy - - r-base - - r-ggplot2 - - r-cowplot - - hdf5 - - graphmap - - bwa - + - python <3 + - pip run: - - python + - python <3 - h5py - rpy2 >=2.4.2 - numpy diff --git a/recipes/nanostat/build.sh b/recipes/nanostat/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/nanostat/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/nanostat/meta.yaml b/recipes/nanostat/meta.yaml index c619ea98179d2..4ac84e4971cb9 100644 --- a/recipes/nanostat/meta.yaml +++ b/recipes/nanostat/meta.yaml @@ -9,18 +9,18 @@ source: sha256: ca53ad16aab0a187fffe7e6a9a764e6fd5ef54b7568b52a8df816304680f28d7 build: + noarch: python entry_points: - NanoStat=nanostat.NanoStat:main number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python >=3 + - pip run: - - python + - python >=3 - nanoget >=0.15.0 - nanomath >=0.19.0 diff --git a/recipes/nanosv/build.sh b/recipes/nanosv/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/nanosv/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/nanosv/meta.yaml b/recipes/nanosv/meta.yaml index 5b41ba9042a94..0881a02a1a22a 100644 --- a/recipes/nanosv/meta.yaml +++ b/recipes/nanosv/meta.yaml @@ -9,17 +9,18 @@ source: sha256: af1b3671d862008b4631c6338fc7dbe3d6a11d4412c55eba4334f305a46a82f2 build: + noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - NanoSV=nanosv.NanoSV:main - noarch: python requirements: host: - - python >3 - - setuptools + - python >=3 + - pip run: - - python >3 + - python >=3 - pysam - pyvcf @@ -34,6 +35,7 @@ about: summary: Structural variation detection tool for Oxford Nanopore data. extra: - recipe-maintainers: 'wdecoster' + recipe-maintainers: + - 'wdecoster' identifiers: - doi:10.1038/s41467-017-01343-4 diff --git a/recipes/nasp/meta.yaml b/recipes/nasp/meta.yaml index c2cb893987cec..8ab1ee2ba3960 100644 --- a/recipes/nasp/meta.yaml +++ b/recipes/nasp/meta.yaml @@ -16,7 +16,7 @@ build: requirements: build: - - go + - {{ compiler('go') }} host: - python >=3 - pip @@ -38,8 +38,6 @@ about: summary: 'NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats' extra: - skip-lints: - - should_be_noarch identifiers: - doi:10.1099/mgen.0.000074 recipe-maintainers: diff --git a/recipes/ndex-python/build.sh b/recipes/ndex-python/build.sh deleted file mode 100644 index e3b0eb7e3ac1a..0000000000000 --- a/recipes/ndex-python/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/ndex-python/meta.yaml b/recipes/ndex-python/meta.yaml index c4030bf7dffa8..78b4a70dfd5d4 100644 --- a/recipes/ndex-python/meta.yaml +++ b/recipes/ndex-python/meta.yaml @@ -9,20 +9,16 @@ source: md5: 767d75ebf462abed0ed5cf9bfb5d29e4 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - requests - - requests-toolbelt - - networkx - - urllib3 >=1.16 - + - python <3 + - pip run: - - python + - python <3 - requests - requests-toolbelt - networkx diff --git a/recipes/neptune/build.sh b/recipes/neptune/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/neptune/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/neptune/meta.yaml b/recipes/neptune/meta.yaml index 1e126bf594bfd..531ce0c6027bd 100644 --- a/recipes/neptune/meta.yaml +++ b/recipes/neptune/meta.yaml @@ -7,21 +7,16 @@ source: md5: ed48846deffefe25784c9f8b7db2de6e build: + noarch: python number: 2 - skip: True #[not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - drmaa - - numpy - - scipy - - biopython - - blast - + - python <3 + - pip run: - - python + - python <3 - drmaa - numpy - scipy diff --git a/recipes/netcdf-metadata-info/meta.yaml b/recipes/netcdf-metadata-info/meta.yaml index 360ccb4b2b713..314b38165fbf7 100644 --- a/recipes/netcdf-metadata-info/meta.yaml +++ b/recipes/netcdf-metadata-info/meta.yaml @@ -15,10 +15,10 @@ build: requirements: build: + - {{ compiler('c') }} + host: - libnetcdf 4.4.* - - gcc run: - - libgcc - libnetcdf 4.4.* test: diff --git a/recipes/networkxgmml/meta.yaml b/recipes/networkxgmml/meta.yaml index 0b12bdbb5d114..6a89476d5200d 100644 --- a/recipes/networkxgmml/meta.yaml +++ b/recipes/networkxgmml/meta.yaml @@ -19,7 +19,6 @@ requirements: - networkx run: - python - - setuptools - networkx test: diff --git a/recipes/ngless/meta.yaml b/recipes/ngless/meta.yaml index 43f08e021d21f..ec10842aeb01f 100644 --- a/recipes/ngless/meta.yaml +++ b/recipes/ngless/meta.yaml @@ -18,7 +18,6 @@ requirements: run: - python - test: commands: - ngless --version @@ -28,3 +27,7 @@ about: home: https://ngless.embl.de license: MIT summary: A tool for metagenomics processing with a focus on metagenomics + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/nglview/meta.yaml b/recipes/nglview/meta.yaml deleted file mode 100644 index b54ec3fa73a41..0000000000000 --- a/recipes/nglview/meta.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{% set version = "1.1.7" %} -{% set sha256 = "7c01586535cb7bf670c8a1d5c5607f5f2c5307bbeeae7435b0716a9032b9a22b" %} -# from: https://github.com/conda-forge/nglview-feedstock/blob/master/recipe/meta.yaml - -package: - name: nglview - version: '{{ version }}' - -source: - url: https://pypi.io/packages/source/n/nglview/nglview-{{ version }}.tar.gz - sha256: '{{ sha256 }}' - -build: - number: 0 - script: python -m pip install --no-deps --ignore-installed . - noarch: python - -requirements: - build: - - python - - pip - run: - - python - - numpy - - ipywidgets >=7 - - notebook - -test: - imports: - - nglview - - notebook - -about: - home: https://github.com/arose/nglview - license: MIT - license_family: MIT - license_file: LICENSE - summary: An IPython widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer - for rendering. - doc_url: https://arose.github.io/nglview/latest/ - dev_url: https://github.com/arose/nglview - -extra: - recipe-maintainers: - - hainm diff --git a/recipes/ngsutils/build.sh b/recipes/ngsutils/build.sh index 2c3fc04aee3d6..71f9d43e63739 100644 --- a/recipes/ngsutils/build.sh +++ b/recipes/ngsutils/build.sh @@ -16,4 +16,4 @@ sed "s~cat VERSION~cat $PREFIX/share/ngsutils/VERSION~g" | \ sed 's~exec "$DIR"/ngsutils/$SUBDIR/$action "$@"~exec python "$DIR"/ngsutils/$SUBDIR/$action "$@"~g' > $SRC_DIR/bin/ngsutils.new mv $SRC_DIR/bin/ngsutils.new $SRC_DIR/bin/ngsutils -python setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/ngsutils/meta.yaml b/recipes/ngsutils/meta.yaml index b544cf97045ce..085530df6048a 100644 --- a/recipes/ngsutils/meta.yaml +++ b/recipes/ngsutils/meta.yaml @@ -11,6 +11,8 @@ build: skip: True # [py3k] requirements: + build: + - {{ compiler('c') }} host: - python - pysam @@ -22,7 +24,6 @@ requirements: run: - python - pysam - - cython - samtools - eta - coverage diff --git a/recipes/nmrglue/build.sh b/recipes/nmrglue/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/nmrglue/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/nmrglue/meta.yaml b/recipes/nmrglue/meta.yaml index f3dbc70a6c4dd..d567b20852c72 100644 --- a/recipes/nmrglue/meta.yaml +++ b/recipes/nmrglue/meta.yaml @@ -8,15 +8,14 @@ source: build: number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - {{ compiler('c') }} host: - python - - numpy - - scipy - + - pip run: - python - numpy diff --git a/recipes/nmrpro/build.sh b/recipes/nmrpro/build.sh deleted file mode 100644 index 4dad93a1c02ab..0000000000000 --- a/recipes/nmrpro/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/nmrpro/meta.yaml b/recipes/nmrpro/meta.yaml index 28a7edb667d06..b334ddc8d7b8e 100644 --- a/recipes/nmrpro/meta.yaml +++ b/recipes/nmrpro/meta.yaml @@ -9,13 +9,12 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + requirements: host: - python - - setuptools - - numpy - - scipy - - nmrglue >=0.5 + - pip run: - python - numpy diff --git a/recipes/nose-capturestderr/build.sh b/recipes/nose-capturestderr/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/nose-capturestderr/build.sh +++ /dev/null @@ -1,9 +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/nose-capturestderr/meta.yaml b/recipes/nose-capturestderr/meta.yaml index f9adee762bec5..05517728830e1 100644 --- a/recipes/nose-capturestderr/meta.yaml +++ b/recipes/nose-capturestderr/meta.yaml @@ -9,17 +9,15 @@ source: build: preserve_egg_dir: True number: 0 - skip: True # [not py27] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - nose >=0.11.1 - + - python <3 + - pip run: - - python - - setuptools + - python <3 - nose >=0.11.1 test: diff --git a/recipes/novoalign/meta.yaml b/recipes/novoalign/meta.yaml index 19bf2011ae20f..be15b53f9ca6e 100644 --- a/recipes/novoalign/meta.yaml +++ b/recipes/novoalign/meta.yaml @@ -9,12 +9,14 @@ package: version: '{{ version }}' source: - url: http://www.novocraft.com/bioconda/novocraftV{{ version }}.Linux2.6.32.tar.gz # [linux] - sha256: {{ sha256_linux }} # [linux] - url: http://www.novocraft.com/bioconda/novocraftV{{ version }}.MacOSX.tar.gz # [osx] - sha256: {{ sha256_osx }} # [osx] - patches: - - 0001-patches-for-compiling-novo2maq.patch + - url: http://www.novocraft.com/bioconda/novocraftV{{ version }}.Linux2.6.32.tar.gz # [linux] + sha256: {{ sha256_linux }} # [linux] + patches: + - 0001-patches-for-compiling-novo2maq.patch # [linux] + - url: http://www.novocraft.com/bioconda/novocraftV{{ version }}.MacOSX.tar.gz # [osx] + sha256: {{ sha256_osx }} # [osx] + patches: + - 0001-patches-for-compiling-novo2maq.patch # [osx] build: number: 2 @@ -23,7 +25,6 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - zlib host: - curl # curl is needed to access Novocraft's website during package install -- see post-link.sh - zlib @@ -49,3 +50,5 @@ extra: notes: Novoalign runs in single-threaded mode by default unless a "novoalign.lic" license file is provided in the same directory as its binaries. The license file can be copied in to the conda environment via the "novoalign-license-register" command. identifiers: - biotools:Novoalign + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/npyscreen/build.sh b/recipes/npyscreen/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/npyscreen/build.sh +++ /dev/null @@ -1,9 +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/npyscreen/meta.yaml b/recipes/npyscreen/meta.yaml index a43f65458cbe5..3d5d3bef5f398 100644 --- a/recipes/npyscreen/meta.yaml +++ b/recipes/npyscreen/meta.yaml @@ -9,13 +9,12 @@ source: build: noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - ncurses - + - pip run: - python - ncurses diff --git a/recipes/nucamino/meta.yaml b/recipes/nucamino/meta.yaml index 6094103ba6776..fe290be19e8ea 100644 --- a/recipes/nucamino/meta.yaml +++ b/recipes/nucamino/meta.yaml @@ -5,10 +5,10 @@ package: version: {{ version }} source: - url: https://github.com/hivdb/nucamino/releases/download/v{{ version }}/nucamino-darwin-amd64 # [osx] - sha256: 7ebb74247d17c4009072f67ff38c5578a96ed5df4246a37ccd038ad3473cfdb3 # [osx] - url: https://github.com/hivdb/nucamino/releases/download/v{{ version }}/nucamino-linux-amd64 # [linux64] - sha256: 6453d87b8b5acb381ef97aec65cbd40e34b63abb20da3d7bf5136881e1ea422c # [linux64] + - url: https://github.com/hivdb/nucamino/releases/download/v{{ version }}/nucamino-darwin-amd64 # [osx] + sha256: 7ebb74247d17c4009072f67ff38c5578a96ed5df4246a37ccd038ad3473cfdb3 # [osx] + - url: https://github.com/hivdb/nucamino/releases/download/v{{ version }}/nucamino-linux-amd64 # [linux64] + sha256: 6453d87b8b5acb381ef97aec65cbd40e34b63abb20da3d7bf5136881e1ea422c # [linux64] build: number: 1 @@ -23,3 +23,8 @@ about: home: https://github.com/hivdb/nucamino license: MIT summary: A nucleotide to amino acid alignment program optimized for virus gene sequences + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/nucleoatac/meta.yaml b/recipes/nucleoatac/meta.yaml index 469ca642469e9..33ceeb2ddee20 100644 --- a/recipes/nucleoatac/meta.yaml +++ b/recipes/nucleoatac/meta.yaml @@ -10,17 +10,18 @@ source: sha256: {{sha256}} build: - noarch: python number: 2 script: python -m pip install --no-deps --ignore-installed . requirements: + build: + - {{ compiler('c') }} host: - python <3 - pip + - cython >=0.22 run: - python <3 - - cython >=0.22 - numpy >=1.9.1 - scipy - matplotlib diff --git a/recipes/nudup/meta.yaml b/recipes/nudup/meta.yaml index 88b3a94c26c4d..b097d318f100a 100644 --- a/recipes/nudup/meta.yaml +++ b/recipes/nudup/meta.yaml @@ -7,14 +7,16 @@ source: sha256: daa4d26380275951ec5675d5a7f0432fa89e4ead868bae2d0eeabd1cb7449736 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python <3 + - pip run: - - python + - python <3 - samtools >=1.2 - coreutils - sed diff --git a/recipes/nullarbor/meta.yaml b/recipes/nullarbor/meta.yaml index adad0bcf1a6cf..62ad34a64a7cf 100644 --- a/recipes/nullarbor/meta.yaml +++ b/recipes/nullarbor/meta.yaml @@ -53,6 +53,8 @@ requirements: test: commands: + - "nullarbor.pl --help" + - "nullarbor.pl --version" - {{ name }}.pl --version | grep '{{ version }}' - {{ name }}-report.pl --version | grep '{{ version }}' - {{ name }}.pl --help @@ -65,3 +67,9 @@ about: license: GPL2 license_file: LICENSE summary: Reads to report pipeline for bacterial isolate NGS data + +extra: + skip-lints: + - missing_hash + - uses_vcs_url + - should_be_noarch_generic diff --git a/recipes/nvc/0.0.3/build.sh b/recipes/nvc/0.0.3/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/nvc/0.0.3/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/nvc/0.0.3/meta.yaml b/recipes/nvc/0.0.3/meta.yaml deleted file mode 100644 index 4320defbb7749..0000000000000 --- a/recipes/nvc/0.0.3/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -package: - name: nvc - version: "0.0.3" - -source: - url: https://pypi.python.org/packages/8a/1d/8632b9c34be231ece0b6671bbb2d3b536c5248be282e8d8ce65c428d0556/nvc-0.0.3.tar.gz - md5: 1d0c48b59888f24076db47b6fe16573b - -build: - skip: True # [not py27] - number: 1 - -requirements: - host: - - python - - setuptools - - numpy - - pybamparser ==0.0.3 - - pybamtools ==0.0.3 - - run: - - python - - numpy - - pybamparser ==0.0.3 - - pybamtools ==0.0.3 - -test: - commands: - - naive_variant_caller.py --help - -about: - home: https://github.com/blankenberg/nvc - license: GNU General Public License v2 (GPLv2) - summary: 'The Naive Variant Caller' - license_family: GPL2 diff --git a/recipes/nvc/build.sh b/recipes/nvc/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/nvc/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/nvc/meta.yaml b/recipes/nvc/meta.yaml index 3e8d27c2cef13..77faf25305df1 100644 --- a/recipes/nvc/meta.yaml +++ b/recipes/nvc/meta.yaml @@ -7,19 +7,16 @@ source: md5: 59a82e9463c5a624dc9cc78b40b3b575 build: - skip: True # [not py27] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - pybamparser ==0.0.3 - - pybamtools ==0.0.4 - + - python <3 + - pip run: - - python + - python <3 - numpy - pybamparser ==0.0.3 - pybamtools ==0.0.4 diff --git a/recipes/obitools/1.0.010/build.sh b/recipes/obitools/1.0.010/build.sh deleted file mode 100644 index f341bce6fcf96..0000000000000 --- a/recipes/obitools/1.0.010/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/sh -$PYTHON setup.py install diff --git a/recipes/obitools/1.0.010/extractreads.patch b/recipes/obitools/1.0.010/extractreads.patch deleted file mode 100644 index 425589f268d53..0000000000000 --- a/recipes/obitools/1.0.010/extractreads.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- src/extractreads.py.bak 2014-09-19 13:18:24.000000000 +0200 -+++ src/extractreads.py 2017-03-20 14:55:55.253800815 +0100 -@@ -1,3 +1,4 @@ -+#!/usr/local/bin/python - ''' - Created on 9 juin 2012 - diff --git a/recipes/obitools/1.0.010/extractreads2.patch b/recipes/obitools/1.0.010/extractreads2.patch deleted file mode 100644 index 7fc1957741f56..0000000000000 --- a/recipes/obitools/1.0.010/extractreads2.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- src/extractreads2.py.bak 2014-09-19 13:18:26.000000000 +0200 -+++ src/extractreads2.py 2017-03-20 14:55:49.797716366 +0100 -@@ -1,3 +1,4 @@ -+#!/usr/local/bin/python - ''' - Created on 9 juin 2012 - diff --git a/recipes/obitools/1.0.010/meta.yaml b/recipes/obitools/1.0.010/meta.yaml deleted file mode 100644 index e69779f9f9d1e..0000000000000 --- a/recipes/obitools/1.0.010/meta.yaml +++ /dev/null @@ -1,69 +0,0 @@ -package: - name: obitools - version: "1.0.010" - -source: - url: https://pypi.python.org/packages/00/33/f2774566fc1c661dcea4015f5423817d39b0dff2a3e3151108cf9100275b/OBITools-1.0.010.tar.gz - md5: 28695dd1334d0b7a4717df64817ef3dd - sha1: ae56828d2b08de8264056ae533ed41f6945c7be8 - sha256: 63766b4543f1e5871cf306811fc06dfaec2928445693e8f1c2768d578daed0e2 - patches: - - extractreads.patch - - extractreads2.patch - -build: - number: 2 - skip: True # [not py27 or osx] - -requirements: - host: - - python - - cython 0.21.* - - setuptools - - sphinx >=1.2.0 - - virtualenv >=1.11.0 - - wheel >=0.24.0 - run: - - python - - esmre - - xorg-libx11 - - xorg-libxau - -test: - commands: - - ali2consensus -h - - ecodbtaxstat -h - - ecotag -h - - ecotaxspecificity -h - - ecotaxstat -h - - ecodbtaxstat -h - - extractreads -h - - extractreads2 -h - - illuminapairedend -h - - ngsfilter -h - - obiaddtaxids -h - - obiannotate -h - - obiclean -h - - obicomplement -h - - obiconvert -h - - obicount -h - - obicut -h - - obidistribute -h - - obigrep -h - - obihead -h - - obijoinpairedend -h - - obisample -h - - obiselect -h - - obisort -h - - obisplit -h - - obistat -h - - obitab -h - - obitail -h - - obitaxonomy -h - - obiuniq -h - - oligotag -h - -about: - home: http://metabarcoding.org/obitools - license: CeCILL-V2 - summary: "The OBITools package is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information" diff --git a/recipes/obitools/1.2.10/build.sh b/recipes/obitools/1.2.10/build.sh deleted file mode 100644 index f341bce6fcf96..0000000000000 --- a/recipes/obitools/1.2.10/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/sh -$PYTHON setup.py install diff --git a/recipes/obitools/1.2.10/meta.yaml b/recipes/obitools/1.2.10/meta.yaml deleted file mode 100644 index 16451626c853a..0000000000000 --- a/recipes/obitools/1.2.10/meta.yaml +++ /dev/null @@ -1,73 +0,0 @@ -package: - name: obitools - version: "1.2.10" - -source: - url: https://pypi.python.org/packages/c6/24/8145846aed626414b19073c95bcf323304206d302e7e8e3e0831eed993dc/OBITools-1.2.10.tar.gz - md5: 4e1f8a39a304224f5c877f7afb845bcd - sha1: cb49f1cc73eef5d97110aa092b78f9143f113249 - sha256: ffa158a31d1bc01ca0ee9b62a27654fc88a01e7fe0a18984f4bbb8a1a72b1f5e - patches: - - extractreads.patch - - extractreads2.patch - -build: - number: 2 - skip: True # [not py27 or osx] - -requirements: - host: - - python - - cython >=0.24 - - setuptools - - sphinx >=1.2.0 - - virtualenv >=1.11.0 - - wheel >=0.24.0 - run: - - python - - esmre - - ipython >=3.0.0 - - xorg-libx11 - - xorg-libxau - -test: - commands: - - ali2consensus -h - - ecodbtaxstat -h - - ecotag -h - - ecotaxspecificity -h - - ecotaxstat -h - - extractreads -h - - extractreads2 -h - - illuminapairedend -h - - ngsfilter -h - - obiaddtaxids -h - - obiannotate -h - - obiclean -h - - obicomplement -h - - obiconvert -h - - obicount -h - - obicut -h - - obidistribute -h - - obiextract -h - - obigrep -h - - obihead -h - - obijoinpairedend -h - - obipr2 -h - - obisample -h - - obiselect -h - - obisilva -h - - obisort -h - - obisplit -h - - obistat -h - - obisubset -h - - obitab -h - - obitail -h - - obitaxonomy -h - - obiuniq -h - - oligotag -h - -about: - home: http://metabarcoding.org/obitools - license: CeCILL-V2 - summary: "The OBITools package is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information" diff --git a/recipes/obitools/1.2.11/build.sh b/recipes/obitools/1.2.11/build.sh deleted file mode 100644 index f341bce6fcf96..0000000000000 --- a/recipes/obitools/1.2.11/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/sh -$PYTHON setup.py install diff --git a/recipes/obitools/1.2.11/extractreads.patch b/recipes/obitools/1.2.11/extractreads.patch deleted file mode 100644 index 583a62597baef..0000000000000 --- a/recipes/obitools/1.2.11/extractreads.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- src/extractreads.py.bak 2015-06-01 12:25:20.000000000 +0200 -+++ src/extractreads.py 2017-03-20 15:16:15.305397545 +0100 -@@ -1,3 +1,4 @@ -+#!/usr/local/bin/python - ''' - Created on 9 juin 2012 - diff --git a/recipes/obitools/1.2.11/extractreads2.patch b/recipes/obitools/1.2.11/extractreads2.patch deleted file mode 100644 index 9dbd44390fc8c..0000000000000 --- a/recipes/obitools/1.2.11/extractreads2.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- src/extractreads2.py.bak 2015-06-01 12:25:20.000000000 +0200 -+++ src/extractreads2.py 2017-03-20 15:16:21.637497364 +0100 -@@ -1,3 +1,4 @@ -+#!/usr/local/bin/python - ''' - Created on 9 juin 2012 - diff --git a/recipes/obitools/1.2.10/extractreads.patch b/recipes/obitools/extractreads.patch similarity index 100% rename from recipes/obitools/1.2.10/extractreads.patch rename to recipes/obitools/extractreads.patch diff --git a/recipes/obitools/1.2.10/extractreads2.patch b/recipes/obitools/extractreads2.patch similarity index 100% rename from recipes/obitools/1.2.10/extractreads2.patch rename to recipes/obitools/extractreads2.patch diff --git a/recipes/obitools/1.2.11/meta.yaml b/recipes/obitools/meta.yaml similarity index 94% rename from recipes/obitools/1.2.11/meta.yaml rename to recipes/obitools/meta.yaml index dfaa4f2ab28d9..d21ec45df4faf 100644 --- a/recipes/obitools/1.2.11/meta.yaml +++ b/recipes/obitools/meta.yaml @@ -14,8 +14,11 @@ source: build: number: 1 skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - python - cython >=0.24 diff --git a/recipes/ogdf/meta.yaml b/recipes/ogdf/meta.yaml index bafbb001f124f..3697f2eac0fd0 100644 --- a/recipes/ogdf/meta.yaml +++ b/recipes/ogdf/meta.yaml @@ -14,10 +14,17 @@ build: requirements: build: - {{ compiler('c') }} + host: - python >=2.7,<3 run: + - python >=2.7,<3 about: home: http://http://ogdf.net/doku.php license: GPLv3 summary: The Open Graph Drawing Framework is a self-contained C++ class library for the automatic layout of diagrams. + +extra: + skip-lints: + - missing_tests + - should_not_be_noarch_source diff --git a/recipes/oligotyping/2.0/build.sh b/recipes/oligotyping/2.0/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/oligotyping/2.0/build.sh +++ /dev/null @@ -1,9 +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/oligotyping/2.0/meta.yaml b/recipes/oligotyping/2.0/meta.yaml index 1fb5902942a37..ed86428f7122f 100644 --- a/recipes/oligotyping/2.0/meta.yaml +++ b/recipes/oligotyping/2.0/meta.yaml @@ -8,19 +8,16 @@ source: build: number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python skip: True # [not py27 or osx] requirements: host: - - python - - setuptools - - matplotlib - - biopython - - scipy - - django - + - python <3 + - pip run: - - python + - python <3 - matplotlib - biopython - scipy diff --git a/recipes/oligotyping/build.sh b/recipes/oligotyping/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/oligotyping/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/oligotyping/meta.yaml b/recipes/oligotyping/meta.yaml index b49f0dea226db..62e169bde2d6b 100644 --- a/recipes/oligotyping/meta.yaml +++ b/recipes/oligotyping/meta.yaml @@ -7,12 +7,13 @@ source: md5: ac5385ec5bd1103ec50b262e463e5990 build: - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python number: 1 requirements: host: - - python + - python <3 - setuptools - matplotlib - biopython @@ -20,7 +21,7 @@ requirements: - django run: - - python + - python <3 - matplotlib - biopython - scipy diff --git a/recipes/oncotator/meta.yaml b/recipes/oncotator/meta.yaml index a2fcc3bd311b6..b927206a6521c 100644 --- a/recipes/oncotator/meta.yaml +++ b/recipes/oncotator/meta.yaml @@ -12,19 +12,21 @@ source: build: number: 1 - noarch: python + skip: True # [py3k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" requirements: + build: + - {{ compiler('c') }} host: - pip - - python <3 + - python - numpy ==1.11.0 + - cython ==0.24 - pyvcf ==0.6.8 run: - - python <3 + - python - biopython ==1.66 - - cython ==0.24 - numpy ==1.11.0 - pandas ==0.18.0 - bcbio-gff ==0.6.2 diff --git a/recipes/ont-tombo/build.sh b/recipes/ont-tombo/build.sh deleted file mode 100644 index 4899c226c8dd0..0000000000000 --- a/recipes/ont-tombo/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - -# 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/ont-tombo/meta.yaml b/recipes/ont-tombo/meta.yaml index dc54502f31c37..1e134c0eed99d 100644 --- a/recipes/ont-tombo/meta.yaml +++ b/recipes/ont-tombo/meta.yaml @@ -14,11 +14,14 @@ build: entry_points: - tombo = tombo.__main__:main number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - python - - setuptools >=18.0 + - pip - h5py - rpy2 # [py3k] - rpy2 <=2.8.6 # [not py3k] @@ -40,7 +43,6 @@ requirements: - rpy2 <=2.8.6 # [not py3k] - numpy - scipy - - cython - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/openbabel/2.3.2/build.sh b/recipes/openbabel/2.3.2/build.sh deleted file mode 100644 index e92fc504c2600..0000000000000 --- a/recipes/openbabel/2.3.2/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/sh - -#strictly use anaconda build environment -CC=${PREFIX}/bin/gcc -CXX=${PREFIX}/bin/g++ - -cmake . -DPYTHON_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=$PREFIX -make -make install diff --git a/recipes/openbabel/2.3.2/meta.yaml b/recipes/openbabel/2.3.2/meta.yaml deleted file mode 100644 index 11ad92fde7bae..0000000000000 --- a/recipes/openbabel/2.3.2/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -about: - home: http://openbabel.org - license: GPL - summary: 'Open Babel is a chemical toolbox designed to speak the many languages - of chemical data. It''s an open, collaborative project allowing anyone to search, - convert, analyze, or store data from molecular modeling, chemistry, solid-state - materials, biochemistry, or related areas.' - -build: - skip: True # [not py27 or osx] - number: 3 - -package: - name: openbabel - version: 2.3.2 - -requirements: - build: - - {{ compiler('cxx') }} - - cmake - host: - - python - - eigen - - libxml2 - - zlib - - cairo - run: - - python - - zlib - -source: - sha256: 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 - url: http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz - -test: - commands: - - obabel --help diff --git a/recipes/openbabel/2.4.1/372.patch b/recipes/openbabel/2.4.1/372.patch deleted file mode 100644 index c3b60b1bbddaf..0000000000000 --- a/recipes/openbabel/2.4.1/372.patch +++ /dev/null @@ -1,57 +0,0 @@ -From 92f4646d5cbf8d3291c66f9bff7ae61b6d535763 Mon Sep 17 00:00:00 2001 -From: Hector Mtz-Seara -Date: Thu, 2 Feb 2017 17:00:58 +0100 -Subject: [PATCH 1/2] Fix bug #368: Python3.6 openbabel: No module named - 'DLFCN' - -The DLFCN module has been removed from python 3.6, as it is not -documented. Same funtionality can be achive with the os module -that makes available the os.RTLD_GLOBAL variable for dlopen() ---- - scripts/CMakeLists.txt | 7 ++----- - 1 file changed, 2 insertions(+), 5 deletions(-) - -diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt -index e98eb16..6c096d0 100644 ---- a/scripts/CMakeLists.txt -+++ b/scripts/CMakeLists.txt -@@ -81,11 +81,8 @@ if (DO_PYTHON_BINDINGS) - COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i - COMMAND ${CMAKE_COMMAND} -E echo "import sys" > ob.py - COMMAND ${CMAKE_COMMAND} -E echo "if sys.platform.find('linux'\) != -1:" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " import dl" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py -+ COMMAND ${CMAKE_COMMAND} -E echo " import os" >> ob.py -+ COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | os.RTLD_GLOBAL)" >> ob.py - COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py - COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py - COMMAND ${CMAKE_COMMAND} -E remove ob.py - -From 776867aa63c389f3140053f3afd4a0ad8a3c58a7 Mon Sep 17 00:00:00 2001 -From: Hector Mtz-Seara -Date: Fri, 3 Feb 2017 08:15:43 +0100 -Subject: [PATCH 2/2] Usage of ctypes module for RTLD_GLOBAL to achieve - python2/3 compatibility - ---- - scripts/CMakeLists.txt | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt -index 6c096d0..4e4ec44 100644 ---- a/scripts/CMakeLists.txt -+++ b/scripts/CMakeLists.txt -@@ -81,8 +81,8 @@ if (DO_PYTHON_BINDINGS) - COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i - COMMAND ${CMAKE_COMMAND} -E echo "import sys" > ob.py - COMMAND ${CMAKE_COMMAND} -E echo "if sys.platform.find('linux'\) != -1:" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " import os" >> ob.py -- COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | os.RTLD_GLOBAL)" >> ob.py -+ COMMAND ${CMAKE_COMMAND} -E echo " import ctypes" >> ob.py -+ COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | ctypes.RTLD_GLOBAL)" >> ob.py - COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py - COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py - COMMAND ${CMAKE_COMMAND} -E remove ob.py diff --git a/recipes/openbabel/2.4.1/build.sh b/recipes/openbabel/2.4.1/build.sh deleted file mode 100644 index 5037a058c95c3..0000000000000 --- a/recipes/openbabel/2.4.1/build.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash -if [ `uname` == Darwin ]; then - SO_EXT='dylib' -else - SO_EXT='so' -fi - -PYTHON_INCLUDE_DIR=$($PYTHON -c 'import distutils.sysconfig, sys; sys.stdout.write(distutils.sysconfig.get_python_inc())') -PYTHON_LIBRARY=$($PYTHON -c 'from distutils.sysconfig import get_config_var; import os, sys; sys.stdout.write(os.path.join(get_config_var("LIBDIR"), get_config_var("LDLIBRARY")))') - -cmake -DCMAKE_INSTALL_PREFIX="$PREFIX" \ - -DCMAKE_BUILD_TYPE=RELEASE \ - -DWITH_INCHI=ON \ - -DPYTHON_LIBRARY="$PYTHON_LIBRARY" \ - -DPYTHON_EXECUTABLE="$PYTHON" \ - -DPYTHON_INCLUDE_DIR="$PYTHON_INCLUDE_DIR" \ - -DPYTHON_BINDINGS=ON \ - -DLIBXML2_INCLUDE_DIR="$PREFIX/include" \ - -DLIBXML2_LIBRARIES="$PREFIX/lib/libxml2.${SO_EXT}" \ - -DZLIB_INCLUDE_DIR="$PREFIX/include" \ - -DZLIB_LIBRARY="$PREFIX/lib/libz.${SO_EXT}" \ - -DRUN_SWIG=ON - - -make -j${CPU_COUNT} -make install diff --git a/recipes/openbabel/2.4.1/fix_babel_test_paths.diff b/recipes/openbabel/2.4.1/fix_babel_test_paths.diff deleted file mode 100644 index 57af50703bb8d..0000000000000 --- a/recipes/openbabel/2.4.1/fix_babel_test_paths.diff +++ /dev/null @@ -1,23 +0,0 @@ -This is to fix up the python scripts that test the various openbabel -executables. They were looking for the executables relative to the -testing folder, under the assumption they were part of the usual -cmake, make, ctest, suite. But we instead want to test the binaries that -we just installed somewhere else (eg. the anaconda _test environment). - -diff --git a/test/testbabel.py b/test/testbabel.py -index 5def841..ccf6bbc 100644 ---- test/testbabel.py -+++ test/testbabel.py -@@ -60,6 +60,12 @@ def executable(name): - if sys.platform == "win32": - suffix = ".exe" - folder = os.path.join(folder, "Release") -+ # For anaconda testing purposes, the correct binary -+ # that we wish to test ought to be on the path, -+ from distutils import spawn -+ path_to_exe = spawn.find_executable(name) -+ return path_to_exe -+ # instead of assuming it's somewhere relative to the testing folder: - return os.path.join("..", folder, name + suffix) - - def log(text): \ No newline at end of file diff --git a/recipes/openbabel/2.4.1/fix_data_path.diff b/recipes/openbabel/2.4.1/fix_data_path.diff deleted file mode 100644 index a682218a5c800..0000000000000 --- a/recipes/openbabel/2.4.1/fix_data_path.diff +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/src/tokenst.cpp b/src/tokenst.cpp -index 2ab6454..badfade 100644 ---- src/tokenst.cpp -+++ src/tokenst.cpp -@@ -206,7 +206,13 @@ namespace OpenBabel - string file; - const char* datadir = getenv(envvar.c_str()); - if(!datadir) -+ { - datadir = BABEL_DATADIR; -+ } -+ //puts(datadir); -+ std::string tempstring = string(datadir); -+ datadir = tempstring.c_str(); -+ //puts(datadir); - - // check the subdirectory for this version number - file = datadir; \ No newline at end of file diff --git a/recipes/openbabel/2.4.1/fix_libinchi_cmakelists.diff b/recipes/openbabel/2.4.1/fix_libinchi_cmakelists.diff deleted file mode 100644 index d4d4c880f33a2..0000000000000 --- a/recipes/openbabel/2.4.1/fix_libinchi_cmakelists.diff +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/formats/libinchi/CMakeLists.txt b/src/formats/libinchi/CMakeLists.txt -index 2a0be6b5..e72083c9 100644 ---- a/src/formats/libinchi/CMakeLists.txt -+++ b/src/formats/libinchi/CMakeLists.txt -@@ -6,7 +6,7 @@ set(INCHI_PATCH_VER 1) - file(GLOB inchi_srcs "*.c") - - if(NOT WIN32) -- set(libs ${libs} c) -+ set(libs ${libs} c m) - endif(NOT WIN32) - - include_directories(${openbabel_SOURCE_DIR}/include/inchi) diff --git a/recipes/openbabel/2.4.1/fix_library_path_search.diff b/recipes/openbabel/2.4.1/fix_library_path_search.diff deleted file mode 100644 index c76df9d7a1ff0..0000000000000 --- a/recipes/openbabel/2.4.1/fix_library_path_search.diff +++ /dev/null @@ -1,30 +0,0 @@ -Devised by Richard West in an attempt to fix the way paths -are manipulated when making anaconda packages. See -https://github.com/conda/conda-recipes/pull/310#issuecomment-106533773 - -diff --git a/src/dlhandler_unix.cpp b/src/dlhandler_unix.cpp -index 5bffac3..bc66235 100644 ---- src/dlhandler_unix.cpp -+++ src/dlhandler_unix.cpp - -@@ -79,7 +79,19 @@ int DLHandler::findFiles (std::vector & file_list, - char buffer[BUFF_SIZE]; - - if (!path.empty()) -- paths.push_back(path); -+ { -+ strncpy(buffer, path.c_str(), BUFF_SIZE - 1); -+ // add a trailing NULL just in case -+ buffer[BUFF_SIZE - 1] = '\0'; -+ OpenBabel::tokenize(vs, buffer, "\r\n:"); -+ if (!vs.empty()) -+ { -+ for (unsigned int i = 0; i < vs.size(); ++i) { -+ paths.push_back(vs[i]); -+ } -+ } -+ } -+ - - if (getenv("BABEL_LIBDIR") != NULL) - { diff --git a/recipes/openbabel/2.4.1/meta.yaml b/recipes/openbabel/2.4.1/meta.yaml deleted file mode 100644 index a4a7fd481309e..0000000000000 --- a/recipes/openbabel/2.4.1/meta.yaml +++ /dev/null @@ -1,57 +0,0 @@ - -package: - name: openbabel - version: 2.4.1 - -source: - url: https://github.com/openbabel/openbabel/archive/openbabel-2-4-1.zip - sha1: 6fefb2355601b665bea5840fe8e6f95bd48023c9 - - patches: - - fix_library_path_search.diff - - fix_data_path.diff - - fix_babel_test_paths.diff - - fix_libinchi_cmakelists.diff - - 372.patch - -build: - # https://bugs.archlinux.org/task/52409 - skip: true # [not py2k and not py35] - number: 5 - detect_binary_files_with_prefix: true - -requirements: - build: - - {{ compiler('c') }} - - cmake - host: - - zlib - - swig - - eigen - - bzip2 - - python - - libxml2 - - cairo # [linux] - run: - - python - - zlib - - libxml2 - - cairo # [linux] - - xorg-libxau - - xorg-libxdmcp - - xorg-libxext - - xorg-libxrender - - xorg-libsm -test: - imports: - - openbabel - - pybel - commands: - - obabel --help - - obabel -:'c1ccccc1' --gen3d -omol2 - - obabel -:'c1ccccc1' --gen3d -oinchi - -about: - home: http://www.openbabel.org/ - license: GPLv2 - summary: "A chemical toolbox designed to speak the many languages of chemical data" diff --git a/recipes/openbabel/2.4.1/run_test.py b/recipes/openbabel/2.4.1/run_test.py deleted file mode 100644 index fe494e8f427a0..0000000000000 --- a/recipes/openbabel/2.4.1/run_test.py +++ /dev/null @@ -1,15 +0,0 @@ -# tests for openbabel in python - -# A test of some smiple SMILES manipulation -# by Richard West -# Three SMILES, first two obviously the same, third one a resonance isomer. -smis=['[CH2]C=CCO', 'C([CH2])=CCO','C=C[CH]CO'] - -import pybel -canonicals = [pybel.readstring("smi", smile).write("can").strip() for smile in smis] -assert len(canonicals) == 3 -assert len(set(canonicals)) == 2 -# go via InChI to recognize resonance isomer -inchis = [pybel.readstring("smi", smile).write("inchi").strip() for smile in smis] -canonicals = [pybel.readstring("inchi", inchi).write("can").strip() for inchi in inchis] -assert len(set(canonicals)) == 1 diff --git a/recipes/optbuild/build.sh b/recipes/optbuild/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/optbuild/build.sh +++ /dev/null @@ -1,9 +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/optbuild/meta.yaml b/recipes/optbuild/meta.yaml index 16b300429936d..c7742b8d85070 100644 --- a/recipes/optbuild/meta.yaml +++ b/recipes/optbuild/meta.yaml @@ -9,14 +9,12 @@ source: build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - autolog - - six - + - pip run: - python - autolog diff --git a/recipes/optitype/1.2.1/meta.yaml b/recipes/optitype/1.2.1/meta.yaml index 344ec054bef41..7a2f140c2491f 100644 --- a/recipes/optitype/1.2.1/meta.yaml +++ b/recipes/optitype/1.2.1/meta.yaml @@ -3,17 +3,17 @@ package: version: '1.2.1' build: number: 1 - skip: True # [not py27 or osx] + noarch: python source: - fn: OptiType-1.2.1.tar.gz url: https://github.com/FRED-2/OptiType/archive/v1.2.1.tar.gz md5: 3e3e3e2675d24ce672f667b5c253161c requirements: - build: - - python + host: + - python <3 + - pip run: - - python + - python <3 - numpy - pyomo - hdf5 diff --git a/recipes/optitype/meta.yaml b/recipes/optitype/meta.yaml index 468a2a8d2eb70..a5ae104ba3f33 100644 --- a/recipes/optitype/meta.yaml +++ b/recipes/optitype/meta.yaml @@ -5,8 +5,9 @@ package: version: {{ version }} build: + noarch: python number: 3 - skip: True # [not py27 or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/FRED-2/OptiType/archive/v{{ version }}.tar.gz @@ -14,9 +15,10 @@ source: requirements: host: - - python + - python <3 + - pip run: - - python + - python <3 - numpy =1.15.4 - pyomo - hdf5 @@ -38,4 +40,3 @@ about: home: https://github.com/FRED-2/OptiType license: BSD summary: Precision HLA typing from next-generation sequencing data - diff --git a/recipes/optplus/build.sh b/recipes/optplus/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/optplus/build.sh +++ /dev/null @@ -1,9 +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/optplus/meta.yaml b/recipes/optplus/meta.yaml index 6c3d8c879ced5..2058a61db9a89 100644 --- a/recipes/optplus/meta.yaml +++ b/recipes/optplus/meta.yaml @@ -9,13 +9,12 @@ source: build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - six - + - pip run: - python - six diff --git a/recipes/orthomcl/meta.yaml b/recipes/orthomcl/meta.yaml index 29f436c3a0c8f..7332c711dde43 100644 --- a/recipes/orthomcl/meta.yaml +++ b/recipes/orthomcl/meta.yaml @@ -3,6 +3,7 @@ package: version: 2.0.9 build: + noarch: generic number: 3 source: diff --git a/recipes/p7zip/build.sh b/recipes/p7zip/build.sh deleted file mode 100755 index c82c39ee2b5d8..0000000000000 --- a/recipes/p7zip/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/lib - -make all_test - -sed -i "s|#! /bin/sh|#!/bin/bash|" install.sh -sed -i "s|DEST_HOME=.*|DEST_HOME=$PREFIX|" install.sh -./install.sh - -rm -r $PREFIX/man -rm -r $PREFIX/share - diff --git a/recipes/p7zip/meta.yaml b/recipes/p7zip/meta.yaml deleted file mode 100644 index 50a3cc2b15d51..0000000000000 --- a/recipes/p7zip/meta.yaml +++ /dev/null @@ -1,28 +0,0 @@ -package: - name: p7zip - version: "15.09" - -build: - number: 4 - skip: True # [osx] - -source: - url: http://iweb.dl.sourceforge.net/project/p7zip/p7zip/15.09/p7zip_15.09_src_all.tar.bz2 - md5: ab69f4f13ba0ec57eca2cf4c9edd9678 - -requirements: - build: - - {{ compiler('cxx') }} - -test: - commands: - - touch xxx - - 7z a xxx.7z xxx - - 7za a xxx.7z xxx - - 7zr a xxx.7z xxx - -about: - home: http://sourceforge.net/projects/p7zip/ - summary: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org ) for Unix. - license: LGPLv2 - diff --git a/recipes/pacbio_falcon/meta.yaml b/recipes/pacbio_falcon/meta.yaml index 4754aef44b97f..4fd6da61f0d13 100644 --- a/recipes/pacbio_falcon/meta.yaml +++ b/recipes/pacbio_falcon/meta.yaml @@ -15,17 +15,17 @@ source: md5: be4a225262ee4bd9729b6b7e81a83615 build: + noarch: python number: 1 - skip: True # [py3k] requirements: host: - - python + - python <3 - setuptools - pypeflow - networkx run: - - python + - python <3 - pypeflow - rdflib - rdfextras diff --git a/recipes/pal_finder/meta.yaml b/recipes/pal_finder/meta.yaml index f0fce3ea4eb8a..b9b22062cff0c 100644 --- a/recipes/pal_finder/meta.yaml +++ b/recipes/pal_finder/meta.yaml @@ -7,6 +7,7 @@ source: url: http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz build: + noarch: generic number: 2 requirements: diff --git a/recipes/pancake/build.sh b/recipes/pancake/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pancake/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/pancake/meta.yaml b/recipes/pancake/meta.yaml index 95f90b2bbebe0..57a2c9f0ca063 100644 --- a/recipes/pancake/meta.yaml +++ b/recipes/pancake/meta.yaml @@ -7,18 +7,16 @@ source: md5: 2bc2b40b6e46477aae5fc9ae4807dcef build: + noarch: python number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - biopython - + - python >=3 + - pip run: - - python + - python >=3 - numpy - biopython diff --git a/recipes/panphlan/1.2/meta.yaml b/recipes/panphlan/1.2/meta.yaml index 4f794bdfde493..4fe9e2d1226c4 100644 --- a/recipes/panphlan/1.2/meta.yaml +++ b/recipes/panphlan/1.2/meta.yaml @@ -11,19 +11,12 @@ source: url: https://bitbucket.org/CibioCM/panphlan/get/{{ version }}.tar.gz build: + noarch: generic number: 4 - skip: true # [osx] requirements: - host: - - python - - setuptools - - bowtie2 >=2.0.0 - - numpy - run: - python - - setuptools - bowtie2 >=2.0.0 - numpy - biopython diff --git a/recipes/panX/1.5.0/build.sh b/recipes/panx/1.5.0/build.sh similarity index 100% rename from recipes/panX/1.5.0/build.sh rename to recipes/panx/1.5.0/build.sh diff --git a/recipes/panX/1.5.0/meta.yaml b/recipes/panx/1.5.0/meta.yaml similarity index 94% rename from recipes/panX/1.5.0/meta.yaml rename to recipes/panx/1.5.0/meta.yaml index 7fbc15931dc5c..3408e85eb6143 100644 --- a/recipes/panX/1.5.0/meta.yaml +++ b/recipes/panx/1.5.0/meta.yaml @@ -13,13 +13,13 @@ source: - panx_sf_gain_loss.patch build: + noarch: generic number: 1 - skip: True # [not py27] requirements: host: run: - - python + - python <3 - biopython - numpy - scipy diff --git a/recipes/panX/1.5.0/panx_sf_gain_loss.patch b/recipes/panx/1.5.0/panx_sf_gain_loss.patch similarity index 100% rename from recipes/panX/1.5.0/panx_sf_gain_loss.patch rename to recipes/panx/1.5.0/panx_sf_gain_loss.patch diff --git a/recipes/panX/1.6.0/build.sh b/recipes/panx/1.6.0/build.sh similarity index 100% rename from recipes/panX/1.6.0/build.sh rename to recipes/panx/1.6.0/build.sh diff --git a/recipes/panX/1.6.0/meta.yaml b/recipes/panx/1.6.0/meta.yaml similarity index 94% rename from recipes/panX/1.6.0/meta.yaml rename to recipes/panx/1.6.0/meta.yaml index adcfc63ce1344..034922b4af1af 100644 --- a/recipes/panX/1.6.0/meta.yaml +++ b/recipes/panx/1.6.0/meta.yaml @@ -11,13 +11,13 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 - skip: True # [not py27] requirements: host: run: - - python + - python <3 - biopython - numpy - scipy diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 0c81052e7d341..09d8c8a526333 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -8,11 +8,10 @@ package: version: '{{version}}' source: - url: '{{base}}/v{{version}}/parsnp-Linux64-v{{version}}.tar.gz' # [linux] - sha256: '{{sha256linux}}' # [linux] - - url: '{{base}}/v{{version}}/parsnp-OSX64-v{{version}}.tar.gz' # [osx] - sha256: '{{sha256osx}}' # [osx] + - url: '{{base}}/v{{version}}/parsnp-Linux64-v{{version}}.tar.gz' # [linux] + sha256: '{{sha256linux}}' # [linux] + - url: '{{base}}/v{{version}}/parsnp-OSX64-v{{version}}.tar.gz' # [osx] + sha256: '{{sha256osx}}' # [osx] build: number: 0 @@ -29,3 +28,7 @@ about: license: "custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE" summary: Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/pasa/meta.yaml b/recipes/pasa/meta.yaml index d99b6107b08d9..318a421e12139 100644 --- a/recipes/pasa/meta.yaml +++ b/recipes/pasa/meta.yaml @@ -11,21 +11,17 @@ build: skip: True # [osx] source: - fn: PASApipeline-v{{ version }}.tar.gz url: https://github.com/PASApipeline/PASApipeline/releases/download/{{ name }}-v{{ version }}/PASApipeline-v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: build: - - gcc # [not osx] - - llvm # [osx] - + - {{ compiler('c') }} run: - blat - cdbtools - fasta3 - gmap - - libgcc # [not osx] - lighttpd - samtools - transdecoder >=5.2.0 diff --git a/recipes/pathoscope/build.sh b/recipes/pathoscope/build.sh deleted file mode 100755 index c0f405b64c876..0000000000000 --- a/recipes/pathoscope/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -# Install using setuptools -$PYTHON setup.py install diff --git a/recipes/pathoscope/meta.yaml b/recipes/pathoscope/meta.yaml index 319ec0bde07d2..aea9e724589d2 100644 --- a/recipes/pathoscope/meta.yaml +++ b/recipes/pathoscope/meta.yaml @@ -1,26 +1,22 @@ -build: - number: 0 - skip: True # [not py27] - -about: - home: 'https://github.com/PathoScope/PathoScope' - license: GPLv3 - summary: Species identification and strain attribution with unassembled sequencing data - package: name: pathoscope version: 2.0.7 +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + source: url: https://github.com/PathoScope/PathoScope/archive/v2.0.7.tar.gz sha256: 59e473d5671b310da9bf9a541b78d15148f279df0635b016503a861905f11bb0 requirements: host: - - python - - setuptools + - python <3 + - pip run: - - python + - python <3 - samtools <1.0 - bowtie2 @@ -31,6 +27,11 @@ test: - pathoscope MAP -h &> /dev/null - pathoscope ID -h &> /dev/null - pathoscope REP -h &> /dev/null + +about: + home: 'https://github.com/PathoScope/PathoScope' + license: GPLv3 + summary: Species identification and strain attribution with unassembled sequencing data extra: maintainers: diff --git a/recipes/pathwaymatcher/meta.yaml b/recipes/pathwaymatcher/meta.yaml index ac6a160a683c0..90034f90cadc8 100644 --- a/recipes/pathwaymatcher/meta.yaml +++ b/recipes/pathwaymatcher/meta.yaml @@ -2,12 +2,12 @@ {% set version = "1.9.1" %} package: - name: pathwaymatcher - version: {{ version }} + name: pathwaymatcher + version: {{ version }} source: - url: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/releases/download/{{ version }}/{{ name }}.jar - sha256: d012cefe842f3c13b8c9bd8c6106224d7d57eeb945b0ee9090892a4109c29c91 + url: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/releases/download/{{ version }}/{{ name }}.jar + sha256: d012cefe842f3c13b8c9bd8c6106224d7d57eeb945b0ee9090892a4109c29c91 build: noarch: generic @@ -20,22 +20,16 @@ requirements: - python test: - commands: + commands: - echo -e "CFTR\nTGFB1\nFCGR2A\nDCTN4\nSCNN1B\nSCNN1G\nSCNN1A\nTNFRSF1A\nCLCA4\nSTX1A\nCXCL8" > genes.txt - pathwaymatcher src.main.java.no.uib.pap.pathwaymatcher.PathwayMatcher -g -gg -i genes.txt - pathwaymatcher.py -g -gg -i genes.txt about: - home: https://github.com/PathwayAnalysisPlatform/PathwayMatcher - license: Apache License, Version 2.0 - summary: | - PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome. - -about: - home: https://github.com/PathwayAnalysisPlatform/PathwayMatcher - license: Apache License, Version 2.0 - summary: | - PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome. + home: https://github.com/PathwayAnalysisPlatform/PathwayMatcher + license: Apache License, Version 2.0 + summary: | + PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome. extra: notes: | diff --git a/recipes/pauda/meta.yaml b/recipes/pauda/meta.yaml index f5c75c6eacbe3..a4193578fada3 100644 --- a/recipes/pauda/meta.yaml +++ b/recipes/pauda/meta.yaml @@ -7,12 +7,12 @@ source: sha256: 7c5feecc226c83f1da124cade547dbe497e939fb04f9927b131afcd66e1cfd81 build: + noarch: generic number: 1 - skip: True #[not linux] requirements: run: - - java-jdk + - openjdk - bowtie2 test: diff --git a/recipes/pb-assembly/meta.yaml b/recipes/pb-assembly/meta.yaml index a5702f93968f8..db74c7e15ede1 100644 --- a/recipes/pb-assembly/meta.yaml +++ b/recipes/pb-assembly/meta.yaml @@ -3,11 +3,8 @@ package: version: "0.0.6" build: number: 5 - script: echo noop - skip: True # [py27 or osx] + noarch: generic requirements: - build: - - python run: - python - pb-falcon>=0.3.0 diff --git a/recipes/pbalign/meta.yaml b/recipes/pbalign/meta.yaml index 8749afa2348e3..1926e6715bcb1 100644 --- a/recipes/pbalign/meta.yaml +++ b/recipes/pbalign/meta.yaml @@ -10,29 +10,16 @@ source: url: https://github.com/PacificBiosciences/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbalign - license: BSD-3-Clause-Clear - summary: Python wrapper for producing PBBAM valid alignments - -extra: - recipe-maintainers: - - pb-cdunn - - ylipacbio - - pb-dseifert - - mhsieh - build: - skip: True # [not py27] + noarch: python number: 0 requirements: host: - - python + - python <3 - setuptools run: - - python - - setuptools + - python <3 - pysam >=0.15.1 - pbcore >=1.6.5 - pbcommand >=1.1.1 @@ -43,3 +30,15 @@ requirements: test: commands: - pbalign -h + +about: + home: https://github.com/PacificBiosciences/pbalign + license: BSD-3-Clause-Clear + summary: Python wrapper for producing PBBAM valid alignments + +extra: + recipe-maintainers: + - pb-cdunn + - ylipacbio + - pb-dseifert + - mhsieh diff --git a/recipes/pbcommand/meta.yaml b/recipes/pbcommand/meta.yaml index 624594b0ff1a4..4465900da9189 100644 --- a/recipes/pbcommand/meta.yaml +++ b/recipes/pbcommand/meta.yaml @@ -10,25 +10,15 @@ source: url: https://github.com/PacificBiosciences/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: Library and Tools for interfacing with PacBio pbsmrtpipe workflow engine - -extra: - recipe-maintainers: - - pb-dseifert - - mhsieh - build: - skip: True # [not py27] + noarch: python number: 2 entry_points: - pbservice = pbcommand.services.cli:main requirements: host: - - python + - python <3 - setuptools - avro-python2 - requests @@ -36,7 +26,7 @@ requirements: - pytz - numpy >=1.15 run: - - python + - python <3 - avro-python2 - requests - iso8601 @@ -58,3 +48,13 @@ test: - tests commands: - pbservice --help + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: Library and Tools for interfacing with PacBio pbsmrtpipe workflow engine + +extra: + recipe-maintainers: + - pb-dseifert + - mhsieh diff --git a/recipes/pbcore/meta.yaml b/recipes/pbcore/meta.yaml index 98f30cd46dfdb..9563db6672a37 100644 --- a/recipes/pbcore/meta.yaml +++ b/recipes/pbcore/meta.yaml @@ -10,21 +10,13 @@ source: url: https://github.com/PacificBiosciences/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: A Python library for reading and writing PacBio data files - -extra: - recipe-maintainers: - - pb-dseifert - - mhsieh - build: skip: True # [not py27] number: 0 requirements: + build: + - {{ compiler('c') }} host: - python - setuptools @@ -34,7 +26,6 @@ requirements: - pysam >=0.15.1 run: - python - - cython - numpy >=1.15 - h5py >=2.7.0 - pysam >=0.15.1 @@ -54,3 +45,13 @@ test: - nose - pyxb - sphinx + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: A Python library for reading and writing PacBio data files + +extra: + recipe-maintainers: + - pb-dseifert + - mhsieh diff --git a/recipes/pbcoretools/meta.yaml b/recipes/pbcoretools/meta.yaml index 1807051af591b..0e615da017874 100644 --- a/recipes/pbcoretools/meta.yaml +++ b/recipes/pbcoretools/meta.yaml @@ -10,21 +10,13 @@ source: url: https://github.com/PacificBiosciences/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: CLI tools and add-ons for PacBio's core APIs - -extra: - recipe-maintainers: - - pb-dseifert - - mhsieh - build: skip: True # [not py27] number: 4 requirements: + build: + - {{ compiler('c') }} host: - python - setuptools @@ -45,3 +37,13 @@ test: - bamSieve -h - dataset -h - pbvalidate -h + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: CLI tools and add-ons for PacBio's core APIs + +extra: + recipe-maintainers: + - pb-dseifert + - mhsieh diff --git a/recipes/pbdagcon/meta.yaml b/recipes/pbdagcon/meta.yaml index 4cc3f298de7f5..67f454bcc7afc 100644 --- a/recipes/pbdagcon/meta.yaml +++ b/recipes/pbdagcon/meta.yaml @@ -37,4 +37,4 @@ about: extra: skip-lints: - missing_hash - - uses_git_url + - uses_vcs_url diff --git a/recipes/pbh5tools/build.sh b/recipes/pbh5tools/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/pbh5tools/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/pbh5tools/meta.yaml b/recipes/pbh5tools/meta.yaml index 8ccccf9ab6a01..cf8d65ad1c9a3 100644 --- a/recipes/pbh5tools/meta.yaml +++ b/recipes/pbh5tools/meta.yaml @@ -12,6 +12,7 @@ source: build: skip: True # [not py27] number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: diff --git a/recipes/pbhoover/meta.yaml b/recipes/pbhoover/meta.yaml index aae2701a8cde0..f720c8c7b792d 100644 --- a/recipes/pbhoover/meta.yaml +++ b/recipes/pbhoover/meta.yaml @@ -9,12 +9,12 @@ source: sha256: b5d5a76c2c045c26acb3ac909dd5c0f4a7805b718a8ae0fca6ccb57b7e5edaeb build: + noarch: python number: 2 - skip: True # [not py27] requirements: host: - - python + - python <3 - setuptools - setuptools_scm - pbcore >=1.2.10 @@ -23,7 +23,7 @@ requirements: - pyvcf run: - - python + - python <3 - pbh5tools - tabix - bcftools diff --git a/recipes/pdfkit/build.sh b/recipes/pdfkit/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/pdfkit/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/pdfkit/meta.yaml b/recipes/pdfkit/meta.yaml index 35bab79d98476..be473b50ba725 100644 --- a/recipes/pdfkit/meta.yaml +++ b/recipes/pdfkit/meta.yaml @@ -1,23 +1,28 @@ -build: - number: 0 - skip: True # [osx] - package: name: pdfkit version: "0.6.1" + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + source: url: https://files.pythonhosted.org/packages/a1/98/6988328f72fe3be4cbfcb6cbfc3066a00bf111ca7821a83dd0ce56e2cf57/pdfkit-0.6.1.tar.gz sha256: ef1da35b78d534197e7ce4a604a4a190e9aa769e56634957535f3479a50d8cd1 + requirements: host: - - wkhtmltopdf + - pip - python run: - wkhtmltopdf - python + test: imports: - pdfkit + about: home: https://pypi.python.org/pypi/pdfkit license: MIT License diff --git a/recipes/ped_parser/1.6.5/build.sh b/recipes/ped_parser/1.6.5/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/ped_parser/1.6.5/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/ped_parser/1.6.5/meta.yaml b/recipes/ped_parser/1.6.5/meta.yaml index 6b5d37fd4d20a..34bf258456f96 100644 --- a/recipes/ped_parser/1.6.5/meta.yaml +++ b/recipes/ped_parser/1.6.5/meta.yaml @@ -1,12 +1,12 @@ -build: - number: 1 - # click needs to be patched in order to properly detect unicode in py3k - skip: true # [py3k or osx] - package: name: ped_parser version: "1.6.5" +build: + noarch: python + number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + source: url: https://pypi.python.org/packages/source/p/ped_parser/ped_parser-1.6.5.tar.gz md5: 1f404e131c3d210d32e6253ac500b200 @@ -14,13 +14,9 @@ source: requirements: host: - python - - setuptools - - pytest - - click - + - pip run: - python - - pytest - click test: diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index 2ef9b38832eab..c59c6aa3aa006 100644 --- a/recipes/ped_parser/meta.yaml +++ b/recipes/ped_parser/meta.yaml @@ -2,11 +2,6 @@ {% set version = "1.6.6" %} {% set sha256hash = "7ce955a5674815ff9383fd5d1e54181ddeadf1bd9c897cc45007edff4125e4fc" %} -build: - number: 1 - # click needs to be patched in order to properly detect unicode in py3k - skip: true # [py3k or osx] - package: name: {{ name }} version: {{ version }} @@ -15,13 +10,14 @@ source: url: https://pypi.python.org/packages/5d/ca/0ad16b9dd17f8115800ef08584bc6119a2ca05654dad456c285d5ca33c67/ped_parser-{{ version }}.tar.gz sha256: {{ sha256hash }} +build: + noarch: python + number: 1 + requirements: host: - python - setuptools - - pytest - - click - run: - python - pytest diff --git a/recipes/peddy/meta.yaml b/recipes/peddy/meta.yaml index 7e27b956533a0..475681cc6a1bf 100644 --- a/recipes/peddy/meta.yaml +++ b/recipes/peddy/meta.yaml @@ -12,11 +12,12 @@ source: build: noarch: python number: 1 - script: python setup.py install + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python + - pip run: - python - networkx diff --git a/recipes/pepnovo/meta.yaml b/recipes/pepnovo/meta.yaml index 3ba9d64a7e523..5dd9b71948bdc 100644 --- a/recipes/pepnovo/meta.yaml +++ b/recipes/pepnovo/meta.yaml @@ -20,6 +20,7 @@ test: about: home: http://proteomics.ucsd.edu/Software/PepNovo/ + license: BSD license_file: LICENSE summary: PepNovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data diff --git a/recipes/pepr/meta.yaml b/recipes/pepr/meta.yaml index 8e3d61f96ba0a..9815bd31450f7 100644 --- a/recipes/pepr/meta.yaml +++ b/recipes/pepr/meta.yaml @@ -1,8 +1,4 @@ {% set version = "1.1.24" %} - -build: - number: 1 - package: name: pepr version: {{ version }} @@ -13,6 +9,8 @@ source: patches: - setup.py.patch +build: + noarch: python entry_points: - PePr=PePr.PePr:argless_main - PePr-preprocess=PePr.PePr:pre_processing_module @@ -23,11 +21,6 @@ requirements: host: - python - setuptools - - numpy >=1.6.0 - - scipy >=0.14.0 - - pysam - - sharedmem - run: - python - numpy >=1.6.0 diff --git a/recipes/perl-aceperl/meta.yaml b/recipes/perl-aceperl/meta.yaml index 86620b9dace93..ab1d37d16545c 100644 --- a/recipes/perl-aceperl/meta.yaml +++ b/recipes/perl-aceperl/meta.yaml @@ -13,6 +13,7 @@ source: - makefile-options.patch build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-algorithm-dependency/meta.yaml b/recipes/perl-algorithm-dependency/meta.yaml index eeebd5dfb027d..5d369eecdebca 100644 --- a/recipes/perl-algorithm-dependency/meta.yaml +++ b/recipes/perl-algorithm-dependency/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-algorithm-diff/meta.yaml b/recipes/perl-algorithm-diff/meta.yaml index 8d67cf1a29f40..59f45f92ac1f3 100644 --- a/recipes/perl-algorithm-diff/meta.yaml +++ b/recipes/perl-algorithm-diff/meta.yaml @@ -7,6 +7,7 @@ source: md5: 0e8add21a641b8d66436df0c2024bf3b build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-algorithm-munkres/meta.yaml b/recipes/perl-algorithm-munkres/meta.yaml index ccedb5d8c6fa9..25a9dc3f880d6 100644 --- a/recipes/perl-algorithm-munkres/meta.yaml +++ b/recipes/perl-algorithm-munkres/meta.yaml @@ -7,6 +7,7 @@ source: md5: 56349287513f955002720c8e2523582b build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-aliased/meta.yaml b/recipes/perl-aliased/meta.yaml index 30be1a4699d3c..e8cd54cab6299 100644 --- a/recipes/perl-aliased/meta.yaml +++ b/recipes/perl-aliased/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-apache-test/meta.yaml b/recipes/perl-apache-test/meta.yaml index 53b81caeb557b..da307b2ffbc43 100644 --- a/recipes/perl-apache-test/meta.yaml +++ b/recipes/perl-apache-test/meta.yaml @@ -3,6 +3,7 @@ package: version: "1.40" build: + noarch: generic number: 1 source: diff --git a/recipes/perl-app-cpanminus/meta.yaml b/recipes/perl-app-cpanminus/meta.yaml index 46c44da06d973..203ec398bf273 100644 --- a/recipes/perl-app-cpanminus/meta.yaml +++ b/recipes/perl-app-cpanminus/meta.yaml @@ -10,6 +10,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-appconfig/meta.yaml b/recipes/perl-appconfig/meta.yaml index 11a25312c835b..64a366ffe00ce 100644 --- a/recipes/perl-appconfig/meta.yaml +++ b/recipes/perl-appconfig/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7747d9241561ed5567d5e134b8648707 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-archive-extract/meta.yaml b/recipes/perl-archive-extract/meta.yaml index 09737814e7f34..f4804d3c48734 100644 --- a/recipes/perl-archive-extract/meta.yaml +++ b/recipes/perl-archive-extract/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-archive-tar-wrapper/0.33/meta.yaml b/recipes/perl-archive-tar-wrapper/0.33/meta.yaml index 848ee385707f5..a21798b026d91 100644 --- a/recipes/perl-archive-tar-wrapper/0.33/meta.yaml +++ b/recipes/perl-archive-tar-wrapper/0.33/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-archive-tar/meta.yaml b/recipes/perl-archive-tar/meta.yaml index 6d5e9d0429a3c..17c483fa0f4bc 100644 --- a/recipes/perl-archive-tar/meta.yaml +++ b/recipes/perl-archive-tar/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 92783780731ab0c9247adf43e70f4801e8317e3915ea87e38b85c8f734e8fca2 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-archive-zip/meta.yaml b/recipes/perl-archive-zip/meta.yaml index 99805d0c6f45d..99c3b990d2c2f 100644 --- a/recipes/perl-archive-zip/meta.yaml +++ b/recipes/perl-archive-zip/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-array-compare/meta.yaml b/recipes/perl-array-compare/meta.yaml index 990b1d65d808a..8927bfc177a86 100644 --- a/recipes/perl-array-compare/meta.yaml +++ b/recipes/perl-array-compare/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-array-set/meta.yaml b/recipes/perl-array-set/meta.yaml index 999144aa7fe51..32d290e7f0465 100644 --- a/recipes/perl-array-set/meta.yaml +++ b/recipes/perl-array-set/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-array-utils/meta.yaml b/recipes/perl-array-utils/meta.yaml index 0d14edecdb7d6..fca7b29dec105 100644 --- a/recipes/perl-array-utils/meta.yaml +++ b/recipes/perl-array-utils/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-attribute-handlers/0.96/meta.yaml b/recipes/perl-attribute-handlers/0.96/meta.yaml index 3299755734bfd..39be73cdcfb98 100644 --- a/recipes/perl-attribute-handlers/0.96/meta.yaml +++ b/recipes/perl-attribute-handlers/0.96/meta.yaml @@ -6,6 +6,7 @@ package: name: {{ name }} version: {{ version }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-authen-sasl-saslprep/meta.yaml b/recipes/perl-authen-sasl-saslprep/meta.yaml index 3e08a354d5b80..4ee9bad55efff 100644 --- a/recipes/perl-authen-sasl-saslprep/meta.yaml +++ b/recipes/perl-authen-sasl-saslprep/meta.yaml @@ -7,6 +7,7 @@ source: sha256: a4cccc34bb3f53acf0ba78c9fc61af8d156d109d1c10487ba5988a55077d1f70 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-autodie/meta.yaml b/recipes/perl-autodie/meta.yaml index dea1886ffeaa0..0e8defae5097e 100644 --- a/recipes/perl-autodie/meta.yaml +++ b/recipes/perl-autodie/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-autoloader/5.74/meta.yaml b/recipes/perl-autoloader/5.74/meta.yaml index 9a555cd6a46e4..6c71fcc3c0027 100644 --- a/recipes/perl-autoloader/5.74/meta.yaml +++ b/recipes/perl-autoloader/5.74/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-b-debug/meta.yaml b/recipes/perl-b-debug/meta.yaml index 8e1effd5af64b..22e1a13bb956d 100644 --- a/recipes/perl-b-debug/meta.yaml +++ b/recipes/perl-b-debug/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-b/1.48/meta.yaml b/recipes/perl-b/1.48/meta.yaml index 2dd27cd98a811..9299a62611257 100644 --- a/recipes/perl-b/1.48/meta.yaml +++ b/recipes/perl-b/1.48/meta.yaml @@ -7,6 +7,7 @@ package: version: {{ version }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-bignum/meta.yaml b/recipes/perl-bignum/meta.yaml index b6ca3b0f23af3..e28830a66578d 100644 --- a/recipes/perl-bignum/meta.yaml +++ b/recipes/perl-bignum/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-bio-asn1-entrezgene/meta.yaml b/recipes/perl-bio-asn1-entrezgene/meta.yaml index 79ca2ab72fa76..34b3638bcf13b 100644 --- a/recipes/perl-bio-asn1-entrezgene/meta.yaml +++ b/recipes/perl-bio-asn1-entrezgene/meta.yaml @@ -7,6 +7,7 @@ source: sha256: f9e778db705ce5c35ad2798e38a8490b644edfdc14253aa1b74a1f5e79fc6a4b build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-bio-automatedannotation/1.182770/meta.yaml b/recipes/perl-bio-automatedannotation/1.182770/meta.yaml index 7c14ea8e2570c..8d3dfadd83b41 100644 --- a/recipes/perl-bio-automatedannotation/1.182770/meta.yaml +++ b/recipes/perl-bio-automatedannotation/1.182770/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-bio-cigar/meta.yaml b/recipes/perl-bio-cigar/meta.yaml index cfe132429c4b6..45e100cebcf50 100644 --- a/recipes/perl-bio-cigar/meta.yaml +++ b/recipes/perl-bio-cigar/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 4 requirements: diff --git a/recipes/perl-bio-coordinate/meta.yaml b/recipes/perl-bio-coordinate/meta.yaml index 3fd2edde0dc96..92152e8be5f11 100644 --- a/recipes/perl-bio-coordinate/meta.yaml +++ b/recipes/perl-bio-coordinate/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-bio-eutilities/meta.yaml b/recipes/perl-bio-eutilities/meta.yaml index d39c3df9cf8ee..8b99feb9d1228 100644 --- a/recipes/perl-bio-eutilities/meta.yaml +++ b/recipes/perl-bio-eutilities/meta.yaml @@ -7,6 +7,7 @@ source: md5: 8814608d46fc6517814f320766c24739 build: + noarch: generic number: 2 # commented versions are tested as working diff --git a/recipes/perl-bio-featureio/meta.yaml b/recipes/perl-bio-featureio/meta.yaml index b5cdd28b50f73..9e9f6ce6fb118 100644 --- a/recipes/perl-bio-featureio/meta.yaml +++ b/recipes/perl-bio-featureio/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7e455995c0a9cff706f43b1412dfdb9c build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-bio-gff3/meta.yaml b/recipes/perl-bio-gff3/meta.yaml index 0724869675ad2..319f5c3dd5342 100644 --- a/recipes/perl-bio-gff3/meta.yaml +++ b/recipes/perl-bio-gff3/meta.yaml @@ -7,6 +7,7 @@ source: md5: 8416fe2b09abddc37aed3df7040b1670 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-bio-mlst-check/meta.yaml b/recipes/perl-bio-mlst-check/meta.yaml index 428c0abfd0822..7e4f347abee88 100644 --- a/recipes/perl-bio-mlst-check/meta.yaml +++ b/recipes/perl-bio-mlst-check/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-bio-phylo/meta.yaml b/recipes/perl-bio-phylo/meta.yaml index 2c56811aa4cdd..dd9d345f04ee8 100644 --- a/recipes/perl-bio-phylo/meta.yaml +++ b/recipes/perl-bio-phylo/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7e7a8956222831282cab7444f6632c0c build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-bio-rna-rnaalisplit/meta.yaml b/recipes/perl-bio-rna-rnaalisplit/meta.yaml index 162fd0abea470..e2e8f8dc31243 100644 --- a/recipes/perl-bio-rna-rnaalisplit/meta.yaml +++ b/recipes/perl-bio-rna-rnaalisplit/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 skip: True # [osx] diff --git a/recipes/perl-bio-samtools/meta.yaml b/recipes/perl-bio-samtools/meta.yaml index e91337b1e855a..2ca7cef0f0cdb 100644 --- a/recipes/perl-bio-samtools/meta.yaml +++ b/recipes/perl-bio-samtools/meta.yaml @@ -9,6 +9,7 @@ source: - build-pl.patch build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-bio-tools-phylo-paml/meta.yaml b/recipes/perl-bio-tools-phylo-paml/meta.yaml index 7a1a21e26c4a1..6ca4245df5bcf 100644 --- a/recipes/perl-bio-tools-phylo-paml/meta.yaml +++ b/recipes/perl-bio-tools-phylo-paml/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml b/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml index 0e754f597e579..b20f463336c8f 100644 --- a/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml +++ b/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml b/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml index b57a55b40fa27..92e9d65bcb675 100644 --- a/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml +++ b/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic skip: True # [osx] number: 1 diff --git a/recipes/perl-bioperl-core/meta.yaml b/recipes/perl-bioperl-core/meta.yaml index b3c2644c27a64..72ab44082c2bb 100644 --- a/recipes/perl-bioperl-core/meta.yaml +++ b/recipes/perl-bioperl-core/meta.yaml @@ -9,6 +9,7 @@ source: - "pr309.patch" build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-bioperl-run/meta.yaml b/recipes/perl-bioperl-run/meta.yaml index 7e77d0d0008b2..82e64d0d264f1 100644 --- a/recipes/perl-bioperl-run/meta.yaml +++ b/recipes/perl-bioperl-run/meta.yaml @@ -7,6 +7,7 @@ source: md5: ca4109ea9d3aa0fdff0efc2058874724 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-bioperl/meta.yaml b/recipes/perl-bioperl/meta.yaml index bfb7d49c36c9d..804506ec5ae25 100644 --- a/recipes/perl-bioperl/meta.yaml +++ b/recipes/perl-bioperl/meta.yaml @@ -3,6 +3,7 @@ package: version: "1.7.2" build: + noarch: generic number: 10 requirements: diff --git a/recipes/perl-biosails/0.02/meta.yaml b/recipes/perl-biosails/0.02/meta.yaml index e6f1d03ba511e..c32a92fc61aee 100644 --- a/recipes/perl-biosails/0.02/meta.yaml +++ b/recipes/perl-biosails/0.02/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-biox-seq/0.006007/meta.yaml b/recipes/perl-biox-seq/0.006007/meta.yaml index f6587c26f9fec..67a7091bee015 100644 --- a/recipes/perl-biox-seq/0.006007/meta.yaml +++ b/recipes/perl-biox-seq/0.006007/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-biox-workflow-command/meta.yaml b/recipes/perl-biox-workflow-command/meta.yaml index 067c6842d62a5..69ac23a52b335 100644 --- a/recipes/perl-biox-workflow-command/meta.yaml +++ b/recipes/perl-biox-workflow-command/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 #skip: True # [osx] diff --git a/recipes/perl-bit-vector/meta.yaml b/recipes/perl-bit-vector/meta.yaml index edf0ed5bd055e..86ea27a208fcf 100644 --- a/recipes/perl-bit-vector/meta.yaml +++ b/recipes/perl-bit-vector/meta.yaml @@ -7,6 +7,7 @@ source: md5: bf67f144e5be5327ed79d4c69e6e0086 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-blib/1.06/meta.yaml b/recipes/perl-blib/1.06/meta.yaml index b75123f6a5ab4..431718ca90cbd 100644 --- a/recipes/perl-blib/1.06/meta.yaml +++ b/recipes/perl-blib/1.06/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-border-style/meta.yaml b/recipes/perl-border-style/meta.yaml index 53c1e0e56fb55..59b01b4ee7be0 100644 --- a/recipes/perl-border-style/meta.yaml +++ b/recipes/perl-border-style/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-bundle-bioperl/meta.yaml b/recipes/perl-bundle-bioperl/meta.yaml index ebd4062f9ae7e..f3469284a3a7e 100644 --- a/recipes/perl-bundle-bioperl/meta.yaml +++ b/recipes/perl-bundle-bioperl/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-business-isbn-data/meta.yaml b/recipes/perl-business-isbn-data/meta.yaml index 4e6f9042cdb01..b41f4aa77e6fc 100644 --- a/recipes/perl-business-isbn-data/meta.yaml +++ b/recipes/perl-business-isbn-data/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-business-isbn/meta.yaml b/recipes/perl-business-isbn/meta.yaml index 0b8515895ecc5..2abd9fc02db67 100644 --- a/recipes/perl-business-isbn/meta.yaml +++ b/recipes/perl-business-isbn/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-cache-cache/meta.yaml b/recipes/perl-cache-cache/meta.yaml index 65c6570c5abdc..02c2f85066fb5 100644 --- a/recipes/perl-cache-cache/meta.yaml +++ b/recipes/perl-cache-cache/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-cairo/meta.yaml b/recipes/perl-cairo/meta.yaml index 0ab3f74e133f7..95077202bb361 100644 --- a/recipes/perl-cairo/meta.yaml +++ b/recipes/perl-cairo/meta.yaml @@ -7,6 +7,7 @@ source: sha256: e64803018bc7cba49e73e258547f5378cc4249797beafec524852140f49c45c4 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-canary-stability/meta.yaml b/recipes/perl-canary-stability/meta.yaml index 0b63bc0573d4c..f7be68e98b5b2 100644 --- a/recipes/perl-canary-stability/meta.yaml +++ b/recipes/perl-canary-stability/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-capture-tiny/0.34/meta.yaml b/recipes/perl-capture-tiny/0.34/meta.yaml index 2c200b22d737a..203429262f872 100644 --- a/recipes/perl-capture-tiny/0.34/meta.yaml +++ b/recipes/perl-capture-tiny/0.34/meta.yaml @@ -7,6 +7,7 @@ source: md5: bca6ac7cd6cd88fa9cd9c99e52833a72 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-capture-tiny/meta.yaml b/recipes/perl-capture-tiny/meta.yaml index de87f2ff7d569..2e90fc4c2dc37 100644 --- a/recipes/perl-capture-tiny/meta.yaml +++ b/recipes/perl-capture-tiny/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-carp-clan/meta.yaml b/recipes/perl-carp-clan/meta.yaml index f71ee3c00dabe..e31886ec8c9b1 100644 --- a/recipes/perl-carp-clan/meta.yaml +++ b/recipes/perl-carp-clan/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-carp/1.38/meta.yaml b/recipes/perl-carp/1.38/meta.yaml index 5ee40a2f5cb21..8b36af8f0d507 100644 --- a/recipes/perl-carp/1.38/meta.yaml +++ b/recipes/perl-carp/1.38/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-class-accessor/meta.yaml b/recipes/perl-class-accessor/meta.yaml index 74400dc6e9e70..c896b940f9978 100644 --- a/recipes/perl-class-accessor/meta.yaml +++ b/recipes/perl-class-accessor/meta.yaml @@ -7,6 +7,7 @@ source: sha256: bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-class-data-inheritable/meta.yaml b/recipes/perl-class-data-inheritable/meta.yaml index 8f5cbc56eead7..5167d2b03d7c7 100644 --- a/recipes/perl-class-data-inheritable/meta.yaml +++ b/recipes/perl-class-data-inheritable/meta.yaml @@ -7,6 +7,7 @@ source: md5: fc0fe65926eb8fb932743559feb54eb9 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-class-inspector/meta.yaml b/recipes/perl-class-inspector/meta.yaml index 7bc12ae9f43dd..37fd4d6120b06 100644 --- a/recipes/perl-class-inspector/meta.yaml +++ b/recipes/perl-class-inspector/meta.yaml @@ -7,6 +7,7 @@ source: sha256: fe9a86dcb3ccc7a99d6865e6b674a14d20164f76bd84f2eb43aafcc6bf1cf0d8 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-class-load/meta.yaml b/recipes/perl-class-load/meta.yaml index d93c7052b7994..7b459520eaf6d 100644 --- a/recipes/perl-class-load/meta.yaml +++ b/recipes/perl-class-load/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-class-method-modifiers/meta.yaml b/recipes/perl-class-method-modifiers/meta.yaml index 6c9b0b63b8ac2..c450693ab7a31 100644 --- a/recipes/perl-class-method-modifiers/meta.yaml +++ b/recipes/perl-class-method-modifiers/meta.yaml @@ -7,6 +7,7 @@ source: sha256: e44c1073020bf55b8c97975ed77235fd7e2a6a56f29b5c702301721184e27ac8 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-class-methodmaker/meta.yaml b/recipes/perl-class-methodmaker/meta.yaml index e61591d0e2e88..ed174374f85b9 100644 --- a/recipes/perl-class-methodmaker/meta.yaml +++ b/recipes/perl-class-methodmaker/meta.yaml @@ -12,6 +12,7 @@ source: build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-class-singleton/meta.yaml b/recipes/perl-class-singleton/meta.yaml index 706461a6b490d..e705a54e2c800 100644 --- a/recipes/perl-class-singleton/meta.yaml +++ b/recipes/perl-class-singleton/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-class-std-fast/meta.yaml b/recipes/perl-class-std-fast/meta.yaml index 9a89377970e1d..d1957d4df631d 100644 --- a/recipes/perl-class-std-fast/meta.yaml +++ b/recipes/perl-class-std-fast/meta.yaml @@ -7,6 +7,7 @@ source: md5: d06d084cb84f295b0aabf2eee78ef746 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-class-std/meta.yaml b/recipes/perl-class-std/meta.yaml index 6f0b0ed572222..ed8a2fec2ba1c 100644 --- a/recipes/perl-class-std/meta.yaml +++ b/recipes/perl-class-std/meta.yaml @@ -7,6 +7,7 @@ source: md5: 82bcc56d9769edce671b0bd0e183ec3a build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-class-xsaccessor/1.19/meta.yaml b/recipes/perl-class-xsaccessor/1.19/meta.yaml index 3db737b439b37..b79fbd23f1dbe 100644 --- a/recipes/perl-class-xsaccessor/1.19/meta.yaml +++ b/recipes/perl-class-xsaccessor/1.19/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-clone-choose/meta.yaml b/recipes/perl-clone-choose/meta.yaml index 1d65e60d523e2..a9ca92ad1daff 100644 --- a/recipes/perl-clone-choose/meta.yaml +++ b/recipes/perl-clone-choose/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-clone-pp/meta.yaml b/recipes/perl-clone-pp/meta.yaml index f5b40c1a21e6b..c9bc60528418b 100644 --- a/recipes/perl-clone-pp/meta.yaml +++ b/recipes/perl-clone-pp/meta.yaml @@ -7,6 +7,7 @@ source: sha256: bf85e109b7d9a10677db82fa65c1720ae95499a49cbb676d4b3d1b183786b395 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-color-theme/meta.yaml b/recipes/perl-color-theme/meta.yaml index 08bc8e91af1f0..29f6e089694fa 100644 --- a/recipes/perl-color-theme/meta.yaml +++ b/recipes/perl-color-theme/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-common-sense/meta.yaml b/recipes/perl-common-sense/meta.yaml index a3aeced7603d1..27f2e1f5d92bb 100644 --- a/recipes/perl-common-sense/meta.yaml +++ b/recipes/perl-common-sense/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-compress-bgzf/0.005/meta.yaml b/recipes/perl-compress-bgzf/0.005/meta.yaml index 1d8169d099f73..bfff41059ffb6 100644 --- a/recipes/perl-compress-bgzf/0.005/meta.yaml +++ b/recipes/perl-compress-bgzf/0.005/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-config-autoconf/meta.yaml b/recipes/perl-config-autoconf/meta.yaml index 5080ef4414dea..6f3ecadb6ab15 100644 --- a/recipes/perl-config-autoconf/meta.yaml +++ b/recipes/perl-config-autoconf/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-config-general/meta.yaml b/recipes/perl-config-general/meta.yaml index fc07eb5a906ef..1a059ced2afed 100644 --- a/recipes/perl-config-general/meta.yaml +++ b/recipes/perl-config-general/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-config-simple/meta.yaml b/recipes/perl-config-simple/meta.yaml index cd50e3754d49d..d4d70da3f621d 100644 --- a/recipes/perl-config-simple/meta.yaml +++ b/recipes/perl-config-simple/meta.yaml @@ -7,6 +7,7 @@ source: md5: f014aec54f0a1e2e880d317180fce502 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-const-fast/meta.yaml b/recipes/perl-const-fast/meta.yaml index 8334739483391..ac1029e5ab629 100644 --- a/recipes/perl-const-fast/meta.yaml +++ b/recipes/perl-const-fast/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-constant/1.33/meta.yaml b/recipes/perl-constant/1.33/meta.yaml index b8723623df48e..bef21531eb0e3 100644 --- a/recipes/perl-constant/1.33/meta.yaml +++ b/recipes/perl-constant/1.33/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-convert-binhex/meta.yaml b/recipes/perl-convert-binhex/meta.yaml index 7c3d74d70c8dc..22e652e0fbe14 100644 --- a/recipes/perl-convert-binhex/meta.yaml +++ b/recipes/perl-convert-binhex/meta.yaml @@ -7,6 +7,7 @@ source: md5: 2f485e1283387ead5b92243e1aacff9d build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-cpan-meta-check/meta.yaml b/recipes/perl-cpan-meta-check/meta.yaml index df2ff6ab35995..b2fa9c6df0661 100644 --- a/recipes/perl-cpan-meta-check/meta.yaml +++ b/recipes/perl-cpan-meta-check/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-cpan-meta-requirements/meta.yaml b/recipes/perl-cpan-meta-requirements/meta.yaml index 04eac1cf7448d..6fef056aa7373 100644 --- a/recipes/perl-cpan-meta-requirements/meta.yaml +++ b/recipes/perl-cpan-meta-requirements/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-cpan-meta-validator/2.140640/meta.yaml b/recipes/perl-cpan-meta-validator/2.140640/meta.yaml index a1e242bcc39b4..13c876797aafc 100644 --- a/recipes/perl-cpan-meta-validator/2.140640/meta.yaml +++ b/recipes/perl-cpan-meta-validator/2.140640/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-cpan-meta-yaml/meta.yaml b/recipes/perl-cpan-meta-yaml/meta.yaml index cc70c7f846838..414c6659f79d1 100644 --- a/recipes/perl-cpan-meta-yaml/meta.yaml +++ b/recipes/perl-cpan-meta-yaml/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-cpan-meta/meta.yaml b/recipes/perl-cpan-meta/meta.yaml index 13aeda35c71d6..d818ea0a56546 100644 --- a/recipes/perl-cpan-meta/meta.yaml +++ b/recipes/perl-cpan-meta/meta.yaml @@ -3,6 +3,7 @@ package: version: 2.150010 build: + noarch: generic number: 0 source: diff --git a/recipes/perl-cpan-shell/5.5004/meta.yaml b/recipes/perl-cpan-shell/5.5004/meta.yaml index b6f8c0252b844..3611ad6b15907 100644 --- a/recipes/perl-cpan-shell/5.5004/meta.yaml +++ b/recipes/perl-cpan-shell/5.5004/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-crypt-openssl-random/0.11/meta.yaml b/recipes/perl-crypt-openssl-random/0.11/meta.yaml index 72ef45cbaae80..dc035c77d246f 100644 --- a/recipes/perl-crypt-openssl-random/0.11/meta.yaml +++ b/recipes/perl-crypt-openssl-random/0.11/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 skip: True # [osx] diff --git a/recipes/perl-crypt-openssl-rsa/0.28/meta.yaml b/recipes/perl-crypt-openssl-rsa/0.28/meta.yaml index b8294068440e3..f2572c3a32de2 100644 --- a/recipes/perl-crypt-openssl-rsa/0.28/meta.yaml +++ b/recipes/perl-crypt-openssl-rsa/0.28/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 skip: True # [osx] diff --git a/recipes/perl-crypt-rc4/meta.yaml b/recipes/perl-crypt-rc4/meta.yaml index e9b8c13fa439b..b24dcb426f43c 100644 --- a/recipes/perl-crypt-rc4/meta.yaml +++ b/recipes/perl-crypt-rc4/meta.yaml @@ -7,6 +7,7 @@ source: md5: 4ca59a7e58ac9597c3b4f3f46ea22629 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-data-compare/1.25/meta.yaml b/recipes/perl-data-compare/1.25/meta.yaml index 2a2cbc104cdf7..9da220950748e 100644 --- a/recipes/perl-data-compare/1.25/meta.yaml +++ b/recipes/perl-data-compare/1.25/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-data-dumper/meta.yaml b/recipes/perl-data-dumper/meta.yaml index 11dfb1c058394..46a45f493e7e1 100644 --- a/recipes/perl-data-dumper/meta.yaml +++ b/recipes/perl-data-dumper/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-data-match/0.06/meta.yaml b/recipes/perl-data-match/0.06/meta.yaml index 876ad929861b9..292a8000a9529 100644 --- a/recipes/perl-data-match/0.06/meta.yaml +++ b/recipes/perl-data-match/0.06/meta.yaml @@ -13,6 +13,7 @@ source: - Match.pm.patch build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-data-munge/meta.yaml b/recipes/perl-data-munge/meta.yaml index 4763bb793e3c2..e7bdab27f03c8 100644 --- a/recipes/perl-data-munge/meta.yaml +++ b/recipes/perl-data-munge/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-data-optlist/meta.yaml b/recipes/perl-data-optlist/meta.yaml index b428694d012e5..94e183c11e93f 100644 --- a/recipes/perl-data-optlist/meta.yaml +++ b/recipes/perl-data-optlist/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-data-stag/meta.yaml b/recipes/perl-data-stag/meta.yaml index c3e6eda517412..c6cb4599be345 100644 --- a/recipes/perl-data-stag/meta.yaml +++ b/recipes/perl-data-stag/meta.yaml @@ -7,6 +7,7 @@ source: md5: f803acf74f1bfccc118aeac5483ee871 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-data-utilities/0.04/meta.yaml b/recipes/perl-data-utilities/0.04/meta.yaml index 909ef0e9aa940..9af916b505271 100644 --- a/recipes/perl-data-utilities/0.04/meta.yaml +++ b/recipes/perl-data-utilities/0.04/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-data-visitor/0.30/meta.yaml b/recipes/perl-data-visitor/0.30/meta.yaml index 975e08479c7f9..3ea705d2cc276 100644 --- a/recipes/perl-data-visitor/0.30/meta.yaml +++ b/recipes/perl-data-visitor/0.30/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-data-walk/2.01/meta.yaml b/recipes/perl-data-walk/2.01/meta.yaml index 41649455005ec..6853b861595c3 100644 --- a/recipes/perl-data-walk/2.01/meta.yaml +++ b/recipes/perl-data-walk/2.01/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-date-format/2.30/meta.yaml b/recipes/perl-date-format/2.30/meta.yaml index 35b0406ded6bc..bee4a9d4e759d 100644 --- a/recipes/perl-date-format/2.30/meta.yaml +++ b/recipes/perl-date-format/2.30/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-date-manip/meta.yaml b/recipes/perl-date-manip/meta.yaml index a85c4e2640d61..a5156b0634b8a 100644 --- a/recipes/perl-date-manip/meta.yaml +++ b/recipes/perl-date-manip/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-datetime-format-strptime/meta.yaml b/recipes/perl-datetime-format-strptime/meta.yaml index ba586ed6c1ac2..d9083e2999f89 100644 --- a/recipes/perl-datetime-format-strptime/meta.yaml +++ b/recipes/perl-datetime-format-strptime/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-dbi/meta.yaml b/recipes/perl-dbi/meta.yaml index 395c9b3e9d8fc..de2b8616e1b65 100644 --- a/recipes/perl-dbi/meta.yaml +++ b/recipes/perl-dbi/meta.yaml @@ -8,6 +8,7 @@ source: url: https://cpan.metacpan.org/authors/id/T/TI/TIMB/DBI-1.642.tar.gz sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: host: diff --git a/recipes/perl-devel-checkbin/meta.yaml b/recipes/perl-devel-checkbin/meta.yaml index f68d8c5901655..9208adcfbaa92 100644 --- a/recipes/perl-devel-checkbin/meta.yaml +++ b/recipes/perl-devel-checkbin/meta.yaml @@ -7,6 +7,7 @@ source: md5: 042b68e48d9b53de7d3ef4c726d57cb2 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-devel-checkos/1.81/meta.yaml b/recipes/perl-devel-checkos/1.81/meta.yaml index ff45e842ab351..48535ca906362 100644 --- a/recipes/perl-devel-checkos/1.81/meta.yaml +++ b/recipes/perl-devel-checkos/1.81/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-devel-cycle/meta.yaml b/recipes/perl-devel-cycle/meta.yaml index 528ce2e8f0057..9cf9b3ca9826a 100644 --- a/recipes/perl-devel-cycle/meta.yaml +++ b/recipes/perl-devel-cycle/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-devel-globaldestruction/meta.yaml b/recipes/perl-devel-globaldestruction/meta.yaml index 64a29bbeb7be2..42d995f1b6f28 100644 --- a/recipes/perl-devel-globaldestruction/meta.yaml +++ b/recipes/perl-devel-globaldestruction/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-devel-overloadinfo/meta.yaml b/recipes/perl-devel-overloadinfo/meta.yaml index 7b33136e54423..5e4266ddae8fc 100644 --- a/recipes/perl-devel-overloadinfo/meta.yaml +++ b/recipes/perl-devel-overloadinfo/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-devel-symdump/2.18/meta.yaml b/recipes/perl-devel-symdump/2.18/meta.yaml index 230734644b01c..75b0571773033 100644 --- a/recipes/perl-devel-symdump/2.18/meta.yaml +++ b/recipes/perl-devel-symdump/2.18/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-digest-crc32/meta.yaml b/recipes/perl-digest-crc32/meta.yaml index 04710a2fd8cda..f7152cc048cc1 100644 --- a/recipes/perl-digest-crc32/meta.yaml +++ b/recipes/perl-digest-crc32/meta.yaml @@ -7,6 +7,7 @@ source: md5: 4808a7fd130218cd1193d8a496d8ec92 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-digest-hmac/meta.yaml b/recipes/perl-digest-hmac/meta.yaml index 6ca4ea3653eb4..18607f354e4d3 100644 --- a/recipes/perl-digest-hmac/meta.yaml +++ b/recipes/perl-digest-hmac/meta.yaml @@ -7,6 +7,7 @@ source: md5: e6a5d6f552da16eacb5157ea4369ff9d build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-digest-md5-file/meta.yaml b/recipes/perl-digest-md5-file/meta.yaml index 9ca62eb6e31b3..f111b73d70983 100644 --- a/recipes/perl-digest-md5-file/meta.yaml +++ b/recipes/perl-digest-md5-file/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-digest-md5/meta.yaml b/recipes/perl-digest-md5/meta.yaml index a604024cef10b..476b0a28fe426 100644 --- a/recipes/perl-digest-md5/meta.yaml +++ b/recipes/perl-digest-md5/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 03b198a2d14425d951e5e50a885d3818c3162c8fe4c21e18d7798a9a179d0e3c build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-digest-perl-md5/meta.yaml b/recipes/perl-digest-perl-md5/meta.yaml index 8b9fb0519f074..58f952ab6cecd 100644 --- a/recipes/perl-digest-perl-md5/meta.yaml +++ b/recipes/perl-digest-perl-md5/meta.yaml @@ -7,6 +7,7 @@ source: md5: 41f1160e11ce0d99021fc8d6c725fa3d build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-digest-sha/5.88/meta.yaml b/recipes/perl-digest-sha/5.88/meta.yaml index 015c542f8d1f5..4458b7fb55400 100644 --- a/recipes/perl-digest-sha/5.88/meta.yaml +++ b/recipes/perl-digest-sha/5.88/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-dist-checkconflicts/meta.yaml b/recipes/perl-dist-checkconflicts/meta.yaml index e1f342d89925a..3f9cbbad20486 100644 --- a/recipes/perl-dist-checkconflicts/meta.yaml +++ b/recipes/perl-dist-checkconflicts/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-dumbbench/0.111/meta.yaml b/recipes/perl-dumbbench/0.111/meta.yaml index 0ec7458ff465c..077f3260182f3 100644 --- a/recipes/perl-dumbbench/0.111/meta.yaml +++ b/recipes/perl-dumbbench/0.111/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-dynaloader/1.25/meta.yaml b/recipes/perl-dynaloader/1.25/meta.yaml index 01efb566c6876..aba817ce07211 100644 --- a/recipes/perl-dynaloader/1.25/meta.yaml +++ b/recipes/perl-dynaloader/1.25/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-email-date-format/meta.yaml b/recipes/perl-email-date-format/meta.yaml index 94a4fc0ee3dcd..4394decf943b5 100644 --- a/recipes/perl-email-date-format/meta.yaml +++ b/recipes/perl-email-date-format/meta.yaml @@ -7,6 +7,7 @@ source: md5: 030dcee3bc1a44674900b0132925bd03 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-encode-locale/meta.yaml b/recipes/perl-encode-locale/meta.yaml index f36130d50fa3b..5163b5ddf7120 100644 --- a/recipes/perl-encode-locale/meta.yaml +++ b/recipes/perl-encode-locale/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 6 requirements: diff --git a/recipes/perl-encode/2.88/meta.yaml b/recipes/perl-encode/2.88/meta.yaml index 3bcc20e16e721..4e8fe7018db5e 100644 --- a/recipes/perl-encode/2.88/meta.yaml +++ b/recipes/perl-encode/2.88/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-env-path/meta.yaml b/recipes/perl-env-path/meta.yaml index 5565bc60b5c18..bd5f47c2d2f9e 100644 --- a/recipes/perl-env-path/meta.yaml +++ b/recipes/perl-env-path/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-env/meta.yaml b/recipes/perl-env/meta.yaml index 75b54d9ac1691..d222ec94ad58d 100644 --- a/recipes/perl-env/meta.yaml +++ b/recipes/perl-env/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-error/meta.yaml b/recipes/perl-error/meta.yaml index c448ff53cbb3e..981de8e7569d2 100644 --- a/recipes/perl-error/meta.yaml +++ b/recipes/perl-error/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 07b2ac8275dfa04144745a6c1900a596280f862b97d22bab0c5ce02682ebd3be build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-exception-class/meta.yaml b/recipes/perl-exception-class/meta.yaml index 20fb23334bb05..759e7978ee858 100644 --- a/recipes/perl-exception-class/meta.yaml +++ b/recipes/perl-exception-class/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 33f3fbf8b138d3b04ea4ec0ba83fb0df6ba898806bcf4ef393d4cafc1a23ee0d build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-experimental/meta.yaml b/recipes/perl-experimental/meta.yaml index 9814893529b53..6e00876cd19cc 100644 --- a/recipes/perl-experimental/meta.yaml +++ b/recipes/perl-experimental/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-exporter-tidy/meta.yaml b/recipes/perl-exporter-tidy/meta.yaml index fb9b4db6948e2..7d130bba79283 100644 --- a/recipes/perl-exporter-tidy/meta.yaml +++ b/recipes/perl-exporter-tidy/meta.yaml @@ -7,6 +7,7 @@ source: md5: 025866016bd6ca361052acb30bcf07f4 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-exporter-tiny/meta.yaml b/recipes/perl-exporter-tiny/meta.yaml index 217f9eebc01f7..b453a2816bf7f 100644 --- a/recipes/perl-exporter-tiny/meta.yaml +++ b/recipes/perl-exporter-tiny/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-exporter/5.72/meta.yaml b/recipes/perl-exporter/5.72/meta.yaml index b91fb774731b3..9b9ec1b4dfc68 100644 --- a/recipes/perl-exporter/5.72/meta.yaml +++ b/recipes/perl-exporter/5.72/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-extutils-cbuilder/0.280230/meta.yaml b/recipes/perl-extutils-cbuilder/0.280230/meta.yaml index 98a1a083cb9cd..964addfa3bd62 100644 --- a/recipes/perl-extutils-cbuilder/0.280230/meta.yaml +++ b/recipes/perl-extutils-cbuilder/0.280230/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-extutils-config/meta.yaml b/recipes/perl-extutils-config/meta.yaml index eacc0a4209f61..5c6e680bdca23 100644 --- a/recipes/perl-extutils-config/meta.yaml +++ b/recipes/perl-extutils-config/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-extutils-depends/meta.yaml b/recipes/perl-extutils-depends/meta.yaml index 15f82fa9ef043..338ecfb73a155 100644 --- a/recipes/perl-extutils-depends/meta.yaml +++ b/recipes/perl-extutils-depends/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 780ff72128c04c2a22e6801187aa9c58cab298407f6e9d062706af1c250bbe98 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-extutils-helpers/meta.yaml b/recipes/perl-extutils-helpers/meta.yaml index a24d8dd2770b4..d1e5b46350f45 100644 --- a/recipes/perl-extutils-helpers/meta.yaml +++ b/recipes/perl-extutils-helpers/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-extutils-installpaths/meta.yaml b/recipes/perl-extutils-installpaths/meta.yaml index 387492e389034..38749a4cebcfa 100644 --- a/recipes/perl-extutils-installpaths/meta.yaml +++ b/recipes/perl-extutils-installpaths/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-extutils-makemaker/meta.yaml b/recipes/perl-extutils-makemaker/meta.yaml index 319329abb08af..973cc4df78b2f 100644 --- a/recipes/perl-extutils-makemaker/meta.yaml +++ b/recipes/perl-extutils-makemaker/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-extutils-manifest/meta.yaml b/recipes/perl-extutils-manifest/meta.yaml index 50e04ba639677..86dc6f3b92943 100644 --- a/recipes/perl-extutils-manifest/meta.yaml +++ b/recipes/perl-extutils-manifest/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 799280074f98ef2d7fdf4f75521ad83ec01c2e068e54a45c92968cd9dc2db45e build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-extutils-parsexs/meta.yaml b/recipes/perl-extutils-parsexs/meta.yaml index 766c4207b68e4..6be2eb593e526 100644 --- a/recipes/perl-extutils-parsexs/meta.yaml +++ b/recipes/perl-extutils-parsexs/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-extutils-pkgconfig/meta.yaml b/recipes/perl-extutils-pkgconfig/meta.yaml index bbd29098ed9c3..dcd20eb510488 100644 --- a/recipes/perl-extutils-pkgconfig/meta.yaml +++ b/recipes/perl-extutils-pkgconfig/meta.yaml @@ -7,6 +7,7 @@ source: sha256: bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-chdir/meta.yaml b/recipes/perl-file-chdir/meta.yaml index 5434c14ebe21e..703f19d3895db 100644 --- a/recipes/perl-file-chdir/meta.yaml +++ b/recipes/perl-file-chdir/meta.yaml @@ -7,6 +7,7 @@ source: md5: aacfafa4a8f13d45be67451e0f9b483e build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-file-compare/1.1006/meta.yaml b/recipes/perl-file-compare/1.1006/meta.yaml index fa0dc4875a7ab..e2357ecc5b01d 100644 --- a/recipes/perl-file-compare/1.1006/meta.yaml +++ b/recipes/perl-file-compare/1.1006/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-copy-recursive-reduced/meta.yaml b/recipes/perl-file-copy-recursive-reduced/meta.yaml index 90ac9c41c8407..57d3ddc703ef0 100644 --- a/recipes/perl-file-copy-recursive-reduced/meta.yaml +++ b/recipes/perl-file-copy-recursive-reduced/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-file-details/meta.yaml b/recipes/perl-file-details/meta.yaml index 4e52337bd6feb..4db54f6899ea0 100644 --- a/recipes/perl-file-details/meta.yaml +++ b/recipes/perl-file-details/meta.yaml @@ -7,6 +7,7 @@ source: md5: 557b420008cf640740932249957c6b89 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-fetch/meta.yaml b/recipes/perl-file-fetch/meta.yaml index cface0a554880..f82e44e4d9b09 100644 --- a/recipes/perl-file-fetch/meta.yaml +++ b/recipes/perl-file-fetch/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-file-find-rule/meta.yaml b/recipes/perl-file-find-rule/meta.yaml index 1822a9edbfe75..f9e8d925830ad 100644 --- a/recipes/perl-file-find-rule/meta.yaml +++ b/recipes/perl-file-find-rule/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 5 requirements: diff --git a/recipes/perl-file-find/1.27/meta.yaml b/recipes/perl-file-find/1.27/meta.yaml index 893ebdc2022ca..530a8da017567 100644 --- a/recipes/perl-file-find/1.27/meta.yaml +++ b/recipes/perl-file-find/1.27/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-grep/meta.yaml b/recipes/perl-file-grep/meta.yaml index c9d642ca33834..e33a4772b72f5 100644 --- a/recipes/perl-file-grep/meta.yaml +++ b/recipes/perl-file-grep/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-file-homedir/meta.yaml b/recipes/perl-file-homedir/meta.yaml index 0b8cb068c7d81..f3d212be37695 100644 --- a/recipes/perl-file-homedir/meta.yaml +++ b/recipes/perl-file-homedir/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-file-listing/meta.yaml b/recipes/perl-file-listing/meta.yaml index 49e5d2ea3c7b8..1eb2d98001c5d 100644 --- a/recipes/perl-file-listing/meta.yaml +++ b/recipes/perl-file-listing/meta.yaml @@ -7,6 +7,7 @@ source: md5: 83f636b477741f3a014585bb9cc079a6 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-next/meta.yaml b/recipes/perl-file-next/meta.yaml index d99312ab9ad44..0acf9cc99eb1b 100644 --- a/recipes/perl-file-next/meta.yaml +++ b/recipes/perl-file-next/meta.yaml @@ -7,6 +7,7 @@ source: md5: 103bc329cd2b64ec270ac53a7dacb378 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-path/meta.yaml b/recipes/perl-file-path/meta.yaml index 559dcf1a975ca..fb95295f9a9ae 100644 --- a/recipes/perl-file-path/meta.yaml +++ b/recipes/perl-file-path/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-file-pushd/meta.yaml b/recipes/perl-file-pushd/meta.yaml index 682edb7a09e95..249b92e6b04ff 100644 --- a/recipes/perl-file-pushd/meta.yaml +++ b/recipes/perl-file-pushd/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-readbackwards/meta.yaml b/recipes/perl-file-readbackwards/meta.yaml index 0684ca53b020f..bb31ac6c3a989 100644 --- a/recipes/perl-file-readbackwards/meta.yaml +++ b/recipes/perl-file-readbackwards/meta.yaml @@ -7,6 +7,7 @@ source: md5: 613d9d02de6c1d86d5fa5b8816a6b214 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-share/0.25/meta.yaml b/recipes/perl-file-share/0.25/meta.yaml index 8408c70444f2e..ad0a6ccc800ac 100644 --- a/recipes/perl-file-share/0.25/meta.yaml +++ b/recipes/perl-file-share/0.25/meta.yaml @@ -3,6 +3,7 @@ package: version: "0.25" build: + noarch: generic number: 2 source: diff --git a/recipes/perl-file-sharedir-install/meta.yaml b/recipes/perl-file-sharedir-install/meta.yaml index 81b525f49e80f..633090cf50d7e 100644 --- a/recipes/perl-file-sharedir-install/meta.yaml +++ b/recipes/perl-file-sharedir-install/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-file-sharedir/meta.yaml b/recipes/perl-file-sharedir/meta.yaml index 28966ca8859e0..a57a5287c3b98 100644 --- a/recipes/perl-file-sharedir/meta.yaml +++ b/recipes/perl-file-sharedir/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-slurp-tiny/meta.yaml b/recipes/perl-file-slurp-tiny/meta.yaml index 051fdf384bc01..6dab427c6061b 100644 --- a/recipes/perl-file-slurp-tiny/meta.yaml +++ b/recipes/perl-file-slurp-tiny/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7575b81543281ea57cdb7e5eb3f73264 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-slurp/meta.yaml b/recipes/perl-file-slurp/meta.yaml index 37c8a633b6c53..0f284310a69fb 100644 --- a/recipes/perl-file-slurp/meta.yaml +++ b/recipes/perl-file-slurp/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-file-slurper/meta.yaml b/recipes/perl-file-slurper/meta.yaml index b8e2b58fb342c..e56d2af2df0a5 100644 --- a/recipes/perl-file-slurper/meta.yaml +++ b/recipes/perl-file-slurper/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 4efb2ea416b110a1bda6f8133549cc6ea3676402e3caf7529fce0313250aa578 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-file-sort/meta.yaml b/recipes/perl-file-sort/meta.yaml index eaf654de03a1f..617d80b077e16 100644 --- a/recipes/perl-file-sort/meta.yaml +++ b/recipes/perl-file-sort/meta.yaml @@ -7,6 +7,7 @@ source: md5: 1feb4128bba2edde68ada7838e55863a build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-file-spec/3.48_01/meta.yaml b/recipes/perl-file-spec/3.48_01/meta.yaml index b07eaf5d2737e..fbbc0b3128a9e 100644 --- a/recipes/perl-file-spec/3.48_01/meta.yaml +++ b/recipes/perl-file-spec/3.48_01/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-tee/0.07/meta.yaml b/recipes/perl-file-tee/0.07/meta.yaml index 7c73c6e294155..5f76ba2fc9fc0 100644 --- a/recipes/perl-file-tee/0.07/meta.yaml +++ b/recipes/perl-file-tee/0.07/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-temp/0.2304/meta.yaml b/recipes/perl-file-temp/0.2304/meta.yaml index 7e219a82e11e5..4a4e9c75f23cc 100644 --- a/recipes/perl-file-temp/0.2304/meta.yaml +++ b/recipes/perl-file-temp/0.2304/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-file-touch/meta.yaml b/recipes/perl-file-touch/meta.yaml index e52bcd068e92e..637d2282466f5 100644 --- a/recipes/perl-file-touch/meta.yaml +++ b/recipes/perl-file-touch/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-file-util/meta.yaml b/recipes/perl-file-util/meta.yaml index 5f767c77712b9..7e9c0888213cf 100644 --- a/recipes/perl-file-util/meta.yaml +++ b/recipes/perl-file-util/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-file-which/meta.yaml b/recipes/perl-file-which/meta.yaml index cd5b61ba3e742..98a6b00b412d9 100644 --- a/recipes/perl-file-which/meta.yaml +++ b/recipes/perl-file-which/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-filter-simple/0.91/meta.yaml b/recipes/perl-filter-simple/0.91/meta.yaml index 39836c3ad36a3..9e3d4aba0035d 100644 --- a/recipes/perl-filter-simple/0.91/meta.yaml +++ b/recipes/perl-filter-simple/0.91/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-findbin-libs/2.017008/meta.yaml b/recipes/perl-findbin-libs/2.017008/meta.yaml index e7d7a0d38b83a..1b5760542ec06 100644 --- a/recipes/perl-findbin-libs/2.017008/meta.yaml +++ b/recipes/perl-findbin-libs/2.017008/meta.yaml @@ -7,6 +7,7 @@ source: md5: 45c36e1de8fb386f262240e6a322e245 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-findbin-real/meta.yaml b/recipes/perl-findbin-real/meta.yaml index 7a23270b65d7e..223c0a8baedb8 100644 --- a/recipes/perl-findbin-real/meta.yaml +++ b/recipes/perl-findbin-real/meta.yaml @@ -7,6 +7,7 @@ source: md5: 686a6d7027237b6984ae8318ed203366 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-font-afm/meta.yaml b/recipes/perl-font-afm/meta.yaml index 1184ea795fafd..918afa47213c5 100644 --- a/recipes/perl-font-afm/meta.yaml +++ b/recipes/perl-font-afm/meta.yaml @@ -7,6 +7,7 @@ source: md5: b14ecf4dc4edbd63940aa354eb13c499 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-font-ttf/meta.yaml b/recipes/perl-font-ttf/meta.yaml index 9c718e2d36e97..b8e5b644fbc4a 100644 --- a/recipes/perl-font-ttf/meta.yaml +++ b/recipes/perl-font-ttf/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-forks/meta.yaml b/recipes/perl-forks/meta.yaml index 6b8a80cf4b2af..67771f5808d06 100644 --- a/recipes/perl-forks/meta.yaml +++ b/recipes/perl-forks/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 4 requirements: diff --git a/recipes/perl-gdgraph-histogram/meta.yaml b/recipes/perl-gdgraph-histogram/meta.yaml index 70138bb20cf97..a184953ad2e78 100644 --- a/recipes/perl-gdgraph-histogram/meta.yaml +++ b/recipes/perl-gdgraph-histogram/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-gdgraph/meta.yaml b/recipes/perl-gdgraph/meta.yaml index 3cb5192e4bc2c..d0426774dce26 100644 --- a/recipes/perl-gdgraph/meta.yaml +++ b/recipes/perl-gdgraph/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-getopt-argvfile/1.11/meta.yaml b/recipes/perl-getopt-argvfile/1.11/meta.yaml index 7794ab69b43a5..fd01596bebddf 100644 --- a/recipes/perl-getopt-argvfile/1.11/meta.yaml +++ b/recipes/perl-getopt-argvfile/1.11/meta.yaml @@ -10,6 +10,7 @@ source: # - fix.patch build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-getopt-long/meta.yaml b/recipes/perl-getopt-long/meta.yaml index b2e8612e8ce8a..16187e391a6ca 100644 --- a/recipes/perl-getopt-long/meta.yaml +++ b/recipes/perl-getopt-long/meta.yaml @@ -7,6 +7,7 @@ source: md5: c4824b8a135be64f1e09df8ebb2391a9 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-git-wrapper-plus/meta.yaml b/recipes/perl-git-wrapper-plus/meta.yaml index f3649e64e014b..bd5a227d3505e 100644 --- a/recipes/perl-git-wrapper-plus/meta.yaml +++ b/recipes/perl-git-wrapper-plus/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-git-wrapper/meta.yaml b/recipes/perl-git-wrapper/meta.yaml index b307b74a59976..e47607fb77aa0 100644 --- a/recipes/perl-git-wrapper/meta.yaml +++ b/recipes/perl-git-wrapper/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-go-perl/meta.yaml b/recipes/perl-go-perl/meta.yaml index 67a3c858603f3..bd55d632fc0a9 100644 --- a/recipes/perl-go-perl/meta.yaml +++ b/recipes/perl-go-perl/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-graph-readwrite/meta.yaml b/recipes/perl-graph-readwrite/meta.yaml index 1873e769dd487..39a5a94cf35d9 100644 --- a/recipes/perl-graph-readwrite/meta.yaml +++ b/recipes/perl-graph-readwrite/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-graph/meta.yaml b/recipes/perl-graph/meta.yaml index 7949d8bd3e539..a7b91351ee1fb 100644 --- a/recipes/perl-graph/meta.yaml +++ b/recipes/perl-graph/meta.yaml @@ -7,6 +7,7 @@ source: md5: 1ab4e49420e56eeb1bc81d842aa8f3af build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-graphics-colornames/meta.yaml b/recipes/perl-graphics-colornames/meta.yaml index 264e6bca1631b..c980e93605e02 100644 --- a/recipes/perl-graphics-colornames/meta.yaml +++ b/recipes/perl-graphics-colornames/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-graphics-colorobject/meta.yaml b/recipes/perl-graphics-colorobject/meta.yaml index 907b03fb135de..78c17e1846dde 100644 --- a/recipes/perl-graphics-colorobject/meta.yaml +++ b/recipes/perl-graphics-colorobject/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-graphviz/meta.yaml b/recipes/perl-graphviz/meta.yaml index e4c900805c644..e41b5312d9e8a 100644 --- a/recipes/perl-graphviz/meta.yaml +++ b/recipes/perl-graphviz/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-hash-merge/meta.yaml b/recipes/perl-hash-merge/meta.yaml index f00a6182b4d6b..434c224317ef6 100644 --- a/recipes/perl-hash-merge/meta.yaml +++ b/recipes/perl-hash-merge/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 402fd52191d51415bb7163b7673fb4a108e3156493d7df931b8db4b2af757c40 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml b/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml index 7b48bcbc8733f..50d7788b2ef9c 100644 --- a/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml +++ b/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-heap-simple-perl/meta.yaml b/recipes/perl-heap-simple-perl/meta.yaml index ef8b3e243ebf4..4f2a77c835629 100644 --- a/recipes/perl-heap-simple-perl/meta.yaml +++ b/recipes/perl-heap-simple-perl/meta.yaml @@ -7,6 +7,7 @@ source: md5: a2723ab28b7fcb35131037525a5b2f93 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-heap-simple/meta.yaml b/recipes/perl-heap-simple/meta.yaml index c2c4e48f25b4b..635a90aeded9d 100644 --- a/recipes/perl-heap-simple/meta.yaml +++ b/recipes/perl-heap-simple/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7a70c8e7e52b35c33bbbb9ad8cdbdeb4 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-heap/meta.yaml b/recipes/perl-heap/meta.yaml index 344742cee68f5..9148f551dcfe6 100644 --- a/recipes/perl-heap/meta.yaml +++ b/recipes/perl-heap/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-hook-lexwrap/0.26/meta.yaml b/recipes/perl-hook-lexwrap/0.26/meta.yaml index 4d3b34c80b3a9..22ad9eaff90d4 100644 --- a/recipes/perl-hook-lexwrap/0.26/meta.yaml +++ b/recipes/perl-hook-lexwrap/0.26/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-hpc-runner-command-plugin-logger-sqlite/0.0.3/meta.yaml b/recipes/perl-hpc-runner-command-plugin-logger-sqlite/0.0.3/meta.yaml index c7c2794a0fede..85b03da56c6f2 100644 --- a/recipes/perl-hpc-runner-command-plugin-logger-sqlite/0.0.3/meta.yaml +++ b/recipes/perl-hpc-runner-command-plugin-logger-sqlite/0.0.3/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 skip: True # [osx] diff --git a/recipes/perl-hpc-runner-command/3.2.13/meta.yaml b/recipes/perl-hpc-runner-command/3.2.13/meta.yaml index 93fbbafc01056..8715e2b77a9b4 100644 --- a/recipes/perl-hpc-runner-command/3.2.13/meta.yaml +++ b/recipes/perl-hpc-runner-command/3.2.13/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 #skip: True # [osx] diff --git a/recipes/perl-html-element-extended/meta.yaml b/recipes/perl-html-element-extended/meta.yaml index 0b2653eaa07c3..61f487c6f1095 100644 --- a/recipes/perl-html-element-extended/meta.yaml +++ b/recipes/perl-html-element-extended/meta.yaml @@ -7,6 +7,7 @@ source: md5: 41ec9dcc7cefa03b204d0e8ca8e1c112 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-html-entities-numbered/meta.yaml b/recipes/perl-html-entities-numbered/meta.yaml index 1556f6fdbf2dc..91de622ced0f8 100644 --- a/recipes/perl-html-entities-numbered/meta.yaml +++ b/recipes/perl-html-entities-numbered/meta.yaml @@ -7,6 +7,7 @@ source: md5: 9bc61132c10aa506d2629b37a2012729 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-html-form/meta.yaml b/recipes/perl-html-form/meta.yaml index 7b6795768ba93..049d3f9cf8db7 100644 --- a/recipes/perl-html-form/meta.yaml +++ b/recipes/perl-html-form/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-html-formatter/meta.yaml b/recipes/perl-html-formatter/meta.yaml index 3f3f0dbee5921..17c9fb769f8d4 100644 --- a/recipes/perl-html-formatter/meta.yaml +++ b/recipes/perl-html-formatter/meta.yaml @@ -7,6 +7,7 @@ source: sha256: cb0a0dd8aa5e8ba9ca214ce451bf4df33aa09c13e907e8d3082ddafeb30151cc build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-html-tableextract/meta.yaml b/recipes/perl-html-tableextract/meta.yaml index 839d327bb221f..93389a4bdd7fe 100644 --- a/recipes/perl-html-tableextract/meta.yaml +++ b/recipes/perl-html-tableextract/meta.yaml @@ -7,6 +7,7 @@ source: md5: 0d1d3f46a6a0336c5d20e61128e59cb6 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-html-tagset/meta.yaml b/recipes/perl-html-tagset/meta.yaml index 2b07fc9713dcd..a896aa02aab57 100644 --- a/recipes/perl-html-tagset/meta.yaml +++ b/recipes/perl-html-tagset/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-html-template/meta.yaml b/recipes/perl-html-template/meta.yaml index 2e62cbf9336b7..b74bbb58c09fe 100644 --- a/recipes/perl-html-template/meta.yaml +++ b/recipes/perl-html-template/meta.yaml @@ -7,6 +7,7 @@ source: md5: ee5f4a78102d2ffe089e047d2dbb0ff8 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-html-tidy/meta.yaml b/recipes/perl-html-tidy/meta.yaml index c04bdc60f8ddd..2750c94f1f272 100644 --- a/recipes/perl-html-tidy/meta.yaml +++ b/recipes/perl-html-tidy/meta.yaml @@ -9,6 +9,7 @@ source: - makefile-pl.patch build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-html-tree/meta.yaml b/recipes/perl-html-tree/meta.yaml index ea6891c4900cc..df34bed9d7f77 100644 --- a/recipes/perl-html-tree/meta.yaml +++ b/recipes/perl-html-tree/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-html-treebuilder-xpath/meta.yaml b/recipes/perl-html-treebuilder-xpath/meta.yaml index db34edeb12b14..ae777a9fcdc6e 100644 --- a/recipes/perl-html-treebuilder-xpath/meta.yaml +++ b/recipes/perl-html-treebuilder-xpath/meta.yaml @@ -7,6 +7,7 @@ source: md5: a3fa3b73ff51dd6ec63be394dcd2a3b5 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-http-cookies/meta.yaml b/recipes/perl-http-cookies/meta.yaml index 57157b9d31f78..aaf0115ecfe15 100644 --- a/recipes/perl-http-cookies/meta.yaml +++ b/recipes/perl-http-cookies/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-http-daemon/meta.yaml b/recipes/perl-http-daemon/meta.yaml index e316aac5f5d54..54b2f147a3d12 100644 --- a/recipes/perl-http-daemon/meta.yaml +++ b/recipes/perl-http-daemon/meta.yaml @@ -7,6 +7,7 @@ source: md5: ed0ae02d25d7f1e89456d4d69732adc2 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-http-date/meta.yaml b/recipes/perl-http-date/meta.yaml index b9f066f7b3f0a..12eddce2479fe 100644 --- a/recipes/perl-http-date/meta.yaml +++ b/recipes/perl-http-date/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-http-message/meta.yaml b/recipes/perl-http-message/meta.yaml index c9327270f6625..615435dde7477 100644 --- a/recipes/perl-http-message/meta.yaml +++ b/recipes/perl-http-message/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-http-negotiate/meta.yaml b/recipes/perl-http-negotiate/meta.yaml index 7459da978f00b..1ba4c7222a3fd 100644 --- a/recipes/perl-http-negotiate/meta.yaml +++ b/recipes/perl-http-negotiate/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-http-server-simple/meta.yaml b/recipes/perl-http-server-simple/meta.yaml index 88db11b51d701..fcfbcb9f48d90 100644 --- a/recipes/perl-http-server-simple/meta.yaml +++ b/recipes/perl-http-server-simple/meta.yaml @@ -8,6 +8,7 @@ source: build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-image-info/meta.yaml b/recipes/perl-image-info/meta.yaml index c83aaed7b020b..493d25173dae4 100644 --- a/recipes/perl-image-info/meta.yaml +++ b/recipes/perl-image-info/meta.yaml @@ -7,6 +7,7 @@ source: md5: 0fa4db4bdf14b6f453655bafa62d766a build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-image-size/meta.yaml b/recipes/perl-image-size/meta.yaml index 0d390d59248ab..e7abb62977092 100644 --- a/recipes/perl-image-size/meta.yaml +++ b/recipes/perl-image-size/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-import-into/meta.yaml b/recipes/perl-import-into/meta.yaml index ae0a11c9fd120..99121581b3c35 100644 --- a/recipes/perl-import-into/meta.yaml +++ b/recipes/perl-import-into/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-importer/meta.yaml b/recipes/perl-importer/meta.yaml index c8560017feea9..85fe5e5a04b9c 100644 --- a/recipes/perl-importer/meta.yaml +++ b/recipes/perl-importer/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 0745138c487d74033d0cbeb36f06595036dc7e688f1a5dbec9cc2fa799e13946 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-indirect/meta.yaml b/recipes/perl-indirect/meta.yaml index fabcbb0dd8705..b825b05b39d4d 100644 --- a/recipes/perl-indirect/meta.yaml +++ b/recipes/perl-indirect/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-inline/meta.yaml b/recipes/perl-inline/meta.yaml index 67495fa5b4ab0..92c07a8b1125f 100644 --- a/recipes/perl-inline/meta.yaml +++ b/recipes/perl-inline/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-integer/1.01/meta.yaml b/recipes/perl-integer/1.01/meta.yaml index decaa3f188502..6203f35210aac 100644 --- a/recipes/perl-integer/1.01/meta.yaml +++ b/recipes/perl-integer/1.01/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-all/meta.yaml b/recipes/perl-io-all/meta.yaml index 9c116be710428..ee23975755863 100644 --- a/recipes/perl-io-all/meta.yaml +++ b/recipes/perl-io-all/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 54e21d250c0229127e30b77a3461e10077854ec244f26fb670f1b445ed4c4d5b build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-io-compress-deflate/2.064/meta.yaml b/recipes/perl-io-compress-deflate/2.064/meta.yaml index f8de5369f62e6..c91d6681c2796 100644 --- a/recipes/perl-io-compress-deflate/2.064/meta.yaml +++ b/recipes/perl-io-compress-deflate/2.064/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-gzip/meta.yaml b/recipes/perl-io-gzip/meta.yaml index c4b19693c1c8f..5e478ffaf613e 100644 --- a/recipes/perl-io-gzip/meta.yaml +++ b/recipes/perl-io-gzip/meta.yaml @@ -7,6 +7,7 @@ source: md5: 0393eae5d0b23df6cf40ed44af7d711c build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-io-handle/1.35/meta.yaml b/recipes/perl-io-handle/1.35/meta.yaml index 8c17475118bd3..71b88c13ca15b 100644 --- a/recipes/perl-io-handle/1.35/meta.yaml +++ b/recipes/perl-io-handle/1.35/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-html/meta.yaml b/recipes/perl-io-html/meta.yaml index a1d37946322af..41fd40840d117 100644 --- a/recipes/perl-io-html/meta.yaml +++ b/recipes/perl-io-html/meta.yaml @@ -7,6 +7,7 @@ source: md5: 3f8958718844dc96b9f6946f21d70d22 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-io-interactive/meta.yaml b/recipes/perl-io-interactive/meta.yaml index 46f4e9837f2b2..2274b541b2dc2 100644 --- a/recipes/perl-io-interactive/meta.yaml +++ b/recipes/perl-io-interactive/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 0ed53b8ae93ae877e98e0d89b7b429e29ccd1ee4c28e952c4ea9aa73d01febdc build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-io-prompt/meta.yaml b/recipes/perl-io-prompt/meta.yaml index 40655e3cd9c71..ae772d22b2023 100644 --- a/recipes/perl-io-prompt/meta.yaml +++ b/recipes/perl-io-prompt/meta.yaml @@ -23,6 +23,7 @@ source: - patches/yesno.pl.patch build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-io-scalar/2.111/meta.yaml b/recipes/perl-io-scalar/2.111/meta.yaml index a4a37ca79e264..87dbd89f675ae 100644 --- a/recipes/perl-io-scalar/2.111/meta.yaml +++ b/recipes/perl-io-scalar/2.111/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-sessiondata/meta.yaml b/recipes/perl-io-sessiondata/meta.yaml index 99773e49e6ad9..447c40ae1c3ca 100644 --- a/recipes/perl-io-sessiondata/meta.yaml +++ b/recipes/perl-io-sessiondata/meta.yaml @@ -7,6 +7,7 @@ source: md5: 790f9e05465c774cf9a6299500463104 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-socket-inet6/meta.yaml b/recipes/perl-io-socket-inet6/meta.yaml index c0190c987ce3e..2032fa8101e05 100644 --- a/recipes/perl-io-socket-inet6/meta.yaml +++ b/recipes/perl-io-socket-inet6/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-io-socket-ssl/meta.yaml b/recipes/perl-io-socket-ssl/meta.yaml index 91bf49a234dab..428def5b9fa0f 100644 --- a/recipes/perl-io-socket-ssl/meta.yaml +++ b/recipes/perl-io-socket-ssl/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-io-string/meta.yaml b/recipes/perl-io-string/meta.yaml index 8f7d8d6963a63..48a321bfafdf0 100644 --- a/recipes/perl-io-string/meta.yaml +++ b/recipes/perl-io-string/meta.yaml @@ -7,6 +7,7 @@ source: md5: 250e5424f290299fc3d6b5d1e9da3835 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-io-stringy/meta.yaml b/recipes/perl-io-stringy/meta.yaml index cdfd977289fad..ece088a9a0012 100644 --- a/recipes/perl-io-stringy/meta.yaml +++ b/recipes/perl-io-stringy/meta.yaml @@ -7,6 +7,7 @@ source: md5: e91acf0a800b190d13585a47de775bdd build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-tty/meta.yaml b/recipes/perl-io-tty/meta.yaml index 4d74fdd357e2c..c7c22c4121af5 100644 --- a/recipes/perl-io-tty/meta.yaml +++ b/recipes/perl-io-tty/meta.yaml @@ -7,6 +7,7 @@ source: md5: 11695a1a516b3bd1b90ce75ff0ce3e6d build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-uncompress-bunzip2/2.064/meta.yaml b/recipes/perl-io-uncompress-bunzip2/2.064/meta.yaml index 8611d3909240a..a2595b8793c8d 100644 --- a/recipes/perl-io-uncompress-bunzip2/2.064/meta.yaml +++ b/recipes/perl-io-uncompress-bunzip2/2.064/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-uncompress-gunzip/2.064/meta.yaml b/recipes/perl-io-uncompress-gunzip/2.064/meta.yaml index 170aab348d9c0..03b488fa96ec1 100644 --- a/recipes/perl-io-uncompress-gunzip/2.064/meta.yaml +++ b/recipes/perl-io-uncompress-gunzip/2.064/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-uncompress-rawinflate/2.064/meta.yaml b/recipes/perl-io-uncompress-rawinflate/2.064/meta.yaml index 741e07dccd0d3..ac4fc020cff0e 100644 --- a/recipes/perl-io-uncompress-rawinflate/2.064/meta.yaml +++ b/recipes/perl-io-uncompress-rawinflate/2.064/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-io-zlib/meta.yaml b/recipes/perl-io-zlib/meta.yaml index dd3f4f0707f3c..ee9911b00bd65 100644 --- a/recipes/perl-io-zlib/meta.yaml +++ b/recipes/perl-io-zlib/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-ipc-cmd/meta.yaml b/recipes/perl-ipc-cmd/meta.yaml index e164fc9463d37..65f0af9413ca6 100644 --- a/recipes/perl-ipc-cmd/meta.yaml +++ b/recipes/perl-ipc-cmd/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-ipc-run/meta.yaml b/recipes/perl-ipc-run/meta.yaml index 540bd42e94272..679e1208c7a90 100644 --- a/recipes/perl-ipc-run/meta.yaml +++ b/recipes/perl-ipc-run/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 3850d7edf8a4671391c6e99bb770698e1c45da55b323b31c76310913349b6c2f build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-ipc-run3/meta.yaml b/recipes/perl-ipc-run3/meta.yaml index d057e0bf068f6..aeae046693772 100644 --- a/recipes/perl-ipc-run3/meta.yaml +++ b/recipes/perl-ipc-run3/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-ipc-system-simple/meta.yaml b/recipes/perl-ipc-system-simple/meta.yaml index 255ec76206bed..2ffc7411c3fd4 100644 --- a/recipes/perl-ipc-system-simple/meta.yaml +++ b/recipes/perl-ipc-system-simple/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 5 requirements: diff --git a/recipes/perl-jcode/meta.yaml b/recipes/perl-jcode/meta.yaml index 5da9a69fd1849..6588f77e9733a 100644 --- a/recipes/perl-jcode/meta.yaml +++ b/recipes/perl-jcode/meta.yaml @@ -7,6 +7,7 @@ source: md5: f6c52253ff69a44c38a9183c469f6eb0 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-json-create/meta.yaml b/recipes/perl-json-create/meta.yaml index 896156249c4e1..95c77f9e2c5ea 100644 --- a/recipes/perl-json-create/meta.yaml +++ b/recipes/perl-json-create/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-json-maybexs/meta.yaml b/recipes/perl-json-maybexs/meta.yaml index 86ae88f24de9d..fe40f320dee66 100644 --- a/recipes/perl-json-maybexs/meta.yaml +++ b/recipes/perl-json-maybexs/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-json/meta.yaml b/recipes/perl-json/meta.yaml index aa0803d098962..18742e73497af 100644 --- a/recipes/perl-json/meta.yaml +++ b/recipes/perl-json/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 444a88755a89ffa2a5424ab4ed1d11dca61808ebef57e81243424619a9e8627c build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-lib/0.63/meta.yaml b/recipes/perl-lib/0.63/meta.yaml index 363c072b6105e..cb686d7ad335b 100644 --- a/recipes/perl-lib/0.63/meta.yaml +++ b/recipes/perl-lib/0.63/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-libxml-perl/meta.yaml b/recipes/perl-libxml-perl/meta.yaml index fff5d340e652d..73c1a8fdc4103 100644 --- a/recipes/perl-libxml-perl/meta.yaml +++ b/recipes/perl-libxml-perl/meta.yaml @@ -7,6 +7,7 @@ source: md5: 0ed5fbdda53d1301ddaed88db10503bb build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-list-compare/0.53/meta.yaml b/recipes/perl-list-compare/0.53/meta.yaml index ebcffa7c16c0c..512b6902dcf1b 100644 --- a/recipes/perl-list-compare/0.53/meta.yaml +++ b/recipes/perl-list-compare/0.53/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-list-moreutils-xs/meta.yaml b/recipes/perl-list-moreutils-xs/meta.yaml index 36b98fdf70802..e6d74ba54b6f6 100644 --- a/recipes/perl-list-moreutils-xs/meta.yaml +++ b/recipes/perl-list-moreutils-xs/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-list-moreutils/meta.yaml b/recipes/perl-list-moreutils/meta.yaml index 484845c0e970f..f93aebfa07c60 100644 --- a/recipes/perl-list-moreutils/meta.yaml +++ b/recipes/perl-list-moreutils/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-list-uniq/meta.yaml b/recipes/perl-list-uniq/meta.yaml index 0dc5c934b0085..ed2cad5300099 100644 --- a/recipes/perl-list-uniq/meta.yaml +++ b/recipes/perl-list-uniq/meta.yaml @@ -7,6 +7,7 @@ source: md5: 06abbe2fddf2522b9100d672a48fae59 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-local-lib/meta.yaml b/recipes/perl-local-lib/meta.yaml index b3bdc1443ac2b..d85392d181c0a 100644 --- a/recipes/perl-local-lib/meta.yaml +++ b/recipes/perl-local-lib/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-locale-maketext-simple/meta.yaml b/recipes/perl-locale-maketext-simple/meta.yaml index bcf79332f1264..57bc581a43a94 100644 --- a/recipes/perl-locale-maketext-simple/meta.yaml +++ b/recipes/perl-locale-maketext-simple/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-locale/1.03/meta.yaml b/recipes/perl-locale/1.03/meta.yaml index f91cec6792800..5bc33a67e2841 100644 --- a/recipes/perl-locale/1.03/meta.yaml +++ b/recipes/perl-locale/1.03/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-log-any/meta.yaml b/recipes/perl-log-any/meta.yaml index 1141f1aa1039f..0e8871fb093c6 100644 --- a/recipes/perl-log-any/meta.yaml +++ b/recipes/perl-log-any/meta.yaml @@ -7,6 +7,7 @@ source: md5: 99ee3bfe069838008110ec52cac8c8c3 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-log-log4perl/meta.yaml b/recipes/perl-log-log4perl/meta.yaml index 5ee1f9041e2f3..b540798365ba5 100644 --- a/recipes/perl-log-log4perl/meta.yaml +++ b/recipes/perl-log-log4perl/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-logger-simple/meta.yaml b/recipes/perl-logger-simple/meta.yaml index 766cd6ad70a7d..2986db1886aec 100644 --- a/recipes/perl-logger-simple/meta.yaml +++ b/recipes/perl-logger-simple/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-lwp-mediatypes/meta.yaml b/recipes/perl-lwp-mediatypes/meta.yaml index e2fc50ea121f7..578c4d8d02b0f 100644 --- a/recipes/perl-lwp-mediatypes/meta.yaml +++ b/recipes/perl-lwp-mediatypes/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-lwp-protocol-https/meta.yaml b/recipes/perl-lwp-protocol-https/meta.yaml index fdec38a62fa0a..8b77196883da2 100644 --- a/recipes/perl-lwp-protocol-https/meta.yaml +++ b/recipes/perl-lwp-protocol-https/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 522cc946cf84a1776304a5737a54b8822ec9e79b264d0ba0722a70473dbfb9e7 build: + noarch: generic number: 4 requirements: diff --git a/recipes/perl-mac-propertylist/meta.yaml b/recipes/perl-mac-propertylist/meta.yaml index ddeb8c470cb01..bb24ddfad4ea6 100644 --- a/recipes/perl-mac-propertylist/meta.yaml +++ b/recipes/perl-mac-propertylist/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-mac-systemdirectory/meta.yaml b/recipes/perl-mac-systemdirectory/meta.yaml index 2824d2c302da2..a32f79f648767 100644 --- a/recipes/perl-mac-systemdirectory/meta.yaml +++ b/recipes/perl-mac-systemdirectory/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 skip: True # [not osx] diff --git a/recipes/perl-math-base-convert/meta.yaml b/recipes/perl-math-base-convert/meta.yaml index 5fdda66f84871..586ddc6c81478 100644 --- a/recipes/perl-math-base-convert/meta.yaml +++ b/recipes/perl-math-base-convert/meta.yaml @@ -7,6 +7,7 @@ source: md5: aed8356d8e2870ee1d27a7b6c5752714 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-math-bezier/meta.yaml b/recipes/perl-math-bezier/meta.yaml index a6731683aa528..33b99588e2826 100644 --- a/recipes/perl-math-bezier/meta.yaml +++ b/recipes/perl-math-bezier/meta.yaml @@ -7,6 +7,7 @@ source: md5: ba6874d8754e2d64ab9c7d15e0eb56c2 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index d5f0286bb0e79..114a4bb6e470c 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-math-bigrat/meta.yaml b/recipes/perl-math-bigrat/meta.yaml index 18949f6c17d95..787232e47a9af 100644 --- a/recipes/perl-math-bigrat/meta.yaml +++ b/recipes/perl-math-bigrat/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-math-combinatorics/meta.yaml b/recipes/perl-math-combinatorics/meta.yaml index 1559e4064270a..1d3755bc009ae 100644 --- a/recipes/perl-math-combinatorics/meta.yaml +++ b/recipes/perl-math-combinatorics/meta.yaml @@ -7,6 +7,7 @@ source: md5: de556a046f00789c94cf58cb7c2d9d89 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-math-complex/meta.yaml b/recipes/perl-math-complex/meta.yaml index ef8b31b3f4a8a..756b2de4a8568 100644 --- a/recipes/perl-math-complex/meta.yaml +++ b/recipes/perl-math-complex/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-math-derivative/meta.yaml b/recipes/perl-math-derivative/meta.yaml index 7c4ffdf524ad5..cee44f848580a 100644 --- a/recipes/perl-math-derivative/meta.yaml +++ b/recipes/perl-math-derivative/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 14c0b3fa05dcb74a44a9de6b4b08c3e58e672826b5f8e47535325b64f6ee69e6 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-math-round/meta.yaml b/recipes/perl-math-round/meta.yaml index 805ee1f0ac49a..76f40dc554ccb 100644 --- a/recipes/perl-math-round/meta.yaml +++ b/recipes/perl-math-round/meta.yaml @@ -7,6 +7,7 @@ source: md5: b74c5d2a3f891c19dafd7ce638732fd1 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-math-spline/meta.yaml b/recipes/perl-math-spline/meta.yaml index 3d7622735e0d3..1b8841a98427a 100644 --- a/recipes/perl-math-spline/meta.yaml +++ b/recipes/perl-math-spline/meta.yaml @@ -7,6 +7,7 @@ source: md5: 64c7bb3829e1fa7e49c2bf50b358c7c7 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-math-utils/meta.yaml b/recipes/perl-math-utils/meta.yaml index 8c8507041704f..f3f4b956d90a1 100644 --- a/recipes/perl-math-utils/meta.yaml +++ b/recipes/perl-math-utils/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-math-vecstat/meta.yaml b/recipes/perl-math-vecstat/meta.yaml index 8df92b157a170..1dce05e52223f 100644 --- a/recipes/perl-math-vecstat/meta.yaml +++ b/recipes/perl-math-vecstat/meta.yaml @@ -7,6 +7,7 @@ source: md5: 3df23fb451f73bb49fd4ea344ba94020 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mce-shared/meta.yaml b/recipes/perl-mce-shared/meta.yaml index 6df15db68c18f..3a30495a8fb8b 100644 --- a/recipes/perl-mce-shared/meta.yaml +++ b/recipes/perl-mce-shared/meta.yaml @@ -12,6 +12,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-mce/meta.yaml b/recipes/perl-mce/meta.yaml index 6e85101e70016..fd78e73776b78 100644 --- a/recipes/perl-mce/meta.yaml +++ b/recipes/perl-mce/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-memoize/meta.yaml b/recipes/perl-memoize/meta.yaml index 44c16f75cd3bc..8a62b23528627 100644 --- a/recipes/perl-memoize/meta.yaml +++ b/recipes/perl-memoize/meta.yaml @@ -7,6 +7,7 @@ source: md5: 6de4628f734fc898429c5b21367c02ab build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-mime-base64/meta.yaml b/recipes/perl-mime-base64/meta.yaml index e061fc34b5daf..3745920667ea5 100644 --- a/recipes/perl-mime-base64/meta.yaml +++ b/recipes/perl-mime-base64/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mime-lite/meta.yaml b/recipes/perl-mime-lite/meta.yaml index f6295e76eab69..fa52cff0b277a 100644 --- a/recipes/perl-mime-lite/meta.yaml +++ b/recipes/perl-mime-lite/meta.yaml @@ -7,6 +7,7 @@ source: md5: 5a6d90329e049eee77248d667343acc7 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mime-quotedprint/3.13/meta.yaml b/recipes/perl-mime-quotedprint/3.13/meta.yaml index f6afb5bb96d80..4e5de903b1228 100644 --- a/recipes/perl-mime-quotedprint/3.13/meta.yaml +++ b/recipes/perl-mime-quotedprint/3.13/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mime-tools/meta.yaml b/recipes/perl-mime-tools/meta.yaml index 5b77dead3393c..f28b7989a0a1f 100644 --- a/recipes/perl-mime-tools/meta.yaml +++ b/recipes/perl-mime-tools/meta.yaml @@ -7,6 +7,7 @@ source: sha256: adffe86cd0b045d5a1553f48e72e89b9834fbda4f334c98215995b98cb17c917 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mime-types/meta.yaml b/recipes/perl-mime-types/meta.yaml index 7f39f22aa98ee..c1754fb402aac 100644 --- a/recipes/perl-mime-types/meta.yaml +++ b/recipes/perl-mime-types/meta.yaml @@ -7,6 +7,7 @@ source: sha256: e04ed7d42f1ff3150a303805f2689c28f80b92c511784d4641cb7f040d3e8ff6 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-mixin-linewise/meta.yaml b/recipes/perl-mixin-linewise/meta.yaml index 18f44ee0fd328..9b80c6adc7b13 100644 --- a/recipes/perl-mixin-linewise/meta.yaml +++ b/recipes/perl-mixin-linewise/meta.yaml @@ -7,6 +7,7 @@ source: md5: c0f62761c6ce2ae6dc3e54153d042009 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-mldbm-sync/meta.yaml b/recipes/perl-mldbm-sync/meta.yaml index f63a4c1c6e181..8e772ade8b744 100644 --- a/recipes/perl-mldbm-sync/meta.yaml +++ b/recipes/perl-mldbm-sync/meta.yaml @@ -7,6 +7,7 @@ source: md5: 1bb4e8d4bd6a30eee3f1126956409321 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mldbm/meta.yaml b/recipes/perl-mldbm/meta.yaml index fdc80960a3d16..ae2585933b3b7 100644 --- a/recipes/perl-mldbm/meta.yaml +++ b/recipes/perl-mldbm/meta.yaml @@ -7,6 +7,7 @@ source: md5: 9b7ec37bfc36b0e83db9323be92beb50 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-module-build-tiny/meta.yaml b/recipes/perl-module-build-tiny/meta.yaml index 797026964476b..8e1f83a406a97 100644 --- a/recipes/perl-module-build-tiny/meta.yaml +++ b/recipes/perl-module-build-tiny/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-module-build/meta.yaml b/recipes/perl-module-build/meta.yaml index bbdf8ddffb7af..ea6869558b67f 100644 --- a/recipes/perl-module-build/meta.yaml +++ b/recipes/perl-module-build/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-module-corelist/meta.yaml b/recipes/perl-module-corelist/meta.yaml index 2a0c87c7b69b8..4d09ebb288845 100644 --- a/recipes/perl-module-corelist/meta.yaml +++ b/recipes/perl-module-corelist/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-module-extract-use/1.043/meta.yaml b/recipes/perl-module-extract-use/1.043/meta.yaml index bee2f254bccb1..8041a6f92d985 100644 --- a/recipes/perl-module-extract-use/1.043/meta.yaml +++ b/recipes/perl-module-extract-use/1.043/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-module-fromperlver/0.008002/meta.yaml b/recipes/perl-module-fromperlver/0.008002/meta.yaml index def8364b803a8..f27d3361e65f3 100644 --- a/recipes/perl-module-fromperlver/0.008002/meta.yaml +++ b/recipes/perl-module-fromperlver/0.008002/meta.yaml @@ -7,6 +7,7 @@ source: md5: d17aba7a26509a0102b9360ac0fdb9c7 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-module-implementation/meta.yaml b/recipes/perl-module-implementation/meta.yaml index 0de2e937f4c99..3d7d1779c0ac9 100644 --- a/recipes/perl-module-implementation/meta.yaml +++ b/recipes/perl-module-implementation/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-module-list/meta.yaml b/recipes/perl-module-list/meta.yaml index 51c1cfb79b1e2..4658061250c8b 100644 --- a/recipes/perl-module-list/meta.yaml +++ b/recipes/perl-module-list/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-module-load-conditional/0.62/meta.yaml b/recipes/perl-module-load-conditional/0.62/meta.yaml index 3b05d73d663be..b1da60a81d06d 100644 --- a/recipes/perl-module-load-conditional/0.62/meta.yaml +++ b/recipes/perl-module-load-conditional/0.62/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-module-load-conditional/0.68/meta.yaml b/recipes/perl-module-load-conditional/0.68/meta.yaml index c457b7dd7f438..8f22c579b2e6f 100644 --- a/recipes/perl-module-load-conditional/0.68/meta.yaml +++ b/recipes/perl-module-load-conditional/0.68/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-module-load/0.32/meta.yaml b/recipes/perl-module-load/0.32/meta.yaml index 5e4eea71dc7bd..88be3cf50900b 100644 --- a/recipes/perl-module-load/0.32/meta.yaml +++ b/recipes/perl-module-load/0.32/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-module-loaded/meta.yaml b/recipes/perl-module-loaded/meta.yaml index c33d9a005ae7f..f4cf1e517fedb 100644 --- a/recipes/perl-module-loaded/meta.yaml +++ b/recipes/perl-module-loaded/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-module-metadata/meta.yaml b/recipes/perl-module-metadata/meta.yaml index 84c5ba21cbb1b..69b8d95060803 100644 --- a/recipes/perl-module-metadata/meta.yaml +++ b/recipes/perl-module-metadata/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-module-pluggable/meta.yaml b/recipes/perl-module-pluggable/meta.yaml index f03a148b7b6df..f0c0165f998f3 100644 --- a/recipes/perl-module-pluggable/meta.yaml +++ b/recipes/perl-module-pluggable/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-module-runtime-conflicts/meta.yaml b/recipes/perl-module-runtime-conflicts/meta.yaml index 7b80fc88abce2..df3803b97067c 100644 --- a/recipes/perl-module-runtime-conflicts/meta.yaml +++ b/recipes/perl-module-runtime-conflicts/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-module-runtime/meta.yaml b/recipes/perl-module-runtime/meta.yaml index f18e8744a858f..b7c8ea860eb8c 100644 --- a/recipes/perl-module-runtime/meta.yaml +++ b/recipes/perl-module-runtime/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-module-scandeps/meta.yaml b/recipes/perl-module-scandeps/meta.yaml index a57ec71bb157b..8aaa2f3f7d141 100644 --- a/recipes/perl-module-scandeps/meta.yaml +++ b/recipes/perl-module-scandeps/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-module-util/meta.yaml b/recipes/perl-module-util/meta.yaml index 973aa2b7a9c27..d3382c8642a61 100644 --- a/recipes/perl-module-util/meta.yaml +++ b/recipes/perl-module-util/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moo/meta.yaml b/recipes/perl-moo/meta.yaml index f7f3a81c6d350..7db7eed80ce70 100644 --- a/recipes/perl-moo/meta.yaml +++ b/recipes/perl-moo/meta.yaml @@ -7,6 +7,7 @@ source: sha256: f8bbb625f8e963eabe05cff9048fdd72bdd26777404ff2c40bc690f558be91e1 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-app-role-log4perl/meta.yaml b/recipes/perl-moosex-app-role-log4perl/meta.yaml index 83d25ac5d2f8f..3907e1cb89d35 100644 --- a/recipes/perl-moosex-app-role-log4perl/meta.yaml +++ b/recipes/perl-moosex-app-role-log4perl/meta.yaml @@ -10,6 +10,7 @@ source: # - fix.patch build: + noarch: generic skip: True # [osx] number: 1 diff --git a/recipes/perl-moosex-app/1.39/meta.yaml b/recipes/perl-moosex-app/1.39/meta.yaml index e444036498e34..d590c7a189b7d 100644 --- a/recipes/perl-moosex-app/1.39/meta.yaml +++ b/recipes/perl-moosex-app/1.39/meta.yaml @@ -7,6 +7,7 @@ source: md5: 36040281ec23ad0dee068c70e57ea106 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-moosex-app/meta.yaml b/recipes/perl-moosex-app/meta.yaml index efda20fe9489c..3ba72dc8d27e4 100644 --- a/recipes/perl-moosex-app/meta.yaml +++ b/recipes/perl-moosex-app/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 57ef199b45fa26bc519a4cc4713783b76ebe5b572b19870ff5df3c56ac0dd77f build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-moosex-clone/0.06/meta.yaml b/recipes/perl-moosex-clone/0.06/meta.yaml index 6f57c2c72f949..42502984b019a 100644 --- a/recipes/perl-moosex-clone/0.06/meta.yaml +++ b/recipes/perl-moosex-clone/0.06/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-moosex-fileattribute/meta.yaml b/recipes/perl-moosex-fileattribute/meta.yaml index 927f4f951192d..c90312b28376e 100644 --- a/recipes/perl-moosex-fileattribute/meta.yaml +++ b/recipes/perl-moosex-fileattribute/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-getopt/meta.yaml b/recipes/perl-moosex-getopt/meta.yaml index a9e98842c7c5e..3c9ec7386f43d 100644 --- a/recipes/perl-moosex-getopt/meta.yaml +++ b/recipes/perl-moosex-getopt/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-nonmoose/meta.yaml b/recipes/perl-moosex-nonmoose/meta.yaml index 1fad606d1d3bb..b055635f400c3 100644 --- a/recipes/perl-moosex-nonmoose/meta.yaml +++ b/recipes/perl-moosex-nonmoose/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-moosex-object-pluggable/0.0014/meta.yaml b/recipes/perl-moosex-object-pluggable/0.0014/meta.yaml index 0aceaeecd3b63..f263b96ea9820 100644 --- a/recipes/perl-moosex-object-pluggable/0.0014/meta.yaml +++ b/recipes/perl-moosex-object-pluggable/0.0014/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-role-parameterized/meta.yaml b/recipes/perl-moosex-role-parameterized/meta.yaml index 1513ab0f5622f..41447b74647a7 100644 --- a/recipes/perl-moosex-role-parameterized/meta.yaml +++ b/recipes/perl-moosex-role-parameterized/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-singleton/meta.yaml b/recipes/perl-moosex-singleton/meta.yaml index 2a8e1f68fe969..13db543f67b3d 100644 --- a/recipes/perl-moosex-singleton/meta.yaml +++ b/recipes/perl-moosex-singleton/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-types-path-class/meta.yaml b/recipes/perl-moosex-types-path-class/meta.yaml index 0f0f0c246e38a..dfb36eb2d68da 100644 --- a/recipes/perl-moosex-types-path-class/meta.yaml +++ b/recipes/perl-moosex-types-path-class/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 4 requirements: diff --git a/recipes/perl-moosex-types-path-tiny/meta.yaml b/recipes/perl-moosex-types-path-tiny/meta.yaml index 4cd5621cc15cd..9c98640e512e6 100644 --- a/recipes/perl-moosex-types-path-tiny/meta.yaml +++ b/recipes/perl-moosex-types-path-tiny/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-moosex-types-stringlike/meta.yaml b/recipes/perl-moosex-types-stringlike/meta.yaml index 943e47c86b19f..b569caefea7ee 100644 --- a/recipes/perl-moosex-types-stringlike/meta.yaml +++ b/recipes/perl-moosex-types-stringlike/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-moosex-types/meta.yaml b/recipes/perl-moosex-types/meta.yaml index a846635bfa1b9..ab2d120f858ab 100644 --- a/recipes/perl-moosex-types/meta.yaml +++ b/recipes/perl-moosex-types/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mozilla-ca/meta.yaml b/recipes/perl-mozilla-ca/meta.yaml index f001167fd7628..1104ced13cf56 100644 --- a/recipes/perl-mozilla-ca/meta.yaml +++ b/recipes/perl-mozilla-ca/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-mro-compat/meta.yaml b/recipes/perl-mro-compat/meta.yaml index 97f8feba8d177..de58a2fd3aab7 100644 --- a/recipes/perl-mro-compat/meta.yaml +++ b/recipes/perl-mro-compat/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-net-ftp-recursive/2.04/meta.yaml b/recipes/perl-net-ftp-recursive/2.04/meta.yaml index 4556a58958712..b3a695dc05822 100644 --- a/recipes/perl-net-ftp-recursive/2.04/meta.yaml +++ b/recipes/perl-net-ftp-recursive/2.04/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-net-ftp/2.79/meta.yaml b/recipes/perl-net-ftp/2.79/meta.yaml index 1fe253bc684c8..1abfdafc7c809 100644 --- a/recipes/perl-net-ftp/2.79/meta.yaml +++ b/recipes/perl-net-ftp/2.79/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-net-netrc/2.14/meta.yaml b/recipes/perl-net-netrc/2.14/meta.yaml index 90a850b0b8f00..e4525f842693b 100644 --- a/recipes/perl-net-netrc/2.14/meta.yaml +++ b/recipes/perl-net-netrc/2.14/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-ntlm/meta.yaml b/recipes/perl-ntlm/meta.yaml index bb0b13bd427ef..a2f6cf7bd70c1 100644 --- a/recipes/perl-ntlm/meta.yaml +++ b/recipes/perl-ntlm/meta.yaml @@ -7,6 +7,7 @@ source: md5: da314ee94b14af2a2f39b6f2c0046e73 build: + noarch: generic number: 4 requirements: diff --git a/recipes/perl-number-compare/meta.yaml b/recipes/perl-number-compare/meta.yaml index ea473a0e430ee..aa30ef6906cfa 100644 --- a/recipes/perl-number-compare/meta.yaml +++ b/recipes/perl-number-compare/meta.yaml @@ -7,6 +7,7 @@ source: md5: ded4085a8fc96328742785574ca65208 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-number-format/meta.yaml b/recipes/perl-number-format/meta.yaml index a5c8178c24637..f1ece6bea6e54 100644 --- a/recipes/perl-number-format/meta.yaml +++ b/recipes/perl-number-format/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-number-misc/1.2/meta.yaml b/recipes/perl-number-misc/1.2/meta.yaml index 4f195d2c03b37..cc15f77278580 100644 --- a/recipes/perl-number-misc/1.2/meta.yaml +++ b/recipes/perl-number-misc/1.2/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7a0009b5be60378f204ed1fc9b2d5a19 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-number-range/meta.yaml b/recipes/perl-number-range/meta.yaml index 1ffe1af7a3f48..77738a05684db 100644 --- a/recipes/perl-number-range/meta.yaml +++ b/recipes/perl-number-range/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-number-witherror/1.01/meta.yaml b/recipes/perl-number-witherror/1.01/meta.yaml index 988ea3d653d8f..f9141f855ca9e 100644 --- a/recipes/perl-number-witherror/1.01/meta.yaml +++ b/recipes/perl-number-witherror/1.01/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-object-insideout/meta.yaml b/recipes/perl-object-insideout/meta.yaml index 65dc7c0a80a30..7570245d8094d 100644 --- a/recipes/perl-object-insideout/meta.yaml +++ b/recipes/perl-object-insideout/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-ole-storage_lite/meta.yaml b/recipes/perl-ole-storage_lite/meta.yaml index 5d4bb3739363d..6739d3dd4061b 100644 --- a/recipes/perl-ole-storage_lite/meta.yaml +++ b/recipes/perl-ole-storage_lite/meta.yaml @@ -7,6 +7,7 @@ source: md5: 1a713f5342c7d90e54ab0d9659650296 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-onto-perl/meta.yaml b/recipes/perl-onto-perl/meta.yaml index 023d99d5ad4f7..88824224cd591 100644 --- a/recipes/perl-onto-perl/meta.yaml +++ b/recipes/perl-onto-perl/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-ostype/meta.yaml b/recipes/perl-ostype/meta.yaml index b13aba9a6afa6..6658816a613cd 100644 --- a/recipes/perl-ostype/meta.yaml +++ b/recipes/perl-ostype/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-package-deprecationmanager/meta.yaml b/recipes/perl-package-deprecationmanager/meta.yaml index ce9c71cf7a846..fc442beea47d3 100644 --- a/recipes/perl-package-deprecationmanager/meta.yaml +++ b/recipes/perl-package-deprecationmanager/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-par-dist/0.49/meta.yaml b/recipes/perl-par-dist/0.49/meta.yaml index ccde939999edb..20ad0fc9a4d70 100644 --- a/recipes/perl-par-dist/0.49/meta.yaml +++ b/recipes/perl-par-dist/0.49/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-par-packer/1.036/meta.yaml b/recipes/perl-par-packer/1.036/meta.yaml index 44085d97fa1e3..386a682ec57d2 100644 --- a/recipes/perl-par-packer/1.036/meta.yaml +++ b/recipes/perl-par-packer/1.036/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 2 skip: True # [osx] diff --git a/recipes/perl-par/1.014/meta.yaml b/recipes/perl-par/1.014/meta.yaml index 005bc2af06286..073b126babb2a 100644 --- a/recipes/perl-par/1.014/meta.yaml +++ b/recipes/perl-par/1.014/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-parallel-forkmanager/meta.yaml b/recipes/perl-parallel-forkmanager/meta.yaml index 4aa8ccc2fda3d..8464e35b3841c 100644 --- a/recipes/perl-parallel-forkmanager/meta.yaml +++ b/recipes/perl-parallel-forkmanager/meta.yaml @@ -7,6 +7,7 @@ source: sha256: c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-parallel-iterator/meta.yaml b/recipes/perl-parallel-iterator/meta.yaml index 1f828d13b58fd..d23e13338049c 100644 --- a/recipes/perl-parallel-iterator/meta.yaml +++ b/recipes/perl-parallel-iterator/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-parallel-loops/meta.yaml b/recipes/perl-parallel-loops/meta.yaml index 12e1eeb0d9ff4..d347a06cd3f99 100644 --- a/recipes/perl-parallel-loops/meta.yaml +++ b/recipes/perl-parallel-loops/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-params-check/0.38/meta.yaml b/recipes/perl-params-check/0.38/meta.yaml index 04c275e4cfdbb..93834b4b3a045 100644 --- a/recipes/perl-params-check/0.38/meta.yaml +++ b/recipes/perl-params-check/0.38/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-params-coerce/0.14/meta.yaml b/recipes/perl-params-coerce/0.14/meta.yaml index 1cbbdfdd90132..61ff3dff9355a 100644 --- a/recipes/perl-params-coerce/0.14/meta.yaml +++ b/recipes/perl-params-coerce/0.14/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-params-validate/1.26/meta.yaml b/recipes/perl-params-validate/1.26/meta.yaml index 0cc7a4a52a131..985d631bed442 100644 --- a/recipes/perl-params-validate/1.26/meta.yaml +++ b/recipes/perl-params-validate/1.26/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-parent/0.236/meta.yaml b/recipes/perl-parent/0.236/meta.yaml index 9dc756c023ab0..8ca7dc6f93d4f 100644 --- a/recipes/perl-parent/0.236/meta.yaml +++ b/recipes/perl-parent/0.236/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-parse-recdescent/meta.yaml b/recipes/perl-parse-recdescent/meta.yaml index 64dd40a9b24fb..9225c72513866 100644 --- a/recipes/perl-parse-recdescent/meta.yaml +++ b/recipes/perl-parse-recdescent/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-parse-yapp/meta.yaml b/recipes/perl-parse-yapp/meta.yaml index 7665a14c88abb..8d58cb6296607 100644 --- a/recipes/perl-parse-yapp/meta.yaml +++ b/recipes/perl-parse-yapp/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-path-class/meta.yaml b/recipes/perl-path-class/meta.yaml index 801c0a0de8514..b8a9c96e7fff6 100644 --- a/recipes/perl-path-class/meta.yaml +++ b/recipes/perl-path-class/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-path-tiny/0.076/meta.yaml b/recipes/perl-path-tiny/0.076/meta.yaml index a8829999ce112..59d3a4ada9062 100644 --- a/recipes/perl-path-tiny/0.076/meta.yaml +++ b/recipes/perl-path-tiny/0.076/meta.yaml @@ -7,6 +7,7 @@ source: md5: 495b965187a59af9b99c0f4709013746 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-path-tiny/meta.yaml b/recipes/perl-path-tiny/meta.yaml index f9f5668be9546..a2dbc3b287308 100644 --- a/recipes/perl-path-tiny/meta.yaml +++ b/recipes/perl-path-tiny/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 3c49482be2b3eb7ddd7e73a5b90cff648393f5d5de334ff126ce7a3632723ff5 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-pbkdf2-tiny/meta.yaml b/recipes/perl-pbkdf2-tiny/meta.yaml index a9d07e08d018e..5c3eab77b7833 100644 --- a/recipes/perl-pbkdf2-tiny/meta.yaml +++ b/recipes/perl-pbkdf2-tiny/meta.yaml @@ -7,6 +7,7 @@ source: md5: 6628cad808d13bedb20054eea84b0f72 build: + noarch: generic number: 1 skip: True # [osx] diff --git a/recipes/perl-pegex/meta.yaml b/recipes/perl-pegex/meta.yaml index 21f6c3bce745a..dc372bd3283d2 100644 --- a/recipes/perl-pegex/meta.yaml +++ b/recipes/perl-pegex/meta.yaml @@ -7,6 +7,7 @@ source: md5: 04ab96185d73bdad02dfbabb1152af40 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-perl-osnames/meta.yaml b/recipes/perl-perl-osnames/meta.yaml index 7ccec57ec3cff..828e8077fd3b5 100644 --- a/recipes/perl-perl-osnames/meta.yaml +++ b/recipes/perl-perl-osnames/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-perl-ostype/1.010/meta.yaml b/recipes/perl-perl-ostype/1.010/meta.yaml index 13b6633fc0338..a7236612894bb 100644 --- a/recipes/perl-perl-ostype/1.010/meta.yaml +++ b/recipes/perl-perl-ostype/1.010/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-perl-version/meta.yaml b/recipes/perl-perl-version/meta.yaml index f399f3f5c6822..ada1d8889db86 100644 --- a/recipes/perl-perl-version/meta.yaml +++ b/recipes/perl-perl-version/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-perl4-corelibs/0.004/meta.yaml b/recipes/perl-perl4-corelibs/0.004/meta.yaml index 4c06dc82da1aa..890470864df43 100644 --- a/recipes/perl-perl4-corelibs/0.004/meta.yaml +++ b/recipes/perl-perl4-corelibs/0.004/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-perlio-encoding/0.18/meta.yaml b/recipes/perl-perlio-encoding/0.18/meta.yaml index d577abd97fd38..dce70ebf7fea5 100644 --- a/recipes/perl-perlio-encoding/0.18/meta.yaml +++ b/recipes/perl-perlio-encoding/0.18/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-perlio/1.09/meta.yaml b/recipes/perl-perlio/1.09/meta.yaml index 2bf946271d3b4..e107fe7a361e3 100644 --- a/recipes/perl-perlio/1.09/meta.yaml +++ b/recipes/perl-perlio/1.09/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-pod-checker/1.60/meta.yaml b/recipes/perl-pod-checker/1.60/meta.yaml index 12aae5ab4bab9..325145283fcbe 100644 --- a/recipes/perl-pod-checker/1.60/meta.yaml +++ b/recipes/perl-pod-checker/1.60/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-pod-coverage/0.23/meta.yaml b/recipes/perl-pod-coverage/0.23/meta.yaml index 8b9dbd9e32e3e..069eefa544207 100644 --- a/recipes/perl-pod-coverage/0.23/meta.yaml +++ b/recipes/perl-pod-coverage/0.23/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-pod-escapes/1.07/meta.yaml b/recipes/perl-pod-escapes/1.07/meta.yaml index 7f78241f53c81..175495011abea 100644 --- a/recipes/perl-pod-escapes/1.07/meta.yaml +++ b/recipes/perl-pod-escapes/1.07/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-pod-parser/1.63/meta.yaml b/recipes/perl-pod-parser/1.63/meta.yaml index e24b57f98bc8e..7afeb14f04fbd 100644 --- a/recipes/perl-pod-parser/1.63/meta.yaml +++ b/recipes/perl-pod-parser/1.63/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-pod-plaintext/2.07/meta.yaml b/recipes/perl-pod-plaintext/2.07/meta.yaml index 16bbf30eabf0b..3a1e5dd9b44f4 100644 --- a/recipes/perl-pod-plaintext/2.07/meta.yaml +++ b/recipes/perl-pod-plaintext/2.07/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-pod-simple-text/3.28/meta.yaml b/recipes/perl-pod-simple-text/3.28/meta.yaml index 1d7562c91afaf..b3acef7802019 100644 --- a/recipes/perl-pod-simple-text/3.28/meta.yaml +++ b/recipes/perl-pod-simple-text/3.28/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-pod-simple/3.35/meta.yaml b/recipes/perl-pod-simple/3.35/meta.yaml index 91736bcc33b81..2b28b1d3dda09 100644 --- a/recipes/perl-pod-simple/3.35/meta.yaml +++ b/recipes/perl-pod-simple/3.35/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-pod-usage/meta.yaml b/recipes/perl-pod-usage/meta.yaml index 2e0cfe2059b19..dd87edb7aee2a 100644 --- a/recipes/perl-pod-usage/meta.yaml +++ b/recipes/perl-pod-usage/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-posix/1.38_03/meta.yaml b/recipes/perl-posix/1.38_03/meta.yaml index f49d07fc0cf8c..c88d6aca1c9cb 100644 --- a/recipes/perl-posix/1.38_03/meta.yaml +++ b/recipes/perl-posix/1.38_03/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-postscript/meta.yaml b/recipes/perl-postscript/meta.yaml index c492a4bb36b42..4f51843a81226 100644 --- a/recipes/perl-postscript/meta.yaml +++ b/recipes/perl-postscript/meta.yaml @@ -9,6 +9,7 @@ source: - elements-version.patch build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-ppi/1.236/meta.yaml b/recipes/perl-ppi/1.236/meta.yaml index 74116917cf9c2..1c9c32ddab242 100644 --- a/recipes/perl-ppi/1.236/meta.yaml +++ b/recipes/perl-ppi/1.236/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-prefork/1.05/meta.yaml b/recipes/perl-prefork/1.05/meta.yaml index a0b8cb390d8b2..640b808de2c8e 100644 --- a/recipes/perl-prefork/1.05/meta.yaml +++ b/recipes/perl-prefork/1.05/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-probe-perl/meta.yaml b/recipes/perl-probe-perl/meta.yaml index a9ef4aeaaeeb4..c60c95c622512 100644 --- a/recipes/perl-probe-perl/meta.yaml +++ b/recipes/perl-probe-perl/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-proc-fork/meta.yaml b/recipes/perl-proc-fork/meta.yaml index 74b893c2ca208..7ba79ac5e1bd2 100644 --- a/recipes/perl-proc-fork/meta.yaml +++ b/recipes/perl-proc-fork/meta.yaml @@ -7,6 +7,7 @@ source: sha256: edd5ee82b4241d9eca68992cfaadb585979fedc216c048c880f12b5cfc9bb6ee build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-readonly/meta.yaml b/recipes/perl-readonly/meta.yaml index d6be235ee2a83..d93350fc23c5f 100644 --- a/recipes/perl-readonly/meta.yaml +++ b/recipes/perl-readonly/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-regexp-common/meta.yaml b/recipes/perl-regexp-common/meta.yaml index 63873f95518de..bf3d632b00766 100644 --- a/recipes/perl-regexp-common/meta.yaml +++ b/recipes/perl-regexp-common/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-return-multilevel/meta.yaml b/recipes/perl-return-multilevel/meta.yaml index a227a74c4d12f..4076a29cef6f2 100644 --- a/recipes/perl-return-multilevel/meta.yaml +++ b/recipes/perl-return-multilevel/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-role-tiny-with/2.000005/meta.yaml b/recipes/perl-role-tiny-with/2.000005/meta.yaml index 831a40673ad29..aac91b31736c4 100644 --- a/recipes/perl-role-tiny-with/2.000005/meta.yaml +++ b/recipes/perl-role-tiny-with/2.000005/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-safe/2.37/meta.yaml b/recipes/perl-safe/2.37/meta.yaml index e80647222c538..bed73cefc17cb 100644 --- a/recipes/perl-safe/2.37/meta.yaml +++ b/recipes/perl-safe/2.37/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-scalar-util-numeric/meta.yaml b/recipes/perl-scalar-util-numeric/meta.yaml index 22db91accd6ff..e42474ed02632 100644 --- a/recipes/perl-scalar-util-numeric/meta.yaml +++ b/recipes/perl-scalar-util-numeric/meta.yaml @@ -7,6 +7,7 @@ source: md5: 6a5451f33c3ec5c17d0672a4d5b0d24c build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-scope-guard/meta.yaml b/recipes/perl-scope-guard/meta.yaml index 18b499c0ee215..515d3fe9e8768 100644 --- a/recipes/perl-scope-guard/meta.yaml +++ b/recipes/perl-scope-guard/meta.yaml @@ -7,6 +7,7 @@ source: md5: be57b915d23ddac7677ef2ad9e52b92a build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-set-intspan/meta.yaml b/recipes/perl-set-intspan/meta.yaml index b12be5a2f26d5..74ccd7247bce1 100644 --- a/recipes/perl-set-intspan/meta.yaml +++ b/recipes/perl-set-intspan/meta.yaml @@ -7,6 +7,7 @@ source: md5: 7c21c2fedce5b7be7d8200e2cf2bdca1 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-set-scalar/meta.yaml b/recipes/perl-set-scalar/meta.yaml index 9b66914378aea..7630108602260 100644 --- a/recipes/perl-set-scalar/meta.yaml +++ b/recipes/perl-set-scalar/meta.yaml @@ -7,6 +7,7 @@ source: md5: 4af73c0d6f562d1eddd4ebf6014ac67f build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-slurp/meta.yaml b/recipes/perl-slurp/meta.yaml index 8ef207af9bccc..443ec0c8c642e 100644 --- a/recipes/perl-slurp/meta.yaml +++ b/recipes/perl-slurp/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-snap/meta.yaml b/recipes/perl-snap/meta.yaml index d8fd4b3b7a947..3e3e110830be5 100644 --- a/recipes/perl-snap/meta.yaml +++ b/recipes/perl-snap/meta.yaml @@ -18,6 +18,7 @@ source: sha256: 04f1901962f72ed9888fd0993bb9549e906279c675b01f75da20789dae685e34 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-soap-lite/meta.yaml b/recipes/perl-soap-lite/meta.yaml index 9514c7fce9426..12381891ea138 100644 --- a/recipes/perl-soap-lite/meta.yaml +++ b/recipes/perl-soap-lite/meta.yaml @@ -7,6 +7,7 @@ source: md5: eceb84ca5aabebf855e37c53f53d39ce build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-socket/2.027/meta.yaml b/recipes/perl-socket/2.027/meta.yaml index dfe2530329c13..8264ff696a6c7 100644 --- a/recipes/perl-socket/2.027/meta.yaml +++ b/recipes/perl-socket/2.027/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-socket6/meta.yaml b/recipes/perl-socket6/meta.yaml index da45375d1d8ea..3cf698c27781a 100644 --- a/recipes/perl-socket6/meta.yaml +++ b/recipes/perl-socket6/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 468915fa3a04dcf6574fc957eff495915e24569434970c91ee8e4e1459fc9114 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-sort-naturally/meta.yaml b/recipes/perl-sort-naturally/meta.yaml index 23ef7f88be4d0..6d44dfa181b75 100644 --- a/recipes/perl-sort-naturally/meta.yaml +++ b/recipes/perl-sort-naturally/meta.yaml @@ -7,6 +7,7 @@ source: md5: fef2e36d1b1ea23ee79ec68b5872453f build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-sort-versions/meta.yaml b/recipes/perl-sort-versions/meta.yaml index 61bcaef59ebf9..d52b29fc14843 100644 --- a/recipes/perl-sort-versions/meta.yaml +++ b/recipes/perl-sort-versions/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-specio-exporter/0.36/meta.yaml b/recipes/perl-specio-exporter/0.36/meta.yaml index 209f2e844fc8d..df69c7784d598 100644 --- a/recipes/perl-specio-exporter/0.36/meta.yaml +++ b/recipes/perl-specio-exporter/0.36/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-specio/meta.yaml b/recipes/perl-specio/meta.yaml index 4f09b9e207dc9..4c9421391d7ff 100644 --- a/recipes/perl-specio/meta.yaml +++ b/recipes/perl-specio/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-spiffy/meta.yaml b/recipes/perl-spiffy/meta.yaml index 4c16b1a3233a3..d08c0fc307705 100644 --- a/recipes/perl-spiffy/meta.yaml +++ b/recipes/perl-spiffy/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-spreadsheet-parseexcel/meta.yaml b/recipes/perl-spreadsheet-parseexcel/meta.yaml index 17346f3c2f27a..c4c44e8767e4d 100644 --- a/recipes/perl-spreadsheet-parseexcel/meta.yaml +++ b/recipes/perl-spreadsheet-parseexcel/meta.yaml @@ -7,6 +7,7 @@ source: md5: 4b8857e3a391d86501c1b742b459ac9e build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-spreadsheet-writeexcel/meta.yaml b/recipes/perl-spreadsheet-writeexcel/meta.yaml index 0b351099c844b..4843352192ecf 100644 --- a/recipes/perl-spreadsheet-writeexcel/meta.yaml +++ b/recipes/perl-spreadsheet-writeexcel/meta.yaml @@ -7,6 +7,7 @@ source: md5: b3262290e96985ee12d81c861a389790 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-statistics-basic/meta.yaml b/recipes/perl-statistics-basic/meta.yaml index 3ef1d4cecd7b9..a6091dd4f537c 100644 --- a/recipes/perl-statistics-basic/meta.yaml +++ b/recipes/perl-statistics-basic/meta.yaml @@ -7,6 +7,7 @@ source: md5: 1ee961c3a4b9c0a594dc3cfccbcd1ed1 build: + noarch: generic number: 2 # Failing on OSX during builds due to KeyError: 'perl' skip: true # [osx] diff --git a/recipes/perl-statistics-descriptive/3.0609/meta.yaml b/recipes/perl-statistics-descriptive/3.0609/meta.yaml index ee86f6a8db895..97b8ddab3d70e 100644 --- a/recipes/perl-statistics-descriptive/3.0609/meta.yaml +++ b/recipes/perl-statistics-descriptive/3.0609/meta.yaml @@ -7,6 +7,7 @@ source: md5: 3fa7a705742d2ba942b9e0b167fdb48b build: + noarch: generic number: 4 requirements: diff --git a/recipes/perl-statistics-descriptive/meta.yaml b/recipes/perl-statistics-descriptive/meta.yaml index 009f4087eed47..535dddfeee3a0 100644 --- a/recipes/perl-statistics-descriptive/meta.yaml +++ b/recipes/perl-statistics-descriptive/meta.yaml @@ -7,6 +7,7 @@ source: sha256: f98a10c625640170cdda408cccc72bdd7f66f8ebe5f59dec1b96185171ef11d0 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-statistics-distributions/meta.yaml b/recipes/perl-statistics-distributions/meta.yaml index 3a7b06a006326..5d1416bcc5baf 100644 --- a/recipes/perl-statistics-distributions/meta.yaml +++ b/recipes/perl-statistics-distributions/meta.yaml @@ -7,6 +7,7 @@ source: md5: 526cb415b30ffeec52563dbcb436ca60 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-statistics-frequency/meta.yaml b/recipes/perl-statistics-frequency/meta.yaml index d7180b15eb674..7e05b8dcad973 100644 --- a/recipes/perl-statistics-frequency/meta.yaml +++ b/recipes/perl-statistics-frequency/meta.yaml @@ -7,6 +7,7 @@ source: md5: e1ecb945b642d574d3708d6ef5d0be0c build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-statistics-lite/meta.yaml b/recipes/perl-statistics-lite/meta.yaml index 5f880afdc35c6..3e37aa9248160 100644 --- a/recipes/perl-statistics-lite/meta.yaml +++ b/recipes/perl-statistics-lite/meta.yaml @@ -7,6 +7,7 @@ source: md5: 63bb672beb9463e35d1abce850508852 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-statistics-r/meta.yaml b/recipes/perl-statistics-r/meta.yaml index 64448af0fb24c..7756bc03daff7 100644 --- a/recipes/perl-statistics-r/meta.yaml +++ b/recipes/perl-statistics-r/meta.yaml @@ -8,6 +8,7 @@ about: summary: Statistics::R - Perl interface with the R statistical program build: + noarch: generic number: 3 source: diff --git a/recipes/perl-statistics-ttest/meta.yaml b/recipes/perl-statistics-ttest/meta.yaml index 1af45956296cc..d99519753392f 100644 --- a/recipes/perl-statistics-ttest/meta.yaml +++ b/recipes/perl-statistics-ttest/meta.yaml @@ -7,6 +7,7 @@ source: md5: 605466db48e2b16063abd16550e7d345 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-string-approx/3.27/meta.yaml b/recipes/perl-string-approx/3.27/meta.yaml index 5d8b1aa428e52..ed7e8ab242669 100644 --- a/recipes/perl-string-approx/3.27/meta.yaml +++ b/recipes/perl-string-approx/3.27/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-string-escape/2010.002/meta.yaml b/recipes/perl-string-escape/2010.002/meta.yaml index cc1086b5c5dcf..3bbf42db5c5ab 100644 --- a/recipes/perl-string-escape/2010.002/meta.yaml +++ b/recipes/perl-string-escape/2010.002/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-string-random/0.30/meta.yaml b/recipes/perl-string-random/0.30/meta.yaml index 36a18f2c93f78..6afe31e52b970 100644 --- a/recipes/perl-string-random/0.30/meta.yaml +++ b/recipes/perl-string-random/0.30/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-string-rewriteprefix/meta.yaml b/recipes/perl-string-rewriteprefix/meta.yaml index 501f1e8465dd4..bc528a95e2dad 100644 --- a/recipes/perl-string-rewriteprefix/meta.yaml +++ b/recipes/perl-string-rewriteprefix/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-string-truncate/meta.yaml b/recipes/perl-string-truncate/meta.yaml index 901bcbb006436..0d2bcb68d5127 100644 --- a/recipes/perl-string-truncate/meta.yaml +++ b/recipes/perl-string-truncate/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-string-util/1.26/meta.yaml b/recipes/perl-string-util/1.26/meta.yaml index 10a00ff2bc934..726e94afaef98 100644 --- a/recipes/perl-string-util/1.26/meta.yaml +++ b/recipes/perl-string-util/1.26/meta.yaml @@ -6,6 +6,7 @@ source: url: https://cpan.metacpan.org/authors/id/M/MI/MIKO/String-Util-1.26.tar.gz md5: d0f13f8688bedef7174634bb57f7fbe4 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-sub-attribute/0.05/meta.yaml b/recipes/perl-sub-attribute/0.05/meta.yaml index fd54ad744083a..03c44dfe36b17 100644 --- a/recipes/perl-sub-attribute/0.05/meta.yaml +++ b/recipes/perl-sub-attribute/0.05/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-sub-exporter-formethods/meta.yaml b/recipes/perl-sub-exporter-formethods/meta.yaml index 6d514c4997797..4c670a37b3ad0 100644 --- a/recipes/perl-sub-exporter-formethods/meta.yaml +++ b/recipes/perl-sub-exporter-formethods/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-sub-exporter-progressive/meta.yaml b/recipes/perl-sub-exporter-progressive/meta.yaml index d8f2b50687cf7..c7da9133c4d9e 100644 --- a/recipes/perl-sub-exporter-progressive/meta.yaml +++ b/recipes/perl-sub-exporter-progressive/meta.yaml @@ -7,6 +7,7 @@ source: sha256: d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-sub-exporter/meta.yaml b/recipes/perl-sub-exporter/meta.yaml index 4ac3edad99ecb..06674cde6af08 100644 --- a/recipes/perl-sub-exporter/meta.yaml +++ b/recipes/perl-sub-exporter/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-sub-info/meta.yaml b/recipes/perl-sub-info/meta.yaml index 09dc0df199392..6fb2e984c0d9b 100644 --- a/recipes/perl-sub-info/meta.yaml +++ b/recipes/perl-sub-info/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-sub-install/meta.yaml b/recipes/perl-sub-install/meta.yaml index 943648c7724b2..d1bedae0c9c8e 100644 --- a/recipes/perl-sub-install/meta.yaml +++ b/recipes/perl-sub-install/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-sub-name/0.21/meta.yaml b/recipes/perl-sub-name/0.21/meta.yaml index 9b51c5d27ff08..f68ceed80e2c1 100644 --- a/recipes/perl-sub-name/0.21/meta.yaml +++ b/recipes/perl-sub-name/0.21/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-sub-quote/meta.yaml b/recipes/perl-sub-quote/meta.yaml index 6b9d0906eae08..77020158720aa 100644 --- a/recipes/perl-sub-quote/meta.yaml +++ b/recipes/perl-sub-quote/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-svg-graph/meta.yaml b/recipes/perl-svg-graph/meta.yaml index 4ea8c48c7bb79..0f02d0ffc351b 100644 --- a/recipes/perl-svg-graph/meta.yaml +++ b/recipes/perl-svg-graph/meta.yaml @@ -7,6 +7,7 @@ source: md5: e922f0b323056ecf306eb8085db283f5 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-svg/meta.yaml b/recipes/perl-svg/meta.yaml index 0c35982fad8a7..3aea4970f2461 100644 --- a/recipes/perl-svg/meta.yaml +++ b/recipes/perl-svg/meta.yaml @@ -7,6 +7,7 @@ source: sha256: ec3d6ddde7a46fa507eaa616b94d217296fdc0d8fbf88741367a9821206f28af build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-symbol/1.07/meta.yaml b/recipes/perl-symbol/1.07/meta.yaml index e60f5c04847e5..df1f6680c8fa6 100644 --- a/recipes/perl-symbol/1.07/meta.yaml +++ b/recipes/perl-symbol/1.07/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-sys-info-base/meta.yaml b/recipes/perl-sys-info-base/meta.yaml index 7f97ab667f418..9fdccc752a09b 100644 --- a/recipes/perl-sys-info-base/meta.yaml +++ b/recipes/perl-sys-info-base/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-sys-info-driver-linux/meta.yaml b/recipes/perl-sys-info-driver-linux/meta.yaml index 9ecea1456c414..92fd9862e47c0 100644 --- a/recipes/perl-sys-info-driver-linux/meta.yaml +++ b/recipes/perl-sys-info-driver-linux/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 skip: true # [not linux] diff --git a/recipes/perl-sys-info-driver-osx/meta.yaml b/recipes/perl-sys-info-driver-osx/meta.yaml index 24a00cb4d4f28..199587ab1aa25 100644 --- a/recipes/perl-sys-info-driver-osx/meta.yaml +++ b/recipes/perl-sys-info-driver-osx/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 skip: true # [not osx] diff --git a/recipes/perl-sys-info/meta.yaml b/recipes/perl-sys-info/meta.yaml index f3b00308fe9f9..76f1caf9163ba 100644 --- a/recipes/perl-sys-info/meta.yaml +++ b/recipes/perl-sys-info/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-sys-sigaction/0.23/meta.yaml b/recipes/perl-sys-sigaction/0.23/meta.yaml index 9960d79c2b13c..0a3f3a069926b 100644 --- a/recipes/perl-sys-sigaction/0.23/meta.yaml +++ b/recipes/perl-sys-sigaction/0.23/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-tap-harness-env/3.30/meta.yaml b/recipes/perl-tap-harness-env/3.30/meta.yaml index a057798499428..69aa12b8c7e13 100644 --- a/recipes/perl-tap-harness-env/3.30/meta.yaml +++ b/recipes/perl-tap-harness-env/3.30/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-task-weaken/meta.yaml b/recipes/perl-task-weaken/meta.yaml index 4afff5dc75134..f6ee09acc5fa9 100644 --- a/recipes/perl-task-weaken/meta.yaml +++ b/recipes/perl-task-weaken/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 2383fedb9dbaef646468ea824afbf7c801076720cfba0df2a7a074726dcd66be build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-template-toolkit/meta.yaml b/recipes/perl-template-toolkit/meta.yaml index 1e84cc1f163b3..7f1a501ddb826 100644 --- a/recipes/perl-template-toolkit/meta.yaml +++ b/recipes/perl-template-toolkit/meta.yaml @@ -7,6 +7,7 @@ source: md5: 4c289856ebee446ebbe2629b24f0734b build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-term-detect-software/meta.yaml b/recipes/perl-term-detect-software/meta.yaml index c5b671d3997b0..e2fb9cb6c993c 100644 --- a/recipes/perl-term-detect-software/meta.yaml +++ b/recipes/perl-term-detect-software/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-term-encoding/meta.yaml b/recipes/perl-term-encoding/meta.yaml index 106566e122392..3eeda24758bdb 100644 --- a/recipes/perl-term-encoding/meta.yaml +++ b/recipes/perl-term-encoding/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-term-progressbar/meta.yaml b/recipes/perl-term-progressbar/meta.yaml index 91e920406a2f9..5bbe0ac60c2d3 100644 --- a/recipes/perl-term-progressbar/meta.yaml +++ b/recipes/perl-term-progressbar/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-term-table/meta.yaml b/recipes/perl-term-table/meta.yaml index b704b6540a402..84f726e6cc21d 100644 --- a/recipes/perl-term-table/meta.yaml +++ b/recipes/perl-term-table/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-base/meta.yaml b/recipes/perl-test-base/meta.yaml index e795fc85bc27e..0c838be077b2b 100644 --- a/recipes/perl-test-base/meta.yaml +++ b/recipes/perl-test-base/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-builder-tester/meta.yaml b/recipes/perl-test-builder-tester/meta.yaml index 1079d8cb2d105..d8d38999fdb1e 100644 --- a/recipes/perl-test-builder-tester/meta.yaml +++ b/recipes/perl-test-builder-tester/meta.yaml @@ -3,6 +3,7 @@ package: version: "1.23_002" build: + noarch: generic number: 1 #source: diff --git a/recipes/perl-test-class-moose/meta.yaml b/recipes/perl-test-class-moose/meta.yaml index 9d2f80ec3fbc0..361720516d74c 100644 --- a/recipes/perl-test-class-moose/meta.yaml +++ b/recipes/perl-test-class-moose/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-classapi/meta.yaml b/recipes/perl-test-classapi/meta.yaml index 047c50f6aaecf..832eb0d0c2ce0 100644 --- a/recipes/perl-test-classapi/meta.yaml +++ b/recipes/perl-test-classapi/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-cleannamespaces/meta.yaml b/recipes/perl-test-cleannamespaces/meta.yaml index 3fddba6077829..7dac4e40d5d85 100644 --- a/recipes/perl-test-cleannamespaces/meta.yaml +++ b/recipes/perl-test-cleannamespaces/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-cpan-meta/0.25/meta.yaml b/recipes/perl-test-cpan-meta/0.25/meta.yaml index 8707121cd600f..a7d63b35c33a0 100644 --- a/recipes/perl-test-cpan-meta/0.25/meta.yaml +++ b/recipes/perl-test-cpan-meta/0.25/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-cpan-meta/meta.yaml b/recipes/perl-test-cpan-meta/meta.yaml index 85bc3613d6b10..ec57832fe53a4 100644 --- a/recipes/perl-test-cpan-meta/meta.yaml +++ b/recipes/perl-test-cpan-meta/meta.yaml @@ -7,6 +7,7 @@ source: md5: d1582df35cc1e8875357702c687ed22f build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-deep/meta.yaml b/recipes/perl-test-deep/meta.yaml index ec5ce420ffe0b..950e7e470584d 100644 --- a/recipes/perl-test-deep/meta.yaml +++ b/recipes/perl-test-deep/meta.yaml @@ -14,6 +14,7 @@ requirements: - perl build: + noarch: generic number: 1 test: diff --git a/recipes/perl-test-eol/meta.yaml b/recipes/perl-test-eol/meta.yaml index 80bb6dd19b567..db5eda176e146 100644 --- a/recipes/perl-test-eol/meta.yaml +++ b/recipes/perl-test-eol/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 8e7f7e5d07d3be0f1d7d51bcda8af0962767eb2897fd48994df274c0f5ed6b50 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-exception/meta.yaml b/recipes/perl-test-exception/meta.yaml index 75a0da0af51e6..32398581b376d 100644 --- a/recipes/perl-test-exception/meta.yaml +++ b/recipes/perl-test-exception/meta.yaml @@ -7,6 +7,7 @@ source: md5: 572d355026fb0b87fc2b8c64b83cada0 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-exec/meta.yaml b/recipes/perl-test-exec/meta.yaml index ab92a524bbb5e..9e200c2294022 100644 --- a/recipes/perl-test-exec/meta.yaml +++ b/recipes/perl-test-exec/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-fatal/meta.yaml b/recipes/perl-test-fatal/meta.yaml index 22cebc232a586..216c5c8c4f2ff 100644 --- a/recipes/perl-test-fatal/meta.yaml +++ b/recipes/perl-test-fatal/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-test-file-contents/0.23/meta.yaml b/recipes/perl-test-file-contents/0.23/meta.yaml index 8fa203779b49c..6939da27db03d 100644 --- a/recipes/perl-test-file-contents/0.23/meta.yaml +++ b/recipes/perl-test-file-contents/0.23/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-file/meta.yaml b/recipes/perl-test-file/meta.yaml index 2e87e9ef317f2..feb928d0287d0 100644 --- a/recipes/perl-test-file/meta.yaml +++ b/recipes/perl-test-file/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-files/meta.yaml b/recipes/perl-test-files/meta.yaml index 7a8471dc144b1..1d698beb37e1f 100644 --- a/recipes/perl-test-files/meta.yaml +++ b/recipes/perl-test-files/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-fork/meta.yaml b/recipes/perl-test-fork/meta.yaml index fe2f881b59b28..973b7045ff4ad 100644 --- a/recipes/perl-test-fork/meta.yaml +++ b/recipes/perl-test-fork/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-harness/3.36/meta.yaml b/recipes/perl-test-harness/3.36/meta.yaml index 2a6f4a136be09..7785717e02fb2 100644 --- a/recipes/perl-test-harness/3.36/meta.yaml +++ b/recipes/perl-test-harness/3.36/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-harness/meta.yaml b/recipes/perl-test-harness/meta.yaml index adfce5bb2d7e0..43f32e268d980 100644 --- a/recipes/perl-test-harness/meta.yaml +++ b/recipes/perl-test-harness/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-inter/meta.yaml b/recipes/perl-test-inter/meta.yaml index f01028859aa95..936c13aac0704 100644 --- a/recipes/perl-test-inter/meta.yaml +++ b/recipes/perl-test-inter/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-lectrotest/0.5001/meta.yaml b/recipes/perl-test-lectrotest/0.5001/meta.yaml index 0cfa5b1f84afb..e43a70c2c7ef9 100644 --- a/recipes/perl-test-lectrotest/0.5001/meta.yaml +++ b/recipes/perl-test-lectrotest/0.5001/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-longstring/meta.yaml b/recipes/perl-test-longstring/meta.yaml index ee64754440455..9fcb417914520 100644 --- a/recipes/perl-test-longstring/meta.yaml +++ b/recipes/perl-test-longstring/meta.yaml @@ -7,6 +7,7 @@ source: md5: 8baab770f61ebd5647a9dd3679f42fbd build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-memory-cycle/meta.yaml b/recipes/perl-test-memory-cycle/meta.yaml index 7ae38c73ca3da..e83e619313f11 100644 --- a/recipes/perl-test-memory-cycle/meta.yaml +++ b/recipes/perl-test-memory-cycle/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-mockmodule/meta.yaml b/recipes/perl-test-mockmodule/meta.yaml index 5baa3efd3841c..64edf7e717f4d 100644 --- a/recipes/perl-test-mockmodule/meta.yaml +++ b/recipes/perl-test-mockmodule/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-most/meta.yaml b/recipes/perl-test-most/meta.yaml index 248cd92622e22..6c8f15ed6c368 100644 --- a/recipes/perl-test-most/meta.yaml +++ b/recipes/perl-test-most/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 9897a6f4d751598d2ed1047e01c1554b01d0f8c96c45e7e845229782bf6f657f build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-needs/meta.yaml b/recipes/perl-test-needs/meta.yaml index 9c19c4780bfe0..bc78aaef94bf7 100644 --- a/recipes/perl-test-needs/meta.yaml +++ b/recipes/perl-test-needs/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-notabs/meta.yaml b/recipes/perl-test-notabs/meta.yaml index 0c01b344c7c25..00b760bf0233e 100644 --- a/recipes/perl-test-notabs/meta.yaml +++ b/recipes/perl-test-notabs/meta.yaml @@ -7,6 +7,7 @@ source: sha256: fb75c6a38721f0169e11c1e7dbe5329ed7216885a0b01123f342dd86d3356030 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-nowarnings/meta.yaml b/recipes/perl-test-nowarnings/meta.yaml index 36edfc7a06c06..7d2e4f753256c 100644 --- a/recipes/perl-test-nowarnings/meta.yaml +++ b/recipes/perl-test-nowarnings/meta.yaml @@ -7,6 +7,7 @@ source: md5: 682ed043f7d3e38f3dfd8745fd21c49a build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-test-object/0.08/meta.yaml b/recipes/perl-test-object/0.08/meta.yaml index 80f53871f0d4d..37942f7d596ff 100644 --- a/recipes/perl-test-object/0.08/meta.yaml +++ b/recipes/perl-test-object/0.08/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-output/meta.yaml b/recipes/perl-test-output/meta.yaml index 49825300c097a..3e9d860b62e5d 100644 --- a/recipes/perl-test-output/meta.yaml +++ b/recipes/perl-test-output/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-pod/1.51/meta.yaml b/recipes/perl-test-pod/1.51/meta.yaml index 5782b8b1b2d89..6a124159d902d 100644 --- a/recipes/perl-test-pod/1.51/meta.yaml +++ b/recipes/perl-test-pod/1.51/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-pod/meta.yaml b/recipes/perl-test-pod/meta.yaml index b11360fb9217f..7b929fb3aa8fb 100644 --- a/recipes/perl-test-pod/meta.yaml +++ b/recipes/perl-test-pod/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-prereq/2.002/meta.yaml b/recipes/perl-test-prereq/2.002/meta.yaml index 13557b9b54641..08f622c5b9bc5 100644 --- a/recipes/perl-test-prereq/2.002/meta.yaml +++ b/recipes/perl-test-prereq/2.002/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-test-requires/meta.yaml b/recipes/perl-test-requires/meta.yaml index 992fcc64c50eb..9830c075fae0a 100644 --- a/recipes/perl-test-requires/meta.yaml +++ b/recipes/perl-test-requires/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-test-requiresinternet/meta.yaml b/recipes/perl-test-requiresinternet/meta.yaml index d602774b29f1b..7ad42ff0394c1 100644 --- a/recipes/perl-test-requiresinternet/meta.yaml +++ b/recipes/perl-test-requiresinternet/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-script/meta.yaml b/recipes/perl-test-script/meta.yaml index fa0e57ea7bee0..17151fbb9226f 100644 --- a/recipes/perl-test-script/meta.yaml +++ b/recipes/perl-test-script/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-simple/meta.yaml b/recipes/perl-test-simple/meta.yaml index 849161be9ab7f..8e8459ebf6491 100644 --- a/recipes/perl-test-simple/meta.yaml +++ b/recipes/perl-test-simple/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-subcalls/1.10/meta.yaml b/recipes/perl-test-subcalls/1.10/meta.yaml index 344a77d417fc8..9cc419e60846e 100644 --- a/recipes/perl-test-subcalls/1.10/meta.yaml +++ b/recipes/perl-test-subcalls/1.10/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-test-sys-info/meta.yaml b/recipes/perl-test-sys-info/meta.yaml index 3aba6d9efd6ff..6a86f04cb92cb 100644 --- a/recipes/perl-test-sys-info/meta.yaml +++ b/recipes/perl-test-sys-info/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-toolbox/0.4/meta.yaml b/recipes/perl-test-toolbox/0.4/meta.yaml index 3dafdc02c06f2..cb37ccb2e2170 100644 --- a/recipes/perl-test-toolbox/0.4/meta.yaml +++ b/recipes/perl-test-toolbox/0.4/meta.yaml @@ -7,6 +7,7 @@ source: md5: b8a83d332dcd0691b68ed9e0a0a53e7b build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-trap/meta.yaml b/recipes/perl-test-trap/meta.yaml index 4a242e5e91208..b5091a7ce0fb9 100644 --- a/recipes/perl-test-trap/meta.yaml +++ b/recipes/perl-test-trap/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-unit-lite/0.1202/meta.yaml b/recipes/perl-test-unit-lite/0.1202/meta.yaml index 65020c7850a8c..ccc282c733b3e 100644 --- a/recipes/perl-test-unit-lite/0.1202/meta.yaml +++ b/recipes/perl-test-unit-lite/0.1202/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-utf8/meta.yaml b/recipes/perl-test-utf8/meta.yaml index 3944ca69e2b9f..11553b5893c90 100644 --- a/recipes/perl-test-utf8/meta.yaml +++ b/recipes/perl-test-utf8/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-warn/meta.yaml b/recipes/perl-test-warn/meta.yaml index 6ae051ca845a6..e7145d6d04a7d 100644 --- a/recipes/perl-test-warn/meta.yaml +++ b/recipes/perl-test-warn/meta.yaml @@ -7,6 +7,7 @@ source: sha256: ecbca346d379cef8d3c0e4ac0c8eb3b2613d737ffaaeae52271c38d7bf3c6cda build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-warnings/meta.yaml b/recipes/perl-test-warnings/meta.yaml index 9f22f533736d8..49fb25b23bb2b 100644 --- a/recipes/perl-test-warnings/meta.yaml +++ b/recipes/perl-test-warnings/meta.yaml @@ -15,6 +15,7 @@ requirements: - perl build: + noarch: generic number: 1 test: diff --git a/recipes/perl-test-without-module/meta.yaml b/recipes/perl-test-without-module/meta.yaml index 18255f1cba693..e2d1cf2a24b1a 100644 --- a/recipes/perl-test-without-module/meta.yaml +++ b/recipes/perl-test-without-module/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test-xml/meta.yaml b/recipes/perl-test-xml/meta.yaml index 53c04265e039d..c3feed9f5f0c8 100644 --- a/recipes/perl-test-xml/meta.yaml +++ b/recipes/perl-test-xml/meta.yaml @@ -7,6 +7,7 @@ source: md5: 490b487e07908358eb64a3c3c5b48143 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test-yaml/meta.yaml b/recipes/perl-test-yaml/meta.yaml index d4f7c170a2910..e3305d1627f96 100644 --- a/recipes/perl-test-yaml/meta.yaml +++ b/recipes/perl-test-yaml/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test/1.26/meta.yaml b/recipes/perl-test/1.26/meta.yaml index b13b75dd8815b..0177816df412d 100644 --- a/recipes/perl-test/1.26/meta.yaml +++ b/recipes/perl-test/1.26/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-test2-suite/meta.yaml b/recipes/perl-test2-suite/meta.yaml index ea4604cf02894..31b4f1d872d76 100644 --- a/recipes/perl-test2-suite/meta.yaml +++ b/recipes/perl-test2-suite/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-test2/1.302075/meta.yaml b/recipes/perl-test2/1.302075/meta.yaml index 5274a41b2cec7..0fb92f810bf3c 100644 --- a/recipes/perl-test2/1.302075/meta.yaml +++ b/recipes/perl-test2/1.302075/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-text-abbrev/meta.yaml b/recipes/perl-text-abbrev/meta.yaml index a08dd736b5c9d..224ec0a5b6e78 100644 --- a/recipes/perl-text-abbrev/meta.yaml +++ b/recipes/perl-text-abbrev/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-text-ansitable/0.48/meta.yaml b/recipes/perl-text-ansitable/0.48/meta.yaml index 0d527f41aabf4..53301a819e03e 100644 --- a/recipes/perl-text-ansitable/0.48/meta.yaml +++ b/recipes/perl-text-ansitable/0.48/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-text-asciitable/0.22/meta.yaml b/recipes/perl-text-asciitable/0.22/meta.yaml index 0a97ab26b6f19..a58ef64e182fb 100644 --- a/recipes/perl-text-asciitable/0.22/meta.yaml +++ b/recipes/perl-text-asciitable/0.22/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-text-balanced/meta.yaml b/recipes/perl-text-balanced/meta.yaml index 1368673a52c6c..77ff315cefab9 100644 --- a/recipes/perl-text-balanced/meta.yaml +++ b/recipes/perl-text-balanced/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-text-diff/meta.yaml b/recipes/perl-text-diff/meta.yaml index 01448e0e3d694..4e48eb50863e7 100644 --- a/recipes/perl-text-diff/meta.yaml +++ b/recipes/perl-text-diff/meta.yaml @@ -7,6 +7,7 @@ source: sha256: e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-text-format/meta.yaml b/recipes/perl-text-format/meta.yaml index f431576a5db04..451578da57ced 100644 --- a/recipes/perl-text-format/meta.yaml +++ b/recipes/perl-text-format/meta.yaml @@ -7,6 +7,7 @@ source: md5: ab4ae26dbbb7eed101dc7a4324ac9c10 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-text-glob/meta.yaml b/recipes/perl-text-glob/meta.yaml index 738727d334eff..485d90dc5d3a5 100644 --- a/recipes/perl-text-glob/meta.yaml +++ b/recipes/perl-text-glob/meta.yaml @@ -7,6 +7,7 @@ source: md5: d001559c504a2625dd117bd1558f07f7 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-text-levenshtein/0.13/meta.yaml b/recipes/perl-text-levenshtein/0.13/meta.yaml index a7e0692d51877..c5282955a5f88 100644 --- a/recipes/perl-text-levenshtein/0.13/meta.yaml +++ b/recipes/perl-text-levenshtein/0.13/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-text-nsp/meta.yaml b/recipes/perl-text-nsp/meta.yaml index c67d9924abfde..ac62032f1cc78 100644 --- a/recipes/perl-text-nsp/meta.yaml +++ b/recipes/perl-text-nsp/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-text-parsewords/meta.yaml b/recipes/perl-text-parsewords/meta.yaml index 3efb9d152b49e..e5e1c3e9b952c 100644 --- a/recipes/perl-text-parsewords/meta.yaml +++ b/recipes/perl-text-parsewords/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 85e0238179dd43997e58c66bd51611182bc7d533505029a2db0d3232edaff5e8 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-text-tabs-wrap/meta.yaml b/recipes/perl-text-tabs-wrap/meta.yaml index 3987c2ba10bc5..42207194ac5ff 100644 --- a/recipes/perl-text-tabs-wrap/meta.yaml +++ b/recipes/perl-text-tabs-wrap/meta.yaml @@ -7,6 +7,7 @@ source: md5: 3e421ed3810803512af8d13bad548993 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-text-tabs/2013.0523/meta.yaml b/recipes/perl-text-tabs/2013.0523/meta.yaml index f0c08b341a006..a89031aeb8521 100644 --- a/recipes/perl-text-tabs/2013.0523/meta.yaml +++ b/recipes/perl-text-tabs/2013.0523/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-text-template-simple/meta.yaml b/recipes/perl-text-template-simple/meta.yaml index 81260b79c7b68..5830cbb12a1b6 100644 --- a/recipes/perl-text-template-simple/meta.yaml +++ b/recipes/perl-text-template-simple/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-text-template/1.46/meta.yaml b/recipes/perl-text-template/1.46/meta.yaml index 3b6b3f9e4f2e2..dbc4ad059bcb1 100644 --- a/recipes/perl-text-template/1.46/meta.yaml +++ b/recipes/perl-text-template/1.46/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-text-wrap/meta.yaml b/recipes/perl-text-wrap/meta.yaml index 747c4ec1e8dd7..59c3e9064c3b1 100644 --- a/recipes/perl-text-wrap/meta.yaml +++ b/recipes/perl-text-wrap/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-threaded/meta.yaml b/recipes/perl-threaded/meta.yaml index 589f0d1651f8e..e702775126f0d 100644 --- a/recipes/perl-threaded/meta.yaml +++ b/recipes/perl-threaded/meta.yaml @@ -5,6 +5,7 @@ package: version: 5.26.0 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-tie-cache/meta.yaml b/recipes/perl-tie-cache/meta.yaml index d28c0987a7b05..82b0684760601 100644 --- a/recipes/perl-tie-cache/meta.yaml +++ b/recipes/perl-tie-cache/meta.yaml @@ -7,6 +7,7 @@ source: md5: 8210f295e8676c8540a5934f88bf5fed build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-tie-cacher/meta.yaml b/recipes/perl-tie-cacher/meta.yaml index b8c42d69caa5a..b2529775cab6b 100644 --- a/recipes/perl-tie-cacher/meta.yaml +++ b/recipes/perl-tie-cacher/meta.yaml @@ -7,6 +7,7 @@ source: md5: ef6b5ead22f10731ae007a921342c959 build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-tie-hash-indexed/meta.yaml b/recipes/perl-tie-hash-indexed/meta.yaml index 03607ad399a02..a33416f7066f7 100644 --- a/recipes/perl-tie-hash-indexed/meta.yaml +++ b/recipes/perl-tie-hash-indexed/meta.yaml @@ -7,6 +7,7 @@ source: md5: 41e2d013df8cfafdd239bc65bbada014 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-tie-hash/1.05/meta.yaml b/recipes/perl-tie-hash/1.05/meta.yaml index 1892de0d10a65..d439aca8502cf 100644 --- a/recipes/perl-tie-hash/1.05/meta.yaml +++ b/recipes/perl-tie-hash/1.05/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-tie-ixhash/meta.yaml b/recipes/perl-tie-ixhash/meta.yaml index f7ff8464012a8..06ff87b3c2ac0 100644 --- a/recipes/perl-tie-ixhash/meta.yaml +++ b/recipes/perl-tie-ixhash/meta.yaml @@ -7,6 +7,7 @@ source: md5: 8393f2ced231533c3e714abad582f291 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-tie-log4perl/meta.yaml b/recipes/perl-tie-log4perl/meta.yaml index 9b84a25e92ce3..e048c88e1ead8 100644 --- a/recipes/perl-tie-log4perl/meta.yaml +++ b/recipes/perl-tie-log4perl/meta.yaml @@ -7,6 +7,7 @@ source: md5: 6f6cef7f335b2326b5c91dbef46d4560 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-tie-refhash-weak/0.09/meta.yaml b/recipes/perl-tie-refhash-weak/0.09/meta.yaml index e0645690ce640..7c47814e47d90 100644 --- a/recipes/perl-tie-refhash-weak/0.09/meta.yaml +++ b/recipes/perl-tie-refhash-weak/0.09/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-tie-refhash/1.39/meta.yaml b/recipes/perl-tie-refhash/1.39/meta.yaml index 60cc2ddc7a80b..eabaa4f2f251e 100644 --- a/recipes/perl-tie-refhash/1.39/meta.yaml +++ b/recipes/perl-tie-refhash/1.39/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-tie-toobject/0.03/meta.yaml b/recipes/perl-tie-toobject/0.03/meta.yaml index 1b4643d4f2c76..4ce4f80ebb32f 100644 --- a/recipes/perl-tie-toobject/0.03/meta.yaml +++ b/recipes/perl-tie-toobject/0.03/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-time-local/meta.yaml b/recipes/perl-time-local/meta.yaml index 9ee8de37383ed..7d5975ef141a2 100644 --- a/recipes/perl-time-local/meta.yaml +++ b/recipes/perl-time-local/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-time-piece/1.27/meta.yaml b/recipes/perl-time-piece/1.27/meta.yaml index ed1686d6e4c02..1e296a1b0ed9b 100644 --- a/recipes/perl-time-piece/1.27/meta.yaml +++ b/recipes/perl-time-piece/1.27/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-timedate/meta.yaml b/recipes/perl-timedate/meta.yaml index a1e0707666015..307d8f33596d7 100644 --- a/recipes/perl-timedate/meta.yaml +++ b/recipes/perl-timedate/meta.yaml @@ -7,6 +7,7 @@ source: md5: b1d91153ac971347aee84292ed886c1c build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-tree-dag_node/meta.yaml b/recipes/perl-tree-dag_node/meta.yaml index 366a6c66355e8..604764a561d15 100644 --- a/recipes/perl-tree-dag_node/meta.yaml +++ b/recipes/perl-tree-dag_node/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 1c8ba69772568b3758054247097512c550efe31517c329fb65eef7afccc9d304 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-try-tiny-retry/meta.yaml b/recipes/perl-try-tiny-retry/meta.yaml index ae0116b7dbc9a..bbfddd860c9f9 100644 --- a/recipes/perl-try-tiny-retry/meta.yaml +++ b/recipes/perl-try-tiny-retry/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 8af70c1bd46d749388738b7ea03c703cac898be939a5ff37117a01ed7eda8bbe build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-try-tiny/meta.yaml b/recipes/perl-try-tiny/meta.yaml index adabe2aef3324..7ebf0a467992f 100644 --- a/recipes/perl-try-tiny/meta.yaml +++ b/recipes/perl-try-tiny/meta.yaml @@ -7,6 +7,7 @@ source: sha256: da5bd0d5c903519bbf10bb9ba0cb7bcac0563882bcfe4503aee3fb143eddef6b build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-type-tiny/meta.yaml b/recipes/perl-type-tiny/meta.yaml index dce0ae86e42b9..cc88d2bac837a 100644 --- a/recipes/perl-type-tiny/meta.yaml +++ b/recipes/perl-type-tiny/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-types-serialiser/meta.yaml b/recipes/perl-types-serialiser/meta.yaml index 5dac3eccb39ee..d15f038e4bc63 100644 --- a/recipes/perl-types-serialiser/meta.yaml +++ b/recipes/perl-types-serialiser/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-unicode-stringprep/meta.yaml b/recipes/perl-unicode-stringprep/meta.yaml index 7fd7c9a32aef3..5bd60ed5446cf 100644 --- a/recipes/perl-unicode-stringprep/meta.yaml +++ b/recipes/perl-unicode-stringprep/meta.yaml @@ -7,6 +7,7 @@ source: md5: bf9ffbc387cc12d67a3875be1cd8e105 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-uri/meta.yaml b/recipes/perl-uri/meta.yaml index de4bb04751130..653c2b1393609 100644 --- a/recipes/perl-uri/meta.yaml +++ b/recipes/perl-uri/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-variable-magic/0.61/meta.yaml b/recipes/perl-variable-magic/0.61/meta.yaml index 88b4af546b4da..c613c7d555e8b 100644 --- a/recipes/perl-variable-magic/0.61/meta.yaml +++ b/recipes/perl-variable-magic/0.61/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-vars/1.03/meta.yaml b/recipes/perl-vars/1.03/meta.yaml index 09fb5d30d69e8..cab6f50d672d9 100644 --- a/recipes/perl-vars/1.03/meta.yaml +++ b/recipes/perl-vars/1.03/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-vcftools-vcf/meta.yaml b/recipes/perl-vcftools-vcf/meta.yaml index 921efde4531a4..c6446cea23b53 100644 --- a/recipes/perl-vcftools-vcf/meta.yaml +++ b/recipes/perl-vcftools-vcf/meta.yaml @@ -9,6 +9,7 @@ source: sha256: dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-velvetoptimiser/meta.yaml b/recipes/perl-velvetoptimiser/meta.yaml index a463270336c77..bffb9fe53a6df 100644 --- a/recipes/perl-velvetoptimiser/meta.yaml +++ b/recipes/perl-velvetoptimiser/meta.yaml @@ -7,6 +7,7 @@ source: md5: 1b7495b54e084672657ff7ac91aa00bf build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-version-next/meta.yaml b/recipes/perl-version-next/meta.yaml index 777eef65814ab..d98f3e5b42daf 100644 --- a/recipes/perl-version-next/meta.yaml +++ b/recipes/perl-version-next/meta.yaml @@ -7,6 +7,7 @@ source: md5: 4bafa527ff40edef40822f1f9a80fe51 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-version/meta.yaml b/recipes/perl-version/meta.yaml index 0f6fb54aaa8f6..20fbb90135cd8 100644 --- a/recipes/perl-version/meta.yaml +++ b/recipes/perl-version/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-want/meta.yaml b/recipes/perl-want/meta.yaml index db2d44f41018b..2d6cb42f36b6d 100644 --- a/recipes/perl-want/meta.yaml +++ b/recipes/perl-want/meta.yaml @@ -10,6 +10,7 @@ source: md5: 33b2dae5db59781b9a0434fa1db04aab build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-warnings-register/1.03/meta.yaml b/recipes/perl-warnings-register/1.03/meta.yaml index 30bc7999231b3..ffb4ad875c23b 100644 --- a/recipes/perl-warnings-register/1.03/meta.yaml +++ b/recipes/perl-warnings-register/1.03/meta.yaml @@ -13,6 +13,7 @@ package: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-www-mechanize/meta.yaml b/recipes/perl-www-mechanize/meta.yaml index 179b66b793370..8a7703e402987 100644 --- a/recipes/perl-www-mechanize/meta.yaml +++ b/recipes/perl-www-mechanize/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-www-robotrules/meta.yaml b/recipes/perl-www-robotrules/meta.yaml index 386a6040e627e..e7b39d6a1b91a 100644 --- a/recipes/perl-www-robotrules/meta.yaml +++ b/recipes/perl-www-robotrules/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-xml-dom-xpath/meta.yaml b/recipes/perl-xml-dom-xpath/meta.yaml index def5b7f5f1df1..cbcb7b4aba451 100644 --- a/recipes/perl-xml-dom-xpath/meta.yaml +++ b/recipes/perl-xml-dom-xpath/meta.yaml @@ -9,6 +9,7 @@ source: md5: 51a40df96c2f92829e1a4f84782fa75e build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-xml-dom/meta.yaml b/recipes/perl-xml-dom/meta.yaml index 1739887085f9d..aa9b07a3512b4 100644 --- a/recipes/perl-xml-dom/meta.yaml +++ b/recipes/perl-xml-dom/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-entities/meta.yaml b/recipes/perl-xml-entities/meta.yaml index c26e23deb41de..6b23f942a917f 100644 --- a/recipes/perl-xml-entities/meta.yaml +++ b/recipes/perl-xml-entities/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-xml-filter-buffertext/meta.yaml b/recipes/perl-xml-filter-buffertext/meta.yaml index 1193186f1f607..37f525bfb396d 100644 --- a/recipes/perl-xml-filter-buffertext/meta.yaml +++ b/recipes/perl-xml-filter-buffertext/meta.yaml @@ -7,6 +7,7 @@ source: md5: 2992c0387632583b966ab9c965b25512 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-xml-libxslt/meta.yaml b/recipes/perl-xml-libxslt/meta.yaml index a59a1b44e2690..a84ae4f0baa60 100644 --- a/recipes/perl-xml-libxslt/meta.yaml +++ b/recipes/perl-xml-libxslt/meta.yaml @@ -7,6 +7,7 @@ source: md5: a32045699c001d960d6f94891f9e853c build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-xml-namespacesupport/meta.yaml b/recipes/perl-xml-namespacesupport/meta.yaml index b6b42156e690e..bea46c8472cbb 100644 --- a/recipes/perl-xml-namespacesupport/meta.yaml +++ b/recipes/perl-xml-namespacesupport/meta.yaml @@ -13,6 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-parser-lite/meta.yaml b/recipes/perl-xml-parser-lite/meta.yaml index a4a31352d1108..bebc7c2f02ee1 100644 --- a/recipes/perl-xml-parser-lite/meta.yaml +++ b/recipes/perl-xml-parser-lite/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 6f90a027e1531a0e5406cf1de13c709b5216966df8f73d0bab9ab919209763ee build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-regexp/meta.yaml b/recipes/perl-xml-regexp/meta.yaml index 15b223ef386a7..9225a08de2d1e 100644 --- a/recipes/perl-xml-regexp/meta.yaml +++ b/recipes/perl-xml-regexp/meta.yaml @@ -7,6 +7,7 @@ source: md5: 2e38ea2340f2d2eb56bd81c4d739fbe0 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-xml-sax-base/meta.yaml b/recipes/perl-xml-sax-base/meta.yaml index 13befb8f52ca4..db58ff3d0d850 100644 --- a/recipes/perl-xml-sax-base/meta.yaml +++ b/recipes/perl-xml-sax-base/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-sax-expat/meta.yaml b/recipes/perl-xml-sax-expat/meta.yaml index 8d21bfeea7d2f..2e8a3d5ec4c96 100644 --- a/recipes/perl-xml-sax-expat/meta.yaml +++ b/recipes/perl-xml-sax-expat/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 3 requirements: diff --git a/recipes/perl-xml-sax-writer/meta.yaml b/recipes/perl-xml-sax-writer/meta.yaml index c8b6f0890a9a3..38aca88aa6992 100644 --- a/recipes/perl-xml-sax-writer/meta.yaml +++ b/recipes/perl-xml-sax-writer/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-semanticdiff/meta.yaml b/recipes/perl-xml-semanticdiff/meta.yaml index cdc4a0defe45a..edf8346c426f7 100644 --- a/recipes/perl-xml-semanticdiff/meta.yaml +++ b/recipes/perl-xml-semanticdiff/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 05fdefefbbc3f6b62fc7c9b5fabafb6b695ed68f0a3d958577251d1f0402a0f5 build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-simple/meta.yaml b/recipes/perl-xml-simple/meta.yaml index 8f336a42d0da6..eaa0461c18efe 100644 --- a/recipes/perl-xml-simple/meta.yaml +++ b/recipes/perl-xml-simple/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8 build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-xml-twig/meta.yaml b/recipes/perl-xml-twig/meta.yaml index e298d9bb14fef..8877d197aecce 100644 --- a/recipes/perl-xml-twig/meta.yaml +++ b/recipes/perl-xml-twig/meta.yaml @@ -9,6 +9,7 @@ source: - xml_parser.patch # depden on xml-parser 2.44 isntead of 2.23, should work xref https://rt.cpan.org/Public/Bug/Display.html?id=101041 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-xml-writer/meta.yaml b/recipes/perl-xml-writer/meta.yaml index 940eef9b3b30c..ff4aa67003b44 100644 --- a/recipes/perl-xml-writer/meta.yaml +++ b/recipes/perl-xml-writer/meta.yaml @@ -7,6 +7,7 @@ source: md5: b9c2420c243c6a36ce45a008740fcede build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-xml-xpath/meta.yaml b/recipes/perl-xml-xpath/meta.yaml index b29919122b290..b7ee9bf6a8a21 100644 --- a/recipes/perl-xml-xpath/meta.yaml +++ b/recipes/perl-xml-xpath/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 1cc9110705165dc09dd09974dd7c0b6709c9351d6b6b1cef5a711055f891dd0f build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-xml-xpathengine/meta.yaml b/recipes/perl-xml-xpathengine/meta.yaml index 834d96680db68..b1a9efa689130 100644 --- a/recipes/perl-xml-xpathengine/meta.yaml +++ b/recipes/perl-xml-xpathengine/meta.yaml @@ -7,6 +7,7 @@ source: md5: d840cbefa57c23041f0bed14940a6b22 build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-xsloader/meta.yaml b/recipes/perl-xsloader/meta.yaml index 19da1d8273489..f66998a55d26c 100644 --- a/recipes/perl-xsloader/meta.yaml +++ b/recipes/perl-xsloader/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/perl-yaml-libyaml/0.63/meta.yaml b/recipes/perl-yaml-libyaml/0.63/meta.yaml index 11429665d4cdd..671e33a78df21 100644 --- a/recipes/perl-yaml-libyaml/0.63/meta.yaml +++ b/recipes/perl-yaml-libyaml/0.63/meta.yaml @@ -7,6 +7,7 @@ source: md5: a6a2d7e2124b101236613e831458172f build: + noarch: generic number: 2 requirements: diff --git a/recipes/perl-yaml-libyaml/0.66/meta.yaml b/recipes/perl-yaml-libyaml/0.66/meta.yaml index 98694ede5556f..a3f1075d332e4 100644 --- a/recipes/perl-yaml-libyaml/0.66/meta.yaml +++ b/recipes/perl-yaml-libyaml/0.66/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/perl-yaml-tiny/meta.yaml b/recipes/perl-yaml-tiny/meta.yaml index 71817a2e50501..a91c915b63a95 100644 --- a/recipes/perl-yaml-tiny/meta.yaml +++ b/recipes/perl-yaml-tiny/meta.yaml @@ -8,6 +8,7 @@ source: build: + noarch: generic number: 0 requirements: diff --git a/recipes/pfam_scan/meta.yaml b/recipes/pfam_scan/meta.yaml index a4dfb187b6e4f..3f3a27fd397f0 100644 --- a/recipes/pfam_scan/meta.yaml +++ b/recipes/pfam_scan/meta.yaml @@ -7,12 +7,10 @@ source: sha256: 365c96bc150d5057349c3016d62667c58cb33afcfb6329457ae16ab5aae4f401 build: + noarch: generic number: 2 requirements: - build: - - perl - run: # Authors tested on 3.0 and 3.1b1 and 3.1b2 - hmmer >=3.0 diff --git a/recipes/phame/meta.yaml b/recipes/phame/meta.yaml index 99e21c20496f9..7051d4bf73bb3 100644 --- a/recipes/phame/meta.yaml +++ b/recipes/phame/meta.yaml @@ -11,8 +11,8 @@ source: url: https://github.com/mshakya/{{ name }}/archive/{{ version }}.tar.gz build: + noarch: generic number: 0 - # skip: true # [osx] requirements: run: diff --git a/recipes/phenix/meta.yaml b/recipes/phenix/meta.yaml index 6cfa61ce6fc5e..473d6ae02b3ed 100644 --- a/recipes/phenix/meta.yaml +++ b/recipes/phenix/meta.yaml @@ -12,24 +12,15 @@ source: build: number: 0 - skip: True # [not py27] + skip: True # [not py27] requirements: build: + - {{ compiler('c') }} + host: - python - cython - - setuptools - pip - - pysam - - argparse - - pyvcf - - pyyaml - - matplotlib - - bintrees - - biopython - - numpy - - matplotlib-venn - - psycopg2 run: - python - pysam diff --git a/recipes/phyloflash/meta.yaml b/recipes/phyloflash/meta.yaml index 730361d809774..3af9a7fbdfc0e 100644 --- a/recipes/phyloflash/meta.yaml +++ b/recipes/phyloflash/meta.yaml @@ -11,10 +11,10 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: - build: [] run: - perl >=5.13.2 - bbmap diff --git a/recipes/phylotoast/build.sh b/recipes/phylotoast/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/phylotoast/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/phylotoast/meta.yaml b/recipes/phylotoast/meta.yaml index 1a4793c158d76..a7750073f5821 100644 --- a/recipes/phylotoast/meta.yaml +++ b/recipes/phylotoast/meta.yaml @@ -12,26 +12,14 @@ source: build: number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - - scipy - - matplotlib <=1.5.3 - - biopython >=1.60 - - scikit-bio <=0.4.2 - - scikit-learn - - pandas - - statsmodels - - palettable - - biom-format >=2.1.5 - - h5py - + - python <3 + - pip run: - - python + - python <3 - numpy - scipy - matplotlib <=1.5.3 diff --git a/recipes/phyluce/build.sh b/recipes/phyluce/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/phyluce/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/phyluce/meta.yaml b/recipes/phyluce/meta.yaml index a04db328b0d19..b642ed1e3b574 100644 --- a/recipes/phyluce/meta.yaml +++ b/recipes/phyluce/meta.yaml @@ -13,15 +13,15 @@ source: build: number: 0 - skip: true # [not py27] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 - abyss 1.5.* - bcftools - bedtools @@ -69,4 +69,4 @@ about: extra: identifiers: - - doi:10.1093/bioinformatics/btv646 \ No newline at end of file + - doi:10.1093/bioinformatics/btv646 diff --git a/recipes/pipmir/meta.yaml b/recipes/pipmir/meta.yaml index d3270e8e91dde..95caa54c8676e 100644 --- a/recipes/pipmir/meta.yaml +++ b/recipes/pipmir/meta.yaml @@ -7,16 +7,12 @@ source: md5: 4103f0a148e4cc0217c616c1606f11c5 build: - skip: True # [not linux] + noarch: generic number: 3 requirements: - build: - - java-jdk - - samtools - - viennarna 1.8.5 run: - - java-jdk + - openjdk - samtools - viennarna 1.8.5 diff --git a/recipes/piret/build.sh b/recipes/piret/build.sh index 2f2b1d0255a22..f40ca2892d26f 100644 --- a/recipes/piret/build.sh +++ b/recipes/piret/build.sh @@ -1,4 +1,3 @@ #!/bin/bash cp -R bin/* $PREFIX/bin -#$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/pizzly/0.37.1/meta.yaml b/recipes/pizzly/0.37.1/meta.yaml index 0922a1aeff510..bb8555c39ab70 100644 --- a/recipes/pizzly/0.37.1/meta.yaml +++ b/recipes/pizzly/0.37.1/meta.yaml @@ -3,10 +3,10 @@ package: version: 0.37.1 source: - url: https://github.com/pmelsted/pizzly/releases/download/v0.37.1/pizzly_linux.tar.gz # [linux] - sha256: 81379b94ce8c648cb36a6cd278fa36977fa1b1008458f75f20de8d253f23d835 # [linux] - url: https://github.com/pmelsted/pizzly/releases/download/v0.37.1/pizzly_mac.tar.gz # [osx] - sha256: d8a922b76445bae79acb41d818dedba51567e7c041e8bb14360fd4cc0f674778 # [osx] + - url: https://github.com/pmelsted/pizzly/releases/download/v0.37.1/pizzly_linux.tar.gz # [linux] + sha256: 81379b94ce8c648cb36a6cd278fa36977fa1b1008458f75f20de8d253f23d835 # [linux] + - url: https://github.com/pmelsted/pizzly/releases/download/v0.37.1/pizzly_mac.tar.gz # [osx] + sha256: d8a922b76445bae79acb41d818dedba51567e7c041e8bb14360fd4cc0f674778 # [osx] build: number: 0 @@ -30,3 +30,7 @@ about: home: https://github.com/pmelsted/pizzly license: BSD-2 license_file: LICENSE + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.0/build.sh b/recipes/plant_tribes_assembly_post_processor/1.0.0/build.sh deleted file mode 100644 index 0419dad237697..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/AssemblyPostProcessor $PREFIX/bin -chmod +x $PREFIX/bin/AssemblyPostProcessor -ln -s $PREFIX/bin/AssemblyPostProcessor $PREFIX/pipelines/AssemblyPostProcessor -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.0/meta.yaml b/recipes/plant_tribes_assembly_post_processor/1.0.0/meta.yaml deleted file mode 100644 index bc7527863cfc0..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.0/meta.yaml +++ /dev/null @@ -1,32 +0,0 @@ -package: - name: plant_tribes_assembly_post_processor - version: "1.0.0" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.0.tar.gz - md5: ef556a78118a03045391464102f8ae18 - -build: - number: 1 - # Requires genometools which is not supported on osx - skip: True # [osx] - -requirements: - run: - - cap3 - - genometools-genometools >=1,<2 - - hmmer >=3 - - mafft >=7,<8 - - perl >=5.22 - - perl-estscan2 2.1 pl5.22.0_1 - - transdecoder >=3,<4 - - trimal >=1.4,<2 - -test: - commands: - - AssemblyPostProcessor 2>&1 | grep Usage - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Transcriptome assembly post processing pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.1/build.sh b/recipes/plant_tribes_assembly_post_processor/1.0.1/build.sh deleted file mode 100644 index 0419dad237697..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.1/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/AssemblyPostProcessor $PREFIX/bin -chmod +x $PREFIX/bin/AssemblyPostProcessor -ln -s $PREFIX/bin/AssemblyPostProcessor $PREFIX/pipelines/AssemblyPostProcessor -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.1/meta.yaml b/recipes/plant_tribes_assembly_post_processor/1.0.1/meta.yaml deleted file mode 100644 index 8a1cbb2159f39..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.1/meta.yaml +++ /dev/null @@ -1,32 +0,0 @@ -package: - name: plant_tribes_assembly_post_processor - version: "1.0.1" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.1.tar.gz - md5: dcef43b19ed8057212e8cb44994c7d37 - -build: - number: 1 - # Requires genometools which is not supported on osx - skip: True # [osx] - -requirements: - run: - - cap3 - - genometools-genometools >=1,<2 - - hmmer >=3 - - mafft >=7,<8 - - perl >=5.22 - - perl-estscan2 2.1 pl5.22.0_1 - - transdecoder >=3,<4 - - trimal >=1.4,<2 - -test: - commands: - - AssemblyPostProcessor 2>&1 | grep Usage - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Transcriptome assembly post processing pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.2/build.sh b/recipes/plant_tribes_assembly_post_processor/1.0.2/build.sh deleted file mode 100644 index 0cce90fceb9cb..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data - -cp ./pipelines/AssemblyPostProcessor $PREFIX/bin -chmod +x $PREFIX/bin/AssemblyPostProcessor -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.2/meta.yaml b/recipes/plant_tribes_assembly_post_processor/1.0.2/meta.yaml deleted file mode 100644 index 9c819ab047785..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.2/meta.yaml +++ /dev/null @@ -1,32 +0,0 @@ -package: - name: plant_tribes_assembly_post_processor - version: "1.0.2" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.2.tar.gz - md5: c0a4217048fe8a18e0c13d67667da638 - -build: - number: 1 - # Requires genometools which is not supported on osx - skip: True # [osx] - -requirements: - run: - - cap3 - - genometools-genometools >=1,<2 - - hmmer >=3 - - mafft >=7,<8 - - perl >=5.22 - - perl-estscan2 2.1 pl5.22.0_1 - - transdecoder >=3,<4 - - trimal >=1.4,<2 - -test: - commands: - - AssemblyPostProcessor 2>&1 | grep Usage - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Transcriptome assembly post processing pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.3/meta.yaml b/recipes/plant_tribes_assembly_post_processor/1.0.3/meta.yaml deleted file mode 100644 index 0a13906183067..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.3/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -package: - name: plant_tribes_assembly_post_processor - version: "1.0.3" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.3.tar.gz - md5: fadbcc5f105eb05156e5068380840460 - -build: - number: 1 - # Requires genometools which is not supported on osx - skip: True # [osx] - -requirements: - run: - - cap3 - - genometools-genometools >=1,<2 - - hmmer >=3 - - mafft >=7,<8 - - perl >=5.22 - - perl-estscan2 2.1 pl5.22.0_1 - - transdecoder >=3,<4 - - trimal >=1.4,<2 - -test: - commands: - - AssemblyPostProcessor 2>&1 | grep Usage - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Transcriptome assembly post processing pipeline' - license: GNU General Public License v3 (GPLv3) - diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.4/build.sh b/recipes/plant_tribes_assembly_post_processor/1.0.4/build.sh deleted file mode 100644 index 3e6564850844a..0000000000000 --- a/recipes/plant_tribes_assembly_post_processor/1.0.4/build.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin - -cp ./pipelines/AssemblyPostProcessor $PREFIX/bin -chmod +x $PREFIX/bin/AssemblyPostProcessor diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.3/build.sh b/recipes/plant_tribes_assembly_post_processor/build.sh similarity index 100% rename from recipes/plant_tribes_assembly_post_processor/1.0.3/build.sh rename to recipes/plant_tribes_assembly_post_processor/build.sh diff --git a/recipes/plant_tribes_assembly_post_processor/1.0.4/meta.yaml b/recipes/plant_tribes_assembly_post_processor/meta.yaml similarity index 93% rename from recipes/plant_tribes_assembly_post_processor/1.0.4/meta.yaml rename to recipes/plant_tribes_assembly_post_processor/meta.yaml index 939a65a3cf037..319140fa4d395 100644 --- a/recipes/plant_tribes_assembly_post_processor/1.0.4/meta.yaml +++ b/recipes/plant_tribes_assembly_post_processor/meta.yaml @@ -31,3 +31,6 @@ about: summary: 'Transcriptome assembly post processing pipeline' license: GNU General Public License v3 (GPLv3) +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/plant_tribes_gene_family_aligner/1.0.0/build.sh b/recipes/plant_tribes_gene_family_aligner/1.0.0/build.sh deleted file mode 100644 index 17f6b29e1cac2..0000000000000 --- a/recipes/plant_tribes_gene_family_aligner/1.0.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/GeneFamilyAligner $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyAligner -ln -s $PREFIX/bin/GeneFamilyAligner $PREFIX/pipelines/GeneFamilyAligner -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_gene_family_aligner/1.0.0/meta.yaml b/recipes/plant_tribes_gene_family_aligner/1.0.0/meta.yaml deleted file mode 100644 index 26f79721bad69..0000000000000 --- a/recipes/plant_tribes_gene_family_aligner/1.0.0/meta.yaml +++ /dev/null @@ -1,26 +0,0 @@ -package: - name: plant_tribes_gene_family_aligner - version: "1.0.0" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.0.tar.gz - md5: ef556a78118a03045391464102f8ae18 - -build: - number: 1 - -requirements: - run: - - mafft >=7,<8 - - pasta >=1.7.8 - - perl - - trimal >=1.4,<2 - -test: - commands: - - GeneFamilyAligner 2>&1 | grep ALIGN - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family aligner pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_aligner/1.0.2/build.sh b/recipes/plant_tribes_gene_family_aligner/1.0.2/build.sh deleted file mode 100644 index f3e7e95d1bf06..0000000000000 --- a/recipes/plant_tribes_gene_family_aligner/1.0.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data - -cp ./pipelines/GeneFamilyAligner $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyAligner -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data diff --git a/recipes/plant_tribes_gene_family_aligner/1.0.2/meta.yaml b/recipes/plant_tribes_gene_family_aligner/1.0.2/meta.yaml deleted file mode 100644 index bb6458ca52afe..0000000000000 --- a/recipes/plant_tribes_gene_family_aligner/1.0.2/meta.yaml +++ /dev/null @@ -1,26 +0,0 @@ -package: - name: plant_tribes_gene_family_aligner - version: "1.0.2" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.2.tar.gz - md5: c0a4217048fe8a18e0c13d67667da638 - -build: - number: 1 - -requirements: - run: - - mafft >=7,<8 - - pasta >=1.7.8 - - perl - - trimal >=1.4,<2 - -test: - commands: - - GeneFamilyAligner 2>&1 | grep ALIGN - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family aligner pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_aligner/1.0.3/build.sh b/recipes/plant_tribes_gene_family_aligner/build.sh similarity index 100% rename from recipes/plant_tribes_gene_family_aligner/1.0.3/build.sh rename to recipes/plant_tribes_gene_family_aligner/build.sh diff --git a/recipes/plant_tribes_gene_family_aligner/1.0.3/meta.yaml b/recipes/plant_tribes_gene_family_aligner/meta.yaml similarity index 93% rename from recipes/plant_tribes_gene_family_aligner/1.0.3/meta.yaml rename to recipes/plant_tribes_gene_family_aligner/meta.yaml index 2f3198f5622bd..5bf3d4f47773d 100644 --- a/recipes/plant_tribes_gene_family_aligner/1.0.3/meta.yaml +++ b/recipes/plant_tribes_gene_family_aligner/meta.yaml @@ -7,12 +7,12 @@ source: md5: fadbcc5f105eb05156e5068380840460 build: - skip: True # [py3k] + noarch: generic number: 1 requirements: run: - - python + - python <3 - mafft >=7,<8 - pasta >=1.7.8 - perl diff --git a/recipes/plant_tribes_gene_family_classifier/1.0.0/build.sh b/recipes/plant_tribes_gene_family_classifier/1.0.0/build.sh deleted file mode 100644 index 49ef3eb86d7ce..0000000000000 --- a/recipes/plant_tribes_gene_family_classifier/1.0.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/GeneFamilyClassifier $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyClassifier -ln -s $PREFIX/bin/GeneFamilyClassifier $PREFIX/pipelines/GeneFamilyClassifier -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_gene_family_classifier/1.0.0/meta.yaml b/recipes/plant_tribes_gene_family_classifier/1.0.0/meta.yaml deleted file mode 100644 index 7848d995b522f..0000000000000 --- a/recipes/plant_tribes_gene_family_classifier/1.0.0/meta.yaml +++ /dev/null @@ -1,25 +0,0 @@ -package: - name: plant_tribes_gene_family_classifier - version: "1.0.0" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.0.tar.gz - md5: ef556a78118a03045391464102f8ae18 - -build: - number: 2 - -requirements: - run: - - blast >=2.2.29 - - hmmer >=3 - - perl - -test: - commands: - - GeneFamilyClassifier 2>&1 | grep GENE - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family classifier pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_classifier/1.0.2/build.sh b/recipes/plant_tribes_gene_family_classifier/1.0.2/build.sh deleted file mode 100644 index f86d95b250772..0000000000000 --- a/recipes/plant_tribes_gene_family_classifier/1.0.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data - -cp ./pipelines/GeneFamilyClassifier $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyClassifier -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data diff --git a/recipes/plant_tribes_gene_family_classifier/1.0.2/meta.yaml b/recipes/plant_tribes_gene_family_classifier/1.0.2/meta.yaml deleted file mode 100644 index f7a12fdc4f984..0000000000000 --- a/recipes/plant_tribes_gene_family_classifier/1.0.2/meta.yaml +++ /dev/null @@ -1,25 +0,0 @@ -package: - name: plant_tribes_gene_family_classifier - version: "1.0.2" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.2.tar.gz - md5: c0a4217048fe8a18e0c13d67667da638 - -build: - number: 1 - -requirements: - run: - - blast >=2.2.29 - - hmmer >=3 - - perl - -test: - commands: - - GeneFamilyClassifier 2>&1 | grep GENE - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family classifier pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_classifier/1.0.3/build.sh b/recipes/plant_tribes_gene_family_classifier/build.sh similarity index 100% rename from recipes/plant_tribes_gene_family_classifier/1.0.3/build.sh rename to recipes/plant_tribes_gene_family_classifier/build.sh diff --git a/recipes/plant_tribes_gene_family_classifier/1.0.3/meta.yaml b/recipes/plant_tribes_gene_family_classifier/meta.yaml similarity index 96% rename from recipes/plant_tribes_gene_family_classifier/1.0.3/meta.yaml rename to recipes/plant_tribes_gene_family_classifier/meta.yaml index 50f845d081627..f6b4e8bacfbe6 100644 --- a/recipes/plant_tribes_gene_family_classifier/1.0.3/meta.yaml +++ b/recipes/plant_tribes_gene_family_classifier/meta.yaml @@ -7,6 +7,7 @@ source: md5: fadbcc5f105eb05156e5068380840460 build: + noarch: generic number: 2 requirements: diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml b/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml index ff35c99d7f6c5..82fc93edffb4d 100644 --- a/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml +++ b/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml @@ -7,6 +7,7 @@ source: md5: ef556a78118a03045391464102f8ae18 build: + noarch: generic number: 1 requirements: diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml b/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml index 87cbdd60d90f0..3e9a14a2edca0 100644 --- a/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml +++ b/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml @@ -7,6 +7,7 @@ source: md5: c0a4217048fe8a18e0c13d67667da638 build: + noarch: generic number: 1 requirements: diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml b/recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml index e8387b3639094..42b83dcf3e5db 100644 --- a/recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml +++ b/recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml @@ -7,6 +7,7 @@ source: md5: fadbcc5f105eb05156e5068380840460 build: + noarch: generic number: 1 requirements: diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml index 3aa53de5c29c8..2bae1e111cc9a 100644 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml +++ b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml @@ -7,6 +7,7 @@ source: md5: ef556a78118a03045391464102f8ae18 build: + noarch: generic number: 1 requirements: diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml index f699d1912563b..281f81f98afe7 100644 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml +++ b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml @@ -7,6 +7,7 @@ source: md5: c0a4217048fe8a18e0c13d67667da638 build: + noarch: generic number: 1 requirements: diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml index 664b2804ca5e2..26bcd29283f4d 100644 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml +++ b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml @@ -7,6 +7,7 @@ source: md5: fadbcc5f105eb05156e5068380840460 build: + noarch: generic number: 1 requirements: diff --git a/recipes/plant_tribes_kaks_analysis/1.0.0/build.sh b/recipes/plant_tribes_kaks_analysis/1.0.0/build.sh deleted file mode 100644 index b09ffe312398d..0000000000000 --- a/recipes/plant_tribes_kaks_analysis/1.0.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/KaKsAnalysis $PREFIX/bin -chmod +x $PREFIX/bin/KaKsAnalysis -ln -s $PREFIX/bin/KaKsAnalysis $PREFIX/pipelines/KaKsAnalysis -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_kaks_analysis/1.0.0/meta.yaml b/recipes/plant_tribes_kaks_analysis/1.0.0/meta.yaml deleted file mode 100644 index 117faf3d5bbc4..0000000000000 --- a/recipes/plant_tribes_kaks_analysis/1.0.0/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: plant_tribes_kaks_analysis - version: "1.0.0" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.0.tar.gz - md5: ef556a78118a03045391464102f8ae18 - -build: - number: 1 - # Requires Emmix which is not supported on osx - skip: True # [osx] - -requirements: - run: - - blast >=2.2.29 - - emmix - - mafft >=7,<8 - - paml - - perl - -test: - commands: - - KaKsAnalysis 2>&1 | grep KaKsAnalysis - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'KaKs Analysis pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_kaks_analysis/1.0.2/build.sh b/recipes/plant_tribes_kaks_analysis/1.0.2/build.sh deleted file mode 100644 index ab4e5cdabd186..0000000000000 --- a/recipes/plant_tribes_kaks_analysis/1.0.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data - -cp ./pipelines/KaKsAnalysis $PREFIX/bin -chmod +x $PREFIX/bin/KaKsAnalysis -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data diff --git a/recipes/plant_tribes_kaks_analysis/1.0.2/meta.yaml b/recipes/plant_tribes_kaks_analysis/1.0.2/meta.yaml deleted file mode 100644 index 89a4129ba122f..0000000000000 --- a/recipes/plant_tribes_kaks_analysis/1.0.2/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: plant_tribes_kaks_analysis - version: "1.0.2" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.2.tar.gz - md5: c0a4217048fe8a18e0c13d67667da638 - -build: - number: 1 - # Requires Emmix which is not supported on osx - skip: True # [osx] - -requirements: - run: - - blast >=2.2.29 - - emmix - - mafft >=7,<8 - - paml - - perl - -test: - commands: - - KaKsAnalysis 2>&1 | grep KaKsAnalysis - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'KaKs Analysis pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_kaks_analysis/1.0.3/build.sh b/recipes/plant_tribes_kaks_analysis/build.sh similarity index 100% rename from recipes/plant_tribes_kaks_analysis/1.0.3/build.sh rename to recipes/plant_tribes_kaks_analysis/build.sh diff --git a/recipes/plant_tribes_kaks_analysis/1.0.3/meta.yaml b/recipes/plant_tribes_kaks_analysis/meta.yaml similarity index 88% rename from recipes/plant_tribes_kaks_analysis/1.0.3/meta.yaml rename to recipes/plant_tribes_kaks_analysis/meta.yaml index 85b5a8b6ec1b6..99eb70f61a9ef 100644 --- a/recipes/plant_tribes_kaks_analysis/1.0.3/meta.yaml +++ b/recipes/plant_tribes_kaks_analysis/meta.yaml @@ -7,9 +7,8 @@ source: md5: fadbcc5f105eb05156e5068380840460 build: + noarch: generic number: 1 - # Requires Emmix which is not supported on osx - skip: True # [osx] requirements: run: diff --git a/recipes/plascope/meta.yaml b/recipes/plascope/meta.yaml index cda5ab6ae40dc..8c2d74fb2b172 100644 --- a/recipes/plascope/meta.yaml +++ b/recipes/plascope/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/plasflow/meta.yaml b/recipes/plasflow/meta.yaml index 660777a95eeed..20b21b53ff4d8 100644 --- a/recipes/plasflow/meta.yaml +++ b/recipes/plasflow/meta.yaml @@ -18,7 +18,9 @@ source: build: number: 0 - skip: True # [not py35 or osx] + skip: True + #If this really only works with python 3.5 then we can't support it + # [not py35 or osx] requirements: host: @@ -50,3 +52,6 @@ about: extra: identifiers: - doi:10.1093/nar/gkx1321 + skip-lints: + - should_not_use_skip_python + - should_be_noarch_generic diff --git a/recipes/plasmidtron/meta.yaml b/recipes/plasmidtron/meta.yaml index 911277f2b0339..03eeba1b25f3e 100644 --- a/recipes/plasmidtron/meta.yaml +++ b/recipes/plasmidtron/meta.yaml @@ -11,19 +11,15 @@ source: sha256: {{ sha256hash }} build: - skip: True # [py27] + noarch: python number: 1 requirements: host: - - python - - setuptools - - pyfastaq >=3.12.0 - - matplotlib - - biopython - + - python >=3 + - pip run: - - python + - python >=3 - pyfastaq >=3.12.0 - matplotlib - biopython diff --git a/recipes/plass/meta.yaml b/recipes/plass/meta.yaml index 20ce6f4422e85..efd34aafa363f 100644 --- a/recipes/plass/meta.yaml +++ b/recipes/plass/meta.yaml @@ -40,6 +40,5 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url - missing_hash - diff --git a/recipes/platypus-conquistador/build.sh b/recipes/platypus-conquistador/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/platypus-conquistador/build.sh +++ /dev/null @@ -1,9 +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/platypus-conquistador/meta.yaml b/recipes/platypus-conquistador/meta.yaml index 6d2e4df68085d..edf6634c94410 100644 --- a/recipes/platypus-conquistador/meta.yaml +++ b/recipes/platypus-conquistador/meta.yaml @@ -11,17 +11,15 @@ source: build: number: 2 - skip: true # [not py27 or osx] - number: 2 + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - scikit-bio >=0.2.1,<0.3.0 - - click - + - python <3 + - pip run: - - python + - python <3 - scikit-bio >=0.2.1,<0.3.0 - click diff --git a/recipes/pneumocat/meta.yaml b/recipes/pneumocat/meta.yaml index 322cc7b4b8601..42189f35533ef 100644 --- a/recipes/pneumocat/meta.yaml +++ b/recipes/pneumocat/meta.yaml @@ -11,8 +11,8 @@ source: url: https://github.com/phe-bioinformatics/pneumocat/archive/v{{version}}.tar.gz sha256: '{{sha256}}' build: + noarch: generic number: 2 - skip: true # [not py27] requirements: host: @@ -20,7 +20,7 @@ requirements: - bowtie2 - samtools ==0.1.19 - pyyaml - - python + - python <3 - numpy - lxml - pysam diff --git a/recipes/poretools/0.5.1/build.sh b/recipes/poretools/0.5.1/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/poretools/0.5.1/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/poretools/0.5.1/meta.yaml b/recipes/poretools/0.5.1/meta.yaml index 58498f8dcd541..5eb2f6cc35b57 100644 --- a/recipes/poretools/0.5.1/meta.yaml +++ b/recipes/poretools/0.5.1/meta.yaml @@ -1,32 +1,28 @@ package: name: poretools version: "0.5.1" + source: url: https://github.com/arq5x/poretools/archive/v0.5.1.tar.gz md5: d246f30b6dd25c1e1580eb81cfd95b85 +build: + number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python + requirements: host: - - python - - setuptools - - hdf5 >=1.8.7 - - h5py >=2.0 - - matplotlib - - seaborn - - pandas - + - python <3 + - pip run: - - python + - python <3 - hdf5 >=1.8.7 - h5py >=2.0 - matplotlib - seaborn - pandas -build: - number: 2 - skip: True # [not py27] - test: commands: - poretools -v diff --git a/recipes/poretools/meta.yaml b/recipes/poretools/meta.yaml index 8713582f31c9f..35b442fc10844 100644 --- a/recipes/poretools/meta.yaml +++ b/recipes/poretools/meta.yaml @@ -11,28 +11,22 @@ source: patches: - poretools.patch +build: + noarch: python + number: 6 + requirements: host: - - python - - h5py >=2.2.0 - - setuptools - - hdf5 - - matplotlib - - seaborn - - pandas - + - python <3 + - pip run: - - python + - python <3 - hdf5 - h5py >=2.2.0 - matplotlib - seaborn - pandas -build: - number: 6 - skip: True # [not py27] - test: commands: - poretools -v diff --git a/recipes/potrace/1.11/meta.yaml b/recipes/potrace/1.11/meta.yaml index f8c0ca204c67b..67e79bffda9f7 100644 --- a/recipes/potrace/1.11/meta.yaml +++ b/recipes/potrace/1.11/meta.yaml @@ -1,11 +1,14 @@ package: name: potrace version: 1.11 + build: number: 1 - #skip: True # [osx] + source: url: https://depot.galaxyproject.org/software/potrace/potrace_1.11_src_all.tar.gz + sha256: 5aa5eb496e00206d68b67edf8f6067999a45d1b69f848c18af5cbdf8e4a17ead + requirements: build: - {{ compiler('c') }} @@ -13,9 +16,11 @@ requirements: - zlib run: - zlib + test: commands: - "potrace --help" + about: home: http://potrace.sourceforge.net license: GPL diff --git a/recipes/pp/1.6.4/build.sh b/recipes/pp/1.6.4/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pp/1.6.4/build.sh +++ /dev/null @@ -1,9 +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/pp/1.6.4/meta.yaml b/recipes/pp/1.6.4/meta.yaml deleted file mode 100644 index e3a3a2ecea045..0000000000000 --- a/recipes/pp/1.6.4/meta.yaml +++ /dev/null @@ -1,28 +0,0 @@ -package: - name: pp - version: "1.6.4" - -source: - url: http://www.parallelpython.com/downloads/pp/pp-1.6.4.zip - md5: 0162fd2813d7218a4159430ca9e6f26a - -build: - number: 1 - skip: True # [not py27] - -requirements: - host: - - python - - run: - - python - -test: - imports: - - pp - -about: - home: http://www.parallelpython.com - license: BSD License - summary: 'Parallel and distributed programming for Python' - license_family: BSD diff --git a/recipes/pp/build.sh b/recipes/pp/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pp/build.sh +++ /dev/null @@ -1,9 +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/pp/meta.yaml b/recipes/pp/meta.yaml index e537f4e100f88..d52407b85298c 100644 --- a/recipes/pp/meta.yaml +++ b/recipes/pp/meta.yaml @@ -7,13 +7,14 @@ source: md5: 9dea3a1b61bead0e1d010ea00cd70703 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - python diff --git a/recipes/pplacer/meta.yaml b/recipes/pplacer/meta.yaml index 04cc47c254f3b..ff751927cac52 100644 --- a/recipes/pplacer/meta.yaml +++ b/recipes/pplacer/meta.yaml @@ -6,11 +6,8 @@ package: version: '{{ version }}' source: - url: https://github.com/matsen/pplacer/releases/download/v{{ version }}/pplacer-linux-v{{ version }}.zip # [linux] - sha256: '{{ sha256 }}' # [linux] - # fn: pplacer-Darwin-v1.1.alpha17.zip # [osx] - # url: https://github.com/matsen/pplacer/releases/download/v1.1.alpha17/pplacer-Darwin-v1.1.alpha17.zip # [osx] - # sha256: db1ac64e1bc9b4d24d17ee2e388c061c283ca9fbec075e022bdeaad1adc6d41c # [osx] + url: https://github.com/matsen/pplacer/releases/download/v{{ version }}/pplacer-linux-v{{ version }}.zip + sha256: '{{ sha256 }}' build: skip: true # [osx] @@ -30,3 +27,7 @@ about: maximize phylogenetic likelihood or posterior probability according to a reference alignment. dev_url: https://github.com/matsen/pplacer/ + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index 86e8709fa7869..6f2df0ecaa158 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -10,15 +10,15 @@ source: md5: 6b231a06f8f7f2d2998ccb780adfae9d build: - skip: False # [not py27] number: 3 requirements: + build: + - {{ compiler('c') }} host: - python - setuptools - cython - run: - python diff --git a/recipes/primerprospector/build.sh b/recipes/primerprospector/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/primerprospector/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/primerprospector/meta.yaml b/recipes/primerprospector/meta.yaml index 89665eb8c8411..3889ffb08f82b 100644 --- a/recipes/primerprospector/meta.yaml +++ b/recipes/primerprospector/meta.yaml @@ -7,7 +7,8 @@ package: build: number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python source: url: http://downloads.sourceforge.net/project/pprospector/pprospector-1.0.1.tar.gz @@ -15,13 +16,10 @@ source: requirements: host: - - python - - cogent >=1.5 - - numpy >=1.3.0 - - matplotlib >=0.98.3 - + - python <3 + - pip run: - - python + - python <3 - cogent >=1.5 - numpy >=1.3.0 - matplotlib >=0.98.3 diff --git a/recipes/probamconvert/meta.yaml b/recipes/probamconvert/meta.yaml index 4294d5adcc2b1..9a7d3d7734fce 100644 --- a/recipes/probamconvert/meta.yaml +++ b/recipes/probamconvert/meta.yaml @@ -2,22 +2,17 @@ package: name: probamconvert version: "1.0.2" -about: - home: 'https://github.com/Biobix/proBAMconvert' - summary: proBAMconvert is a conversion tool to convert common peptide identification files (mzIdentML, pepXML, mzTAB) to the proBAM or proBED format - license: Apache License - source: url: https://github.com/Biobix/proBAMconvert/archive/a94913a16339ca58ae43a8e40d26acfd6725da40.tar.gz md5: 17d68ecec97405e8c2198dfd2e7d2383 build: + noarch: generic number: 2 - skip: True # [py3k or osx] requirements: run: - - python + - python <3 - cogent - pysam >=0.9 - mysql-python @@ -32,3 +27,8 @@ requirements: test: commands: - proBAM.py --help + +about: + home: 'https://github.com/Biobix/proBAMconvert' + summary: proBAMconvert is a conversion tool to convert common peptide identification files (mzIdentML, pepXML, mzTAB) to the proBAM or proBED format + license: Apache License diff --git a/recipes/prodigal/meta.yaml b/recipes/prodigal/meta.yaml index 2270f25315ff4..ef6ff4bece66a 100644 --- a/recipes/prodigal/meta.yaml +++ b/recipes/prodigal/meta.yaml @@ -5,8 +5,8 @@ source: url: https://github.com/hyattpd/Prodigal/archive/v2.6.3.zip sha256: 4f73f64ea09be8421e08afabdc641db7775632210f5ef896f5fab4604c9dfcd9 build: + noarch: generic number: 1 - skip: False requirements: build: run: diff --git a/recipes/progressivemauve/meta.yaml b/recipes/progressivemauve/meta.yaml index c8eaef0cfa46c..701450799244f 100644 --- a/recipes/progressivemauve/meta.yaml +++ b/recipes/progressivemauve/meta.yaml @@ -20,3 +20,7 @@ about: home: http://darlinglab.org/mauve/user-guide/progressivemauve.html license: GNU General Public License version 2.0 (GPLv2) summary: 'progressiveMauve computes multiple genome alignment with gene gain, loss and rearrangement' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/prokka/1.12/meta.yaml b/recipes/prokka/1.12/meta.yaml index 2379f60428ae8..6485050e0c3eb 100644 --- a/recipes/prokka/1.12/meta.yaml +++ b/recipes/prokka/1.12/meta.yaml @@ -10,10 +10,12 @@ source: sha256: '{{ sha256 }}' build: + noarch: generic number: 0 requirements: - build: + host: + - perl - perl-bioperl >=1.7.2 - blast >=2.7.1 - infernal >=1.1.2 diff --git a/recipes/pronto/0.3.3/meta.yaml b/recipes/pronto/0.3.3/meta.yaml index fea16172fd9b4..6704e9250ece8 100644 --- a/recipes/pronto/0.3.3/meta.yaml +++ b/recipes/pronto/0.3.3/meta.yaml @@ -7,18 +7,17 @@ source: md5: 512eee78637add914a1b62195007aa2c build: - skip: True # [py3k] + noarch: python number: 2 requirements: host: - - python + - python <3 - setuptools - lxml - six - run: - - python + - python <3 - lxml - six diff --git a/recipes/prophyle/0.1.0/meta.yaml b/recipes/prophyle/0.1.0/meta.yaml index 77ff797145030..282237d1d681e 100644 --- a/recipes/prophyle/0.1.0/meta.yaml +++ b/recipes/prophyle/0.1.0/meta.yaml @@ -10,23 +10,16 @@ source: sha256: {{ sha256 }} build: + noarch: python number: 2 - skip: True # [py27] script: python -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python >=3 - pip - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil run: - - python + - python >=3 - samtools - ete3 - bitarray diff --git a/recipes/protrac/meta.yaml b/recipes/protrac/meta.yaml index f7cae1d86767f..2fb2ec3070c10 100644 --- a/recipes/protrac/meta.yaml +++ b/recipes/protrac/meta.yaml @@ -9,10 +9,11 @@ source: sha256: b8d09faf1c92e02f3d82acdac04675d48e7aa7123101d004d4558c5e5716abd9 build: + noarch: generic number: 0 requirements: - build: + host: - perl run: - perl diff --git a/recipes/pubchempy/meta.yaml b/recipes/pubchempy/meta.yaml index 7e2b97ace46c5..9a1c1233dd0bf 100644 --- a/recipes/pubchempy/meta.yaml +++ b/recipes/pubchempy/meta.yaml @@ -11,7 +11,6 @@ source: sha256: {{ sha256 }} build: - noarch: python noarch: python number: 1 script: python -m pip install --no-deps --ignore-installed . @@ -20,7 +19,6 @@ requirements: host: - python - pip - - setuptools run: - python diff --git a/recipes/pureclip/meta.yaml b/recipes/pureclip/meta.yaml index 9db6678daf765..c1ca706b21dd7 100644 --- a/recipes/pureclip/meta.yaml +++ b/recipes/pureclip/meta.yaml @@ -8,10 +8,10 @@ package: version: {{ version }} source: - url: https://github.com/skrakau/{{ name }}/releases/download/v{{ version }}/{{ name | lower }}-{{ version }}-linux64-static.tar.gz # [linux] - url: https://github.com/skrakau/{{ name }}/releases/download/v{{ version }}/{{ name | lower }}-{{ version }}-mac64.tar.gz # [osx] - sha256: {{ sha256_linux64_static }} # [linux] - sha256: {{ sha256_osx }} # [osx] + - url: https://github.com/skrakau/{{ name }}/releases/download/v{{ version }}/{{ name | lower }}-{{ version }}-linux64-static.tar.gz # [linux] + sha256: {{ sha256_linux64_static }} # [linux] + - url: https://github.com/skrakau/{{ name }}/releases/download/v{{ version }}/{{ name | lower }}-{{ version }}-mac64.tar.gz # [osx] + sha256: {{ sha256_osx }} # [osx] build: number: 0 @@ -35,3 +35,6 @@ about: extra: identifiers: - doi:10.1186/s13059-017-1364-2 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/pvacseq/meta.yaml b/recipes/pvacseq/meta.yaml index 9100c749fa162..224cf07ac7787 100644 --- a/recipes/pvacseq/meta.yaml +++ b/recipes/pvacseq/meta.yaml @@ -10,8 +10,8 @@ source: sha256: '{{ sha256 }}' build: + noarch: python number: 2 - skip: true # [py27] script: python -m pip install --no-deps --ignore-installed . entry_points: - pvacseq = pvacseq.pvacseq:main @@ -19,12 +19,10 @@ build: requirements: host: - - python + - python >=3 - pip - - setuptools - run: - - python + - python >=3 - pyvcf - requests - pyyaml diff --git a/recipes/pyalveo/build.sh b/recipes/pyalveo/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/pyalveo/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/pyalveo/meta.yaml b/recipes/pyalveo/meta.yaml deleted file mode 100644 index aa3f288cfc731..0000000000000 --- a/recipes/pyalveo/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: pyalveo - version: "1.0.5" - -build: - number: 0 - noarch: python - -source: - url: https://files.pythonhosted.org/packages/a8/1f/1aae80f120eb4c53b4d666007c781dff2dcb2555bbe8c2dff96bc9c15c0c/pyalveo-1.0.5.tar.gz - sha256: 9087f7a16c47a7d4365c89333d90b4546b1e9c193c9da78c34d20960237579a7 - -requirements: - host: - - python - - setuptools - - python-dateutil - - requests - - requests-oauthlib - - run: - - python - - python-dateutil - - requests - - requests-oauthlib - -test: - # Python imports - imports: - - pyalveo - - -about: - home: https://github.com/Alveo/pyalveo - license: BSD - summary: 'A Python library for interfacing with the Alveo API' diff --git a/recipes/pyasp/1.4.3/build.sh b/recipes/pyasp/1.4.3/build.sh deleted file mode 100644 index a6609066d90c9..0000000000000 --- a/recipes/pyasp/1.4.3/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/pyasp/1.4.3/meta.yaml b/recipes/pyasp/meta.yaml similarity index 83% rename from recipes/pyasp/1.4.3/meta.yaml rename to recipes/pyasp/meta.yaml index acd933d83958b..b53f228e0617d 100644 --- a/recipes/pyasp/1.4.3/meta.yaml +++ b/recipes/pyasp/meta.yaml @@ -3,6 +3,8 @@ package: version: "1.4.3" build: + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 source: @@ -12,7 +14,7 @@ source: requirements: host: - python - - setuptools + - pip run: - python diff --git a/recipes/pybamparser/meta.yaml b/recipes/pybamparser/meta.yaml index 53b443273d840..2e8bc0259da27 100644 --- a/recipes/pybamparser/meta.yaml +++ b/recipes/pybamparser/meta.yaml @@ -7,16 +7,16 @@ source: md5: 6d7fa3bd46a902d6acf4f6ad61fc29c2 build: - skip: True # [not py27] + noarch: python number: 1 requirements: host: - - python + - python <3 - setuptools run: - - python + - python <3 test: # Python imports diff --git a/recipes/pybamtools/0.0.3/build.sh b/recipes/pybamtools/0.0.3/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/pybamtools/0.0.3/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/pybamtools/0.0.3/meta.yaml b/recipes/pybamtools/0.0.3/meta.yaml deleted file mode 100644 index 424cba7bf5ab0..0000000000000 --- a/recipes/pybamtools/0.0.3/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -package: - name: pybamtools - version: "0.0.3" - -source: - url: https://pypi.python.org/packages/7a/08/052a1f5d53e80f42b94c8e41508c078962e5efd20fdde140414795a29727/pyBamTools-0.0.3.tar.gz - md5: 00858cb6b65f87ac2a87bca0150e203c - -build: - skip: True # [not py27] - number: 1 - -requirements: - host: - - python - - setuptools - - numpy - - pybamparser ==0.0.3 - - run: - - python - - numpy - - pybamparser ==0.0.3 - -test: - # Python imports - imports: - - pyBamTools - - pyBamTools.coverage - - pyBamTools.genotyping - - pyBamTools.util - -about: - home: https://github.com/blankenberg/pyBamTools - license: GNU General Public License v2 (GPLv2) - summary: 'Tools for working on BAM data' - license_family: GPL2 diff --git a/recipes/pybamtools/meta.yaml b/recipes/pybamtools/meta.yaml index 5ce029e55a7cd..4b885c99de6c5 100644 --- a/recipes/pybamtools/meta.yaml +++ b/recipes/pybamtools/meta.yaml @@ -7,18 +7,15 @@ source: md5: 7a43557f1f99adcd989016445427d0a0 build: - skip: True # [not py27] + noarch: python number: 2 requirements: host: - - python + - python <3 - setuptools - - numpy - - pybamparser ==0.0.3 - run: - - python + - python <3 - numpy - pybamparser ==0.0.3 diff --git a/recipes/pybedtools/0.6.9/meta.yaml b/recipes/pybedtools/0.6.9/meta.yaml index 5a4a02e278b1a..1f373aec448c7 100644 --- a/recipes/pybedtools/0.6.9/meta.yaml +++ b/recipes/pybedtools/0.6.9/meta.yaml @@ -12,6 +12,7 @@ build: requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} host: - python diff --git a/recipes/pybel/meta.yaml b/recipes/pybel/meta.yaml index e031f6b86e97a..7aac57e7ac17d 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -7,35 +7,25 @@ source: md5: 4c9f3a0f64b3f32dc3df70d890172752 build: + noarch: python entry_points: - pybel = pybel.cli:main number: 1 # tests fail on osx: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235726973#L3656 # click needs to be patched in order to properly detect unicode in py3k - skip: true # [osx or py3k] requirements: host: - - python - - setuptools - - requests - - ndex-python - - requests-file - - networkx - - pyparsing - - configparser # [py27] - - py2neo - - click - - sqlalchemy - - onto2nx + - python <3 + - pip run: - - python + - python <3 - requests - ndex-python - requests-file - networkx - pyparsing - - configparser # [py27] + - configparser - py2neo - click - sqlalchemy diff --git a/recipes/pycli/build.sh b/recipes/pycli/build.sh deleted file mode 100644 index 4dad93a1c02ab..0000000000000 --- a/recipes/pycli/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/pycli/meta.yaml b/recipes/pycli/meta.yaml index f6bfdda2aa868..87585b1b6c41d 100644 --- a/recipes/pycli/meta.yaml +++ b/recipes/pycli/meta.yaml @@ -9,12 +9,12 @@ source: build: noarch: python number: 1 - skip: False + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools + - python <3 + - pip run: - python <3 diff --git a/recipes/pycluster/build.sh b/recipes/pycluster/build.sh deleted file mode 100644 index d0f35d4aea6ee..0000000000000 --- a/recipes/pycluster/build.sh +++ /dev/null @@ -1,8 +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/pycluster/meta.yaml b/recipes/pycluster/meta.yaml index d8d0d1a122189..a27d3ff8f8c40 100644 --- a/recipes/pycluster/meta.yaml +++ b/recipes/pycluster/meta.yaml @@ -8,13 +8,14 @@ source: build: number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - {{ compiler('c') }} host: - python - - numpy + - pip run: - python - numpy diff --git a/recipes/pycsg/build.sh b/recipes/pycsg/build.sh deleted file mode 100644 index c1d38d2c3ab1b..0000000000000 --- a/recipes/pycsg/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -python setup.py install diff --git a/recipes/pycsg/meta.yaml b/recipes/pycsg/meta.yaml index 0601d78dccf5d..53f4a02895a30 100644 --- a/recipes/pycsg/meta.yaml +++ b/recipes/pycsg/meta.yaml @@ -2,11 +2,6 @@ package: name: pycsg version: "0.3.12" -about: - home: 'https://github.com/pletzer/pycsg' - summary: 'Python port of csg.js from Evan Wallace' - license: MIT - source: git_url: https://github.com/pletzer/pycsg git_rev: cee697f @@ -14,14 +9,26 @@ source: build: noarch: python number: 1 - -test: - # Python imports - imports: - - csg + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python + - pip run: - python + +test: + # Python imports + imports: + - csg + +about: + home: 'https://github.com/pletzer/pycsg' + summary: 'Python port of csg.js from Evan Wallace' + license: MIT + +extra: + skip-lints: + - uses_vcs_url + - missing_hash diff --git a/recipes/pydemult/meta.yaml b/recipes/pydemult/meta.yaml index ba7362cdaf6fc..34e6f2529c092 100644 --- a/recipes/pydemult/meta.yaml +++ b/recipes/pydemult/meta.yaml @@ -10,22 +10,20 @@ source: sha256: 5a44dc6c819fd4394b282d6aeff4b571b61654486ce6e4b782d3cc0731c3a0e2 build: + noarch: python number: 0 - skip: True # [py27] entry_points: - pydemult = pydemult.pydemult:demultiplex script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " requirements: host: - - mputil - - pandas - - pip + - pip >=3 - python run: - mputil - pandas - - python + - python >=3 test: imports: diff --git a/recipes/pydnase/meta.yaml b/recipes/pydnase/meta.yaml index 84bea18007f3b..b8e9174457158 100644 --- a/recipes/pydnase/meta.yaml +++ b/recipes/pydnase/meta.yaml @@ -14,9 +14,11 @@ build: skip: True # [not py3k] requirements: + build: + - {{ compiler('c') }} host: - python - - setuptools + - pip - cython run: - python diff --git a/recipes/pyexcelerator/build.sh b/recipes/pyexcelerator/build.sh deleted file mode 100755 index 1aea1a7737ea5..0000000000000 --- a/recipes/pyexcelerator/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/pyexcelerator/meta.yaml b/recipes/pyexcelerator/meta.yaml index 208dff56288e7..90f2d304076dc 100644 --- a/recipes/pyexcelerator/meta.yaml +++ b/recipes/pyexcelerator/meta.yaml @@ -7,14 +7,14 @@ source: md5: 478c79a74be39d27eee9bd1b3032dffe build: + noarch: pip number: 2 - skip: True # [not py27] - + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - python diff --git a/recipes/pyfaidx/0.4.7.1/build.sh b/recipes/pyfaidx/0.4.7.1/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/pyfaidx/0.4.7.1/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pyfaidx/0.4.7.1/meta.yaml b/recipes/pyfaidx/0.4.7.1/meta.yaml index 999470128e0bd..2fdc69e49d330 100644 --- a/recipes/pyfaidx/0.4.7.1/meta.yaml +++ b/recipes/pyfaidx/0.4.7.1/meta.yaml @@ -9,16 +9,14 @@ source: build: number: 2 noarch: python - skip: False + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - faidx = pyfaidx.cli:main requirements: host: - python - - setuptools - - six - + - pip run: - python - six diff --git a/recipes/pyfasta/build.sh b/recipes/pyfasta/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/pyfasta/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/pyfasta/meta.yaml b/recipes/pyfasta/meta.yaml index cd431ac8144a4..96f710191cc4a 100644 --- a/recipes/pyfasta/meta.yaml +++ b/recipes/pyfasta/meta.yaml @@ -9,15 +9,14 @@ source: build: noarch: python number: 1 - skip: False + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - pyfasta = pyfasta:main requirements: host: - python - - setuptools - + - pip run: - python - numpy diff --git a/recipes/pygresql/build.sh b/recipes/pygresql/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pygresql/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pygresql/meta.yaml b/recipes/pygresql/meta.yaml index cdc0631a76773..640e18259129b 100644 --- a/recipes/pygresql/meta.yaml +++ b/recipes/pygresql/meta.yaml @@ -4,6 +4,8 @@ package: build: number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python source: url: https://pypi.python.org/packages/25/f7/dd8a191de9a7f90b8b262ecf54bff31ca2422b4d564f0ab57e39924aea21/PyGreSQL-5.0.1.zip @@ -12,9 +14,7 @@ source: requirements: host: - python - - setuptools - - postgresql - + - pip run: - python - postgresql diff --git a/recipes/pyhashxx/build.sh b/recipes/pyhashxx/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pyhashxx/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/pyhashxx/meta.yaml b/recipes/pyhashxx/meta.yaml index 71400380ce7b2..eee9194d78f5b 100644 --- a/recipes/pyhashxx/meta.yaml +++ b/recipes/pyhashxx/meta.yaml @@ -3,7 +3,9 @@ package: version: "0.1.3" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/c4/a9/630e7c00c4766b0fa03ca9c4c1c3774ab2fa52646711918632daa403b52c/pyhashxx-0.1.3.tar.gz @@ -12,8 +14,7 @@ source: requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/pyloh/build.sh b/recipes/pyloh/build.sh deleted file mode 100644 index 4dad93a1c02ab..0000000000000 --- a/recipes/pyloh/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/pyloh/meta.yaml b/recipes/pyloh/meta.yaml index 9a20a15ace240..b2748b43ed86f 100644 --- a/recipes/pyloh/meta.yaml +++ b/recipes/pyloh/meta.yaml @@ -11,15 +11,16 @@ source: sha256: {{ hash }} build: + noarch: pip number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 - numpy >=1.6.1 - scipy >=0.10 - matplotlib >=1.2 diff --git a/recipes/pymisc-utils/build.sh b/recipes/pymisc-utils/build.sh index e318b73a7857c..8662a8e3ed6e4 100644 --- a/recipes/pymisc-utils/build.sh +++ b/recipes/pymisc-utils/build.sh @@ -1,4 +1,4 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv cp misc/*.py ${PREFIX}/bin/ chmod 755 ${PREFIX}/bin/*.py diff --git a/recipes/pymisc-utils/meta.yaml b/recipes/pymisc-utils/meta.yaml index 8f75da0944f66..4100ebc1c7d67 100644 --- a/recipes/pymisc-utils/meta.yaml +++ b/recipes/pymisc-utils/meta.yaml @@ -14,7 +14,7 @@ source: build: number: 0 - skip: True [osx or py27] + skip: True # [osx or py27] requirements: build: @@ -46,7 +46,6 @@ requirements: - python - numpy - scipy - - cython - statsmodels - matplotlib - pandas diff --git a/recipes/pymix/build.sh b/recipes/pymix/build.sh deleted file mode 100644 index e10006f79d5a5..0000000000000 --- a/recipes/pymix/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -python setup.py build -python setup.py install diff --git a/recipes/pymix/meta.yaml b/recipes/pymix/meta.yaml index 7cf1d7ede4ebf..a3959052d0aed 100644 --- a/recipes/pymix/meta.yaml +++ b/recipes/pymix/meta.yaml @@ -2,6 +2,10 @@ {% set version = "0.8" %} {% set md5 = "4e2b7db99251d9ce6d0527528224a45b" %} +package: + name: {{ name }} + version: {{ version }} + source: md5: {{ md5 }} url: http://www.pymix.org/{{ name }}-{{ version }}a.tar.gz @@ -11,10 +15,7 @@ source: build: number: 1 skip: True # [not py27] - -package: - name: {{ name }} - version: {{ version }} + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: diff --git a/recipes/pymot/build.sh b/recipes/pymot/build.sh index 7d72897a7eb46..955afc69d81d3 100644 --- a/recipes/pymot/build.sh +++ b/recipes/pymot/build.sh @@ -1,4 +1,4 @@ #!/bin/bash cp $RECIPE_DIR/setup.py . -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/pymot/meta.yaml b/recipes/pymot/meta.yaml index 27e4d9475b937..1c4d4be9bb6ef 100644 --- a/recipes/pymot/meta.yaml +++ b/recipes/pymot/meta.yaml @@ -9,15 +9,15 @@ source: md5: 3641a81623d0bd37689abe69fd9ed924 build: + noarch: python number: 1 - skip: True # [py3k] requirements: host: - - setuptools - - python + - python <3 + - pip run: - - python + - python <3 - munkres test: diff --git a/recipes/pymummer/0.10.1/build.sh b/recipes/pymummer/0.10.1/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/pymummer/0.10.1/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/pymummer/0.10.1/meta.yaml b/recipes/pymummer/0.10.1/meta.yaml index 44efa00090d97..760a6d24606ef 100644 --- a/recipes/pymummer/0.10.1/meta.yaml +++ b/recipes/pymummer/0.10.1/meta.yaml @@ -7,18 +7,16 @@ source: md5: 1a16e2d27b58f6fdc47f648f977fafd0 build: - skip: True # [py27] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pyfastaq >=3.10.0 - - mummer - + - python >=3 + - pip run: - - python + - python >=3 - pyfastaq >=3.10.0 - mummer diff --git a/recipes/pynast/1.2.2/build.sh b/recipes/pynast/1.2.2/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/pynast/1.2.2/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pynast/1.2.2/meta.yaml b/recipes/pynast/1.2.2/meta.yaml index 939e2a8042a5d..90b4e392d9874 100644 --- a/recipes/pynast/1.2.2/meta.yaml +++ b/recipes/pynast/1.2.2/meta.yaml @@ -7,17 +7,16 @@ source: md5: 6f1744d8d3f333eb2dbe81026d4dcb1b build: + noarch: python number: 1 - skip: True [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - numpy >=1.5.1 - - cogent >=1.5.3 - + - python <3 + - pip run: - - python + - python <3 - numpy >=1.5.1 - cogent >=1.5.3 diff --git a/recipes/pyopt/build.sh b/recipes/pyopt/build.sh deleted file mode 100755 index 8e25a1455f914..0000000000000 --- a/recipes/pyopt/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/pyopt/meta.yaml b/recipes/pyopt/meta.yaml index 830e8c2d4c4e8..12a4cb9bb9fb2 100644 --- a/recipes/pyopt/meta.yaml +++ b/recipes/pyopt/meta.yaml @@ -5,16 +5,16 @@ package: source: url: http://www.pyopt.org/_downloads/pyOpt-1.2.0.tar.gz md5: 84f7574cb40919009312ad52d30109db + build: + noarch: python number: 1 - skip: True # [py3k or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - numpy >=1.0 - - swig >=1.3 - - mpi4py + - python <3 + - pip run: - python - numpy >=1.0 @@ -24,3 +24,4 @@ about: home: http://www.pyopt.org/index.html license: LGPLv3 license_file: LICENSE + summary: a Python-based package for formulating and solving nonlinear constrained optimization problems in an efficient, reusable and portable manner. diff --git a/recipes/pypore/0.0.5.dev20160304220337/build.sh b/recipes/pypore/0.0.5.dev20160304220337/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/pypore/0.0.5.dev20160304220337/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pypore/0.0.5.dev20160304220337/meta.yaml b/recipes/pypore/0.0.5.dev20160304220337/meta.yaml deleted file mode 100644 index 734ad28010b5f..0000000000000 --- a/recipes/pypore/0.0.5.dev20160304220337/meta.yaml +++ /dev/null @@ -1,46 +0,0 @@ -build: - number: 1 - skip: True # [osx] - -package: - name: pypore - version: "0.0.5.dev20160304220337" - -source: - url: https://pypi.python.org/packages/source/p/pypore/pypore-0.0.5.dev20160304220337.tar.gz - md5: 173ebb6a8ca721630468ffd5940029fd - -requirements: - host: - - python - - setuptools - - numpy - - run: - - python - - numpy - -test: - imports: - - pypore - - pypore.filetypes - - pypore.filetypes.tests - - pypore.i_o - - pypore.i_o.tests - - pypore.sampledata - - pypore.sampledata.tests - - pypore.strategies - - pypore.strategies.tests - - pypore.tests - - pyporegui - - pyporegui.graphicsItems - - pyporegui.graphicsItems.tests - - pyporegui.tests - - pyporegui.widgets - - pyporegui.widgets.tests - -about: - home: http://parkin.github.io/pypore/ - license: Apache License, Version 2.0 - summary: 'Pythonic/Cythonic Nanopore Translocation Analysis' - diff --git a/recipes/pypore/build.sh b/recipes/pypore/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pypore/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/pypore/meta.yaml b/recipes/pypore/meta.yaml index bf83e4c19a6e2..6ce654c66b402 100644 --- a/recipes/pypore/meta.yaml +++ b/recipes/pypore/meta.yaml @@ -7,17 +7,16 @@ source: sha256: 47827b073317cee8a22d38cde5fba11f722bde3cc594ecd632c157469dc8ab00 build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - + - python <3 + - pip run: - - python + - python <3 - numpy test: diff --git a/recipes/pyrad/meta.yaml b/recipes/pyrad/meta.yaml index 2969fd7519c3e..fc3b7ffc490c8 100644 --- a/recipes/pyrad/meta.yaml +++ b/recipes/pyrad/meta.yaml @@ -11,17 +11,17 @@ source: sha256: {{ hash }} build: + noarch: python number: 2 - skip: True # [not py27] entry_points: - pyrad = pyrad.pyRAD:main requirements: host: - - python + - python <3 - setuptools run: - - python + - python <3 - numpy - scipy - muscle diff --git a/recipes/pysam/0.10.0/meta.yaml b/recipes/pysam/0.10.0/meta.yaml index dfc4f124817e0..01a5c86dc8d7b 100644 --- a/recipes/pysam/0.10.0/meta.yaml +++ b/recipes/pysam/0.10.0/meta.yaml @@ -6,7 +6,7 @@ source: url: https://pypi.python.org/packages/87/8e/d2d8238558970df37c7aa01ddec63057a98042334e939b4c1c69cb9a2504/pysam-0.10.0.tar.gz md5: a1f3333ce60f8de542624cb07c792fc0 patches: # [osx] - - osx_rpath.patch [osx] + - osx_rpath.patch # [osx] build: number: 8 @@ -48,3 +48,5 @@ extra: identifiers: - biotools:pysam - doi:10.1093/bioinformatics/btp352 + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/pysam/0.8.3/build.sh b/recipes/pysam/0.8.3/build.sh index ff93357eafe4e..35c1b37d7d575 100644 --- a/recipes/pysam/0.8.3/build.sh +++ b/recipes/pysam/0.8.3/build.sh @@ -7,4 +7,4 @@ export C_INCLUDE_PATH=${PREFIX}/include # support, from https://github.com/chapmanb/bcbio-conda/blob/master/pysam/build.sh sed -i'' -e 's/"-Wno-error=declaration-after-statement",//g' setup.py sed -i'' -e 's/"-Wno-error=declaration-after-statement"//g' setup.py -$PYTHON setup.py install \ No newline at end of file +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/pysam/0.9.1/build.sh b/recipes/pysam/0.9.1/build.sh index 571d3c55db842..41681a1551f81 100644 --- a/recipes/pysam/0.9.1/build.sh +++ b/recipes/pysam/0.9.1/build.sh @@ -12,4 +12,4 @@ export LDFLAGS="-L$PREFIX/lib" export HTSLIB_LIBRARY_DIR=$PREFIX/lib export HTSLIB_INCLUDE_DIR=$PREFIX/include -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/pyscaf/build.sh b/recipes/pyscaf/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/pyscaf/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pyscaf/meta.yaml b/recipes/pyscaf/meta.yaml index c4c40d9a3675a..323e74218985e 100644 --- a/recipes/pyscaf/meta.yaml +++ b/recipes/pyscaf/meta.yaml @@ -7,19 +7,18 @@ source: md5: c67526747eb04d1e28279ac310916d40 build: + noarch: python number: 2 entry_points: - pyScaf = pyScaf:main - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - fastaindex - + - python <3 + - pip run: - - python + - python <3 - fastaindex test: diff --git a/recipes/pysnptools/meta.yaml b/recipes/pysnptools/meta.yaml index cac13ba7b25f7..3a35b1e00f575 100644 --- a/recipes/pysnptools/meta.yaml +++ b/recipes/pysnptools/meta.yaml @@ -11,19 +11,15 @@ source: md5: {{ hash }} build: + noarch: python number: 2 - skip: True # [not py27] requirements: host: - - python - - setuptools - - scipy >=0.15.1 - - numpy >=1.9.2 - - pandas >=0.16.2 - + - python <3 + - pip run: - - python + - python <3 - scipy >=0.15.1 - numpy >=1.9.2 - pandas >=0.16.2 diff --git a/recipes/pysvg/meta.yaml b/recipes/pysvg/meta.yaml index 51e73bcf5a324..10025c7bee928 100644 --- a/recipes/pysvg/meta.yaml +++ b/recipes/pysvg/meta.yaml @@ -7,18 +7,17 @@ source: md5: 9f9b637f5d7205a200d00856df1b2ae2 build: + noarch: python number: 2 - skip: True # [not py27] requirements: host: - - python - + - python <3 + - pip run: - - python - - 'lxml >=2.1' - - 'cssselect' - + - python <3 + - lxml >=2.1 + - cssselect test: imports: diff --git a/recipes/pysvmlight/build.sh b/recipes/pysvmlight/build.sh deleted file mode 100644 index b9962a29eda83..0000000000000 --- a/recipes/pysvmlight/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/pysvmlight/meta.yaml b/recipes/pysvmlight/meta.yaml index ffe9219a25703..842ee8646e790 100644 --- a/recipes/pysvmlight/meta.yaml +++ b/recipes/pysvmlight/meta.yaml @@ -9,14 +9,14 @@ source: build: number: 2 skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - {{ compiler('c') }} host: - python - - setuptools - + - pip run: - python diff --git a/recipes/pytest-marks/build.sh b/recipes/pytest-marks/build.sh deleted file mode 100644 index 6663875f9ce59..0000000000000 --- a/recipes/pytest-marks/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/pytest-marks/meta.yaml b/recipes/pytest-marks/meta.yaml index f470a1732ad62..3542de8074754 100644 --- a/recipes/pytest-marks/meta.yaml +++ b/recipes/pytest-marks/meta.yaml @@ -10,18 +10,17 @@ build: noarch: python number: 1 preserve_egg_dir: True + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - pytest >2.0.2 - - funcsigs + - pip run: - python - - setuptools - pytest >2.0.2 - funcsigs + test: imports: - marks diff --git a/recipes/python-bioext/meta.yaml b/recipes/python-bioext/meta.yaml index 5d1a478a8b8e8..c10291a4a8acb 100644 --- a/recipes/python-bioext/meta.yaml +++ b/recipes/python-bioext/meta.yaml @@ -80,3 +80,7 @@ about: home: https://github.com/veg/BioExt.git license: GPL-3 summary: 'A few handy bioinformatics tools not already in BioPython' + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/python-chado/meta.yaml b/recipes/python-chado/meta.yaml index 84ad63d5bc737..64da60002cd73 100644 --- a/recipes/python-chado/meta.yaml +++ b/recipes/python-chado/meta.yaml @@ -19,17 +19,8 @@ build: requirements: host: - - bcbio-gff ==0.6.4 - - biopython - - click - - future - pip - - psycopg2 - python - - pyyaml - - setuptools - - sqlalchemy - - wrapt run: - bcbio-gff ==0.6.4 - biopython @@ -38,7 +29,6 @@ requirements: - psycopg2 - python - pyyaml - - setuptools - sqlalchemy - wrapt diff --git a/recipes/python-consensuscore/meta.yaml b/recipes/python-consensuscore/meta.yaml index a50ff8e21a931..3dd1d3cc1e23e 100644 --- a/recipes/python-consensuscore/meta.yaml +++ b/recipes/python-consensuscore/meta.yaml @@ -10,16 +10,6 @@ source: url: https://github.com/PacificBiosciences/ConsensusCore/archive/{{ version }}.tar.gz sha256: {{ sha256 }} -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: PacBio Quiver Consensus library for RSII data - -extra: - recipe-maintainers: - - pb-dseifert - - mhsieh - build: skip: True # [not py27] number: 3 @@ -44,3 +34,13 @@ test: - ConsensusCore commands: - python -c 'import ConsensusCore; ConsensusCore.Version.VersionString()' + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: PacBio Quiver Consensus library for RSII data + +extra: + recipe-maintainers: + - pb-dseifert + - mhsieh diff --git a/recipes/python-consensuscore2/meta.yaml b/recipes/python-consensuscore2/meta.yaml index c2f42f8694a27..d2114f1405c41 100644 --- a/recipes/python-consensuscore2/meta.yaml +++ b/recipes/python-consensuscore2/meta.yaml @@ -8,23 +8,13 @@ package: version: {{ version }} source: - url: https://github.com/PacificBiosciences/unanimity/releases/download/v{{ version }}/ConsensusCore2-{{ version }}-cp27-cp27mu-linux_x86_64.whl # [linux] - sha256: {{ linux_sha256 }} # [linux] - url: https://github.com/PacificBiosciences/unanimity/releases/download/v{{ version }}/ConsensusCore2-{{ version }}-cp27-cp27m-macosx_10_9_x86_64.whl # [osx] - sha256: {{ mac_sha256 }} # [osx] - -about: - home: https://github.com/PacificBiosciences/pbbioconda - license: BSD-3-Clause-Clear - summary: PacBio Arrow Consensus library for Sequel data - -extra: - recipe-maintainers: - - pb-dseifert - - mhsieh + - url: https://github.com/PacificBiosciences/unanimity/releases/download/v{{ version }}/ConsensusCore2-{{ version }}-cp27-cp27mu-linux_x86_64.whl # [linux] + sha256: {{ linux_sha256 }} # [linux] + - url: https://github.com/PacificBiosciences/unanimity/releases/download/v{{ version }}/ConsensusCore2-{{ version }}-cp27-cp27m-macosx_10_9_x86_64.whl # [osx] + sha256: {{ mac_sha256 }} # [osx] build: - skip: True # [not py27] + skip: True # [not py27] number: 0 requirements: @@ -41,3 +31,16 @@ test: - ConsensusCore2 commands: - python -c 'import ConsensusCore2; ConsensusCore2.__version__' + +about: + home: https://github.com/PacificBiosciences/pbbioconda + license: BSD-3-Clause-Clear + summary: PacBio Arrow Consensus library for Sequel data + +extra: + recipe-maintainers: + - pb-dseifert + - mhsieh + skip-lints: + - should_not_be_noarch_source + - should_be_noarch_python diff --git a/recipes/python-fakemp/build.sh b/recipes/python-fakemp/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/python-fakemp/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/python-fakemp/meta.yaml b/recipes/python-fakemp/meta.yaml index 6d7aeaf3d64b9..92bd86917e49d 100644 --- a/recipes/python-fakemp/meta.yaml +++ b/recipes/python-fakemp/meta.yaml @@ -3,7 +3,9 @@ package: version: 0.9.1 build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/source/f/fakemp/fakemp-0.9.1.tar.gz @@ -12,8 +14,7 @@ source: requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/python-hppy/meta.yaml b/recipes/python-hppy/meta.yaml index f16193dafe2b3..d8fcb8cc07680 100644 --- a/recipes/python-hppy/meta.yaml +++ b/recipes/python-hppy/meta.yaml @@ -4,13 +4,14 @@ package: build: number: 0 - noarch: python source: url: https://github.com/veg/hppy/archive/0.9.8.tar.gz sha256: 3662eef64098f0a1e692b32f58bf3fa32e33fae123e648b7998af88865bba1be requirements: + build: + - {{ compiler('c') }} host: - python - setuptools @@ -19,7 +20,6 @@ requirements: - python-fakemp run: - python - - cython - python-hyphy-python - python-fakemp diff --git a/recipes/python-libsbml/build.sh b/recipes/python-libsbml/build.sh deleted file mode 100644 index 4dad93a1c02ab..0000000000000 --- a/recipes/python-libsbml/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/python-libsbml/meta.yaml b/recipes/python-libsbml/meta.yaml index 94e2ee92c4526..df945ceaa59f2 100644 --- a/recipes/python-libsbml/meta.yaml +++ b/recipes/python-libsbml/meta.yaml @@ -10,6 +10,7 @@ source: build: number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: @@ -17,6 +18,7 @@ requirements: - {{ compiler('cxx') }} host: - python + - pip - libxml2 - bzip2 run: diff --git a/recipes/python-mailund-newick/build.sh b/recipes/python-mailund-newick/build.sh deleted file mode 100644 index 64fb95d92b085..0000000000000 --- a/recipes/python-mailund-newick/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --record=record.txt diff --git a/recipes/python-mailund-newick/meta.yaml b/recipes/python-mailund-newick/meta.yaml index 2c6d60f1aa39c..22884892a6b9e 100644 --- a/recipes/python-mailund-newick/meta.yaml +++ b/recipes/python-mailund-newick/meta.yaml @@ -9,15 +9,16 @@ source: sha256: af8cfb4ba53daae59ff727a6c41a291c84cf3ebeedde888706c53d44d4c9f516 build: + noarch: python number: 1 - skip: Yes [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/python-omero/meta.yaml b/recipes/python-omero/meta.yaml index 9db937e6eab43..4dfec57581fc8 100644 --- a/recipes/python-omero/meta.yaml +++ b/recipes/python-omero/meta.yaml @@ -10,15 +10,15 @@ source: sha1: 0cca42b8f6e41293f6821d94bd8847f2c9712370 build: + noarch: python number: 1 - skip: True # [py3k] requirements: host: - setuptools - - python + - python <3 run: - - python + - python <3 - zeroc-ice >3.5,<3.7 test: diff --git a/recipes/python-rnacentral/meta.yaml b/recipes/python-rnacentral/meta.yaml index 9791adef79170..fb11f048450b0 100644 --- a/recipes/python-rnacentral/meta.yaml +++ b/recipes/python-rnacentral/meta.yaml @@ -2,16 +2,6 @@ package: name: python-rnacentral version: "1.0.0" -about: - home: https://github.com/fabio-cumbo/RNAcentral-data-retrieval-tool - license: BSD 2-Clause License - license_family: BSD - license_file: '{{ RECIPE_DIR }}/LICENSE.txt' - summary: 'This tool exploits the RNAcentral public APIs to - automatically retrieve sequences (converted to the FASTA format) - and the related metadata, starting with one or a list of - RNAcentral IDs' - source: url: https://github.com/fabio-cumbo/RNAcentral-data-retrieval-tool/archive/1.0.0.tar.gz sha256: 87c06285b7e1e96743cafbb314630e25a5c6da32b45fc16b22844143ea6f30c3 @@ -19,12 +9,21 @@ source: build: noarch: python number: 0 - skip: False requirements: run: - python >=2.7,<3 test: - command: + commands: - rnacentral.py --version + +about: + home: https://github.com/fabio-cumbo/RNAcentral-data-retrieval-tool + license: BSD 2-Clause License + license_family: BSD + license_file: '{{ RECIPE_DIR }}/LICENSE.txt' + summary: 'This tool exploits the RNAcentral public APIs to + automatically retrieve sequences (converted to the FASTA format) + and the related metadata, starting with one or a list of + RNAcentral IDs' diff --git a/recipes/pythonpy/meta.yaml b/recipes/pythonpy/meta.yaml index 659a5687db4a9..bff57e46daf10 100644 --- a/recipes/pythonpy/meta.yaml +++ b/recipes/pythonpy/meta.yaml @@ -9,16 +9,13 @@ source: build: noarch: python number: 0 - skip: False requirements: host: - python - setuptools - run: - python - - setuptools test: commands: diff --git a/recipes/pytriangle/build.sh b/recipes/pytriangle/build.sh deleted file mode 100644 index c1d38d2c3ab1b..0000000000000 --- a/recipes/pytriangle/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -python setup.py install diff --git a/recipes/pytriangle/meta.yaml b/recipes/pytriangle/meta.yaml index 72300d82faaef..95ce925b3cc2f 100644 --- a/recipes/pytriangle/meta.yaml +++ b/recipes/pytriangle/meta.yaml @@ -2,17 +2,13 @@ package: name: pytriangle version: "1.0.9" -about: - home: 'https://github.com/pletzer/pytriangle' - summary: 'A python interface to the 2D triangulation program TRIANGLE' - license: MIT - source: git_url: https://github.com/pletzer/pytriangle git_rev: f87b411 build: number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv test: imports: @@ -23,5 +19,16 @@ requirements: - {{ compiler('c') }} host: - python + - pip run: - python + +about: + home: 'https://github.com/pletzer/pytriangle' + summary: 'A python interface to the 2D triangulation program TRIANGLE' + license: MIT + +extra: + skip-lints: + - missing_hash + - uses_vcs_url diff --git a/recipes/pyx/build.sh b/recipes/pyx/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/pyx/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pyx/meta.yaml b/recipes/pyx/meta.yaml index 190931c8dace1..1d399afa2c818 100644 --- a/recipes/pyx/meta.yaml +++ b/recipes/pyx/meta.yaml @@ -7,15 +7,16 @@ source: sha256: 05d1b7fc813379d2c12fcb5bd0195cab522b5aabafac88f72913f1d47becd912 build: + noarch: python number: 1 - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python >=3 + - pip run: - - python + - python >=3 test: imports: diff --git a/recipes/qcli/build.sh b/recipes/qcli/build.sh index b1d700b506801..cb00afb8f1455 100644 --- a/recipes/qcli/build.sh +++ b/recipes/qcli/build.sh @@ -2,8 +2,6 @@ if [[ "${PY_VER}" =~ 3 ]] then - 2to3 -w qcli/ scripts/* - $PYTHON setup.py install -else - $PYTHON setup.py install + 2to3 -w qcli/ scripts/* fi +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/qcli/meta.yaml b/recipes/qcli/meta.yaml index 7f32f2ecc2dc7..f0131852c5680 100644 --- a/recipes/qcli/meta.yaml +++ b/recipes/qcli/meta.yaml @@ -5,18 +5,17 @@ package: source: url: https://pypi.python.org/packages/source/q/qcli/qcli-0.1.1.tar.gz md5: 25b7bc209c1e52be16efad295bd37ed4 - patches: - - python3.patch [py3k] + - python3.patch build: + noarch: python number: 2 - skip: False requirements: host: - python - + - pip run: - python @@ -32,3 +31,4 @@ test: about: license: GPL summary: qcli + home: https://pypi.org/project/qcli/ diff --git a/recipes/qiime-default-reference/0.1.3/build.sh b/recipes/qiime-default-reference/0.1.3/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/qiime-default-reference/0.1.3/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/qiime-default-reference/0.1.3/meta.yaml b/recipes/qiime-default-reference/0.1.3/meta.yaml index e11644f06e440..fe39ea9c9f046 100644 --- a/recipes/qiime-default-reference/0.1.3/meta.yaml +++ b/recipes/qiime-default-reference/0.1.3/meta.yaml @@ -9,13 +9,12 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - six - + - pip run: - python - six diff --git a/recipes/qiime/1.9.1/build.sh b/recipes/qiime/1.9.1/build.sh deleted file mode 100644 index f341bce6fcf96..0000000000000 --- a/recipes/qiime/1.9.1/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/sh -$PYTHON setup.py install diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index a663fbfe8fd8b..2e044a89c0d85 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -4,39 +4,20 @@ package: source: url: https://pypi.python.org/packages/source/q/qiime/qiime-1.9.1.tar.gz - md5: 32d4db2b2c888dbbfc6aa33f02725526 - sha1: 2ab4ac9beb745ed3eca3243312cc9ce14e8a20d8 sha256: c12dcdae1fe44762a49668276d7e93f487d87a0dc2ff8ca696ac0eff9d92a8a8 build: number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python requirements: host: - python <3 - - setuptools - - numpy - - scipy >=0.14.0 - - cogent ==1.5.3 - - natsort <4.0.0 - - pynast ==1.2.2 - - qcli >=0.1.1,<0.2.0 - - gdata - - biom-format >=2.1.4,<2.2.0 - - emperor >=0.9.51,<1.0.0 - - scikit-bio >=0.2.3,<0.3.0 - - matplotlib <=1.9 - - burrito-fillings >=0.1.1,<0.2.0 - - pandas >=0.13.1 - - burrito >=0.9.1,<1.0.0 - - qiime-default-reference >=0.1.2,<0.2.0 - - mock - - nose - - xz - + - pip run: - python <3 - - {{ pin_compatible('numpy') }} + - numpy - scipy >=0.14.0 - cogent ==1.5.3 - natsort <4.0.0 @@ -51,8 +32,6 @@ requirements: - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 - qiime-default-reference >=0.1.2,<0.2.0 - - mock - - nose - glib - xorg-libxext - xorg-libxdmcp diff --git a/recipes/qiimetomaaslin/build.sh b/recipes/qiimetomaaslin/build.sh deleted file mode 100644 index 6ef9c7cafe71c..0000000000000 --- a/recipes/qiimetomaaslin/build.sh +++ /dev/null @@ -1,2 +0,0 @@ - #!/bin/bash - $PYTHON setup.py install diff --git a/recipes/qiimetomaaslin/meta.yaml b/recipes/qiimetomaaslin/meta.yaml index bc2a650b691ea..1428aeb29322c 100644 --- a/recipes/qiimetomaaslin/meta.yaml +++ b/recipes/qiimetomaaslin/meta.yaml @@ -6,8 +6,9 @@ package: version: {{ version }} build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://bitbucket.org/biobakery/{{ name|lower }}/get/{{ version }}.tar.gz @@ -15,12 +16,11 @@ source: requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python - - blist + - python <3 + - blist test: commands: diff --git a/recipes/quast/build.sh b/recipes/quast/build.sh index cdf0c4e6f6d53..71716a65f6a7b 100644 --- a/recipes/quast/build.sh +++ b/recipes/quast/build.sh @@ -14,7 +14,7 @@ mkdir -p $QUAST_HOME rm -r $SRC_DIR/quast_libs/site_packages/joblib* rm -r $SRC_DIR/quast_libs/site_packages/simplejson -python "setup.py" install +$PYTHON -m pip install . --ignore-installed --no-deps -vv cp -R $SRC_DIR/*quast*.py $QUAST_HOME/ cp -R $SRC_DIR/icarus.py $QUAST_HOME/ diff --git a/recipes/r-adephylo/meta.yaml b/recipes/r-adephylo/meta.yaml index 058deec66139e..a17bb51f5ab32 100644 --- a/recipes/r-adephylo/meta.yaml +++ b/recipes/r-adephylo/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.1-11' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-adephylo version: {{ version|replace("-", "_") }} @@ -14,24 +11,14 @@ source: sha256: 154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a build: - merge_build_host: True # [win] - number: 3 - 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] - + - {{ compiler('c') }} host: - r-base - r-ade4 >=1.7_10 @@ -41,7 +28,6 @@ requirements: run: - r-base - - {{native}}gcc-libs # [win] - r-ade4 >=1.7_10 - r-adegenet - r-ape @@ -49,7 +35,6 @@ requirements: test: commands: - - $R -e "library('adephylo')" # [not win] - "\"%R%\" -e \"library('adephylo')\"" # [win] @@ -59,12 +44,3 @@ about: 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-cellassign/meta.yaml b/recipes/r-cellassign/meta.yaml index b34a0d56a1ee6..0525a4c685593 100644 --- a/recipes/r-cellassign/meta.yaml +++ b/recipes/r-cellassign/meta.yaml @@ -10,6 +10,7 @@ source: build: + noarch: generic number: 0 rpaths: - lib/R/lib/ diff --git a/recipes/r-chbutils/meta.yaml b/recipes/r-chbutils/meta.yaml index e9ff627e886d9..c3b935d07966e 100644 --- a/recipes/r-chbutils/meta.yaml +++ b/recipes/r-chbutils/meta.yaml @@ -1,6 +1,5 @@ package: name: r-chbutils - version: "0.1_2017_10_26" source: @@ -8,9 +7,8 @@ source: sha256: 72f5e5c2e15177864a5fa8d05cdd1aef6d9e2a300f45e55fdb096fe640c5b138 build: + noarch: generic number: 0 - skip: True # [osx] - rpaths: - lib/R/lib/ - lib/ @@ -34,12 +32,3 @@ 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-classdiscovery/meta.yaml b/recipes/r-classdiscovery/meta.yaml index ae05bb8d78e10..3703281700c9c 100644 --- a/recipes/r-classdiscovery/meta.yaml +++ b/recipes/r-classdiscovery/meta.yaml @@ -14,6 +14,7 @@ source: sha256: fe4e7ec4283f6820f2c84c1c05a1b9c71c837137edea126769f06f5a53cc2ee5 build: + noarch: generic merge_build_host: True # [win] # If this is a new build for the same version, increment the build number. number: 0 diff --git a/recipes/r-coloc/meta.yaml b/recipes/r-coloc/meta.yaml index 866ac7f7a0122..f3a37f0c624d9 100644 --- a/recipes/r-coloc/meta.yaml +++ b/recipes/r-coloc/meta.yaml @@ -1,8 +1,5 @@ {% set version = '3.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-coloc version: {{ version|replace("-", "_") }} @@ -14,19 +11,13 @@ source: sha256: 882ae56514e93839bd2d9c630a6eb5dc0e146062a46ad1583e7687cfcb31418c build: - merge_build_host: True # [win] - + noarch: generic number: 1 - skip: true # [win32] - rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{posix}}zip # [win] - host: - r-base - r-bma @@ -35,7 +26,6 @@ requirements: - r-reshape - bioconductor-snpstats - r-speedglm - run: - r-base - r-bma @@ -47,7 +37,6 @@ requirements: test: commands: - - $R -e "library('coloc')" # [not win] - "\"%R%\" -e \"library('coloc')\"" # [win] diff --git a/recipes/r-deconstructsigs/meta.yaml b/recipes/r-deconstructsigs/meta.yaml index 7b8cc2bda03bf..0eb43b38e828d 100644 --- a/recipes/r-deconstructsigs/meta.yaml +++ b/recipes/r-deconstructsigs/meta.yaml @@ -16,6 +16,7 @@ source: sha256: 0e31aed3e4428e0026b33e663deee71d9bba81db56a1306e0a81666aa4a0e39d build: + noarch: generic number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml index 5f9e5235a75a1..05532dd3b5e77 100644 --- a/recipes/r-diffcorr/meta.yaml +++ b/recipes/r-diffcorr/meta.yaml @@ -1,6 +1,4 @@ {% set version = '0.4.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} package: name: r-diffcorr @@ -13,7 +11,6 @@ source: sha256: 15125ae871949ef2be89916384e46c665079e6826ecbba6b3608701e574bb7cf build: - merge_build_host: True # [win] number: 1 noarch: generic rpaths: @@ -21,8 +18,6 @@ build: - lib/ requirements: - build: - host: - r-base - r-fdrtool @@ -43,7 +38,7 @@ test: about: home: https://CRAN.R-project.org/package=DiffCorr - license: GPL (> 3) + license: GPL3 summary: 'A method for identifying pattern changes between 2 experimental conditions in correlation networks (e.g., gene co-expression networks), which builds on a commonly used association measure, such as Pearson''s correlation coefficient. This package includes functions @@ -51,5 +46,4 @@ about: correlation, which means the changes in the correlation relationship among variables (e.g., genes and metabolites) between 2 experimental conditions. ' license_family: GPL3 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' # [unix] - license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3' # [win] + license_file: {{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3 diff --git a/recipes/r-empiricalfdr.deseq2/meta.yaml b/recipes/r-empiricalfdr.deseq2/meta.yaml index a40d6150f92c5..5327c925bb63e 100644 --- a/recipes/r-empiricalfdr.deseq2/meta.yaml +++ b/recipes/r-empiricalfdr.deseq2/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 831be77d3b40fcc41e70c0dadcb50871fda6093de3130d6c334c8d4d78635540 build: + noarch: generic merge_build_host: True # [win] number: 4 rpaths: diff --git a/recipes/r-fgwas/meta.yaml b/recipes/r-fgwas/meta.yaml index a25ddc03507ea..00c0099470260 100644 --- a/recipes/r-fgwas/meta.yaml +++ b/recipes/r-fgwas/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 # This is required to make R link correctly on Linux. rpaths: diff --git a/recipes/r-gkmsvm/meta.yaml b/recipes/r-gkmsvm/meta.yaml index 3512c08076b5c..868efd4564d9f 100644 --- a/recipes/r-gkmsvm/meta.yaml +++ b/recipes/r-gkmsvm/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.79.0' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-gkmsvm version: {{ version|replace("-", "_") }} @@ -21,15 +18,9 @@ build: 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' @@ -61,7 +52,6 @@ requirements: test: commands: - - $R -e "library('gkmSVM')" # [not win] - "\"%R%\" -e \"library('gkmSVM')\"" # [win] @@ -72,12 +62,3 @@ about: 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-gpca/build.sh b/recipes/r-gpca/build.sh deleted file mode 100644 index aeaad348da1d2..0000000000000 --- a/recipes/r-gpca/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/gPCA - mv * $PREFIX/lib/R/library/gPCA -fi diff --git a/recipes/r-gpca/meta.yaml b/recipes/r-gpca/meta.yaml deleted file mode 100644 index 5ed4b6d983165..0000000000000 --- a/recipes/r-gpca/meta.yaml +++ /dev/null @@ -1,46 +0,0 @@ -{% set version = '1.0' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - -package: - name: r-gpca - version: {{ version|replace("-", "_") }} - -source: - url: - - {{ cran_mirror }}/src/contrib/gPCA_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/gPCA/gPCA_{{ version }}.tar.gz - sha256: 7ce6c5f90758f9c208bc192ee1a7a423cb1f3de456ad9534bfdff646440b8bfa - -build: - 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('gPCA')" # [not win] - - "\"%R%\" -e \"library('gPCA')\"" # [win] - -about: - home: https://CRAN.R-project.org/package=gPCA - license: GPL (>= 2) - summary: This package implements guided principal components analysis for the detection of - batch effects in high-throughput data. - license_family: GPL3 - - diff --git a/recipes/r-grbase/meta.yaml b/recipes/r-grbase/meta.yaml index 75c5df35a2ddb..ac69693ca8f8e 100644 --- a/recipes/r-grbase/meta.yaml +++ b/recipes/r-grbase/meta.yaml @@ -1,6 +1,4 @@ {% set version = '1.8-3.4' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} package: name: r-grbase @@ -13,7 +11,6 @@ source: sha256: d35f94c2fb7cbd4ce3991570424dfe6723a849658da32e13df29f53b6ea2cc2c build: - merge_build_host: True # [win] number: 1 rpaths: - lib/R/lib/ @@ -21,14 +18,9 @@ build: 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] + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-matrix @@ -41,7 +33,6 @@ requirements: - r-magrittr run: - r-base - - {{native}}gcc-libs # [win] - r-matrix - bioconductor-rbgl - r-rcpp >=0.11.1 diff --git a/recipes/r-hemdag/meta.yaml b/recipes/r-hemdag/meta.yaml index e8e765870ab18..07334355ffaa2 100644 --- a/recipes/r-hemdag/meta.yaml +++ b/recipes/r-hemdag/meta.yaml @@ -1,8 +1,5 @@ {% set version = '2.4.8' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-hemdag version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: a2d8a4d92009d903e7cc8bcfa5d908c830fb6b9dcde4084046e03ded60011106 build: - merge_build_host: True # [win] number: 0 rpaths: - lib/R/lib/ @@ -22,14 +18,9 @@ build: 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] + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - bioconductor-rbgl @@ -42,7 +33,6 @@ requirements: - bioconductor-preprocesscore run: - r-base - - {{native}}gcc-libs # [win] - bioconductor-rbgl - r-doparallel - r-foreach diff --git a/recipes/r-loom/meta.yaml b/recipes/r-loom/meta.yaml index 5e2e32d4a6bae..69fe9eb58ad6b 100644 --- a/recipes/r-loom/meta.yaml +++ b/recipes/r-loom/meta.yaml @@ -8,6 +8,7 @@ source: sha256: 7ad37bee3f91cc7d0cfb7e31b2de33e4bf7dd03ed2205732c34f150c97faa652 build: + noarch: generic number: 0 noarch: generic rpaths: diff --git a/recipes/r-micropan/meta.yaml b/recipes/r-micropan/meta.yaml index c51346ea29bcb..3d8bc440c64fd 100644 --- a/recipes/r-micropan/meta.yaml +++ b/recipes/r-micropan/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.2' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-micropan version: {{ version|replace("-", "_") }} @@ -14,26 +11,16 @@ source: sha256: 7ee2a31928e454defe2b37b0da65aef8e6157d76187e7186b6d2266a586970ac build: - merge_build_host: True # [win] - number: 1 - 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-bh @@ -43,7 +30,6 @@ requirements: run: - r-base - - {{native}}gcc-libs # [win] - r-bh - r-rcpp >=0.12.0 - r-igraph diff --git a/recipes/r-minionqc/meta.yaml b/recipes/r-minionqc/meta.yaml index f7df18be4dfb0..f2209963f867a 100644 --- a/recipes/r-minionqc/meta.yaml +++ b/recipes/r-minionqc/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 230019982f65507e280d025bfa31d7ca82dc44f50fca436d269b72342964622b build: + noarch: generic number: 1 requirements: diff --git a/recipes/r-mixkernel/meta.yaml b/recipes/r-mixkernel/meta.yaml index 4294cb765ac57..59f39725faa6f 100644 --- a/recipes/r-mixkernel/meta.yaml +++ b/recipes/r-mixkernel/meta.yaml @@ -11,6 +11,7 @@ source: sha256: aec11eeb5791c784000be478bdcd2ea1795f5fba139af841b027394c6fb4c8cd build: + noarch: generic number: 0 # This is required to make R link correctly on Linux. rpaths: diff --git a/recipes/r-msqrob/meta.yaml b/recipes/r-msqrob/meta.yaml index 604c8b7dbdbbf..efb580c15ebfa 100644 --- a/recipes/r-msqrob/meta.yaml +++ b/recipes/r-msqrob/meta.yaml @@ -5,8 +5,8 @@ source: url: https://github.com/statOmics/MSqRob/archive/MSqRob_standalone_Win_0.7.6.tar.gz sha256: 334a7d2b323058b61b8cdf651a6daf6e28e0310bc8c61e83075561da8cad93e9 build: + noarch: generic number: 0 - skip: True # [osx] rpaths: - lib/R/lib/ - lib/ @@ -109,7 +109,6 @@ requirements: - r-miniui - r-httpuv - test: commands: - '$R -e "library(''MSqRob'')"' diff --git a/recipes/r-mutoss/meta.yaml b/recipes/r-mutoss/meta.yaml index f7421a34d3718..e8abff45e3081 100644 --- a/recipes/r-mutoss/meta.yaml +++ b/recipes/r-mutoss/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.1-12' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-mutoss version: {{ version|replace("-", "_") }} @@ -14,26 +11,19 @@ source: sha256: 2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa build: - merge_build_host: True # [win] - + noarch: generic number: 1 - skip: true # [win32] - rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{posix}}zip # [win] - host: - r-base - r-multcomp >=1.1_0 - bioconductor-multtest >=2.2.0 - r-mvtnorm - r-plotrix - run: - r-base - r-multcomp >=1.1_0 @@ -43,7 +33,6 @@ requirements: test: commands: - - $R -e "library('mutoss')" # [not win] - "\"%R%\" -e \"library('mutoss')\"" # [win] @@ -54,12 +43,3 @@ about: 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-nabor/meta.yaml b/recipes/r-nabor/meta.yaml index 624087a25b08f..cfa113b7f12c0 100644 --- a/recipes/r-nabor/meta.yaml +++ b/recipes/r-nabor/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 47938dcc987279281c13abfd667660bf1b3b76af116136a27eb066ee1a4b43da build: + noarch: generic number: 2 rpaths: - lib/R/lib/ diff --git a/recipes/r-nanostringnorm/meta.yaml b/recipes/r-nanostringnorm/meta.yaml index 750d51f5a53a8..9903b4acdc8a6 100644 --- a/recipes/r-nanostringnorm/meta.yaml +++ b/recipes/r-nanostringnorm/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.2.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-nanostringnorm version: {{ version|replace("-", "_") }} @@ -14,16 +11,13 @@ source: sha256: f2d4773a67c609a85ad12635252310e1e190444a66997d07665544def3862117 build: - merge_build_host: True # [win] + noarch: generic number: 1 - skip: true # [win32] rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{posix}}zip # [win] host: - r-base - r-xml >=3.98_1.5 @@ -37,7 +31,6 @@ requirements: test: commands: - - $R -e "library('NanoStringNorm')" # [not win] - "\"%R%\" -e \"library('NanoStringNorm')\"" # [win] diff --git a/recipes/r-perfmeas/meta.yaml b/recipes/r-perfmeas/meta.yaml index b43a59bba8571..dd342334ab6dd 100644 --- a/recipes/r-perfmeas/meta.yaml +++ b/recipes/r-perfmeas/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.2.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-perfmeas version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: 2371d9f8949d8c570d8b772ff1c3615eebf5e825a96722b40ced07b22ab3eaf4 build: - merge_build_host: True # [win] number: 3 rpaths: - lib/R/lib/ @@ -23,22 +19,14 @@ build: requirements: build: - {{ compiler('c') }} # [not win] - - {{native}}toolchain # [win] - - {{posix}}filesystem # [win] - - {{posix}}make - - {{posix}}sed # [win] - - {{posix}}coreutils # [win] - - {{posix}}zip # [win] - + - make host: - r-base - bioconductor-rbgl - bioconductor-graph - bioconductor-limma - run: - r-base - - {{native}}gcc-libs # [win] - bioconductor-rbgl - bioconductor-graph - bioconductor-limma diff --git a/recipes/r-phyext2/meta.yaml b/recipes/r-phyext2/meta.yaml index f1f10abf0409c..5ef82f923d438 100644 --- a/recipes/r-phyext2/meta.yaml +++ b/recipes/r-phyext2/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 2ba35543bf7b4bfab5d41ad4de2ff2a1ac78ce0f07c0d736a0d4a58adf0c0749 build: + noarch: generic merge_build_host: True # [win] number: 3 diff --git a/recipes/r-phylobase/meta.yaml b/recipes/r-phylobase/meta.yaml index ef207dbeeb02f..a29f2ea545556 100644 --- a/recipes/r-phylobase/meta.yaml +++ b/recipes/r-phylobase/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.8.6' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-phylobase version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: e7117b210ef406115e5523b794d8c2c5779640cee8c06e73751dc14c69322fd9 build: - merge_build_host: True # [win] number: 1 rpaths: - lib/R/lib/ @@ -22,15 +18,9 @@ build: 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-rnexml @@ -38,10 +28,8 @@ requirements: - r-ade4 - r-ape >=3.0 - r-rncl >=0.6.0 - run: - r-base - - {{native}}gcc-libs # [win] - r-rnexml - r-rcpp >=0.11.0 - r-ade4 diff --git a/recipes/r-phylomeasures/meta.yaml b/recipes/r-phylomeasures/meta.yaml index bfb34e818a24e..b82dd039e62b2 100644 --- a/recipes/r-phylomeasures/meta.yaml +++ b/recipes/r-phylomeasures/meta.yaml @@ -1,8 +1,5 @@ {% set version = '2.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-phylomeasures version: {{ version|replace("-", "_") }} @@ -14,32 +11,21 @@ source: sha256: 1982f47cb5bfa61e56f47cae78e199f13778edde49af86fa5cc183a0d1d15d05 build: - 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-ape - run: - r-base - - {{native}}gcc-libs # [win] - r-ape test: diff --git a/recipes/r-phylosignal/meta.yaml b/recipes/r-phylosignal/meta.yaml index 4b7c24c9af9c6..5ccbbe5978210 100644 --- a/recipes/r-phylosignal/meta.yaml +++ b/recipes/r-phylosignal/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.2.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-phylosignal version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: 9acdfc724cff531590c5b6ba23cb25c5efb84659c08aa7f7cb76f05cec26ba81 build: - merge_build_host: True # [win] number: 0 rpaths: - lib/R/lib/ @@ -22,15 +18,9 @@ build: 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-dbi @@ -41,7 +31,6 @@ requirements: - r-boot - r-igraph - r-phylobase - run: - r-base - {{native}}gcc-libs # [win] diff --git a/recipes/r-popgenreport/meta.yaml b/recipes/r-popgenreport/meta.yaml index 8b81436f12149..79e08119a1318 100644 --- a/recipes/r-popgenreport/meta.yaml +++ b/recipes/r-popgenreport/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 12e86d9d6e4ee3da17df46531657804e5f204452b867df1dc92e1733934b3275 build: + noarch: generic number: 0 rpaths: diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index 7b577fbdebc64..650015349163b 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a build: + noarch: generic number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-raceid3/build.sh b/recipes/r-raceid/build.sh similarity index 100% rename from recipes/r-raceid3/build.sh rename to recipes/r-raceid/build.sh diff --git a/recipes/r-raceid3/meta.yaml b/recipes/r-raceid/meta.yaml similarity index 100% rename from recipes/r-raceid3/meta.yaml rename to recipes/r-raceid/meta.yaml diff --git a/recipes/r-rapidr/meta.yaml b/recipes/r-rapidr/meta.yaml index 4944888a2f785..7d7d8a958b2bb 100644 --- a/recipes/r-rapidr/meta.yaml +++ b/recipes/r-rapidr/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 2d286bdf13f27a040f16f8c5aa740e25fbc4b0913e3cfa4b5956152d25e19691 build: + noarch: generic merge_build_host: True # [win] number: 3 rpaths: diff --git a/recipes/r-riborex/meta.yaml b/recipes/r-riborex/meta.yaml index cfadb504db2bf..a67037583abe6 100644 --- a/recipes/r-riborex/meta.yaml +++ b/recipes/r-riborex/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{sha256}} build: + noarch: generic number: 0 rpaths: diff --git a/recipes/r-ridigbio/meta.yaml b/recipes/r-ridigbio/meta.yaml index 12105022ce572..4c6dfdfd15bdc 100644 --- a/recipes/r-ridigbio/meta.yaml +++ b/recipes/r-ridigbio/meta.yaml @@ -14,6 +14,7 @@ source: sha256: e5cfb2e4dd8ddd1452a5afcf24fcc260889179d0f52eff4f41835adf99b64614 build: + noarch: generic merge_build_host: True # [win] number: 3 rpaths: diff --git a/recipes/r-rnexml/meta.yaml b/recipes/r-rnexml/meta.yaml index e7c642f9e8a3e..3b4c31691e629 100644 --- a/recipes/r-rnexml/meta.yaml +++ b/recipes/r-rnexml/meta.yaml @@ -11,10 +11,8 @@ source: sha256: 8a52e141f2f47f4cfcb617c1a2866fdff26db4b56d47c914c9f12917c39edb73 build: - merge_build_host: True # [win] + noarch: generic number: 1 - skip: true # [win32] - rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-rubic/1.0.2/meta.yaml b/recipes/r-rubic/1.0.2/meta.yaml index 4012df5e0bb1e..b49dc365b6447 100644 --- a/recipes/r-rubic/1.0.2/meta.yaml +++ b/recipes/r-rubic/1.0.2/meta.yaml @@ -5,6 +5,7 @@ source: url: https://github.com/NKI-CCB/RUBIC/archive/v1.0.2.tar.gz sha256: cb24478b58c8b5800da4a1d8594c19a8eec56ef51efd92e7e14ce3b0dbb6141e build: + noarch: generic number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-rubic/1.0.3/meta.yaml b/recipes/r-rubic/1.0.3/meta.yaml index 6d9f3b3a0031e..639970f40e85e 100644 --- a/recipes/r-rubic/1.0.3/meta.yaml +++ b/recipes/r-rubic/1.0.3/meta.yaml @@ -5,6 +5,7 @@ source: url: https://github.com/NKI-CCB/RUBIC/archive/v1.0.3.tar.gz sha256: 36dda0bd2f388e610f551a19b177be08e5a1c2cf68b23a3626dcbd5be1705837 build: + noarch: generic number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-rvertnet/meta.yaml b/recipes/r-rvertnet/meta.yaml index 0ab6b548cd4cd..70d5ddca5a30e 100644 --- a/recipes/r-rvertnet/meta.yaml +++ b/recipes/r-rvertnet/meta.yaml @@ -14,6 +14,7 @@ source: sha256: f2e1d78067bbafa0a641a0af43adf832a94bf2382151f261006907f18b8ce307 build: + noarch: generic merge_build_host: True # [win] number: 3 rpaths: diff --git a/recipes/r-sbpiper/meta.yaml b/recipes/r-sbpiper/meta.yaml index 6133037e5d55a..b5c04e452c905 100644 --- a/recipes/r-sbpiper/meta.yaml +++ b/recipes/r-sbpiper/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 8f053383eb0f73fef7809898f27882b5a662f5b2aa404b3ee52491d92342585e build: + noarch: generic merge_build_host: True # [win] number: 2 diff --git a/recipes/r-scrm/build.sh b/recipes/r-scrm/build.sh deleted file mode 100644 index 5bf492ab9fc06..0000000000000 --- a/recipes/r-scrm/build.sh +++ /dev/null @@ -1 +0,0 @@ -$R CMD INSTALL --build . diff --git a/recipes/r-scrm/meta.yaml b/recipes/r-scrm/meta.yaml deleted file mode 100644 index a89b745c2186f..0000000000000 --- a/recipes/r-scrm/meta.yaml +++ /dev/null @@ -1,70 +0,0 @@ -{% set version = '1.7.2-4' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - -package: - name: r-scrm - version: {{ version|replace("-", "_") }} - -source: - url: - - {{ cran_mirror }}/src/contrib/scrm_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/scrm/scrm_{{ version }}.tar.gz - sha256: c780450d91b671499b703588336bac23293e938ae3d33b1e54db0306091040ba - -build: - merge_build_host: True # [win] - - number: 1 - 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-rcpp >=0.11.2 - - run: - - r-base - - {{native}}gcc-libs # [win] - - r-rcpp >=0.11.2 - -test: - commands: - - - $R -e "library('scrm')" # [not win] - - "\"%R%\" -e \"library('scrm')\"" # [win] - -about: - home: https://github.com/scrm/scrm-r - license: GPL (>= 3) - summary: A coalescent simulator that allows the rapid simulation of biological sequences under - neutral models of evolution. Different to other coalescent based simulations, it - has an optional approximation parameter that allows for high accuracy while maintaining - a linear run time cost for long sequences. It is optimized for simulating massive - data sets as produced by Next- Generation Sequencing technologies for up to several - thousand sequences. - license_family: GPL3 -extra: - recipe-maintainers: - - MathiasHaudgaard - - FrodePedersen - - ArneKr - - johanneskoester - - bgruening - - daler - - jdblischak diff --git a/recipes/r-seqminer/build.sh b/recipes/r-seqminer/build.sh deleted file mode 100644 index 5bf492ab9fc06..0000000000000 --- a/recipes/r-seqminer/build.sh +++ /dev/null @@ -1 +0,0 @@ -$R CMD INSTALL --build . diff --git a/recipes/r-seqminer/meta.yaml b/recipes/r-seqminer/meta.yaml deleted file mode 100644 index 992ae3e7f290e..0000000000000 --- a/recipes/r-seqminer/meta.yaml +++ /dev/null @@ -1,72 +0,0 @@ -{% set version = '7.1' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - -package: - name: r-seqminer - version: {{ version|replace("-", "_") }} - -source: - url: - - {{ cran_mirror }}/src/contrib/seqminer_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/seqminer/seqminer_{{ version }}.tar.gz - sha256: befa015f98096cc186fd3f9175935620e4adf78d73203950ba8e67c2e765cdcb - -build: - 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}}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 - - run: - - r-base - - {{native}}gcc-libs # [win] - -test: - commands: - - - $R -e "library('seqminer')" # [not win] - - "\"%R%\" -e \"library('seqminer')\"" # [win] - -about: - 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-shaman/meta.yaml b/recipes/r-shaman/meta.yaml index 6dd1d141f30fa..c55df2773e8d1 100644 --- a/recipes/r-shaman/meta.yaml +++ b/recipes/r-shaman/meta.yaml @@ -9,8 +9,8 @@ source: sha256: 525880e920a1e90a84f4cfcf3743019f3e5e70eb6287acb3a93bb7ee38dcc091 build: + noarch: generic number: 0 - skip: true #[osx] rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sigQC/build.sh b/recipes/r-sigqc/build.sh similarity index 100% rename from recipes/r-sigQC/build.sh rename to recipes/r-sigqc/build.sh diff --git a/recipes/r-sigQC/meta.yaml b/recipes/r-sigqc/meta.yaml similarity index 84% rename from recipes/r-sigQC/meta.yaml rename to recipes/r-sigqc/meta.yaml index c6846815ed51a..96d5014428135 100644 --- a/recipes/r-sigQC/meta.yaml +++ b/recipes/r-sigqc/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.1.21' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-sigqc version: {{ version|replace("-", "_") }} @@ -14,20 +11,14 @@ source: sha256: 1deec4c855e05bdae3fd854ae0bbb364b4b1a52df6f78bf10ba839f2e7ee241d build: - merge_build_host: True # [win] - # If this is a new build for the same version, increment the build number. + noarch: generic number: 1 - - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ # Suggests: knitr, rmarkdown requirements: - build: - - {{posix}}zip # [win] - host: - r-base - bioconductor-complexheatmap @@ -46,7 +37,6 @@ requirements: - r-mclust - r-moments - r-nnet - run: - r-base - bioconductor-complexheatmap diff --git a/recipes/r-sigtree/meta.yaml b/recipes/r-sigtree/meta.yaml index df47f76fd78a9..ff9c9f42a8149 100644 --- a/recipes/r-sigtree/meta.yaml +++ b/recipes/r-sigtree/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.10.6' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-sigtree version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: 3ce57e37d1c328720bb3ffc8c1f349c62b22e4d4de132f988ce9a42cbf3af0a1 build: - merge_build_host: True # [win] number: 4 rpaths: - lib/R/lib/ @@ -22,14 +18,8 @@ build: requirements: build: - - {{ compiler('c') }} # [not win] - - {{native}}toolchain # [win] - - {{posix}}filesystem # [win] - - {{posix}}make - - {{posix}}sed # [win] - - {{posix}}coreutils # [win] - - {{posix}}zip # [win] - + - {{ compiler('c') }} + - make host: - r-base - r-mass @@ -39,10 +29,8 @@ requirements: - r-phylobase - bioconductor-phyloseq - r-vegan - run: - r-base - - {{native}}gcc-libs # [win] - r-mass - r-rcolorbrewer - r-ape diff --git a/recipes/r-sleuth/meta.yaml b/recipes/r-sleuth/meta.yaml index 3a0b5f717d239..09d4508556c76 100644 --- a/recipes/r-sleuth/meta.yaml +++ b/recipes/r-sleuth/meta.yaml @@ -7,6 +7,7 @@ source: sha256: c25158dff35416865931f7c95f02c64be764c5b2ce964fe9f40972d96150ddb2 build: + noarch: generic number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-spocc/meta.yaml b/recipes/r-spocc/meta.yaml index ee341a74ff629..59476f44f7180 100644 --- a/recipes/r-spocc/meta.yaml +++ b/recipes/r-spocc/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 5e1f4defa7b537d91c59f989537ed7b7e9d5afa439a64e247044d61c1f6af1ab build: + noarch: generic merge_build_host: True # [win] number: 1 rpaths: diff --git a/recipes/r-spp/meta.yaml b/recipes/r-spp/meta.yaml index a535e57f47de5..4eb9d073991ce 100644 --- a/recipes/r-spp/meta.yaml +++ b/recipes/r-spp/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.16.0' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-spp version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: 3c890f3c414183167f9643b556621dcdc14ce6a1b54a04d618c74070fdebfd23 build: - merge_build_host: True # [win] number: 1 rpaths: - lib/R/lib/ @@ -22,30 +18,19 @@ build: requirements: build: - - {{ 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - autoconf + - pkg-config + - make host: - r-base - r-bh >=1.66 - r-rcpp - bioconductor-rsamtools - r-catools - run: - r-base - - {{native}}gcc-libs # [win] - r-bh >=1.66 - r-rcpp - bioconductor-rsamtools diff --git a/recipes/r-stampp/meta.yaml b/recipes/r-stampp/meta.yaml index 3a4fab2863486..3b28f0fef070c 100644 --- a/recipes/r-stampp/meta.yaml +++ b/recipes/r-stampp/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 6ebe4cadbd265953bc76ccef8def71ef0c580626eb1963d5d28cd0d199d6da7b build: + noarch: generic merge_build_host: True # [win] number: 3 rpaths: diff --git a/recipes/r-structssi/meta.yaml b/recipes/r-structssi/meta.yaml index e96aeb2b8a9d8..c5fdd52e1a321 100644 --- a/recipes/r-structssi/meta.yaml +++ b/recipes/r-structssi/meta.yaml @@ -14,6 +14,7 @@ source: sha256: bbcdeac4b9eb8545217d928796b22bb7ba2e75935053b840271e13865fae3c1b build: + noarch: generic merge_build_host: True # [win] number: 4 rpaths: diff --git a/recipes/r-swamp/meta.yaml b/recipes/r-swamp/meta.yaml index 3a0e65cf57f12..d618524a27283 100644 --- a/recipes/r-swamp/meta.yaml +++ b/recipes/r-swamp/meta.yaml @@ -14,6 +14,7 @@ source: sha256: a6462f4fe99837317752b6d2c8f31275414a7f3e6fb4ab2e4fd8409c4f238407 build: + noarch: generic merge_build_host: True # [win] number: 2 rpaths: diff --git a/recipes/r-tcga2stat/meta.yaml b/recipes/r-tcga2stat/meta.yaml index c643726c14d8e..fcb756acef3a4 100644 --- a/recipes/r-tcga2stat/meta.yaml +++ b/recipes/r-tcga2stat/meta.yaml @@ -14,6 +14,7 @@ source: sha256: 7b46ba685839a44923d764c9c6cdbdcf87b9754eb5487e246f9db56c01a44595 build: + noarch: generic merge_build_host: True # [win] number: 4 rpaths: diff --git a/recipes/r-traminer/meta.yaml b/recipes/r-traminer/meta.yaml index 81d8aafac9c80..d7521c1e44736 100644 --- a/recipes/r-traminer/meta.yaml +++ b/recipes/r-traminer/meta.yaml @@ -1,8 +1,5 @@ {% set version = '2.0-9' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-traminer version: {{ version|replace("-", "_") }} @@ -14,36 +11,24 @@ source: sha256: 6e9c017ac11d131c4cfe1009ed1f33704cc9a771b5270bf10477055f5b714b07 build: - merge_build_host: True # [win] - number: 1 - 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-hmisc - r-rcolorbrewer - r-boot - r-cluster - run: - r-base - - {{native}}gcc-libs # [win] - r-hmisc - r-rcolorbrewer - r-boot diff --git a/recipes/r-umi4c/meta.yaml b/recipes/r-umi4c/meta.yaml index 6ab98bf5859fa..302277e272f89 100644 --- a/recipes/r-umi4c/meta.yaml +++ b/recipes/r-umi4c/meta.yaml @@ -1,4 +1,5 @@ {% set version = "0.0.0.9000" %} + package: name: 'r-umi4c' version: '{{ version }}' @@ -8,8 +9,8 @@ source: sha256: e039134249e348843e191a46e2c2421003b3709156f0c9119a75a8450eecb40f build: + noarch: generic number: 0 - skip: true #[osx] rpaths: - lib/R/lib/ - lib/ @@ -20,7 +21,6 @@ requirements: - r-devtools - r-zoo - r-misha - run: - r-base - r-zoo diff --git a/recipes/r-vcfr/meta.yaml b/recipes/r-vcfr/meta.yaml index e7f6b2fbd56fd..b637b54451efe 100644 --- a/recipes/r-vcfr/meta.yaml +++ b/recipes/r-vcfr/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.8.0' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-vcfr version: {{ version|replace("-", "_") }} @@ -14,7 +11,6 @@ source: sha256: 5ffcf9980c1936b9be41b92d5887c56a7ec6e3cf197e5ef7c78aefa8aba20499 build: - merge_build_host: True # [win] number: 2 rpaths: - lib/R/lib/ @@ -22,15 +18,9 @@ build: 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-rcpp @@ -43,10 +33,8 @@ requirements: - r-tibble - r-vegan - r-viridislite - run: - r-base - - {{native}}gcc-libs # [win] - r-rcpp - r-ape - r-dplyr @@ -60,7 +48,6 @@ requirements: test: commands: - - $R -e "library('vcfR')" # [not win] - "\"%R%\" -e \"library('vcfR')\"" # [win] @@ -75,12 +62,3 @@ 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-whopgenome/meta.yaml b/recipes/r-whopgenome/meta.yaml index 25fcfe65f8e16..9b78e2f0e8a2c 100644 --- a/recipes/r-whopgenome/meta.yaml +++ b/recipes/r-whopgenome/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.9.7' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-whopgenome version: {{ version|replace("-", "_") }} @@ -14,35 +11,23 @@ source: sha256: 58bb001a831eff64955e424f07de7775d4d463d9674fc7743a0f795b7a6a47f5 build: - 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] - + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - run: - r-base - - {{native}}gcc-libs # [win] test: commands: - - $R -e "library('WhopGenome')" # [not win] - "\"%R%\" -e \"library('WhopGenome')\"" # [win] diff --git a/recipes/ragout/build.sh b/recipes/ragout/build.sh index d677572ff4626..2b49b3c283d3c 100644 --- a/recipes/ragout/build.sh +++ b/recipes/ragout/build.sh @@ -3,4 +3,4 @@ python setup.py build #installs ragout as a python pachage -python setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/rapid/0.8/meta.yaml b/recipes/rapid/0.8/meta.yaml index 5c483a1979a99..cd5edab6ad4fe 100644 --- a/recipes/rapid/0.8/meta.yaml +++ b/recipes/rapid/0.8/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/SchulzLab/RAPID/archive/v{{ version }}.tar.gz sha256: caddaa79d9be8012bc1ab09bdc431b863c80414eb471ac3a79ce5c940a03d4b5 build: + noarch: generic number: 2 requirements: diff --git a/recipes/rapid/v0.7/meta.yaml b/recipes/rapid/v0.7/meta.yaml index b5c1342434210..414dbfdaa2ed0 100644 --- a/recipes/rapid/v0.7/meta.yaml +++ b/recipes/rapid/v0.7/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/SchulzLab/RAPID/archive/v{{ version }}.tar.gz sha256: 922df6a7dbcd04d72121408e06a491c3946d7fc38a4c980789b311a565b1c59f build: + noarch: generic number: 0 requirements: diff --git a/recipes/rapid/v0.8/meta.yaml b/recipes/rapid/v0.8/meta.yaml index e3558ea87185d..b934d6240ffd8 100644 --- a/recipes/rapid/v0.8/meta.yaml +++ b/recipes/rapid/v0.8/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/SchulzLab/RAPID/archive/v{{ version }}.tar.gz sha256: caddaa79d9be8012bc1ab09bdc431b863c80414eb471ac3a79ce5c940a03d4b5 build: + noarch: generic number: 3 requirements: diff --git a/recipes/rapid/v1.0/meta.yaml b/recipes/rapid/v1.0/meta.yaml index 837ef3fff2a8d..13b7fcc0c2734 100644 --- a/recipes/rapid/v1.0/meta.yaml +++ b/recipes/rapid/v1.0/meta.yaml @@ -8,6 +8,7 @@ source: url: https://github.com/SchulzLab/RAPID/archive/v{{ version }}.tar.gz sha256: 1de2f22b0e0b312e3882e03b043b73a8abd7bfa51b83604422d624f5ce397308 build: + noarch: generic number: 0 requirements: diff --git a/recipes/raxml/7.3.0/meta.yaml b/recipes/raxml/7.3.0/meta.yaml index d0fd5c10c37b7..9a01a948356f4 100644 --- a/recipes/raxml/7.3.0/meta.yaml +++ b/recipes/raxml/7.3.0/meta.yaml @@ -21,3 +21,6 @@ extra: identifiers: - biotools:raxml - doi:10.1093/bioinformatics/btu033 + skip-lints: + - should_be_noarch_generic + - missing_hash diff --git a/recipes/rdfextras/meta.yaml b/recipes/rdfextras/meta.yaml index beb347c1c2bfa..3f036d5877ed6 100644 --- a/recipes/rdfextras/meta.yaml +++ b/recipes/rdfextras/meta.yaml @@ -7,8 +7,8 @@ source: md5: c9905b062568ab5607dcf60573b55c2b build: + noarch: python number: 3 - skip: True # [py3k] preserve_egg_dir: True entry_points: - rdfpipe = rdfextras.tools.rdfpipe:main @@ -18,14 +18,10 @@ build: requirements: host: - - python + - python <3 - setuptools - - rdflib >=3.2.1 - - pyparsing <=1.5.7 - - isodate - run: - - python + - python <3 - isodate - rdflib >=3.2.1 - pyparsing <=1.5.7 diff --git a/recipes/rdp_classifier/meta.yaml b/recipes/rdp_classifier/meta.yaml index b418654cf19af..11222c0eeec0d 100644 --- a/recipes/rdp_classifier/meta.yaml +++ b/recipes/rdp_classifier/meta.yaml @@ -3,12 +3,11 @@ package: version: 2.2 source: - fn: rdp_classifier_2.2.zip - md5: 745db57e1644ca4cca8330bb954d0b2c - sha256: 330a56cc6199a872723a9fee48dd5ae03c5f021c3fa26053c79338f7446a4599 url: https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip + sha256: 330a56cc6199a872723a9fee48dd5ae03c5f021c3fa26053c79338f7446a4599 build: + noarch: generic number: 1 requirements: diff --git a/recipes/rdptools/meta.yaml b/recipes/rdptools/meta.yaml index 4ed9ce065d1ab..9fa71d5adbbae 100644 --- a/recipes/rdptools/meta.yaml +++ b/recipes/rdptools/meta.yaml @@ -42,3 +42,7 @@ about: license: GPL summary: Metaproject for RDP Tools +extra: + skip-lints: + - uses_vcs_url + - missing_hash diff --git a/recipes/recalladapters/meta.yaml b/recipes/recalladapters/meta.yaml index b7a1aae0cc758..8c5e2bf622d45 100644 --- a/recipes/recalladapters/meta.yaml +++ b/recipes/recalladapters/meta.yaml @@ -10,6 +10,14 @@ source: url: https://github.com/PacificBiosciences/recalladapters/releases/download/v{{ version }}/recalladapters sha256: {{ sha256 }} +build: + number: 0 + skip: True # [osx] + +test: + commands: + - recalladapters -h + about: home: https://github.com/PacificBiosciences/pbbioconda license: BSD-3-Clause-Clear @@ -20,11 +28,5 @@ extra: - armintoepfer - pb-dseifert - mhsieh - -build: - number: 0 - skip: True # [osx] - -test: - commands: - - recalladapters -h + skip-lints: + - should_be_noarch_generic diff --git a/recipes/recycler/meta.yaml b/recipes/recycler/meta.yaml index c8680fe5a3c5c..b0732dee24f69 100644 --- a/recipes/recycler/meta.yaml +++ b/recipes/recycler/meta.yaml @@ -6,24 +6,19 @@ package: version: '{{version}}' build: + noarch: python number: 2 - skip: true # [not py27] source: - fn: recycler_{{version}}.tar.gz url: https://github.com/Shamir-Lab/Recycler/archive/v{{version}}.tar.gz sha256: '{{sha256}}' requirements: host: - - python - - networkx - - pysam - - nose - - numpy - + - python <3 + - pip run: - - python + - python <3 - networkx - pysam - nose diff --git a/recipes/refseq_masher/meta.yaml b/recipes/refseq_masher/meta.yaml index 8853b78aed16f..d9572d4d5e3cc 100644 --- a/recipes/refseq_masher/meta.yaml +++ b/recipes/refseq_masher/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256sum }} build: - skip: True # [py27] + noarch: python number: 1 script: python -m pip install --no-deps --ignore-installed . entry_points: @@ -19,11 +19,10 @@ build: requirements: host: - - python + - python >=3 - pip - - setuptools run: - - python + - python >=3 - numpy >=1.12.1 - pandas >=0.20.1 - click diff --git a/recipes/repeatmasker/meta.yaml b/recipes/repeatmasker/meta.yaml index 165df80565cd3..aa4d2091aa879 100644 --- a/recipes/repeatmasker/meta.yaml +++ b/recipes/repeatmasker/meta.yaml @@ -1,19 +1,21 @@ package: name: repeatmasker version: 4.0.9_p2 + source: url: http://www.repeatmasker.org/RepeatMasker-open-4-0-9-p2.tar.gz sha256: 7b40e7c95531c03c009ee4ea0fdb467f85e55df2fd20b5c24ef72d5906c07cd1 patches: - patch1 + build: number: 0 detect_binary_files_with_prefix: False has_prefix_files: - - bin/RepeatMasker + - bin/RepeatMasker requirements: - build: + host: - perl - rmblast run: @@ -42,3 +44,5 @@ about: extra: identifiers: - biotools:RepeatMasker + skip-lints: + - should_be_noarch_generic diff --git a/recipes/repeatmodeler/meta.yaml b/recipes/repeatmodeler/meta.yaml index 078a7716cedae..2e69bc1b4c9e2 100644 --- a/recipes/repeatmodeler/meta.yaml +++ b/recipes/repeatmodeler/meta.yaml @@ -8,10 +8,10 @@ source: build: number: 1 - skip: True #[osx] + skip: True #[osx] requirements: - build: + host: - perl - rmblast run: @@ -35,3 +35,5 @@ about: extra: identifiers: - biotools:RepeatModeler + skip-lints: + - should_be_noarch_generic diff --git a/recipes/repenrich/meta.yaml b/recipes/repenrich/meta.yaml index 4aecfc45160d7..aaf72a0d475a8 100644 --- a/recipes/repenrich/meta.yaml +++ b/recipes/repenrich/meta.yaml @@ -9,19 +9,12 @@ source: - paths.patch build: + noarch: generic number: 1 - skip: True # [py3k] requirements: - host: - - python - - bowtie - - bedtools <2.24.0 - - samtools - - biopython - run: - - python + - python <3 - bowtie - bedtools <2.24.0 - samtools diff --git a/recipes/retry_decorator/build.sh b/recipes/retry_decorator/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/retry_decorator/build.sh +++ /dev/null @@ -1,9 +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/retry_decorator/meta.yaml b/recipes/retry_decorator/meta.yaml index f3cbfca351db8..4e844ac847f11 100644 --- a/recipes/retry_decorator/meta.yaml +++ b/recipes/retry_decorator/meta.yaml @@ -8,13 +8,13 @@ source: build: noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/revtrans/meta.yaml b/recipes/revtrans/meta.yaml index 5f8ce3b081027..7cc10428adc0c 100644 --- a/recipes/revtrans/meta.yaml +++ b/recipes/revtrans/meta.yaml @@ -11,22 +11,22 @@ source: - url: http://www.cbs.dtu.dk/services/RevTrans-2.0/web/releases/revtrans-1.4.tgz sha256: {{ sha256 }} patches: - - interpreter.patch + - interpreter.patch - url: http://www.cbs.dtu.dk/services/RevTrans-2.0/web/releases/contributed/revtrans_jarmo.py sha256: {{ sha256_2 }} patches: - - interpreter_jarmo.patch + - interpreter_jarmo.patch build: + noarch: python number: 0 - skip: True # [py3k] requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 test: commands: diff --git a/recipes/ribodiff/meta.yaml b/recipes/ribodiff/meta.yaml index 44c1e75146cb5..4fdf107cf26a6 100644 --- a/recipes/ribodiff/meta.yaml +++ b/recipes/ribodiff/meta.yaml @@ -9,19 +9,15 @@ source: md5: b02833b4412959746032f0cf23a944d8 build: + noarch: python number: 1 - skip: True # [not py27] requirements: host: - - python + - python <3 - pip - - numpy >=1.8.0 - - scipy >=0.13.3 - - matplotlib >=1.3.0 - - statsmodels >=0.5.0 run: - - python + - python <3 - numpy >=1.8.0 - scipy >=0.13.3 - matplotlib >=1.3.0 diff --git a/recipes/riboplot/build.sh b/recipes/riboplot/build.sh deleted file mode 100644 index 1aea1a7737ea5..0000000000000 --- a/recipes/riboplot/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/riboplot/meta.yaml b/recipes/riboplot/meta.yaml index 68c7d9aa749ac..a3f12b2716e42 100644 --- a/recipes/riboplot/meta.yaml +++ b/recipes/riboplot/meta.yaml @@ -3,27 +3,22 @@ package: version: "0.3.1" source: - url: https://pypi.python.org/packages/87/d7/e67c64d7ea6312437013be23e91c9478543ca0b29a8dc69aa92676f12bd0/riboplot-0.3.1.tar.gz [py2k] - md5: 6903d5fa1e5e5390f6d8dff8b62307ff [py2k] + url: https://pypi.python.org/packages/87/d7/e67c64d7ea6312437013be23e91c9478543ca0b29a8dc69aa92676f12bd0/riboplot-0.3.1.tar.gz + md5: 6903d5fa1e5e5390f6d8dff8b62307ff build: + noarch: python number: 2 entry_points: - riboplot = riboplot.riboplot:run - ribocount = riboplot.ribocount:run - skip: True # [not py27] requirements: host: - - python - - setuptools - - matplotlib <=1.4.3 - - pysam <=0.8.3 - - mock ==1.0.1 - - nose - + - python <3 + - pip run: - - python + - python <3 - matplotlib <=1.4.3 - pysam <=0.8.3 - mock ==1.0.1 @@ -32,7 +27,6 @@ requirements: test: imports: - riboplot - commands: - riboplot --help - ribocount --help diff --git a/recipes/riboraptor/meta.yaml b/recipes/riboraptor/meta.yaml index 8d69be5492966..3c9257e71ebfb 100644 --- a/recipes/riboraptor/meta.yaml +++ b/recipes/riboraptor/meta.yaml @@ -13,33 +13,18 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: python number: 1 entry_points: - riboraptor=riboraptor.cli:cli - script: pip install --no-deps . - skip: True # [py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - matplotlib >=2.1.0 - - numpy >=1.11.0 - - pandas >=0.20.3 - - pybedtools >=0.7.10 - - pybigwig >=0.2.8 - - pyfaidx >=0.5.0 - - pysam >=0.11.2.2 - - scipy >=0.19.1 - - seaborn >=0.8.1 - - statsmodels >=0.8.0 - - six >=1.11.0 - - click >=6.0 - - click-help-colors >=0.3 - - htseq >=0.9.1 - - biopython >=1.70 + - python >=3 + - pip run: - - python + - python >=3 - matplotlib >=2.1.0 - numpy >=1.11.0 - pandas >=0.20.3 diff --git a/recipes/riboseq-rust/meta.yaml b/recipes/riboseq-rust/meta.yaml index 0e9d986814e0f..0e58d62d5dbb3 100644 --- a/recipes/riboseq-rust/meta.yaml +++ b/recipes/riboseq-rust/meta.yaml @@ -12,11 +12,11 @@ source: build: number: 1 - skip: True # [not py27 or osx] + skip: True # [osx] requirements: run: - - python + - python <3 - argparse - matplotlib - numpy @@ -30,3 +30,7 @@ about: license: GPL-3.0 license_file: COPYING summary: 'Ribo-seq Unit Step Transformation. Tools to characterise the determinants of ribosome profiling read density across mRNA. May be used to examine relative decoding rates and and for quality assessment' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/ribotaper/meta.yaml b/recipes/ribotaper/meta.yaml index ddf3dc08d00f6..6e3dda375da25 100644 --- a/recipes/ribotaper/meta.yaml +++ b/recipes/ribotaper/meta.yaml @@ -12,6 +12,8 @@ build: requirements: build: + - {{ compiler('c') }} + host: - bedtools ==2.17.0 - samtools - r-iterators diff --git a/recipes/rmats2sashimiplot/build.sh b/recipes/rmats2sashimiplot/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/rmats2sashimiplot/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/rmats2sashimiplot/meta.yaml b/recipes/rmats2sashimiplot/meta.yaml index 03b3357a1352b..cf3472e661803 100644 --- a/recipes/rmats2sashimiplot/meta.yaml +++ b/recipes/rmats2sashimiplot/meta.yaml @@ -1,5 +1,6 @@ {% set version = "2.0.3" %} {% set sha256 = "8422bbe7bdff2aef5ecbccde58666b35587902f94edaa1c05cb37cdd2e2013c0" %} + package: name: rmats2sashimiplot version: '{{version}}' # Version number indicated in the setup.py file. @@ -7,21 +8,24 @@ package: source: url: https://github.com/Xinglab/rmats2sashimiplot/archive/v{{version}}.tar.gz sha256: '{{sha256}}' + +build: + noarch: python + number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + preserve_egg_dir: true + requirements: host: - - python + - python <3 + - pip run: - - python ==2.6*|2.7* + - python <3 - matplotlib - scipy - pysam ==0.9.0 - samtools ==1.3.1 -build: - number: 2 - skip: true # [not py27] - preserve_egg_dir: true - test: commands: - rmats2sashimiplot -h diff --git a/recipes/rnacode/meta.yaml b/recipes/rnacode/meta.yaml index e3f22bb1fc77b..fb16f3c26a128 100644 --- a/recipes/rnacode/meta.yaml +++ b/recipes/rnacode/meta.yaml @@ -20,8 +20,12 @@ test: about: home: http://wash.github.io/rnacode/ - license: '' + license: unknown summary: 'RNAcode - Analyze the protein coding potential in multiple sequence alignments RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/rnaquast/meta.yaml b/recipes/rnaquast/meta.yaml index 99b0d3acc1f4b..55f3c43a08271 100644 --- a/recipes/rnaquast/meta.yaml +++ b/recipes/rnaquast/meta.yaml @@ -12,7 +12,7 @@ source: build: number: 0 - skip: True # [osx] + skip: True # [osx] requirements: run: @@ -38,3 +38,7 @@ about: summary: rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software. home: http://cab.spbu.ru/software/rnaquast/ license: GPLv2 + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/rnasketch/build.sh b/recipes/rnasketch/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/rnasketch/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/rnasketch/meta.yaml b/recipes/rnasketch/meta.yaml index 2cd616c5fc54d..581c05d9061a7 100644 --- a/recipes/rnasketch/meta.yaml +++ b/recipes/rnasketch/meta.yaml @@ -10,20 +10,21 @@ source: md5: {{ md5 }} build: - skip: True # [not py27 or osx] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 requirements: host: - - python - + - python <3 + - pip run: - - python - - rnablueprint >=1.2 - - viennarna >=2.4* - - python-igraph - - numpy >=1.15* - - scipy >=1.1* + - python <3 + - rnablueprint >=1.2 + - viennarna >=2.4* + - python-igraph + - numpy >=1.15* + - scipy >=1.1* test: imports: diff --git a/recipes/roary2fripan/build.sh b/recipes/roary2fripan.py/build.sh similarity index 100% rename from recipes/roary2fripan/build.sh rename to recipes/roary2fripan.py/build.sh diff --git a/recipes/roary2fripan/meta.yaml b/recipes/roary2fripan.py/meta.yaml similarity index 91% rename from recipes/roary2fripan/meta.yaml rename to recipes/roary2fripan.py/meta.yaml index 6da524603628a..cd88846b9ea24 100644 --- a/recipes/roary2fripan/meta.yaml +++ b/recipes/roary2fripan.py/meta.yaml @@ -6,18 +6,16 @@ package: version: {{ version }} build: + noarch: generic number: 1 - skip: True # [not py27] source: url: https://github.com/kwongj/roary2fripan/archive/298c32a56f8696898fd3a94ef252e57ebe464119.tar.gz md5: 1d99d4a5af37a3ea617cdff7e05f039f requirements: - host: - run: - - python + - python <3 test: commands: diff --git a/recipes/roprofile/meta.yaml b/recipes/roprofile/meta.yaml index 90a155248ff7c..25470c7e17333 100644 --- a/recipes/roprofile/meta.yaml +++ b/recipes/roprofile/meta.yaml @@ -6,18 +6,16 @@ package: version: {{ version }} build: + noarch: generic number: 1 - skip: True # [not py27] source: url: https://github.com/cimendes/roProfile/archive/2a8c52fafc5ae47fe0e7f2b29999579352fdfed1.tar.gz md5: 52a4b174d5d862f0f4b0f203bfe3dc16 requirements: - host: - run: - - python + - python <3 - biopython >=1.66 - matplotlib >=1.5.2 - mpld3 >=0.2 diff --git a/recipes/rpfcountcds/build.sh b/recipes/rpf-count-cds/build.sh similarity index 100% rename from recipes/rpfcountcds/build.sh rename to recipes/rpf-count-cds/build.sh diff --git a/recipes/rpfcountcds/meta.yaml b/recipes/rpf-count-cds/meta.yaml similarity index 90% rename from recipes/rpfcountcds/meta.yaml rename to recipes/rpf-count-cds/meta.yaml index fc173a719a2a6..98fd493bb5648 100644 --- a/recipes/rpfcountcds/meta.yaml +++ b/recipes/rpf-count-cds/meta.yaml @@ -12,15 +12,14 @@ source: build: noarch: python - skip: True # [not py27] number: 1 requirements: host: - - python - - htseq + - python <3 + - pip run: - - python + - python <3 - htseq test: commands: diff --git a/recipes/rpkmforgenes/meta.yaml b/recipes/rpkmforgenes/meta.yaml index d7043df970fd6..283756ba7b374 100644 --- a/recipes/rpkmforgenes/meta.yaml +++ b/recipes/rpkmforgenes/meta.yaml @@ -3,20 +3,16 @@ package: version: "1.0.1" build: + noarch: generic number: 1 - skip: True # [py3k] source: url: https://github.com/danielramskold/S3_species-specific_sequencing/archive/1.0.1.tar.gz md5: 114afd083b2f11bd57c57e68ec4b607d requirements: - host: - - python - - pysam - - numpy run: - - python + - python <3 - pysam - numpy test: diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml index 7af2b71add142..179375c392abc 100644 --- a/recipes/rseqc/meta.yaml +++ b/recipes/rseqc/meta.yaml @@ -11,22 +11,23 @@ source: build: number: 0 - noarch: python + skip: True # [py2k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " requirements: + build: + - {{ compiler('c') }} host: - pip - - python >=3 + - python - cython >=0.12 - - nose run: - bx-python - numpy - pip - pybigwig - pysam - - python >=3 + - python - r-base test: diff --git a/recipes/ruby-dna-tools/meta.yaml b/recipes/ruby-dna-tools/meta.yaml index 10142e9dd8819..cff4356e9e39a 100644 --- a/recipes/ruby-dna-tools/meta.yaml +++ b/recipes/ruby-dna-tools/meta.yaml @@ -1,19 +1,19 @@ {% set version = "1.0" %} {% set sha256 = "9d593872715bf510e66163267ce14e1208ecbdd7017695738610f25b74930f9b" %} -build: - number: 1 - package: name: ruby-dna-tools version: {{ version }} +build: + noarch: generic + number: 1 + source: url: https://github.com/Carldeboer/Ruby-DNA-Tools/archive/{{ version }}.tar.gz sha256: {{ sha256 }} requirements: - host: run: - ruby >=2.4 - jemalloc diff --git a/recipes/ruffus/2.4.1/build.sh b/recipes/ruffus/2.4.1/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/ruffus/2.4.1/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/ruffus/2.4.1/meta.yaml b/recipes/ruffus/2.4.1/meta.yaml index ad2622577225e..8dd6fc40045fa 100644 --- a/recipes/ruffus/2.4.1/meta.yaml +++ b/recipes/ruffus/2.4.1/meta.yaml @@ -7,16 +7,16 @@ source: sha256: 6978532d040f1ea98f1c7b8ef9e7f2bfbac2f18f407ef5e9277fc1eaa3ce0cb5 build: + noarch: python number: 0 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/s3gof3r/meta.yaml b/recipes/s3gof3r/meta.yaml index 6b3acc14930c2..76525b2c436ca 100644 --- a/recipes/s3gof3r/meta.yaml +++ b/recipes/s3gof3r/meta.yaml @@ -3,14 +3,13 @@ package: version: '0.5.0' source: - url: https://github.com/rlmcpherson/s3gof3r/releases/download/v0.5.0/gof3r_0.5.0_linux_amd64.tar.gz # [linux] - sha256: d88f199d1580d8c8cac26ba39e15dc6e2126d20e56c3894bd37a226e8b3e665c - url: https://github.com/rlmcpherson/s3gof3r/releases/download/v0.5.0/gof3r_0.5.0_darwin_amd64.zip # [osx] - sha256: 85ace61bd58cf57034e748af22b8a3c9ca82ed194da3a4c1c646989d78ee2947 + - url: https://github.com/rlmcpherson/s3gof3r/releases/download/v0.5.0/gof3r_0.5.0_linux_amd64.tar.gz # [linux] + sha256: d88f199d1580d8c8cac26ba39e15dc6e2126d20e56c3894bd37a226e8b3e665c + - url: https://github.com/rlmcpherson/s3gof3r/releases/download/v0.5.0/gof3r_0.5.0_darwin_amd64.zip # [osx] + sha256: 85ace61bd58cf57034e748af22b8a3c9ca82ed194da3a4c1c646989d78ee2947 build: number: 1 - skip: False requirements: build: @@ -24,3 +23,8 @@ about: home: https://github.com/rlmcpherson/s3gof3r license: MIT summary: Fast, concurrent, streaming access to Amazon S3, including gof3r, a CLI + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/saffrontree/build.sh b/recipes/saffrontree/build.sh deleted file mode 100644 index 05e8aa5c5fcdf..0000000000000 --- a/recipes/saffrontree/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -python3 setup.py install diff --git a/recipes/saffrontree/meta.yaml b/recipes/saffrontree/meta.yaml index df47470443ecc..390fe9b6bc242 100644 --- a/recipes/saffrontree/meta.yaml +++ b/recipes/saffrontree/meta.yaml @@ -13,6 +13,7 @@ source: build: skip: True # [py27] number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: diff --git a/recipes/sak/meta.yaml b/recipes/sak/meta.yaml index 3c550fdc0266c..bce18fbece0b9 100644 --- a/recipes/sak/meta.yaml +++ b/recipes/sak/meta.yaml @@ -1,19 +1,26 @@ -build: - number: 1 - package: name: sak version: "0.4.6" + source: - url: http://packages.seqan.de/sak/sak-0.4.6-Mac-x86_64.zip # [osx] - md5: 09411d5538fb63dfed9568e75bc8c51a # [osx] - url: http://packages.seqan.de/sak/sak-0.4.6-Linux-x86_64.tar.xz # [linux64] - md5: cfd68084994e666116971dd681b7fe20 # [linux64] + - url: http://packages.seqan.de/sak/sak-0.4.6-Mac-x86_64.zip # [osx] + md5: 09411d5538fb63dfed9568e75bc8c51a # [osx] + - url: http://packages.seqan.de/sak/sak-0.4.6-Linux-x86_64.tar.xz # [linux] + md5: cfd68084994e666116971dd681b7fe20 # [linux] + +build: + number: 1 test: commands: - sak --help 2>&1 > /dev/null + about: home: https://github.com/seqan/seqan/tree/master/apps/sak/README license: https://github.com/seqan/seqan/tree/master/apps/sak/LICENSE summary: This tool allows one to cut sequences and parts of sequences out of sequence files. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/sambamba/0.5.9/meta.yaml b/recipes/sambamba/0.5.9/meta.yaml index eab8ad41e7761..263bddd2b25d9 100644 --- a/recipes/sambamba/0.5.9/meta.yaml +++ b/recipes/sambamba/0.5.9/meta.yaml @@ -4,10 +4,10 @@ package: version: {{ version }} source: - url: https://github.com/lomereiter/sambamba/releases/download/v{{ version }}/sambamba_v{{ version }}_linux.tar.bz2 # [linux] - md5: f4f8bc03c78c3d1edf9d76bdda4bae47 # [linux] - url: https://github.com/lomereiter/sambamba/releases/download/v{{ version }}/sambamba_v{{ version }}_osx.tar.bz2 # [osx] - md5: 5a82a3790717f5bc5ba29ca43a0d8d0e # [osx] + - url: https://github.com/lomereiter/sambamba/releases/download/v{{ version }}/sambamba_v{{ version }}_linux.tar.bz2 # [linux] + md5: f4f8bc03c78c3d1edf9d76bdda4bae47 # [linux] + - url: https://github.com/lomereiter/sambamba/releases/download/v{{ version }}/sambamba_v{{ version }}_osx.tar.bz2 # [osx] + md5: 5a82a3790717f5bc5ba29ca43a0d8d0e # [osx] build: number: 1 @@ -20,3 +20,8 @@ about: home: https://github.com/lomereiter/sambamba license: GPLv2 summary: Tools for working with SAM/BAM data + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/samclip/meta.yaml b/recipes/samclip/meta.yaml index c1eaf0eadca22..e7e868cf079ac 100644 --- a/recipes/samclip/meta.yaml +++ b/recipes/samclip/meta.yaml @@ -10,11 +10,10 @@ source: sha256: 70cf12ec758d5c43fb98dedb9dba0649a851338b19e2290a55288cbf498b6a67 build: + noarch: generic number: 1 requirements: - build: - run: - perl diff --git a/recipes/samsift/0.2.0/meta.yaml b/recipes/samsift/0.2.0/meta.yaml deleted file mode 100644 index 94cb80cc3db98..0000000000000 --- a/recipes/samsift/0.2.0/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set version = "0.2.0" %} -{% set sha256 = "3cc39d4999e9cec9557d4c47919585a90d58b79cd71c762cf98e624cc7d0db44" %} - -package: - name: samsift - version: {{ version }} - -source: - url: https://pypi.io/packages/source/s/samsift/samsift-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 1 - skip: True # [py27] - script: python -m pip install --no-deps --ignore-installed . - #entry-points: - # samsift = samsift:main - -requirements: - host: - - python - - pip - - pysam - run: - - python - - pysam - -test: - commands: - - samsift -v - - samsift -h - # invalid test file, missing PG tag - # - BAM=https://github.com/karel-brinda/samsift/raw/{{ version }}/tests/test.bam; curl -L ${BAM} | samsift - -about: - home: https://github.com/karel-brinda/samsift - license: MIT - summary: 'Advanced filtering and tagging of SAM/BAM alignments using Python expressions.' diff --git a/recipes/samsift/0.2.1/meta.yaml b/recipes/samsift/0.2.1/meta.yaml deleted file mode 100644 index 7ec56382b81cb..0000000000000 --- a/recipes/samsift/0.2.1/meta.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{% set version = "0.2.1" %} -{% set sha256 = "aa30f27d5dc8258e0bfd3eff1fcf6b290815865028ce8fce45e0c216f793a887" %} - -package: - name: samsift - version: {{ version }} - -source: - url: https://pypi.io/packages/source/s/samsift/samsift-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 1 - skip: True # [py27] - entry_points: - - samsift = samsift.samsift:main - - samsift-norm-sam = samsift.samsift_norm_sam:main - script: python -m pip install --no-deps --ignore-installed . - -requirements: - host: - - python - - pip - - pysam - - wheel - - setuptools - run: - - python - - pysam - -test: - commands: - - samsift -v - - samsift -h - - samsift-norm-sam --help - # invalid test file, missing PG tag - #- BAM=https://github.com/karel-brinda/samsift/raw/{{ version }}/tests/test.bam; curl -L ${BAM} | samsift - -about: - home: https://github.com/karel-brinda/samsift - license: MIT - summary: 'Advanced filtering and tagging of SAM/BAM alignments using Python expressions.' diff --git a/recipes/samsift/0.2.2/meta.yaml b/recipes/samsift/0.2.2/meta.yaml deleted file mode 100644 index 9b188418a5c61..0000000000000 --- a/recipes/samsift/0.2.2/meta.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{% set version = "0.2.2" %} -{% set sha256 = "52bda69f13c33c2441833fde7b317ecc62caac8990da7eb20aa3071dd926d3b1" %} - -package: - name: samsift - version: {{ version }} - -source: - url: https://pypi.io/packages/source/s/samsift/samsift-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 1 - skip: True # [py27] - entry_points: - - samsift = samsift.samsift:main - - samsift-norm-sam = samsift.samsift_norm_sam:main - script: python -m pip install --no-deps --ignore-installed . - -requirements: - host: - - python - - pip - - pysam - - wheel - - setuptools - run: - - python - - pysam - -test: - commands: - - samsift -v - - samsift -h - - samsift-norm-sam --help - # invalid test file, missing PG tag - #- BAM=https://github.com/karel-brinda/samsift/raw/{{ version }}/tests/test.bam; curl -L ${BAM} | samsift - -about: - home: https://github.com/karel-brinda/samsift - license: MIT - summary: 'Advanced filtering and tagging of SAM/BAM alignments using Python expressions.' diff --git a/recipes/samsift/0.2.3/meta.yaml b/recipes/samsift/0.2.3/meta.yaml deleted file mode 100644 index ad73acdd4957f..0000000000000 --- a/recipes/samsift/0.2.3/meta.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{% set version = "0.2.3" %} -{% set sha256 = "893617fda0d4be2c2339848f2f7e9d93c4f45e98ace5729a796eb9e29c1d3d31" %} - -package: - name: samsift - version: {{ version }} - -source: - url: https://pypi.io/packages/source/s/samsift/samsift-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 1 - skip: True # [py27] - entry_points: - - samsift = samsift.samsift:main - - samsift-norm-sam = samsift.samsift_norm_sam:main - script: python -m pip install --no-deps --ignore-installed . - -requirements: - host: - - python - - pip - - pysam - - wheel - - setuptools - run: - - python - - pysam - -test: - commands: - - samsift -v - - samsift -h - - samsift-norm-sam --help - # invalid test file, missing PG tag - #- BAM=https://github.com/karel-brinda/samsift/raw/{{ version }}/tests/tests/test.bam; curl -L ${BAM} | samsift - -about: - home: https://github.com/karel-brinda/samsift - license: MIT - summary: 'Advanced filtering and tagging of SAM/BAM alignments using Python expressions.' diff --git a/recipes/samsift/meta.yaml b/recipes/samsift/meta.yaml index 2afa583400da7..e06546ca434a6 100644 --- a/recipes/samsift/meta.yaml +++ b/recipes/samsift/meta.yaml @@ -10,8 +10,8 @@ source: sha256: {{ sha256 }} build: + noarch: python number: 2 - skip: True # [py27] entry_points: - samsift = samsift.samsift:main - samsift-norm-sam = samsift.samsift_norm_sam:main @@ -19,14 +19,10 @@ build: requirements: host: - - python + - python >=3 - pip - - pysam - - wheel - - python-dateutil - - setuptools run: - - python + - python >=3 - python-dateutil - pysam diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 99e487c47b908..00a23491e2c09 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -7,7 +7,7 @@ source: md5: 883df68d2f989c4c431ebb253ca104f7 build: - skip: True # [py27] + noarch: python number: 3 entry_points: - compile_stats=samsifter.stats.compile_stats:main @@ -26,19 +26,10 @@ build: requirements: host: - - python - - setuptools - - matplotlib >=1.3.1 - - python-dateutil - - pandas >=0.14.1 - - numpy >=1.6.1 - - pyqt 4.11.* - - glib - - pytz - - xorg-libsm - - xorg-libxrender + - python >=3 + - pip run: - - python + - python >=3 - matplotlib >=1.3.1 - pandas >=0.14.1 - numpy >=1.6.1 diff --git a/recipes/satsuma/build.sh b/recipes/satsuma2/build.sh similarity index 100% rename from recipes/satsuma/build.sh rename to recipes/satsuma2/build.sh diff --git a/recipes/satsuma/meta.yaml b/recipes/satsuma2/meta.yaml similarity index 95% rename from recipes/satsuma/meta.yaml rename to recipes/satsuma2/meta.yaml index d8866404247b1..c15d8ca0e6864 100644 --- a/recipes/satsuma/meta.yaml +++ b/recipes/satsuma2/meta.yaml @@ -16,7 +16,7 @@ build: requirements: build: - - gxx_linux-64 # [linux64] + - {{ compiler('c') }} - cmake run: diff --git a/recipes/sbt/meta.yaml b/recipes/sbt/meta.yaml index 08a1cdb54b3eb..c8238f95e3cb4 100644 --- a/recipes/sbt/meta.yaml +++ b/recipes/sbt/meta.yaml @@ -2,21 +2,26 @@ package: name: sbt version: "0.13.12" -about: - home: 'http://www.scala-sbt.org/' - license: BSD - build: + noarch: generic number: 1 -requirements: - build: - - java-jdk >=6 - run: - - java-jdk >=6 source: url: https://dl.bintray.com/sbt/native-packages/sbt/0.13.12/sbt-0.13.12.tgz md5: cec3071d46ef13334c8097cc3467ff28 + +requirements: + run: + - openjdk >=6 + test: commands: - "sbt -version" + +about: + home: 'http://www.scala-sbt.org/' + license: BSD + +extra: + skip-lints: + - missing_summary diff --git a/recipes/scaffold_builder/meta.yaml b/recipes/scaffold_builder/meta.yaml index bc5cafe1d651c..bffcbf2686650 100644 --- a/recipes/scaffold_builder/meta.yaml +++ b/recipes/scaffold_builder/meta.yaml @@ -10,14 +10,15 @@ source: sha256: '{{ sha256 }}' build: + noarch: python number: 0 - skip: True # [not py27] requirements: host: - - python + - python <3 + - pip run: - - python + - python <3 - mummer test: diff --git a/recipes/scala/meta.yaml b/recipes/scala/meta.yaml index cc09e2a13686f..0df8905a55114 100644 --- a/recipes/scala/meta.yaml +++ b/recipes/scala/meta.yaml @@ -1,23 +1,24 @@ package: name: "scala" version: "2.11.8" -about: - home: 'http://www.scala-lang.org/' - summary: "Scala combines object-oriented and functional programming in one concise, high-level language. Scala's static types help avoid bugs in complex applications, and its JVM and JavaScript runtimes let you build high-performance systems with easy access to huge ecosystems of libraries." - license: BSD build: + noarch: generic number: 1 +source: + url: http://downloads.lightbend.com/scala/2.11.8/scala-2.11.8.tgz + md5: e7e1f7ddc8873d228d611e801b8d2795 + requirements: - build: - - openjdk >=8 run: - openjdk >=8 -source: - url: http://downloads.lightbend.com/scala/2.11.8/scala-2.11.8.tgz - md5: e7e1f7ddc8873d228d611e801b8d2795 test: commands: - scalac -help + +about: + home: 'http://www.scala-lang.org/' + summary: "Scala combines object-oriented and functional programming in one concise, high-level language. Scala's static types help avoid bugs in complex applications, and its JVM and JavaScript runtimes let you build high-performance systems with easy access to huge ecosystems of libraries." + license: BSD diff --git a/recipes/scanindel/meta.yaml b/recipes/scanindel/meta.yaml index 71bb7900192c1..8c7b74b32ff8b 100644 --- a/recipes/scanindel/meta.yaml +++ b/recipes/scanindel/meta.yaml @@ -12,11 +12,10 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: generic number: 1 - skip: True # [osx or py3k] requirements: - host: run: - scipy - numpy @@ -25,12 +24,11 @@ requirements: - bwa ==0.7.12 - blat - freebayes ==0.9.21.7 - - python + - python <3 - pysam ==0.7.7 - pyvcf ==0.6.7 - biopython ==1.64 - test: commands: - ScanIndel.py -v diff --git a/recipes/scanpy/meta.yaml b/recipes/scanpy/meta.yaml index c63662387de76..0f99702f7f589 100644 --- a/recipes/scanpy/meta.yaml +++ b/recipes/scanpy/meta.yaml @@ -19,7 +19,6 @@ requirements: - pip run: - python >=3.6 - - setuptools - seaborn - scikit-learn - statsmodels diff --git a/recipes/scg/meta.yaml b/recipes/scg/meta.yaml index 8f4017608aa5b..84abfc8db9d87 100644 --- a/recipes/scg/meta.yaml +++ b/recipes/scg/meta.yaml @@ -10,21 +10,16 @@ source: md5: 6f0fb91266de66d6a9d73fb741f49e13 build: + noarch: python script: python -m pip install --no-deps --ignore-installed . number: 1 - skip: True # [not py27] requirements: host: - - python + - python <3 - pip - - pandas >=0.16 - - numpy >=1.9.2 - - scipy >=0.15 - - pyyaml - run: - - python + - python <3 - pandas >=0.16 - numpy >=1.9.2 - scipy >=0.15 diff --git a/recipes/schema/build.sh b/recipes/schema/build.sh deleted file mode 100755 index 8e25a1455f914..0000000000000 --- a/recipes/schema/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/schema/meta.yaml b/recipes/schema/meta.yaml deleted file mode 100644 index 4f8019c3b2094..0000000000000 --- a/recipes/schema/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -package: - name: schema - version: "0.7.0" - -source: - url: https://files.pythonhosted.org/packages/a5/ac/29e4a4d5be1fc8ba1a840853dbec1ab242f6e0bdd09fedb21e8383999fd3/schema-0.7.0.tar.gz - sha256: 44add3ef9016c85ac4b0291b45286a657d0df309b31528ca8d0a9c6d0aa68186 - -requirements: - host: - - python - - setuptools - - contextlib2 - - run: - - python - - contextlib2 - -build: - noarch: python - number: 0 - -test: - imports: - - schema - -about: - home: https://github.com/keleshev/schema - license: MIT License - summary: 'Simple data validation library' - diff --git a/recipes/scnic/meta.yaml b/recipes/scnic/meta.yaml index cc3e3333c0e1a..20139724f5866 100644 --- a/recipes/scnic/meta.yaml +++ b/recipes/scnic/meta.yaml @@ -45,4 +45,6 @@ about: extra: recipe-maintainers: - - shafferm + - shafferm + skip-lints: + - missing_tests diff --git a/recipes/scoary/meta.yaml b/recipes/scoary/meta.yaml index 6d1b14a708c8a..e204af424cd59 100644 --- a/recipes/scoary/meta.yaml +++ b/recipes/scoary/meta.yaml @@ -16,7 +16,6 @@ build: - scoary=scoary.methods:main - scoary_GUI=scoary.GUI:main script: python setup.py install --single-version-externally-managed --record=record.txt - number: 1 requirements: host: diff --git a/recipes/scoop/build.sh b/recipes/scoop/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/scoop/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/scoop/meta.yaml b/recipes/scoop/meta.yaml index c158588320a86..90683c878a559 100644 --- a/recipes/scoop/meta.yaml +++ b/recipes/scoop/meta.yaml @@ -11,6 +11,7 @@ source: build: noarch: python number: 3 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/screamingbackpack/build.sh b/recipes/screamingbackpack/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/screamingbackpack/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/screamingbackpack/meta.yaml b/recipes/screamingbackpack/meta.yaml index 3e1a0a2eca62a..8279b0ba0e30a 100644 --- a/recipes/screamingbackpack/meta.yaml +++ b/recipes/screamingbackpack/meta.yaml @@ -5,19 +5,16 @@ package: source: url: https://pypi.python.org/packages/source/S/ScreamingBackpack/ScreamingBackpack-0.2.333.tar.gz md5: 22d776c6d49eb6e6b2f387af99cc471f -# patches: - # List any patch files here - # - fix.patch build: noarch: python - skip: False number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - + - pip run: - python @@ -26,23 +23,7 @@ test: imports: - screamingbackpack - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called 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: http://pypi.python.org/pypi/ScreamingBackpack/ license: GPLv3 summary: 'ScreamingBackpack' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/screed/0.9/build.sh b/recipes/screed/0.9/build.sh deleted file mode 100644 index 8bf1cb09364a6..0000000000000 --- a/recipes/screed/0.9/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh - -$PYTHON setup.py install diff --git a/recipes/screed/0.9/meta.yaml b/recipes/screed/0.9/meta.yaml index 3969629b94336..73866011f776f 100644 --- a/recipes/screed/0.9/meta.yaml +++ b/recipes/screed/0.9/meta.yaml @@ -9,11 +9,12 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - bz2file ==0.98 + - pip run: - python - bz2file ==0.98 diff --git a/recipes/scrublet/meta.yaml b/recipes/scrublet/meta.yaml index 2574c7036e122..ee1192f2db094 100644 --- a/recipes/scrublet/meta.yaml +++ b/recipes/scrublet/meta.yaml @@ -11,10 +11,11 @@ source: build: number: 0 - noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " requirements: + build: + - {{ compiler('c') }} host: - python-annoy - cython diff --git a/recipes/scvis/build.sh b/recipes/scvis/build.sh deleted file mode 100644 index 5a5aeeb48b45e..0000000000000 --- a/recipes/scvis/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install diff --git a/recipes/scvis/meta.yaml b/recipes/scvis/meta.yaml index 75cd113d1c049..a307688eb8626 100644 --- a/recipes/scvis/meta.yaml +++ b/recipes/scvis/meta.yaml @@ -5,28 +5,26 @@ package: source: url: https://bitbucket.org/jerry00/scvis-dev/get/af73849.tar.gz sha256: ce07c4795ebd1eb5e002727ed1a6052c45b1543063a28dd2444e2c966a86342f - git_rev: master build: noarch: python number: 0 - string: scvis + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: run: - - python - - setuptools - - tensorflow >=1.12 - - pyYAML >=3.11 - - matplotlib >=1.5.1 - - numpy >=1.11.1 - - pandas >=0.19.1 - - nomkl - - pip - - wheel + - python + - tensorflow >=1.12 + - pyYAML >=3.11 + - matplotlib >=1.5.1 + - numpy >=1.11.1 + - pandas >=0.19.1 + - nomkl + - pip + - wheel host: - - python - - pip + - python + - pip about: home: https://bitbucket.org/jerry00/scvis-dev/commits/all diff --git a/recipes/scvis_galaxy/build.sh b/recipes/scvis_galaxy/build.sh deleted file mode 100644 index 5a5aeeb48b45e..0000000000000 --- a/recipes/scvis_galaxy/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install diff --git a/recipes/scvis_galaxy/meta.yaml b/recipes/scvis_galaxy/meta.yaml index 0a06a2a948ce4..a5a541d05505c 100644 --- a/recipes/scvis_galaxy/meta.yaml +++ b/recipes/scvis_galaxy/meta.yaml @@ -5,17 +5,15 @@ package: source: url: https://github.com/astrovsky01/scvis/archive/0.1.0.tar.gz sha256: d0e7bda5a027b5e54d595cf2711b303221daea873e57d63ae2c5bc866bb235ef - git_rev: master build: noarch: python number: 0 - string: scvis_galaxy + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: run: - python - - setuptools - tensorflow >=1.13 - pyYAML >=3.11 - matplotlib >=1.5.1 diff --git a/recipes/searchgui/3.2.11/build.sh b/recipes/searchgui/3.2.11/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.11/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.11/meta.yaml b/recipes/searchgui/3.2.11/meta.yaml deleted file mode 100644 index 9739c6354e684..0000000000000 --- a/recipes/searchgui/3.2.11/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.11" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz - md5: 79daafa1be7c43ad515d38dab5b182c4 - -requirements: - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.11/searchgui.py b/recipes/searchgui/3.2.11/searchgui.py deleted file mode 100755 index e32b10d52d631..0000000000000 --- a/recipes/searchgui/3.2.11/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.11.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.13/build.sh b/recipes/searchgui/3.2.13/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.13/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.13/meta.yaml b/recipes/searchgui/3.2.13/meta.yaml deleted file mode 100644 index 99264373609c3..0000000000000 --- a/recipes/searchgui/3.2.13/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.13" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz - md5: d7f9e271e2b86bba1f9d641cadf380ce - -requirements: - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.13/searchgui.py b/recipes/searchgui/3.2.13/searchgui.py deleted file mode 100755 index 81ea306ba8206..0000000000000 --- a/recipes/searchgui/3.2.13/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.13.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and (pass_args[0].startswith('eu') or pass_args[0].startswith('com')): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.20/build.sh b/recipes/searchgui/3.2.20/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.20/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.20/meta.yaml b/recipes/searchgui/3.2.20/meta.yaml deleted file mode 100644 index 0eccb99cf4b57..0000000000000 --- a/recipes/searchgui/3.2.20/meta.yaml +++ /dev/null @@ -1,46 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.20" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} - -build: - noarch: python - number: 1 - -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz - sha256: 0e8ebf087036fd4680d45207e6be388282b6b5948f6992146608cc891ffbef94 - -requirements: - build: - - {{ compiler('cxx') }} - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python - -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g - -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.20/searchgui.py b/recipes/searchgui/3.2.20/searchgui.py deleted file mode 100755 index f2fc208aa6622..0000000000000 --- a/recipes/searchgui/3.2.20/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.20.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and (pass_args[0].startswith('eu') or pass_args[0].startswith('com')): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.3/build.sh b/recipes/searchgui/3.2.3/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.3/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.3/meta.yaml b/recipes/searchgui/3.2.3/meta.yaml deleted file mode 100644 index 72f5d67ef5e6c..0000000000000 --- a/recipes/searchgui/3.2.3/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.3" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz -requirements: - host: - run: - - java-jdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.3/searchgui.py b/recipes/searchgui/3.2.3/searchgui.py deleted file mode 100755 index ce214995aa505..0000000000000 --- a/recipes/searchgui/3.2.3/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.3.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.5/build.sh b/recipes/searchgui/3.2.5/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.5/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.5/meta.yaml b/recipes/searchgui/3.2.5/meta.yaml deleted file mode 100644 index 1360933839108..0000000000000 --- a/recipes/searchgui/3.2.5/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.5" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz -requirements: - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.5/searchgui.py b/recipes/searchgui/3.2.5/searchgui.py deleted file mode 100755 index 8306b56240778..0000000000000 --- a/recipes/searchgui/3.2.5/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.5.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.6/build.sh b/recipes/searchgui/3.2.6/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.6/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.6/meta.yaml b/recipes/searchgui/3.2.6/meta.yaml deleted file mode 100644 index c1670ae8ba37e..0000000000000 --- a/recipes/searchgui/3.2.6/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.6" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz -requirements: - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.6/searchgui.py b/recipes/searchgui/3.2.6/searchgui.py deleted file mode 100755 index f55c2a0bd3894..0000000000000 --- a/recipes/searchgui/3.2.6/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.6.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.7/build.sh b/recipes/searchgui/3.2.7/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.7/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.7/meta.yaml b/recipes/searchgui/3.2.7/meta.yaml deleted file mode 100644 index 9c28e0b818b71..0000000000000 --- a/recipes/searchgui/3.2.7/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.7" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz -requirements: - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.7/searchgui.py b/recipes/searchgui/3.2.7/searchgui.py deleted file mode 100755 index f2ba142c22925..0000000000000 --- a/recipes/searchgui/3.2.7/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.7.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/3.2.8/build.sh b/recipes/searchgui/3.2.8/build.sh deleted file mode 100644 index b5fda5612c227..0000000000000 --- a/recipes/searchgui/3.2.8/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -R * $outdir/ -cp $RECIPE_DIR/searchgui.py $outdir/searchgui -ls -l $outdir -ln -s $outdir/searchgui $PREFIX/bin -chmod 0755 "${PREFIX}/bin/searchgui" diff --git a/recipes/searchgui/3.2.8/meta.yaml b/recipes/searchgui/3.2.8/meta.yaml deleted file mode 100644 index 1a23978b61bd2..0000000000000 --- a/recipes/searchgui/3.2.8/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "SearchGUI" %} -{% set version = "3.2.8" %} -# Do not forget to update the version string in the searchgui.py file - -about: - home: https://github.com/compomics/searchgui - license: Apache License, Version 2.0 - summary: | - SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. -package: - name: searchgui - version: {{ version }} -build: - number: 1 - skip: True # [osx] -source: - url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz - md5: 3c1c82325e19d30dbe8bb7233e9d8c0e - -requirements: - host: - run: - - openjdk >=6 - - mono >=4.0.0 - - python -test: - commands: - - searchgui eu.isas.searchgui.cmd.FastaCLI - - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g -extra: - notes: | - SearchGUI is Java program that comes with a custom wrapper shell script. - This shell wrapper is called "opsin" and is on $PATH by default. By default - "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can - specify these values directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. - For example run it with "searchgui -Xms512m -Xmx1g" - identifiers: - - biotools:searchgui - - doi:10.1002/pmic.201000595 diff --git a/recipes/searchgui/3.2.8/searchgui.py b/recipes/searchgui/3.2.8/searchgui.py deleted file mode 100755 index 9f366fe9303ba..0000000000000 --- a/recipes/searchgui/3.2.8/searchgui.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for Java Conda packages that ensures that the java runtime -# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). - -# -# Program Parameters -# -import os -import subprocess -import sys -import shutil -from os import access -from os import getenv -from os import X_OK -jar_file = 'SearchGUI-3.2.8.jar' - -default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - java = java_executable() - """ - SearchGui updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 00304ef2749ec..523ebf277d8b1 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -9,15 +9,11 @@ package: build: number: 0 -# url: http://genesis.ugent.be/maven2/eu/isas/searchgui/{{ name }}/{{ version }}/{{ name }}-{{ version }}-mac_and_linux.tar.gz -# sha256: 76c0dc1470c6ff549d14f0b3f4ec19f82e02bbdd80c695873ca09074b0c5f88b - source: url: https://github.com/CarlosHorro/PeptideShaker2-tests/raw/master/SearchGUI-4.0.1-SNAPSHOT-mac_and_linux.tar.gz sha256: 8faf059aa097e9d98bb965b78da06abf901079692d05a9b2b9fca80162fd139b requirements: - host: build: - {{ compiler('c') }} run: @@ -30,7 +26,6 @@ test: - searchgui eu.isas.searchgui.cmd.FastaCLI - searchgui eu.isas.searchgui.cmd.FastaCLI -Xms512m -Xmx1g - about: home: https://github.com/compomics/searchgui license: Apache License 2.0 diff --git a/recipes/secapr/meta.yaml b/recipes/secapr/meta.yaml index 3e82a9833b6c7..8c7a8da9e9da3 100644 --- a/recipes/secapr/meta.yaml +++ b/recipes/secapr/meta.yaml @@ -9,7 +9,7 @@ source: sha256: "d7897719f1b4256ab7d46961340ef584dfe254714096dd9a21099df952634f21" build: - skip: True # [not py27] + noarch: python number: 1 script: python -m pip install --no-deps --ignore-installed . entry_points: @@ -17,14 +17,10 @@ build: requirements: host: - - python + - python <3 - pip - - setuptools - - biopython - - pandas - run: - - python + - python <3 - biopython - emboss - bcftools ==1.8 diff --git a/recipes/seedme/1.2.0/build.sh b/recipes/seedme/1.2.0/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/seedme/1.2.0/build.sh +++ /dev/null @@ -1,9 +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/seedme/1.2.0/meta.yaml b/recipes/seedme/1.2.0/meta.yaml index 42e601006c2d4..3a161e83a8393 100644 --- a/recipes/seedme/1.2.0/meta.yaml +++ b/recipes/seedme/1.2.0/meta.yaml @@ -9,17 +9,16 @@ source: - license.patch build: + noarch: python number: 1 - skip: True # [py3k or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - requests ==2.7.0 - + - python <3 + - pip run: - - python + - python <3 - requests ==2.7.0 - curl diff --git a/recipes/seedme/build.sh b/recipes/seedme/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/seedme/build.sh +++ /dev/null @@ -1,9 +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/seedme/meta.yaml b/recipes/seedme/meta.yaml index 79e34e9c2a7fc..523619ef0faf1 100644 --- a/recipes/seedme/meta.yaml +++ b/recipes/seedme/meta.yaml @@ -9,17 +9,16 @@ source: - license.patch build: + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv number: 1 - skip: True # [py3k] requirements: host: - - python - - setuptools - - requests ==2.7.0 - + - python <3 + - pip run: - - python + - python <3 - requests ==2.7.0 - curl diff --git a/recipes/segemehl/0.2.0/meta.yaml b/recipes/segemehl/0.2.0/meta.yaml index 335c906221a8a..6d81d32816197 100644 --- a/recipes/segemehl/0.2.0/meta.yaml +++ b/recipes/segemehl/0.2.0/meta.yaml @@ -2,9 +2,6 @@ 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] @@ -36,5 +33,4 @@ extra: 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/0.3.1/meta.yaml b/recipes/segemehl/0.3.1/meta.yaml index b3dc824fdede0..498b6bd26bbca 100644 --- a/recipes/segemehl/0.3.1/meta.yaml +++ b/recipes/segemehl/0.3.1/meta.yaml @@ -5,9 +5,6 @@ package: name: segemehl version: {{ version }} -about: - home: http://www.bioinf.uni-leipzig.de/Software/segemehl/ - summary: Short read mapping with gaps build: number: 0 skip: True # [osx] diff --git a/recipes/segemehl/meta.yaml b/recipes/segemehl/meta.yaml index ce3adc255e5d5..841078bf6c490 100644 --- a/recipes/segemehl/meta.yaml +++ b/recipes/segemehl/meta.yaml @@ -5,9 +5,6 @@ package: name: segemehl version: {{ version }} -about: - home: http://www.bioinf.uni-leipzig.de/Software/segemehl/ - summary: Short read mapping with gaps build: number: 0 skip: True # [osx] diff --git a/recipes/segmentation-fold/build.sh b/recipes/segmentation-fold/build.sh deleted file mode 100644 index 88f37a50208a8..0000000000000 --- a/recipes/segmentation-fold/build.sh +++ /dev/null @@ -1,29 +0,0 @@ -#!/bin/sh - -#cmake -DCMAKE_BUILD_TYPE=debug -DCMAKE_INSTALL_PREFIX=$PREFIX . -#make clean - -if [ "$(uname)" == "Darwin" ]; then - # c++11 compatibility - - export CXXFLAGS=' -stdlib=libc++' - export CXX_FLAGS=' -stdlib=libc++' - export CMAKE_CXX_FLAGS=' -stdlib=libc++' - export LDFLAGS=' -stdlib=libc++' - export LD_FLAGS=' -stdlib=libc++' - export CMAKE_LDFLAGS=' -stdlib=libc++' -fi - -cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON . - - -make VERBOSE=1 -make install - -cd scripts/energy-estimation-utility - -# 'setup_requires' and 'install_requires' break setuptools stuff -sed -i.bak -E "s/setup_requires.+\],//" setup.py -sed -i.bak -E "s/install_requires.+\],//" setup.py - -$PYTHON setup.py install diff --git a/recipes/segmentation-fold/meta.yaml b/recipes/segmentation-fold/meta.yaml index ddfe62cb22b5f..ff6f42d77b588 100644 --- a/recipes/segmentation-fold/meta.yaml +++ b/recipes/segmentation-fold/meta.yaml @@ -2,14 +2,10 @@ package: name: segmentation-fold version: 1.7.0 -about: - home: https://github.com/yhoogstrate/segmentation-fold - license: GNU General Public License v3 or later (GPLv3+) - summary: RNA-Folding with predefined segments including K-turns and loop-E-motifs - build: number: 1 skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: "https://github.com/yhoogstrate/segmentation-fold/archive/d1b24fec1da405ba70e07ef27046b385b13e8d1f.tar.gz" @@ -26,9 +22,7 @@ requirements: - pysam >=0.8.1,<=0.8.3 - htseq >=0.6.1 - click >=4.0 - run: - - libcxx # [osx] - boost ==1.63.0 - python - pysam >=0.8.1,<=0.8.3 @@ -40,3 +34,8 @@ test: # click requires a unicode locale - LANG=C.UTF-8 segmentation-fold --version - LANG=C.UTF-8 segmentation-fold-utils --help + +about: + home: https://github.com/yhoogstrate/segmentation-fold + license: GNU General Public License v3 or later (GPLv3+) + summary: RNA-Folding with predefined segments including K-turns and loop-E-motifs diff --git a/recipes/selectsequencesfrommsa/meta.yaml b/recipes/selectsequencesfrommsa/meta.yaml index e4355de66c52c..052c69f16e01f 100644 --- a/recipes/selectsequencesfrommsa/meta.yaml +++ b/recipes/selectsequencesfrommsa/meta.yaml @@ -33,3 +33,7 @@ about: home: https://github.com/eggzilla/SelectSequencesFromMSA license: GPL-3 summary: Tool to select representative sequences from a multiple sequence alignment + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/selscan/meta.yaml b/recipes/selscan/meta.yaml index 32c9d8424b092..2e658d13a21be 100644 --- a/recipes/selscan/meta.yaml +++ b/recipes/selscan/meta.yaml @@ -37,3 +37,5 @@ extra: identifiers: - biotools:selscan - doi:10.1093/molbev/msu211 + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/semidbm/build.sh b/recipes/semidbm/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/semidbm/build.sh +++ /dev/null @@ -1,9 +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/semidbm/meta.yaml b/recipes/semidbm/meta.yaml index 86f9ef96c9fad..8d2528d15e2a7 100644 --- a/recipes/semidbm/meta.yaml +++ b/recipes/semidbm/meta.yaml @@ -9,12 +9,12 @@ source: build: noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/sepp/build.sh b/recipes/sepp/build.sh index 5274febdca95c..f97c5cf1e0909 100644 --- a/recipes/sepp/build.sh +++ b/recipes/sepp/build.sh @@ -8,7 +8,7 @@ mkdir -p $PREFIX/share/sepp/sepp # ... and holds correct path names mv -v sepp-package/sepp/default.main.config $PREFIX/share/sepp/sepp/main.config -python setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv # copy bundled binaries, but hmmer which should be provided by conda, into $PREFIX/bin/ mkdir -p $PREFIX/bin/ diff --git a/recipes/seq-seq-pan/1.0.0/meta.yaml b/recipes/seq-seq-pan/1.0.0/meta.yaml index 146762fc191ba..5e4944b506392 100644 --- a/recipes/seq-seq-pan/1.0.0/meta.yaml +++ b/recipes/seq-seq-pan/1.0.0/meta.yaml @@ -9,12 +9,12 @@ source: md5: 7a0c00d8de984f7129c7bcbe4fa26892 build: + noarch: generic number: 3 - skip: True # [osx or py27] requirements: run: - - python + - python >=3 - biopython ==1.69 - blat ==35 - snakemake ==4.3 diff --git a/recipes/seq2hla/meta.yaml b/recipes/seq2hla/meta.yaml index 9ef53849b2447..362afdfeba483 100644 --- a/recipes/seq2hla/meta.yaml +++ b/recipes/seq2hla/meta.yaml @@ -2,18 +2,16 @@ package: name: seq2hla version: '2.2' build: + noarch: generic number: 1 - skip: True # [not py27 ] source: url: https://bitbucket.org/sebastian_boegel/seq2hla/get/95e554b1d191.zip sha256: 2dbafd409ecb2a1d0dac9a6d6c33cd0044503263b00a8e2cd662f82437112555 patches: - seq2HLA.patch requirements: - host: - - python run: - - python + - python <3 - biopython >=1.58 - bowtie ==1.1.2 - r-base diff --git a/recipes/seqan/2.1.1/meta.yaml b/recipes/seqan/2.1.1/meta.yaml index fa0c260e5e633..e76b19a5754da 100644 --- a/recipes/seqan/2.1.1/meta.yaml +++ b/recipes/seqan/2.1.1/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 test: diff --git a/recipes/seqan/meta.yaml b/recipes/seqan/meta.yaml index 2cefdf985a901..3237a15dda3c2 100644 --- a/recipes/seqan/meta.yaml +++ b/recipes/seqan/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 test: diff --git a/recipes/seqmagick/meta.yaml b/recipes/seqmagick/meta.yaml index 7007eecd8457d..64aa1bb95d93d 100644 --- a/recipes/seqmagick/meta.yaml +++ b/recipes/seqmagick/meta.yaml @@ -7,21 +7,18 @@ source: sha256: e5bd29a5bf69cc352ca77b4d383c0ee03af5bc0285c89acd6810446cd1f56e89 build: + noarch: python entry_points: - seqmagick = seqmagick.scripts.cli:main - skip: True # [py27] number: 2 script: python -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python >3 - pip - - setuptools - - biopython >=1.70 - - nose run: - - python + - python >3 - biopython >=1.70 test: diff --git a/recipes/seqprep/1.1/meta.yaml b/recipes/seqprep/1.1/meta.yaml index 58cbf892f33a1..8147c800653a4 100644 --- a/recipes/seqprep/1.1/meta.yaml +++ b/recipes/seqprep/1.1/meta.yaml @@ -1,6 +1,5 @@ build: number: 2 - skip: True # [osx] package: name: seqprep @@ -9,12 +8,13 @@ package: source: url: https://github.com/jstjohn/SeqPrep/archive/v1.1.tar.gz md5: 42bd8e62e8bf99befb37ed29ce047115 - patches: - cflags.patch requirements: build: + - {{ compiler('c') }} + host: - zlib run: - zlib diff --git a/recipes/sequana/meta.yaml b/recipes/sequana/meta.yaml index 2df825c925a5a..25c94d1b51dde 100644 --- a/recipes/sequana/meta.yaml +++ b/recipes/sequana/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha }} build: - skip: True # [py27] + noarch: python preserve_egg_dir: True number: 1 entry_points: @@ -32,10 +32,10 @@ build: requirements: host: - - python + - python >=3 - setuptools run: - - python + - python >=3 - atropos ==1.1.16 - bcftools - bedtools diff --git a/recipes/sequenceTools/build.sh b/recipes/sequencetools/build.sh similarity index 100% rename from recipes/sequenceTools/build.sh rename to recipes/sequencetools/build.sh diff --git a/recipes/sequenceTools/meta.yaml b/recipes/sequencetools/meta.yaml similarity index 100% rename from recipes/sequenceTools/meta.yaml rename to recipes/sequencetools/meta.yaml diff --git a/recipes/setuptools_cython/build.sh b/recipes/setuptools_cython/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/setuptools_cython/build.sh +++ /dev/null @@ -1,9 +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/setuptools_cython/meta.yaml b/recipes/setuptools_cython/meta.yaml index c26a10af94167..80f567572d581 100644 --- a/recipes/setuptools_cython/meta.yaml +++ b/recipes/setuptools_cython/meta.yaml @@ -5,46 +5,28 @@ package: source: url: https://pypi.python.org/packages/source/s/setuptools_cython/setuptools_cython-0.2.1.tar.gz md5: c29fc5bf2894e69cbd98e3800cef4707 -# patches: - # List any patch files here - # - fix.patch build: preserve_egg_dir: True number: 1 requirements: + build: + - {{ compiler('c') }} host: - python - - setuptools + - pip - cython - run: - python - setuptools - - cython - -# test: - # Python imports - # imports: - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called 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: http://pypi.python.org/pypi/setuptools_cython/ license: http://www.gnu.org/licenses/gpl-2.0.html summary: 'Cython setuptools integration' -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + skip-lints: + - missing_tests + - uses_setuptools diff --git a/recipes/shape-it/1.0.1/build.sh b/recipes/shape_it/1.0.1/build.sh similarity index 100% rename from recipes/shape-it/1.0.1/build.sh rename to recipes/shape_it/1.0.1/build.sh diff --git a/recipes/shape-it/1.0.1/meta.yaml b/recipes/shape_it/1.0.1/meta.yaml similarity index 100% rename from recipes/shape-it/1.0.1/meta.yaml rename to recipes/shape_it/1.0.1/meta.yaml diff --git a/recipes/shapeit/meta.yaml b/recipes/shapeit/meta.yaml index ad4b411870ec9..d237d7e4aeace 100644 --- a/recipes/shapeit/meta.yaml +++ b/recipes/shapeit/meta.yaml @@ -3,12 +3,12 @@ package: version: '2.r837' source: - url: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.static.tgz # [linux] - md5: d778d2e6963a5fdbf4edb1f2dafa9f63 # [linux] + url: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.static.tgz + md5: d778d2e6963a5fdbf4edb1f2dafa9f63 build: number: 1 - skip: True # [osx] + skip: True # [osx] requirements: build: diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml index 478c0880c0074..eb2cafbd6d174 100644 --- a/recipes/shortstack/meta.yaml +++ b/recipes/shortstack/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/sicer/meta.yaml b/recipes/sicer/meta.yaml index 067bd299d0f74..6c696afb41bcb 100644 --- a/recipes/sicer/meta.yaml +++ b/recipes/sicer/meta.yaml @@ -13,17 +13,13 @@ source: - genome_additions_v1.patch build: - skip: True # [not py27] + noarch: generic number: 3 requirements: - host: - - python - - numpy - - scipy run: - numpy - - python + - python <3 - scipy test: commands: diff --git a/recipes/sickle/meta.yaml b/recipes/sickle/meta.yaml index fe0dcc5998699..2c405e2a85226 100644 --- a/recipes/sickle/meta.yaml +++ b/recipes/sickle/meta.yaml @@ -1,11 +1,6 @@ {% set version = "0.6.4" %} {% set sha256 = "b0aaa41d97a0c355aa6099b4dfa46c03f0bf828e6171960a15d68bd0548215ec" %} -build: - number: 0 - skip: true # [osx] - script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt - package: name: sickle version: '{{version}}' @@ -14,14 +9,15 @@ source: url: https://pypi.python.org/packages/source/S/Sickle/Sickle-{{version}}.tar.gz sha256: '{{sha256}}' +build: + noarch: python + number: 0 + script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt requirements: host: - python - - setuptools - - requests >=1.1.0 - - lxml >=3.2.3 - + - pip run: - python - requests >=1.1.0 @@ -31,12 +27,10 @@ test: # Python imports imports: - sickle - requires: - mock >=1.0.1 - nose >=1.0 - about: home: http://github.com/mloesch/sickle license: BSD License diff --git a/recipes/sierrapy/meta.yaml b/recipes/sierrapy/meta.yaml index 917581e149825..5c058f94f1f0b 100644 --- a/recipes/sierrapy/meta.yaml +++ b/recipes/sierrapy/meta.yaml @@ -10,7 +10,6 @@ source: md5: 5a5861fd7795997c5cbe43f9fac5ed64 build: - noarch: python noarch: python script: python -m pip install --no-deps --ignore-installed . entry_points: diff --git a/recipes/simlord/meta.yaml b/recipes/simlord/meta.yaml index 883e310416792..06ba14167afe1 100644 --- a/recipes/simlord/meta.yaml +++ b/recipes/simlord/meta.yaml @@ -7,12 +7,13 @@ source: sha256: 40abec8e31c88f69b485a262abae200b27ebe4e937fe58a3d7508dfa22739dac build: - noarch: python number: 2 entry_points: - simlord = simlord.simlord:main requirements: + build: + - {{ compiler('c') }} host: - python >=3 - setuptools diff --git a/recipes/simwalk/build.sh b/recipes/simwalk2/build.sh similarity index 100% rename from recipes/simwalk/build.sh rename to recipes/simwalk2/build.sh diff --git a/recipes/simwalk/meta.yaml b/recipes/simwalk2/meta.yaml similarity index 67% rename from recipes/simwalk/meta.yaml rename to recipes/simwalk2/meta.yaml index 6b5f680a4e53c..e6fd0c8280dc7 100644 --- a/recipes/simwalk/meta.yaml +++ b/recipes/simwalk2/meta.yaml @@ -3,8 +3,8 @@ package: version: "2.91" source: - url: https://github.com/BioTools-Tek/packages/blob/master/simwalk2/SimWalk2-2.91-lin.tar.gz?raw=true # [linux] - md5: 2a529d50ca48cd7ea2b67f85c290f203 # [linux] + url: https://github.com/BioTools-Tek/packages/blob/master/simwalk2/SimWalk2-2.91-lin.tar.gz?raw=true + md5: 2a529d50ca48cd7ea2b67f85c290f203 build: number: 1 @@ -15,9 +15,7 @@ requirements: - {{ compiler('c') }} - {{ compiler('fortran') }} host: - - libgfortran run: - - libgfortran test: commands: @@ -27,8 +25,3 @@ about: home: http://www.genetics.ucla.edu/software/ license: INDIVIDUAL summary: Stochastic Statistical Analysis of Qualitative Traits - -extra: - skip-lints: - # The wrong libgfortran version is present otherwise - - should_use_compilers diff --git a/recipes/singlecell-barcodes/meta.yaml b/recipes/singlecell-barcodes/meta.yaml index fd6265468f731..265bbbad20574 100644 --- a/recipes/singlecell-barcodes/meta.yaml +++ b/recipes/singlecell-barcodes/meta.yaml @@ -3,6 +3,7 @@ package: version: '0.2' build: + noarch: generic number: 1 source: @@ -19,3 +20,7 @@ about: home: https://github.com/roryk/singlecell-barcodes license: MIT summary: whitelisted singlecell barcodes and information regarding where molecular/sample/cellular barcodes are in each read, for various singlecell protocols + +extra: + skip-lints: + - missing_tests diff --git a/recipes/sis/meta.yaml b/recipes/sis/meta.yaml index 473e5ed94c063..5a67f2b35cd1f 100644 --- a/recipes/sis/meta.yaml +++ b/recipes/sis/meta.yaml @@ -11,28 +11,21 @@ source: sha256: {{ sha256 }} build: + noarch: python number: 2 - skip: yes [py2k] requirements: host: - - mummer - - perl - - python + - python >=3 + - pip run: - mummer - perl - - python + - python >=3 test: - # copying files does not work properly on travis - # source_files: - # - examples/nucmer.coords - # commands: - # - sis.py examples/nucmer.coords imports: - scaffoldsis - about: home: http://marte.ic.unicamp.br:8747/ license: GPLv2+ diff --git a/recipes/sistr_cmd/build.sh b/recipes/sistr_cmd/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/sistr_cmd/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/sistr_cmd/meta.yaml b/recipes/sistr_cmd/meta.yaml index 26b1c1c62610b..c5e59adbb476d 100644 --- a/recipes/sistr_cmd/meta.yaml +++ b/recipes/sistr_cmd/meta.yaml @@ -13,17 +13,14 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: + noarch: python number: 3 - skip: True # [not linux] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - numpy >=1.11.1 - - pandas >=0.18.1 - - pytables >=3.3.0 - - python-dateutil + - pip run: - python - numpy >=1.11.1 diff --git a/recipes/sixgill/build.sh b/recipes/sixgill/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/sixgill/build.sh +++ /dev/null @@ -1,9 +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/sixgill/meta.yaml b/recipes/sixgill/meta.yaml index 0c52b8be9205f..b22dc11c633c8 100644 --- a/recipes/sixgill/meta.yaml +++ b/recipes/sixgill/meta.yaml @@ -9,14 +9,12 @@ source: build: noarch: python number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - biopython - - pysam >=0.9.0 - + - pip run: - python - biopython @@ -33,3 +31,7 @@ about: license: Apache Software License summary: 'six-frame genome-inferred libraries for LC-MS/MS' license_family: Apache + +extra: + skip-lints: + - missing_home diff --git a/recipes/skewer/0.1.126/meta.yaml b/recipes/skewer/0.1.126/meta.yaml index 60e132096f323..2bd853626085e 100644 --- a/recipes/skewer/0.1.126/meta.yaml +++ b/recipes/skewer/0.1.126/meta.yaml @@ -1,13 +1,12 @@ - package: name: skewer version: '0.1.126' + source: url: 'https://github.com/relipmoc/skewer/archive/0.1.126.zip' build: number: 1 - skip: False requirements: build: @@ -23,8 +22,8 @@ about: license: MIT summary: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. - - extra: identifiers: - biotools:skewer + skip-lints: + - missing_hash diff --git a/recipes/slamdunk/meta.yaml b/recipes/slamdunk/meta.yaml index 0db642192e5e4..068d1ef33290a 100644 --- a/recipes/slamdunk/meta.yaml +++ b/recipes/slamdunk/meta.yaml @@ -19,6 +19,7 @@ build: requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} - cmake - wget @@ -51,7 +52,6 @@ requirements: - pandas >=0.13.1 - biopython >=1.63 - pysam >=0.8.3 - - cython >=0.20.1 - zlib - openjdk - r-base diff --git a/recipes/slicedimage/build.sh b/recipes/slicedimage/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/slicedimage/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/slicedimage/meta.yaml b/recipes/slicedimage/meta.yaml deleted file mode 100644 index 8dff41a694615..0000000000000 --- a/recipes/slicedimage/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set SLICEDIMAGE_VERSION = "3.1.2" %} - -package: - name: slicedimage - version: {{ SLICEDIMAGE_VERSION }} - -source: - url: https://github.com/spacetx/slicedimage/archive/{{ SLICEDIMAGE_VERSION }}.zip - sha256: cd3be65cb50500b74a8d9b957eaa7766a360b2a24016d6e1aaaa2ecae35b8bc4 - -build: - noarch: python - number: 0 - -requirements: - build: - - python >=3.6 - - setuptools - run: - - python >=3.6 - - numpy !=1.13.0 - - diskcache - - packaging - - requests - - scikit-image - - six - -test: - imports: - - slicedimage - -about: - home: https://github.com/spacetx/slicedimage - license: MIT - summary: Python module to access sliced imaging data diff --git a/recipes/slimm/meta.yaml b/recipes/slimm/meta.yaml index daeda4058a818..67e75c3d305e9 100644 --- a/recipes/slimm/meta.yaml +++ b/recipes/slimm/meta.yaml @@ -1,28 +1,17 @@ -build: - number: 0 - -about: - home: https://github.com/seqan/slimm/blob/master/README.md - license: https://github.com/seqan/slimm/blob/master/LICENSE - summary: SLIMM - Species Level Identification of Microbes from Metagenomes - package: name: slimm version: 0.3.4 -source: - url: https://github.com/seqan/slimm/releases/download/v0.3.4/slimm-0.3.4-Linux-x86_64_sse4.tar.bz2 # [linux] - sha256: 8b4fccda3768d4e646924244369642fde735c38fd9bdd348cc2f6ff250e2f61d # [linux] - url: https://github.com/seqan/slimm/releases/download/v0.3.4/slimm-0.3.4-Mac-x86_64_sse4.zip # [osx] - sha256: f6c0a3b30642815ed546c9e4ea42e24e5bcc1857d4bf9f1228385b774c47c38b # [osx] +build: + number: 0 +source: + - url: https://github.com/seqan/slimm/releases/download/v0.3.4/slimm-0.3.4-Linux-x86_64_sse4.tar.bz2 # [linux] + sha256: 8b4fccda3768d4e646924244369642fde735c38fd9bdd348cc2f6ff250e2f61d # [linux] + - url: https://github.com/seqan/slimm/releases/download/v0.3.4/slimm-0.3.4-Mac-x86_64_sse4.zip # [osx] + sha256: f6c0a3b30642815ed546c9e4ea42e24e5bcc1857d4bf9f1228385b774c47c38b # [osx] requirements: - build: - - host: - - bzip2 - - zlib run: - bzip2 - zlib @@ -32,9 +21,17 @@ test: - slimm --help 2>&1 > /dev/null - slimm_build --help 2>&1 > /dev/null +about: + home: https://github.com/seqan/slimm/blob/master/README.md + license: https://github.com/seqan/slimm/blob/master/LICENSE + summary: SLIMM - Species Level Identification of Microbes from Metagenomes + extra: identifiers: - biotools:slimm - doi:10.7717/peerj.3138 recipe-maintainers: - temehi + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/slivar/meta.yaml b/recipes/slivar/meta.yaml index 96aa0d3cbaf98..6efe1dc8ca062 100644 --- a/recipes/slivar/meta.yaml +++ b/recipes/slivar/meta.yaml @@ -15,7 +15,7 @@ build: skip: True # [osx] requirements: - host: + run: - htslib - zlib @@ -27,3 +27,7 @@ about: home: https://github.com/brentp/slivar license: MIT summary: 'filter/annotate variants in VCF/BCF format with simple expressions' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/slncky/meta.yaml b/recipes/slncky/meta.yaml index a746db9d5a413..e4af1e10ff1cf 100644 --- a/recipes/slncky/meta.yaml +++ b/recipes/slncky/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' source: - url: https://github.com/slncky/slncky/archive/v{{version}}.tar.gz # [unix] + url: https://github.com/slncky/slncky/archive/v{{version}}.tar.gz sha256: '{{sha256}}' build: diff --git a/recipes/smallgenomeutilities/0.1/build.sh b/recipes/smallgenomeutilities/0.1/build.sh deleted file mode 100644 index 48ff3850d7a39..0000000000000 --- a/recipes/smallgenomeutilities/0.1/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -"${PYTHON}" setup.py install diff --git a/recipes/smallgenomeutilities/0.1/meta.yaml b/recipes/smallgenomeutilities/0.1/meta.yaml index 4e07299a200c3..b8b1696de529b 100644 --- a/recipes/smallgenomeutilities/0.1/meta.yaml +++ b/recipes/smallgenomeutilities/0.1/meta.yaml @@ -7,19 +7,16 @@ source: md5: 339439b1f97ecb1fc91378f78a06bebe build: - skip: True # [py2k] + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - biopython - - numpy - - progress - - pysam + - python >=3 + - pip run: - - python + - python >=3 - biopython - numpy - progress diff --git a/recipes/smallgenomeutilities/0.2.1/meta.yaml b/recipes/smallgenomeutilities/0.2.1/meta.yaml index aff6dbf9a4eaf..57daa69a49d6f 100644 --- a/recipes/smallgenomeutilities/0.2.1/meta.yaml +++ b/recipes/smallgenomeutilities/0.2.1/meta.yaml @@ -13,24 +13,15 @@ source: sha256: {{ sha256 }} build: + noarch: python number: 1 - # not 'noarch python', because of skip version, and because of command line utils - skip: True # [py2k] requirements: host: - - python - - setuptools - - biopython - - numpy - - progress - - pysam - - scikit-learn - - scipy - - matplotlib - + - python >=3 + - pip run: - - python + - python >=3 - biopython - numpy - progress diff --git a/recipes/smashbenchmarking/build.sh b/recipes/smashbenchmarking/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/smashbenchmarking/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/smashbenchmarking/meta.yaml b/recipes/smashbenchmarking/meta.yaml index 1632089a5d761..6dd3e8a382a7d 100644 --- a/recipes/smashbenchmarking/meta.yaml +++ b/recipes/smashbenchmarking/meta.yaml @@ -8,18 +8,15 @@ source: build: number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python requirements: host: - - python - - setuptools - - pyvcf - - pyfasta - - numpy - + - python <3 + - pip run: - - python + - python <3 - pyvcf - pyfasta - numpy diff --git a/recipes/smcounter2/meta.yaml b/recipes/smcounter2/meta.yaml index a7de008e92e93..13389082339e3 100644 --- a/recipes/smcounter2/meta.yaml +++ b/recipes/smcounter2/meta.yaml @@ -5,9 +5,10 @@ package: name: smcounter2 version: {{ version }} + build: + noarch: generic number: 1 - skip: True # [not py27] source: url: https://github.com/qiaseq/qiaseq-smcounter-v2/archive/{{ revision }}.tar.gz @@ -17,13 +18,10 @@ source: - get_pvalue-input.patch requirements: - host: - - python - - r-base build: - wget run: - - python + - python <3 - r-base - r-plyr - scipy diff --git a/recipes/smeg/meta.yaml b/recipes/smeg/meta.yaml index dda754ce2a54a..7a712bb4d13e6 100644 --- a/recipes/smeg/meta.yaml +++ b/recipes/smeg/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1.4" build: - skip: True # [osx] + noarch: generic number: 0 source: diff --git a/recipes/smhasher/build.sh b/recipes/smhasher/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/smhasher/build.sh +++ /dev/null @@ -1,9 +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/smhasher/meta.yaml b/recipes/smhasher/meta.yaml index 85e8bee050abb..9b678eb8f162c 100644 --- a/recipes/smhasher/meta.yaml +++ b/recipes/smhasher/meta.yaml @@ -4,6 +4,7 @@ package: build: number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/5f/b2/421c060300f1449646787273ecd7df558f6f8e4caee3d6fbe8b193cd60d4/smhasher-0.150.1.tar.gz @@ -14,6 +15,7 @@ requirements: - {{ compiler('cxx') }} host: - python + - pip run: - python diff --git a/recipes/snakeparse/meta.yaml b/recipes/snakeparse/meta.yaml index cb1a8f0d383cb..4521518043d33 100644 --- a/recipes/snakeparse/meta.yaml +++ b/recipes/snakeparse/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - skip: True # [not py36] + noarch: python number: 1 script: python -m pip install --no-deps --ignore-installed . entry_points: @@ -17,11 +17,10 @@ source: requirements: host: - - python + - python >=3.6 - pip - - setuptools run: - - python + - python >=3.6 - pyhocon >=0.3.38 - pyyaml >=3.12 diff --git a/recipes/snmf/meta.yaml b/recipes/snmf/meta.yaml index 7a0391ec8c86d..2d16091dea5ba 100644 --- a/recipes/snmf/meta.yaml +++ b/recipes/snmf/meta.yaml @@ -6,15 +6,21 @@ package: build: number: 1 - skip: false source: url: http://membres-timc.imag.fr/Olivier.Francois/snmf/files/sNMF_CL_v{{ version }}.zip md5: 280df791c1c50ac15244cc86f6abf69e - requirements: build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - perl + - perl-bioperl + - perl-lib + run: + - perl - perl-bioperl - perl-lib diff --git a/recipes/snns/meta.yaml b/recipes/snns/meta.yaml index 5cdfdad821073..434827614b4e9 100644 --- a/recipes/snns/meta.yaml +++ b/recipes/snns/meta.yaml @@ -3,7 +3,7 @@ package: version: 4.3 build: - skip: True # [not linux64] + skip: True # [not linux] number: 1 source: @@ -13,11 +13,6 @@ source: sha256: 54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62 requirements: - #build: - # - xorg-makedepend - # - xorg-libxaw3d - # - bison - # - flex run: - xorg-libxaw3d - bison @@ -44,3 +39,7 @@ test: - mkpat 2>&1 | grep usage - snns2c 2>&1 | grep usage - td_bignet 2>&1 | grep usage + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/snostrip/meta.yaml b/recipes/snostrip/meta.yaml index f2aac3cec309e..8c861f5266f69 100644 --- a/recipes/snostrip/meta.yaml +++ b/recipes/snostrip/meta.yaml @@ -49,3 +49,5 @@ about: extra: recipe-maintainers: - jfallmann + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/snpiphy/meta.yaml b/recipes/snpiphy/meta.yaml index c071c6502fadf..bfed51f3e0e4a 100644 --- a/recipes/snpiphy/meta.yaml +++ b/recipes/snpiphy/meta.yaml @@ -10,21 +10,20 @@ source: build: number: 0 - skip: True # [not (linux and py3k)] + noarch: python requirements: - build: - - python - + host: + - python <3 + - pip run: - - python + - python <3 - biopython - numpy - pandas - snippy - gubbins - test: commands: - snpiphy -h diff --git a/recipes/snpsift/4.2/meta.yaml b/recipes/snpsift/4.2/meta.yaml index 871d12908efd5..0cd351d6a4243 100644 --- a/recipes/snpsift/4.2/meta.yaml +++ b/recipes/snpsift/4.2/meta.yaml @@ -3,18 +3,13 @@ {% set version = "4.2" %} {% set md5= "25ae5b062d57072de6cfb8677ca3625a" %} -about: - home: 'http://snpeff.sourceforge.net/SnpSift.html' - license: "LGPLv3" - summary: "Toolbox that allows you to filter and manipulate annotated files" - package: name: snpsift version: {{ version }} build: + noarch: generic number: 3 - skip: False source: url: https://downloads.sourceforge.net/project/snpeff/snpEff_{{ snpeff_ver }}_core.zip @@ -31,6 +26,11 @@ test: - echo | SnpSift filter "(CHROM == '2')" >/dev/null 2>&1 - touch a.vcf && echo | SnpSift annotate a.vcf +about: + home: 'http://snpeff.sourceforge.net/SnpSift.html' + license: "LGPLv3" + summary: "Toolbox that allows you to filter and manipulate annotated files" + extra: notes: 'Note that the package version is slightly different from upstream, this is to make sure conda will order the package versions correctly.' identifiers: diff --git a/recipes/snpsplit/0.3.3/meta.yaml b/recipes/snpsplit/0.3.3/meta.yaml index 08200bf1360e5..ebf0b79a03e3d 100644 --- a/recipes/snpsplit/0.3.3/meta.yaml +++ b/recipes/snpsplit/0.3.3/meta.yaml @@ -9,8 +9,8 @@ source: sha256: 7912581e0aa08155f140edf55ef0a19a9dd3b4d568fe13c2d1e38192b3cc6981 build: + noarch: generic number: 1 - skip: False requirements: run: diff --git a/recipes/snpsplit/meta.yaml b/recipes/snpsplit/meta.yaml index c2935f70561b6..fd3e4723c6280 100644 --- a/recipes/snpsplit/meta.yaml +++ b/recipes/snpsplit/meta.yaml @@ -9,8 +9,8 @@ source: sha256: d5141da711fc52eb9ebdd47ac256ae29edcd41702924f914c526d7393fc0444d build: + noarch: generic number: 1 - skip: False requirements: run: diff --git a/recipes/soapdenovo2-prepare/meta.yaml b/recipes/soapdenovo2-prepare/meta.yaml index 5dff3cfe5d5c8..026738d8ba1d2 100644 --- a/recipes/soapdenovo2-prepare/meta.yaml +++ b/recipes/soapdenovo2-prepare/meta.yaml @@ -29,3 +29,7 @@ about: license_family: GPL license_file: '{{ RECIPE_DIR }}/LICENSE' summary: SoapDenovo2 data prepare module using assembled contig to do scaffold assembly. + +extra: + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/soapsplice/meta.yaml b/recipes/soapsplice/meta.yaml index c9020946e2cec..67add977227cc 100644 --- a/recipes/soapsplice/meta.yaml +++ b/recipes/soapsplice/meta.yaml @@ -30,3 +30,5 @@ extra: identifiers: - biotools:SOAPsplice - doi:10.3389/fgene.2011.00046 + skip-lints: + - should_be_noarch_generic diff --git a/recipes/socksipy-branch/build.sh b/recipes/socksipy-branch/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/socksipy-branch/build.sh +++ /dev/null @@ -1,9 +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/socksipy-branch/meta.yaml b/recipes/socksipy-branch/meta.yaml index 7b0c008215307..261b463717124 100644 --- a/recipes/socksipy-branch/meta.yaml +++ b/recipes/socksipy-branch/meta.yaml @@ -9,11 +9,12 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - + - pip run: - python test: diff --git a/recipes/sompy/LICENSE b/recipes/sompy/LICENSE deleted file mode 100644 index 3662046ce8f75..0000000000000 --- a/recipes/sompy/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -The MIT License (MIT) - -Copyright (c) 2016 Yota Ishikawa - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/recipes/sompy/meta.yaml b/recipes/sompy/meta.yaml deleted file mode 100644 index 1f84a6d7fa152..0000000000000 --- a/recipes/sompy/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "sompy" %} -{% set version = "0.1.1" %} - -package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 846626a39e27cca171a81f4388cb30a32cdcd3bedf170c91227cf5a958aaabec - -build: - number: 1 - noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " - -requirements: - host: - - numpy - - pip - - python <3 - run: - - numpy - - python <3 - - matplotlib - -test: - imports: - - sompy - -about: - home: https://github.com/ttlg/sompy - license: MIT - license_family: MIT - license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE' - summary: "Numpy based SOM Library." diff --git a/recipes/sonicparanoid/meta.yaml b/recipes/sonicparanoid/meta.yaml index efb6699aff312..37ee348bf5683 100644 --- a/recipes/sonicparanoid/meta.yaml +++ b/recipes/sonicparanoid/meta.yaml @@ -2,9 +2,6 @@ {% set version = "1.0.14" %} {% set commit = "71606dae6146" %} -build: - number: 0 - package: name: "{{ name|lower }}" version: "{{ version }}" @@ -13,22 +10,24 @@ source: url: https://bitbucket.org/salvocos/sonicparanoid/get/{{ commit }}.zip sha256: 7ec5737d5cbebbf58e4f970dae5de1075da7a549a66f9b2cf22192acb95b9353 +build: + number: 0 + skip: True # [py2k] + requirements: build: + - {{ compiler("c") }} - {{ compiler("cxx") }} host: - make - - python >=3.5 + - python - numpy - cython - mmseqs2 ==6.f5a1c run: - mmseqs2 ==6.f5a1c - make - - python >=3.5 - - pip >=9.0.1 - - cython >=0.27.0 - - setuptools >=24.2.0 + - python - biopython >=1.67 - pandas >=0.22.0 - numpy >=1.13.0 diff --git a/recipes/sonlib/meta.yaml b/recipes/sonlib/meta.yaml index ca8746034c54a..520d847ddea0d 100644 --- a/recipes/sonlib/meta.yaml +++ b/recipes/sonlib/meta.yaml @@ -7,16 +7,15 @@ source: md5: b6051a1c664ad51f8620d80a3652aa05 build: + noarch: python number: 1 - skip: True # [not py27] requirements: host: - - python - - setuptools - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/sourcetracker/meta.yaml b/recipes/sourcetracker/meta.yaml index a1f337517d303..796a0407d9d78 100644 --- a/recipes/sourcetracker/meta.yaml +++ b/recipes/sourcetracker/meta.yaml @@ -22,17 +22,9 @@ build: requirements: host: - python - - setuptools - - numpy - - h5py - - biom-format >=2.1.5,<2.2.0 - - click - - ipyparallel - - scikit-bio - - pandas + - pip run: - python - - setuptools - numpy - h5py - biom-format >=2.1.5,<2.2.0 @@ -60,8 +52,6 @@ about: extra: recipe-maintainers: - nick-youngblut - -extra: container: # matplotlib depends on libGL.so.1 from the system - extended-base: true \ No newline at end of file + extended-base: true diff --git a/recipes/spades/3.10.1/meta.yaml b/recipes/spades/3.10.1/meta.yaml index 087c43622dd81..80c69c367462b 100644 --- a/recipes/spades/3.10.1/meta.yaml +++ b/recipes/spades/3.10.1/meta.yaml @@ -3,19 +3,17 @@ package: version: '3.10.1' source: - url: http://spades.bioinf.spbau.ru/release3.10.1/SPAdes-3.10.1-Linux.tar.gz # [linux] - md5: fb58d48a0545211aab91f43b7d17ad1b # [linux] - url: http://spades.bioinf.spbau.ru/release3.10.1/SPAdes-3.10.1-Darwin.tar.gz # [osx] - md5: f23bbad7921cff2c283e6589ccee83a2 # [osx] + - url: http://spades.bioinf.spbau.ru/release3.10.1/SPAdes-3.10.1-Linux.tar.gz # [linux] + md5: fb58d48a0545211aab91f43b7d17ad1b # [linux] + - url: http://spades.bioinf.spbau.ru/release3.10.1/SPAdes-3.10.1-Darwin.tar.gz # [osx] + md5: f23bbad7921cff2c283e6589ccee83a2 # [osx] build: number: 1 - skip: True # [not py2k and not py35] requirements: - host: run: - - python + - python <3 test: commands: @@ -30,3 +28,6 @@ extra: identifiers: - biotools:Spades - doi:10.1089/cmb.2012.0021 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/spades/3.11.1/meta.yaml b/recipes/spades/3.11.1/meta.yaml index 5050bf5a66278..713dfcf125d4e 100644 --- a/recipes/spades/3.11.1/meta.yaml +++ b/recipes/spades/3.11.1/meta.yaml @@ -5,10 +5,10 @@ package: version: {{ version }} source: - url: http://cab.spbu.ru/files/release{{ version }}/SPAdes-{{ version }}-Darwin.tar.gz # [osx] - sha256: c7e1bb6065e836c466007a235ffad907fb5f2b634fd2fe86535ed233408aa317 # [osx] - url: http://cab.spbu.ru/files/release{{ version }}/SPAdes-{{ version }}.tar.gz # [linux] - sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474 # [linux] + - url: http://cab.spbu.ru/files/release{{ version }}/SPAdes-{{ version }}-Darwin.tar.gz # [osx] + sha256: c7e1bb6065e836c466007a235ffad907fb5f2b634fd2fe86535ed233408aa317 # [osx] + - url: http://cab.spbu.ru/files/release{{ version }}/SPAdes-{{ version }}.tar.gz # [linux] + sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474 # [linux] build: number: 3 @@ -39,8 +39,9 @@ about: home: http://cab.spbu.ru/software/spades/ license: GPLv2 license_family: GPL - license_file: LICENSE # [linux] - license_file: share/spades/LICENSE # [osx] + license_file: + - LICENSE # [linux] + - share/spades/LICENSE # [osx] 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 @@ -53,3 +54,5 @@ extra: identifiers: - biotools:Spades - doi:10.1089/cmb.2012.0021 + skip-lints: + - should_not_be_noarch_source diff --git a/recipes/spades/3.12.0/meta.yaml b/recipes/spades/3.12.0/meta.yaml index 8392711adb22b..476591a889804 100644 --- a/recipes/spades/3.12.0/meta.yaml +++ b/recipes/spades/3.12.0/meta.yaml @@ -5,12 +5,10 @@ package: 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] + - 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 @@ -47,3 +45,6 @@ extra: - biotools:Spades - doi:10.1089/cmb.2012.0021 - doi:10.1101/gr.213959.116 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/spades/3.5.0/meta.yaml b/recipes/spades/3.5.0/meta.yaml index ebcbc5358711f..19cdc56cbb471 100755 --- a/recipes/spades/3.5.0/meta.yaml +++ b/recipes/spades/3.5.0/meta.yaml @@ -3,17 +3,16 @@ package: version: '3.5.0' source: - fn: SPAdes-3.5.0-Linux.tar.gz url: http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0-Linux.tar.gz md5: 1a4ef6e9c9da8894353fb76ed1a31c9d build: number: 1 - skip: True # [py3k or osx] + skip: True # [osx] requirements: run: - - python + - python <3 test: commands: @@ -28,3 +27,5 @@ extra: identifiers: - biotools:Spades - doi:10.1089/cmb.2012.0021 + skip-lints: + - should_be_noarch_generic diff --git a/recipes/spades/3.9.0/meta.yaml b/recipes/spades/3.9.0/meta.yaml index 261ee25a8786c..6448fb293e8f4 100644 --- a/recipes/spades/3.9.0/meta.yaml +++ b/recipes/spades/3.9.0/meta.yaml @@ -3,18 +3,17 @@ package: version: '3.9.0' source: - url: http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Linux.tar.gz # [linux] - md5: 7d4729764a6e21d9289ff438830b4ae5 # [linux] - url: http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Darwin.tar.gz # [osx] - md5: 9e4d280fefe67589c028170fcb6749b3 # [osx] + - url: http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Linux.tar.gz # [linux] + md5: 7d4729764a6e21d9289ff438830b4ae5 # [linux] + - url: http://spades.bioinf.spbau.ru/release3.9.0/SPAdes-3.9.0-Darwin.tar.gz # [osx] + md5: 9e4d280fefe67589c028170fcb6749b3 # [osx] build: number: 3 - skip: True # [py36] requirements: run: - - python + - python <3 test: commands: @@ -29,3 +28,6 @@ extra: identifiers: - biotools:Spades - doi:10.1089/cmb.2012.0021 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/spades/3.9.1/meta.yaml b/recipes/spades/3.9.1/meta.yaml index 8475fddae055c..ae44523d88acb 100644 --- a/recipes/spades/3.9.1/meta.yaml +++ b/recipes/spades/3.9.1/meta.yaml @@ -3,10 +3,10 @@ package: version: '3.9.1' source: - url: http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Linux.tar.gz # [linux] - sha256: 92b9d70666989e9ed5f27dbbc03ce90826d7297bd6894e3ab534cc6ca8976d9a # [linux] - url: http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Darwin.tar.gz # [osx] - sha256: 7471a9dc9c815a57f67df8d3890396b3b8c198c83fe6f2f6fd148386327a60a6 # [osx] + - url: http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Linux.tar.gz # [linux] + sha256: 92b9d70666989e9ed5f27dbbc03ce90826d7297bd6894e3ab534cc6ca8976d9a # [linux] + - url: http://cab.spbu.ru/files/release3.9.1/SPAdes-3.9.1-Darwin.tar.gz # [osx] + sha256: 7471a9dc9c815a57f67df8d3890396b3b8c198c83fe6f2f6fd148386327a60a6 # [osx] build: number: 0 @@ -14,6 +14,7 @@ build: requirements: run: - python 3.5.* + test: commands: - spades.py --test && rm -rf spades_test @@ -33,3 +34,6 @@ extra: - biotools:Spades - doi:10.1089/cmb.2012.0021 - doi:10.1101/gr.213959.116 + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/spanki/build.sh b/recipes/spanki/build.sh deleted file mode 100644 index d0f35d4aea6ee..0000000000000 --- a/recipes/spanki/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/spanki/meta.yaml b/recipes/spanki/meta.yaml index 135b40165f069..9aa7d95bed5b8 100644 --- a/recipes/spanki/meta.yaml +++ b/recipes/spanki/meta.yaml @@ -8,20 +8,15 @@ source: build: number: 1 - skip: True # [not py27] + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - pyfasta - - numpy - - biopython - - statsmodels - - fisher - - pysam - + - python <3 + - pip run: - - python + - python <3 - pyfasta - numpy - biopython diff --git a/recipes/sparse-neighbors-search/meta.yaml b/recipes/sparse-neighbors-search/meta.yaml index 044ecb039dc43..adb025aa53c1c 100644 --- a/recipes/sparse-neighbors-search/meta.yaml +++ b/recipes/sparse-neighbors-search/meta.yaml @@ -20,13 +20,11 @@ requirements: - numpy - scikit-learn - cython - run: - python - scipy - numpy - scikit-learn - - cython test: imports: diff --git a/recipes/spectacle/meta.yaml b/recipes/spectacle/meta.yaml index 6de41c646810f..d98fea2f2ace3 100644 --- a/recipes/spectacle/meta.yaml +++ b/recipes/spectacle/meta.yaml @@ -8,13 +8,11 @@ package: source: url: https://github.com/jiminsong/Spectacle/archive/v{{version}}.tar.gz sha256: '{{sha256}}' -# patches: -# - shebang.patch build: + noarch: generic detect_binary_files_with_prefix: true number: 1 - skip: true # [osx] requirements: host: diff --git a/recipes/spectrassembler/build.sh b/recipes/spectrassembler/build.sh deleted file mode 100644 index 4dad93a1c02ab..0000000000000 --- a/recipes/spectrassembler/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install diff --git a/recipes/spectrassembler/meta.yaml b/recipes/spectrassembler/meta.yaml index 953940edbb3fa..63db891dd7910 100644 --- a/recipes/spectrassembler/meta.yaml +++ b/recipes/spectrassembler/meta.yaml @@ -6,8 +6,9 @@ package: version: {{ version }} build: + noarch: python number: 3 - skip: True # [osx or not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/antrec/spectrassembler/archive/3ef76977896c65af4059d164853295ffecacc687.tar.gz @@ -15,14 +16,10 @@ source: requirements: host: - - python - - setuptools - - numpy - - scipy - - biopython - + - python <3 + - pip run: - - python + - python <3 - numpy - scipy - biopython diff --git a/recipes/SpliceMap/build.sh b/recipes/splicemap/build.sh similarity index 100% rename from recipes/SpliceMap/build.sh rename to recipes/splicemap/build.sh diff --git a/recipes/splicemap/meta.yaml b/recipes/splicemap/meta.yaml new file mode 100644 index 0000000000000..e13f56805804a --- /dev/null +++ b/recipes/splicemap/meta.yaml @@ -0,0 +1,31 @@ +package: + name: splicemap + version: 3.3.5.2 + +build: + number: 1 + +source: + url: https://web.stanford.edu/group/wonglab/SpliceMap/SpliceMap3352_linux-64.zip + sha256: 090a7e0ae99c45b98bfe50e5113415fd9d94c3c5431ecccac65e9ebc45216dcd + +requirements: + build: + - {{ compiler('c') }} + run: + - bowtie + +test: + commands: + - runSpliceMap + +about: + home: http://www.stanford.edu/group/wonglab/SpliceMap/ + license: file + license_file: LICENSE + summary: Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. + +extra: + identifiers: + - biotools:splicemap + - doi:10.1093/nar/gkq211 diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml index bc34e4afb841c..944af69b12563 100644 --- a/recipes/spoa/meta.yaml +++ b/recipes/spoa/meta.yaml @@ -31,4 +31,4 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url diff --git a/recipes/spotyping/meta.yaml b/recipes/spotyping/meta.yaml index db0378a18540a..b8270f98c1664 100644 --- a/recipes/spotyping/meta.yaml +++ b/recipes/spotyping/meta.yaml @@ -13,14 +13,12 @@ source: - patch-ref-location build: - skip: True # [not py2k] + noarch: generic number: 2 requirements: - host: - - python run: - - python + - python <3 - blast - r-gdata @@ -34,6 +32,7 @@ about: summary: 'SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads' license_family: GPL license: GPL-3 + extra: recipe-maintainers: - pvanheus diff --git a/recipes/sprinkles/build.sh b/recipes/sprinkles/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/sprinkles/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/sprinkles/meta.yaml b/recipes/sprinkles/meta.yaml index 6c79a10ad5998..6a48c541fbe07 100644 --- a/recipes/sprinkles/meta.yaml +++ b/recipes/sprinkles/meta.yaml @@ -8,33 +8,21 @@ source: build: number: 2 + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - + - pip run: - python -test: - # Python imports - # imports: - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: http://an9.org/w/SprinklesPy license: MIT License summary: 'Plugins! Easy!' +extra: + skip-lints: + - missing_tests diff --git a/recipes/srnapipe/1.1/build.sh b/recipes/srnapipe/build.sh similarity index 100% rename from recipes/srnapipe/1.1/build.sh rename to recipes/srnapipe/build.sh diff --git a/recipes/srnapipe/1.1/meta.yaml b/recipes/srnapipe/meta.yaml similarity index 98% rename from recipes/srnapipe/1.1/meta.yaml rename to recipes/srnapipe/meta.yaml index 52bed3532e68e..56120094a97d7 100644 --- a/recipes/srnapipe/1.1/meta.yaml +++ b/recipes/srnapipe/meta.yaml @@ -11,6 +11,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 requirements: diff --git a/recipes/srst2/0.1.6/build.sh b/recipes/srst2/0.1.6/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/srst2/0.1.6/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/srst2/0.1.6/meta.yaml b/recipes/srst2/0.1.6/meta.yaml deleted file mode 100644 index b568ab108fede..0000000000000 --- a/recipes/srst2/0.1.6/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -package: - name: srst2 - version: 0.1.6 - -source: - url: https://github.com/katholt/srst2/archive/v0.1.6.tar.gz - sha256: 24cbd03933d4cc14bbfa7f8a073c9b0caafb13d55afb3bfa25f8b093fc5bc615 - patches: - - use_setuptools.patch - - srst_sample_name_v0.1.6.patch - -build: - number: 1 - skip: True #[not py27 or osx] - -requirements: - host: - - python - - setuptools - - numpy >=1.7.1 - - scipy >=0.12.0 - - run: - - python - - numpy >=1.7.1 - - scipy >=0.12.0 - - bowtie2 <=2.2.4 - - samtools ==0.1.18 - -test: - commands: - - srst2 -h 2>&1 | grep "SRST2 - Short Read Sequence Typer" > /dev/null - - getmlst.py -h 2>&1 | grep "usage" > /dev/null - -about: - home: https://github.com/katholt/srst2 - license: BSD - summary: 'Short Read Sequence Typing for Bacterial Pathogens' diff --git a/recipes/srst2/0.1.6/srst_sample_name_v0.1.6.patch b/recipes/srst2/0.1.6/srst_sample_name_v0.1.6.patch deleted file mode 100644 index fc9c012b4f71b..0000000000000 --- a/recipes/srst2/0.1.6/srst_sample_name_v0.1.6.patch +++ /dev/null @@ -1,63 +0,0 @@ -diff --git a/scripts/srst2.py b/scripts/srst2.py -index 67e48ae..916792e 100755 ---- a/scripts/srst2.py -+++ b/scripts/srst2.py -@@ -233,7 +233,7 @@ def parse_fai(fai_file,db_type,delimiter): - return size, gene_clusters, unique_gene_symbols, unique_allele_symbols, gene_cluster_symbols - - --def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): -+def read_pileup_data(pileup_file, size, prob_err, sample_name, consensus_file = ""): - with open(pileup_file) as pileup: - prob_success = 1 - prob_err # Set by user, default is prob_err = 0.01 - hash_alignment = {} -@@ -372,7 +372,7 @@ def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): - elif consensus_file.split(".")[-2] == "all_consensus_alleles": - consensus_type = "consensus" - with open(consensus_file, "a") as consensus_outfile: -- consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, pileup_file.split(".")[1].split("__")[1])) -+ consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, sample_name)) - outstring = consensus_seq + "\n" - consensus_outfile.write(outstring) - -@@ -782,7 +782,7 @@ def create_allele_pileup(allele_name, all_pileup_file): - def parse_scores(run_type,args,scores, hash_edge_depth, - avg_depth_allele, coverage_allele, mismatch_allele, indel_allele, - missing_allele, size_allele, next_to_del_depth_allele, -- unique_cluster_symbols,unique_allele_symbols, pileup_file): -+ unique_cluster_symbols,unique_allele_symbols, pileup_file, sample_name): - - # sort into hash for each gene locus - scores_by_gene = collections.defaultdict(dict) # key1 = gene, key2 = allele, value = score -@@ -868,11 +868,11 @@ def parse_scores(run_type,args,scores, hash_edge_depth, - if args.report_new_consensus or args.report_all_consensus: - new_alleles_filename = args.output + ".new_consensus_alleles.fasta" - allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file) -- read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename) -+ read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename) - if args.report_all_consensus: - new_alleles_filename = args.output + ".all_consensus_alleles.fasta" - allele_pileup_file = create_allele_pileup(results[gene][0], pileup_file) -- read_pileup_data(allele_pileup_file, size_allele, args.prob_err, consensus_file = new_alleles_filename) -+ read_pileup_data(allele_pileup_file, size_allele, args.prob_err, sample_name, consensus_file = new_alleles_filename) - - return results # (allele, diffs, depth_problem, divergence) - -@@ -1265,7 +1265,7 @@ def map_fileSet_to_db(args,sample_name,fastq_inputs,db_name,fasta,size,gene_name - logging.info(' Processing SAMtools pileup...') - hash_alignment, hash_max_depth, hash_edge_depth, avg_depth_allele, coverage_allele, \ - mismatch_allele, indel_allele, missing_allele, size_allele, next_to_del_depth_allele= \ -- read_pileup_data(pileup_file, size, args.prob_err) -+ read_pileup_data(pileup_file, size, args.prob_err, sample_name) - - # Generate scores for all alleles (prints these and associated info if verbose) - # result = dict, with key=allele, value=score -@@ -1283,7 +1283,7 @@ def map_fileSet_to_db(args,sample_name,fastq_inputs,db_name,fasta,size,gene_name - allele_scores = parse_scores(run_type, args, scores, \ - hash_edge_depth, avg_depth_allele, coverage_allele, mismatch_allele, \ - indel_allele, missing_allele, size_allele, next_to_del_depth_allele, -- unique_gene_symbols, unique_allele_symbols, pileup_file) -+ unique_gene_symbols, unique_allele_symbols, pileup_file, sample_name) - - # REPORT/RECORD RESULTS - diff --git a/recipes/srst2/0.1.6/use_setuptools.patch b/recipes/srst2/0.1.6/use_setuptools.patch deleted file mode 100644 index 6ea0da0fa0aad..0000000000000 --- a/recipes/srst2/0.1.6/use_setuptools.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/setup.py b/setup.py -index 37f4ca0..dbd1308 100644 ---- a/setup.py -+++ b/setup.py -@@ -1,6 +1,6 @@ - #!/usr/bin/env python - --from distutils.core import setup -+from setuptools import setup - - setup( - name='srst2', diff --git a/recipes/srst2/build.sh b/recipes/srst2/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/srst2/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/srst2/meta.yaml b/recipes/srst2/meta.yaml index 90886aafff16e..d8c9cc6c21171 100644 --- a/recipes/srst2/meta.yaml +++ b/recipes/srst2/meta.yaml @@ -10,18 +10,16 @@ source: - srst_sample_name_v0.2.0.patch build: + noarch: pip number: 3 - skip: True #[not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy >=1.7.1 - - scipy >=0.12.0 - + - python <3 + - pip run: - - python + - python <3 - numpy >=1.7.1 - scipy >=0.12.0 - bowtie2 <=2.2.9 diff --git a/recipes/ssake/meta.yaml b/recipes/ssake/meta.yaml index 668fe098fa2f3..1f6a1992b2f3f 100644 --- a/recipes/ssake/meta.yaml +++ b/recipes/ssake/meta.yaml @@ -13,17 +13,14 @@ source: - pl_py_paths.patch build: + noarch: generic number: 2 - skip: True # [py3k] requirements: - host: - - python - - perl run: - perl-statistics-descriptive - perl - - python + - python <3 test: commands: diff --git a/recipes/stacks_summary/1.0/build.sh b/recipes/stacks_summary/1.0/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/stacks_summary/1.0/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/stacks_summary/1.0/meta.yaml b/recipes/stacks_summary/1.0/meta.yaml deleted file mode 100644 index f9a5f56ca383e..0000000000000 --- a/recipes/stacks_summary/1.0/meta.yaml +++ /dev/null @@ -1,34 +0,0 @@ -package: - name: stacks_summary - version: "1.0" - -source: - url: https://pypi.python.org/packages/fd/4d/b66c0171669e42a92b6961cf769fcd7186b60e126868fb7c216d9d9a07ec/stacks_summary-1.0.tar.gz - md5: 47393995a2ce15fe2d48eedebfde011c - -build: - number: 1 - skip: True # [not py27] - -requirements: - host: - - python - - setuptools - - numpy - - run: - - python - - numpy - -test: - imports: - - stacks - - commands: - - stacks_summary.py --help - -about: - home: https://github.com/mariabernard/galaxy_wrappers - license: GNU General Public License v3 or later (GPLv3+) - summary: 'Stacks reports generator' - license_family: Public-Domain diff --git a/recipes/stacks_summary/build.sh b/recipes/stacks_summary/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/stacks_summary/build.sh +++ /dev/null @@ -1,9 +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/stacks_summary/meta.yaml b/recipes/stacks_summary/meta.yaml index b632ce198facd..788820d6cda86 100644 --- a/recipes/stacks_summary/meta.yaml +++ b/recipes/stacks_summary/meta.yaml @@ -7,17 +7,16 @@ source: md5: 20e72a66a52502954894168f1cf197c3 build: + noarch: python number: 1 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - numpy - + - python <3 + - pip run: - - python + - python <3 - numpy test: diff --git a/recipes/staden-io-lib/build.sh b/recipes/staden_io_lib/build.sh similarity index 100% rename from recipes/staden-io-lib/build.sh rename to recipes/staden_io_lib/build.sh diff --git a/recipes/staden-io-lib/meta.yaml b/recipes/staden_io_lib/meta.yaml similarity index 100% rename from recipes/staden-io-lib/meta.yaml rename to recipes/staden_io_lib/meta.yaml diff --git a/recipes/star-fusion/0.7.0/meta.yaml b/recipes/star-fusion/0.7.0/meta.yaml index 4ef2abe74551c..fe0fbcc0fdd10 100644 --- a/recipes/star-fusion/0.7.0/meta.yaml +++ b/recipes/star-fusion/0.7.0/meta.yaml @@ -10,6 +10,7 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 1 requirements: diff --git a/recipes/star/2.4.0j/meta.yaml b/recipes/star/2.4.0j/meta.yaml index 8d0557512d071..d2ca1154e2d5c 100644 --- a/recipes/star/2.4.0j/meta.yaml +++ b/recipes/star/2.4.0j/meta.yaml @@ -24,3 +24,5 @@ about: extra: identifiers: - biotools:star + skip-lints: + - should_be_noarch_generic diff --git a/recipes/star/2.6.0c/meta.yaml b/recipes/star/2.6.0c/meta.yaml index 28de6fe733e04..d3fc0509ba6b5 100644 --- a/recipes/star/2.6.0c/meta.yaml +++ b/recipes/star/2.6.0c/meta.yaml @@ -24,3 +24,5 @@ about: extra: identifiers: - biotools:star + skip-lints: + - should_be_noarch_generic diff --git a/recipes/star/2.6.1d/meta.yaml b/recipes/star/2.6.1d/meta.yaml index d2e193aac71f1..cc00d2e09c86a 100644 --- a/recipes/star/2.6.1d/meta.yaml +++ b/recipes/star/2.6.1d/meta.yaml @@ -24,3 +24,5 @@ about: extra: identifiers: - biotools:star + skip-lints: + - should_be_noarch_generic diff --git a/recipes/starseqr/meta.yaml b/recipes/starseqr/meta.yaml index 0b55437c7f709..f15a0e6367909 100644 --- a/recipes/starseqr/meta.yaml +++ b/recipes/starseqr/meta.yaml @@ -24,10 +24,8 @@ requirements: - pysam >=0.9.1.4 - primer3-py - intervaltree_bio - run: - python - - cython - six - networkx - gffread diff --git a/recipes/stellar/meta.yaml b/recipes/stellar/meta.yaml index 56d2ea8be6b54..cdaf89b22f34b 100644 --- a/recipes/stellar/meta.yaml +++ b/recipes/stellar/meta.yaml @@ -1,20 +1,28 @@ -build: - number: 1 - package: name: stellar version: "1.4.9" + +build: + noarch: generic + number: 1 + source: - url: http://packages.seqan.de/stellar/stellar-1.4.9-Mac-x86_64.zip # [osx] - md5: fe9dd472d67524748cd882e2872cbb53 # [osx] - url: http://packages.seqan.de/stellar/stellar-1.4.9-Linux-x86_64.tar.xz # [linux64] - md5: 44eb71b174b516bac0bc884467d8bd8f # [linux64] + - url: http://packages.seqan.de/stellar/stellar-1.4.9-Mac-x86_64.zip # [osx] + md5: fe9dd472d67524748cd882e2872cbb53 # [osx] + - url: http://packages.seqan.de/stellar/stellar-1.4.9-Linux-x86_64.tar.xz # [linux] + md5: 44eb71b174b516bac0bc884467d8bd8f # [linux] test: commands: - stellar --help 2>&1 > /dev/null + about: home: https://github.com/seqan/seqan/tree/master/apps/stellar/README license: LGPLv3+ license_file: LICENSE summary: STELLAR is a tool for finding pairwise local alignments between long genomic or very many short sequences. + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/stoatydive/build.sh b/recipes/stoatydive/build.sh deleted file mode 100755 index b9962a29eda83..0000000000000 --- a/recipes/stoatydive/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install \ No newline at end of file diff --git a/recipes/stoatydive/meta.yaml b/recipes/stoatydive/meta.yaml index 5b510ea853f83..d154bd964bc44 100755 --- a/recipes/stoatydive/meta.yaml +++ b/recipes/stoatydive/meta.yaml @@ -3,38 +3,40 @@ {% set sha256 = "cb82fc07cf661d82c69429a64f0281c5f0d5125fe7b59e8b50c15eb87500b42c" %} package: - name: {{ name|lower }} - version: {{ version }} + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/BackofenLab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} + url: https://github.com/BackofenLab/{{ name }}/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 1 - noarch: python + number: 1 + noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: - host: - - python - run: - - python - - bedtools >=2.27.1 - - numpy - - matplotlib - - scipy >=1.3 - - r-base - - r-umap - - r-data.table - - r-zoo + host: + - python + - pip + run: + - python + - bedtools >=2.27.1 + - numpy + - matplotlib + - scipy >=1.3 + - r-base + - r-umap + - r-data.table + - r-zoo test: - commands: - - StoatyDive.py --help - - bedtools --help + commands: + - StoatyDive.py --help + - bedtools --help about: - home: https://github.com/BackofenLab/StoatyDive - license: GPLv3 - license_file: License.txt - summary: StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. + home: https://github.com/BackofenLab/StoatyDive + license: GPLv3 + license_file: License.txt + summary: StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. diff --git a/recipes/stream_atac/meta.yaml b/recipes/stream_atac/meta.yaml index a7cea3a26bd59..10b09537e4da6 100644 --- a/recipes/stream_atac/meta.yaml +++ b/recipes/stream_atac/meta.yaml @@ -12,7 +12,6 @@ build: requirements: build: - - python - {{ compiler('c') }} - {{ compiler('cxx') }} - {{ compiler('fortran') }} @@ -31,7 +30,6 @@ requirements: - rpy2 run: - python - - setuptools - unzip - zip - wget diff --git a/recipes/strelka/meta.yaml b/recipes/strelka/meta.yaml index 0a1392b8fa068..4472c16336f33 100644 --- a/recipes/strelka/meta.yaml +++ b/recipes/strelka/meta.yaml @@ -7,7 +7,6 @@ package: source: url: https://github.com/Illumina/strelka/releases/download/v{{ version }}/strelka-{{ version }}.centos6_x86_64.tar.bz2 - #url: https://github.com/Illumina/strelka/releases/download/untagged-839da48539154c23a780/strelka-{{version}}.centos6_x86_64.tar.bz2 sha256: '{{ sha256 }}' build: @@ -32,3 +31,5 @@ about: extra: identifiers: - biotools:strelka + skip-lints: + - should_be_noarch_generic diff --git a/recipes/stringmlst/meta.yaml b/recipes/stringmlst/meta.yaml index 9a6626f137ac1..994ff185559c7 100644 --- a/recipes/stringmlst/meta.yaml +++ b/recipes/stringmlst/meta.yaml @@ -10,18 +10,15 @@ source: sha256: b408b1b332f540fdd15e136d91e5a831e5c676dccf102ec2d67199b7931d9163 build: + noarch: python number: 0 - skip: True # [py27] requirements: host: - - python - - setuptools - - pyfaidx - - lxml - + - python >=3 + - pip run: - - python + - python >=3 - bwa - bedtools - samtools >=1.0 diff --git a/recipes/strip-it/1.0.2/build.sh b/recipes/strip_it/1.0.2/build.sh similarity index 100% rename from recipes/strip-it/1.0.2/build.sh rename to recipes/strip_it/1.0.2/build.sh diff --git a/recipes/strip-it/1.0.2/meta.yaml b/recipes/strip_it/1.0.2/meta.yaml similarity index 100% rename from recipes/strip-it/1.0.2/meta.yaml rename to recipes/strip_it/1.0.2/meta.yaml index a0b2f99bc5f56..8efa24c2775c4 100644 --- a/recipes/strip-it/1.0.2/meta.yaml +++ b/recipes/strip_it/1.0.2/meta.yaml @@ -1,3 +1,7 @@ +package: + name: strip_it + version: 1.0.2 + source: url: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/_downloads/strip-it-1.0.2.tar.gz md5: 963da0b005774a7a2eba4b4c384dca2a @@ -6,10 +10,6 @@ build: number: 4 skip: True # [osx] -package: - name: strip_it - version: 1.0.2 - requirements: build: - {{ compiler('cxx') }} diff --git a/recipes/structureharvester/meta.yaml b/recipes/structureharvester/meta.yaml index 048269f920d6c..85a33c8d41381 100644 --- a/recipes/structureharvester/meta.yaml +++ b/recipes/structureharvester/meta.yaml @@ -10,14 +10,12 @@ source: url: https://github.com/dentearl/structureHarvester/archive/{{ commit }}.zip build: + noarch: generic number: 1 - skip: True # [not py27] requirements: - host: - - python run: - - python + - python <3 test: commands: diff --git a/recipes/super_distance/meta.yaml b/recipes/super_distance/meta.yaml index 824a7b09ed6ef..d5a0e17a4d85e 100644 --- a/recipes/super_distance/meta.yaml +++ b/recipes/super_distance/meta.yaml @@ -40,4 +40,4 @@ extra: identifiers: - biotools:super_distance skip-lints: - - uses_git_url + - uses_vcs_url diff --git a/recipes/suppa/meta.yaml b/recipes/suppa/meta.yaml index b7ee7ac2cda3f..06388a5c4fe3f 100644 --- a/recipes/suppa/meta.yaml +++ b/recipes/suppa/meta.yaml @@ -8,15 +8,15 @@ source: patches: patches build: + noarch: python number: 1 - skip: True # [not py3k] requirements: host: - - python - - setuptools + - python >=3 + - pip run: - - python + - python >=3 - scipy >=0.15.1 - numpy >=1.11.0 - pandas >=0.18.0 diff --git a/recipes/sv2/build.sh b/recipes/sv2/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/sv2/build.sh +++ /dev/null @@ -1,9 +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/sv2/meta.yaml b/recipes/sv2/meta.yaml index df106f29f77c2..950839b34c9a8 100644 --- a/recipes/sv2/meta.yaml +++ b/recipes/sv2/meta.yaml @@ -5,6 +5,7 @@ package: build: number: 2 skip: true # [py3k or osx] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/dantaki/SV2/releases/download/sv2v1.4.4/sv2-1.4.3.4.tar.gz @@ -37,7 +38,6 @@ requirements: - wget run: - bedtools - - cython - numpy - pandas - pybedtools diff --git a/recipes/svdb/meta.yaml b/recipes/svdb/meta.yaml index bec9fb5138eb6..a0cb4bea1126c 100644 --- a/recipes/svdb/meta.yaml +++ b/recipes/svdb/meta.yaml @@ -19,13 +19,12 @@ requirements: build: - {{ compiler('c') }} host: - - python <3 + - python - pip - numpy - cython run: - - python <3 - - cython + - python - numpy - scipy diff --git a/recipes/svtools/meta.yaml b/recipes/svtools/meta.yaml index 3e078722890cd..1ea3cbb034ce3 100644 --- a/recipes/svtools/meta.yaml +++ b/recipes/svtools/meta.yaml @@ -7,8 +7,7 @@ source: md5: c96c640e428d9728dc9d618937459ecd build: - number: 0 - skip: True # [not py27 ] + noarch: python preserve_egg_dir: True entry_points: - svtools=svtools.cli:main @@ -16,16 +15,15 @@ build: requirements: host: - - python + - python <3 - numpy - scipy - statsmodels - pandas - svtyper ==0.7.0 - setuptools - run: - - python + - python <3 - numpy - scipy - statsmodels diff --git a/recipes/svviz/meta.yaml b/recipes/svviz/meta.yaml index 0556d3a483b1a..2c1deaca9c114 100644 --- a/recipes/svviz/meta.yaml +++ b/recipes/svviz/meta.yaml @@ -7,24 +7,17 @@ source: sha256: 16a419b9be5f25a0d2393ed13eeccadcdbaf8047c244be108f891c897c5349ed build: - skip: True # [not py27 or osx] + noarch: python entry_points: - svviz = svviz.app:main number: 0 requirements: host: - - python - - setuptools - - requests - - numpy - - pyfaidx - - pysam >=0.7.8 - - flask - - joblib - + - python <3 + - pip run: - - python + - python <3 - requests - numpy - pyfaidx diff --git a/recipes/swalign/build.sh b/recipes/swalign/build.sh deleted file mode 100644 index 0d620c5240825..0000000000000 --- a/recipes/swalign/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/swalign/meta.yaml b/recipes/swalign/meta.yaml index 45878d39ff755..1d0f149a2f4fa 100644 --- a/recipes/swalign/meta.yaml +++ b/recipes/swalign/meta.yaml @@ -7,15 +7,16 @@ source: sha256: bc383f9a2c410e5933fd9a217c41c7607e04ad7cda4c3de8ee99ee22103756d3 build: + noarch: python number: 0 - skip: True # [py3k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - + - python <3 + - pip run: - - python + - python <3 test: imports: diff --git a/recipes/tabview/build.sh b/recipes/tabview/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/tabview/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/tabview/meta.yaml b/recipes/tabview/meta.yaml index 97c94ed35e034..96c8ee0b99077 100644 --- a/recipes/tabview/meta.yaml +++ b/recipes/tabview/meta.yaml @@ -9,7 +9,7 @@ source: build: noarch: python number: 0 - skip: False + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/taeper/meta.yaml b/recipes/taeper/meta.yaml index 8046ef35c403a..b1b761fb37bdc 100644 --- a/recipes/taeper/meta.yaml +++ b/recipes/taeper/meta.yaml @@ -11,21 +11,18 @@ source: sha256: '{{ hash_value }}' build: + noarch: python number: 1 - skip: True # [py27] entry_points: - taeper=taeper.cli:main script: python -m pip install --no-deps --ignore-installed . requirements: host: - - python + - python >=3 - pip - - setuptools - - ont-fast5-api - - numpy run: - - python + - python >=3 - ont-fast5-api - numpy diff --git a/recipes/targetfinder/meta.yaml b/recipes/targetfinder/meta.yaml index 54659d0e6eaf8..b97801c83d435 100644 --- a/recipes/targetfinder/meta.yaml +++ b/recipes/targetfinder/meta.yaml @@ -3,8 +3,8 @@ package: version: 1.7 build: + noarch: generic number: 2 - skip: True # [osx] source: url: https://github.com/carringtonlab/TargetFinder/archive/v1.7.tar.gz @@ -13,9 +13,6 @@ source: - targetfinder.patch requirements: - build: - - perl - run: - perl - fasta3 diff --git a/recipes/targqc/meta.yaml b/recipes/targqc/meta.yaml index 4ee808e11f8c7..6d03f56df4e9a 100644 --- a/recipes/targqc/meta.yaml +++ b/recipes/targqc/meta.yaml @@ -11,25 +11,21 @@ build: number: 0 requirements: - build: - {{ compiler('c') }} - {{ compiler('cxx') }} - host: - python >=3.6 - pip - setuptools - numpy - cython - run: - python >=3.6 - qualimap - sambamba >=0.7.0 - bwa - bedtools >=2.25 - - setuptools >=18.5 - pip - {{ pin_compatible('numpy') }} - tempita diff --git a/recipes/tassel/3.0.174/meta.yaml b/recipes/tassel/3.0.174/meta.yaml index 878951b6ebc92..e771ae564354c 100644 --- a/recipes/tassel/3.0.174/meta.yaml +++ b/recipes/tassel/3.0.174/meta.yaml @@ -14,7 +14,7 @@ source: - patches/start_tassel.patch build: - skip: True # [osx] + noarch: generic number: 1 requirements: @@ -34,5 +34,5 @@ about: extra: skip-lints: # SourceForge Git snapshots do not persist - - uses_git_url + - uses_vcs_url - missing_hash diff --git a/recipes/tassel/4.3.15/meta.yaml b/recipes/tassel/4.3.15/meta.yaml index c1a7edcd1bb82..fa739105a1965 100644 --- a/recipes/tassel/4.3.15/meta.yaml +++ b/recipes/tassel/4.3.15/meta.yaml @@ -14,7 +14,7 @@ source: - patches/start_tassel.patch build: - skip: True # [osx] + noarch: generic number: 1 requirements: @@ -34,5 +34,5 @@ about: extra: skip-lints: # SourceForge Git snapshots do not persist - - uses_git_url + - uses_vcs_url - missing_hash diff --git a/recipes/tassel/meta.yaml b/recipes/tassel/meta.yaml index 540b8e7826f52..522ff7e0ad45b 100644 --- a/recipes/tassel/meta.yaml +++ b/recipes/tassel/meta.yaml @@ -14,7 +14,7 @@ source: - patches/start_tassel.patch build: - skip: True # [osx] + noarch: generic number: 1 requirements: diff --git a/recipes/taxator-tk/meta.yaml b/recipes/taxator-tk/meta.yaml index f1e93d33b5b28..50483335a2efb 100644 --- a/recipes/taxator-tk/meta.yaml +++ b/recipes/taxator-tk/meta.yaml @@ -10,8 +10,8 @@ source: md5: 6575138bb60503e9fdb76ff463be9df3 build: + noarch: generic number: 0 - skip: True # [osx] requirements: build: diff --git a/recipes/taxmapper/meta.yaml b/recipes/taxmapper/meta.yaml index 86adb5318421f..3515b61aa6d87 100644 --- a/recipes/taxmapper/meta.yaml +++ b/recipes/taxmapper/meta.yaml @@ -7,21 +7,17 @@ source: md5: debeb04b01fb17f0db47ee46fd94e760 build: + noarch: python number: 2 - skip: True # [py27 or osx] entry_points: - taxmapper=taxmapper:main requirements: host: - - python - - setuptools - - numpy - - pandas - - matplotlib - - deepdish + - python >=3 + - pip run: - - python + - python >=3 - numpy - pandas - matplotlib diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml index 5c60ce64b2287..dbee08b129d7a 100644 --- a/recipes/taxonkit/meta.yaml +++ b/recipes/taxonkit/meta.yaml @@ -4,22 +4,25 @@ package: name: taxonkit version: {{ version }} -about: - home: https://github.com/shenwei356/taxonkit - summary: A Cross-platform and Efficient NCBI Taxonomy Toolkit - license: MIT - build: number: 0 - skip: False source: - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx] - md5: cb87673d7fb1c28d4eb252a509bd7a89 # [osx] - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux] - md5: 922bae36ced77bd218e0119025f6d6ec # [linux] - + - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx] + md5: cb87673d7fb1c28d4eb252a509bd7a89 # [osx] + - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux] + md5: 922bae36ced77bd218e0119025f6d6ec # [linux] test: commands: - taxonkit version --help + +about: + home: https://github.com/shenwei356/taxonkit + summary: A Cross-platform and Efficient NCBI Taxonomy Toolkit + license: MIT + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/tbl2asn/meta.yaml b/recipes/tbl2asn/meta.yaml index 04d9e0fa61531..ce58a5d275473 100644 --- a/recipes/tbl2asn/meta.yaml +++ b/recipes/tbl2asn/meta.yaml @@ -3,10 +3,10 @@ package: version: "25.7" source: - url: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/mac.tbl2asn.gz # [osx] - sha256: 8dab2f4ff804ad0678de1eebbdd4a3515b0740f5f2116bf91d55cc808f520cbc # [osx] - url: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz # [linux] - sha256: 1f41acb9eacd6e0fa78657b17727b8f94d97490617563686d28b3f6c24d39117 # [linux] + - url: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/mac.tbl2asn.gz # [osx] + sha256: 8dab2f4ff804ad0678de1eebbdd4a3515b0740f5f2116bf91d55cc808f520cbc # [osx] + - url: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux.tbl2asn.gz # [linux] + sha256: 1f41acb9eacd6e0fa78657b17727b8f94d97490617563686d28b3f6c24d39117 # [linux] build: number: 0 @@ -24,3 +24,8 @@ about: home: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2 license: Public Domain summary: 'tbl2asn is a program that automates the creation of sequence records for submission to GenBank' + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/tdrmapper/meta.yaml b/recipes/tdrmapper/meta.yaml index 2f43a2b54a649..50c1a67bd1370 100644 --- a/recipes/tdrmapper/meta.yaml +++ b/recipes/tdrmapper/meta.yaml @@ -7,12 +7,10 @@ source: sha256: 31c8f25050264d2125bdd2706014c102917021c6f3a72f42abec626a8f26ea3e build: + noarch: generic number: 3 - skip: True # [osx] requirements: - build: - - perl run: - perl diff --git a/recipes/telescope/meta.yaml b/recipes/telescope/meta.yaml index b1e2b551d1cc0..51ce031cf65a2 100644 --- a/recipes/telescope/meta.yaml +++ b/recipes/telescope/meta.yaml @@ -34,7 +34,6 @@ requirements: - pysam >=0.15.2 - future >=0.17.1 - pyyaml >=5.1 - - cython - intervaltree >=3.0.2 test: diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml index 9532ae99ec7b8..915713381529b 100644 --- a/recipes/teloclip/meta.yaml +++ b/recipes/teloclip/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27] + noarch: pip number: 0 entry_points: - teloclip=teloclip.run_self:main @@ -22,10 +22,10 @@ build: requirements: host: - - python + - python >=3 - setuptools run: - - python + - python >=3 test: imports: diff --git a/recipes/tepid/build.sh b/recipes/tepid/build.sh deleted file mode 100644 index fad635886c005..0000000000000 --- a/recipes/tepid/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -# install program -$PYTHON setup.py install diff --git a/recipes/tepid/meta.yaml b/recipes/tepid/meta.yaml index 59b24e0d7bf5a..3f09b9ed56f33 100644 --- a/recipes/tepid/meta.yaml +++ b/recipes/tepid/meta.yaml @@ -9,6 +9,7 @@ source: build: number: 1 skip: True # [not py27 or not linux] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv # numpy 1.9.2 was built against libgfortran 1.9.2 requirements: diff --git a/recipes/tetoolkit/build.sh b/recipes/tetoolkit/build.sh deleted file mode 100644 index 0d620c5240825..0000000000000 --- a/recipes/tetoolkit/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/tetoolkit/meta.yaml b/recipes/tetoolkit/meta.yaml index 3162f9b8bc5ff..99f6aac4ccee5 100644 --- a/recipes/tetoolkit/meta.yaml +++ b/recipes/tetoolkit/meta.yaml @@ -7,19 +7,18 @@ source: sha256: 1d0f5928b30c6cd9dbef8e092ae0c11e9e707faf92a19af8eed3e360da7d4e46 build: + noarch: python number: 0 - skip: True # [not py27] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python + - python <3 - setuptools - - argparse - - pysam >=0.9 run: - - python - - argparse + - python <3 - pysam >=0.9 + - r-base - bioconductor-deseq >=1.10 test: diff --git a/recipes/textinput/build.sh b/recipes/textinput/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/textinput/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$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/textinput/meta.yaml b/recipes/textinput/meta.yaml index 49482c3df0979..7bcc9c9c6e33a 100644 --- a/recipes/textinput/meta.yaml +++ b/recipes/textinput/meta.yaml @@ -9,12 +9,12 @@ source: build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - six + - pip - python - run: - six - python diff --git a/recipes/tgt/meta.yaml b/recipes/tgt/meta.yaml index dd02168c2be28..f79b1d55e9de3 100644 --- a/recipes/tgt/meta.yaml +++ b/recipes/tgt/meta.yaml @@ -10,13 +10,14 @@ source: sha256: '{{sha256}}' build: + noarch: pip number: 2 - script: python setup.py install --record=record.txt + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - + - pip run: - python - numpy diff --git a/recipes/theta2/meta.yaml b/recipes/theta2/meta.yaml index 04464298951ca..ef266b7c5edcb 100644 --- a/recipes/theta2/meta.yaml +++ b/recipes/theta2/meta.yaml @@ -3,14 +3,14 @@ package: version: '0.7' build: number: 1 - skip: True # [not py27 or osx] + noarch: python source: url: https://github.com/raphael-group/THetA/archive/v0.7.tar.gz sha256: 474452fa87a1ca0228137693bfede3200b91e4e166b2216c4bd24f8b270c1dea requirements: build: - - python + - python <3 - numpy - scipy - matplotlib @@ -19,7 +19,7 @@ requirements: - wget - unzip run: - - python + - python <3 - numpy - scipy - matplotlib diff --git a/recipes/tidyp/meta.yaml b/recipes/tidyp/meta.yaml index 9a8f41fee87be..8e50cc2432477 100644 --- a/recipes/tidyp/meta.yaml +++ b/recipes/tidyp/meta.yaml @@ -2,9 +2,6 @@ package: name: tidyp version: "1.04" -requirements: - build: - source: url: "http://github.com/downloads/petdance/tidyp/tidyp-1.04.tar.gz" md5: "00a6b804f6625221391d010ca37178e1" @@ -12,7 +9,15 @@ source: build: number: 1 +requirements: + build: + - {{ compiler('c') }} + about: home: "http://www.tidyp.com/" license: BSD-like summary: "Program for cleaning up and validating HTML" + +extra: + skip-lints: + - missing_tests diff --git a/recipes/tinscan/meta.yaml b/recipes/tinscan/meta.yaml index a553e44f5b6fe..5792b14c34592 100644 --- a/recipes/tinscan/meta.yaml +++ b/recipes/tinscan/meta.yaml @@ -7,8 +7,8 @@ source: md5: 3e420a6dd9ac68563324cc8dad0d2612 build: + noarch: python number: 1 - skip: True # [py27] entry_points: - tinscan-prep=tinscan.run_prep:main - tinscan-align=tinscan.run_align:main @@ -16,12 +16,10 @@ build: requirements: host: - - python - - setuptools - - biopython >=1.70 - + - python >=3 + - pip run: - - python + - python >=3 - biopython >=1.70 test: diff --git a/recipes/tinysink/meta.yaml b/recipes/tinysink/meta.yaml index 5e6e5f1f4439f..70be6f7135ced 100644 --- a/recipes/tinysink/meta.yaml +++ b/recipes/tinysink/meta.yaml @@ -9,6 +9,7 @@ source: sha256: c146bc6987b1c12e1ba3b7029b0ae6c6dc6486e0dca9b6f94b8ffa0a88116c6e build: + noarch: generic number: 1 requirements: diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml index dc286f4c1d1dd..ea44d5f7f664c 100644 --- a/recipes/tirmite/meta.yaml +++ b/recipes/tirmite/meta.yaml @@ -13,23 +13,20 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27] + noarch: python 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 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - pandas >=0.20.3 - - biopython >=1.70 - - pymummer >=0.10.3 + - python >=3 + - pip run: - - python + - python >=3 - pandas >=0.20.3 - biopython >=1.70 - pymummer >=0.10.3 diff --git a/recipes/toolshed/build.sh b/recipes/toolshed/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/toolshed/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/toolshed/meta.yaml b/recipes/toolshed/meta.yaml index f2363aa584ffe..eb72223082a3d 100644 --- a/recipes/toolshed/meta.yaml +++ b/recipes/toolshed/meta.yaml @@ -9,16 +9,15 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools + - pip run: - python - - test: requires: - nose diff --git a/recipes/tophat-recondition/meta.yaml b/recipes/tophat-recondition/meta.yaml index 3d59c15a29b9a..c3950deaabf51 100644 --- a/recipes/tophat-recondition/meta.yaml +++ b/recipes/tophat-recondition/meta.yaml @@ -3,6 +3,7 @@ package: version: 1.4 build: + noarch: generic number: 1 source: @@ -10,8 +11,6 @@ source: md5: 4062d5fa0a6f22eb7abed759d278bb34 requirements: - host: - - python run: - python - pysam diff --git a/recipes/tophat2/2.0.13/build.sh b/recipes/tophat/2.0.13/build.sh similarity index 100% rename from recipes/tophat2/2.0.13/build.sh rename to recipes/tophat/2.0.13/build.sh diff --git a/recipes/tophat/2.0.13/meta.yaml b/recipes/tophat/2.0.13/meta.yaml new file mode 100644 index 0000000000000..d24138692c00e --- /dev/null +++ b/recipes/tophat/2.0.13/meta.yaml @@ -0,0 +1,31 @@ +package: + name: tophat + version: 2.0.13 + +source: + - url: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz # [linux] + sha256: a6a73aa3061515ae73da39302c94f61aaf4d7cea0e0f5b3f25ea596718886025 # [linux] + - url: https://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.OSX_x86_64.tar.gz # [osx] + sha256: 2056a446af78c045bd443b5eb13eb6e9222fd3cbce728fa6bb8f0d81451b0143 # [osx] + +build: + number: 4 + +requirements: + run: + - python <3 + - bowtie2 <=2.2.5 + +test: + commands: + - (tophat --version 2>&1) > /dev/null + +about: + home: http://ccb.jhu.edu/software/tophat/index.shtml + license: Boost Software License + summary: A spliced read mapper for RNA-Seq + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/tophat2/build.sh b/recipes/tophat/build.sh similarity index 100% rename from recipes/tophat2/build.sh rename to recipes/tophat/build.sh diff --git a/recipes/tophat/meta.yaml b/recipes/tophat/meta.yaml new file mode 100644 index 0000000000000..95667fe82e42b --- /dev/null +++ b/recipes/tophat/meta.yaml @@ -0,0 +1,31 @@ +package: + name: tophat + version: 2.1.1 + +source: + - url: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz # [linux] + md5: 97fe58465a01cb0a860328fdb1993660 # [linux] + - url: https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.OSX_x86_64.tar.gz # [osx] + md5: 1e4e7f8d08f182d2db3202975f284294 # [osx] + +build: + number: 3 + +requirements: + run: + - python + - bowtie2 <=2.2.5 + +test: + commands: + - (tophat --version 2>&1) > /dev/null + +about: + home: http://ccb.jhu.edu/software/tophat/index.shtml + license: Boost Software License + summary: A spliced read mapper for RNA-Seq + +extra: + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/tophat2/2.0.13/meta.yaml b/recipes/tophat2/2.0.13/meta.yaml deleted file mode 100644 index 61e5971e06166..0000000000000 --- a/recipes/tophat2/2.0.13/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: tophat - version: 2.0.13 - -source: - url: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz # [linux] - sha256: a6a73aa3061515ae73da39302c94f61aaf4d7cea0e0f5b3f25ea596718886025 # [linux] - url: https://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.OSX_x86_64.tar.gz # [osx] - sha256: 2056a446af78c045bd443b5eb13eb6e9222fd3cbce728fa6bb8f0d81451b0143 # [osx] - -build: - skip: True # [py3k] - number: 4 - -requirements: - host: - - python - run: - - python - - bowtie2 <=2.2.5 - -test: - commands: - - (tophat --version 2>&1) > /dev/null - -about: - home: http://ccb.jhu.edu/software/tophat/index.shtml - license: Boost Software License - summary: A spliced read mapper for RNA-Seq diff --git a/recipes/tophat2/meta.yaml b/recipes/tophat2/meta.yaml deleted file mode 100644 index b2b70b23789d3..0000000000000 --- a/recipes/tophat2/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -package: - name: tophat - version: 2.1.1 - -source: - url: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz # [linux] - md5: 97fe58465a01cb0a860328fdb1993660 # [linux] - url: https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.OSX_x86_64.tar.gz # [osx] - md5: 1e4e7f8d08f182d2db3202975f284294 # [osx] - -build: - skip: True # [py3k] - number: 3 - -requirements: - host: - - python - run: - - python - - bowtie2 <=2.2.5 - -test: - commands: - - (tophat --version 2>&1) > /dev/null - -about: - home: http://ccb.jhu.edu/software/tophat/index.shtml - license: Boost Software License - summary: A spliced read mapper for RNA-Seq diff --git a/recipes/transabyss/build.sh b/recipes/transabyss/build.sh index 5be05869c7e21..bbd234f033fef 100644 --- a/recipes/transabyss/build.sh +++ b/recipes/transabyss/build.sh @@ -27,4 +27,4 @@ cp -rf utilities/* transabyss/ cp $RECIPE_DIR/setup.py ./ python setup.py build -python setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/transabyss/meta.yaml b/recipes/transabyss/meta.yaml index 3a9f02d305970..9ac3e44ed273c 100644 --- a/recipes/transabyss/meta.yaml +++ b/recipes/transabyss/meta.yaml @@ -11,19 +11,19 @@ source: - package_info.patch build: - skip: True # [py3k] + noarch: python number: 4 requirements: host: - - python + - python <3 run: - abyss 2.0.* - python-igraph 0.7.* - samtools 1.3.1 - bowtie2 - blat - - python + - python <3 test: commands: diff --git a/recipes/transdecoder/2.1.0/meta.yaml b/recipes/transdecoder/2.1.0/meta.yaml index 28afb5e7c80c1..a163fdf3dde09 100644 --- a/recipes/transdecoder/2.1.0/meta.yaml +++ b/recipes/transdecoder/2.1.0/meta.yaml @@ -6,6 +6,7 @@ package: version: {{ version }} build: + noarch: generic number: 4 source: diff --git a/recipes/transdecoder/3.0.1/meta.yaml b/recipes/transdecoder/3.0.1/meta.yaml index 64d7e0379539a..2158c40c2780a 100644 --- a/recipes/transdecoder/3.0.1/meta.yaml +++ b/recipes/transdecoder/3.0.1/meta.yaml @@ -6,6 +6,7 @@ package: version: {{ version }} build: + noarch: generic number: 2 source: diff --git a/recipes/transdecoder/meta.yaml b/recipes/transdecoder/meta.yaml index b8c49dff95702..ab767f90619b1 100644 --- a/recipes/transdecoder/meta.yaml +++ b/recipes/transdecoder/meta.yaml @@ -10,6 +10,7 @@ source: sha256: '{{sha256}}' build: + noarch: generic number: 1 requirements: diff --git a/recipes/npm-translate-gard/meta.yaml b/recipes/translate-gard/meta.yaml similarity index 93% rename from recipes/npm-translate-gard/meta.yaml rename to recipes/translate-gard/meta.yaml index cb3f4011dcf3d..62426a7a6d8e5 100644 --- a/recipes/npm-translate-gard/meta.yaml +++ b/recipes/translate-gard/meta.yaml @@ -30,3 +30,7 @@ about: home: https://github.com/veg/translate-gard/ license: MIT summary: 'Converts HyPhy 2.3.2 GARD output to JSON' + +extra: + skip-lints: + - should_be_noarch_generic diff --git a/recipes/translatorx/meta.yaml b/recipes/translatorx/meta.yaml index 46ac747c14673..d8bc1df91b7b4 100644 --- a/recipes/translatorx/meta.yaml +++ b/recipes/translatorx/meta.yaml @@ -9,11 +9,10 @@ source: - translatorx.patch build: + noarch: generic number: 1 - skip: False requirements: - run: - perl - muscle @@ -24,7 +23,7 @@ test: about: home: http://pc16141.mncn.csic.es/ - license: + license: unknown summary: Multiple alignment of nucleotide sequences guided by amino acid information extra: diff --git a/recipes/trawler/meta.yaml b/recipes/trawler/meta.yaml index b2dd5d0091611..0e69705648a42 100644 --- a/recipes/trawler/meta.yaml +++ b/recipes/trawler/meta.yaml @@ -7,16 +7,10 @@ source: sha256: 4eebafdb7c2fcb92551f9e6e396222ecd2419bde3a6db1df6f711024b729b328 build: + noarch: generic number: 2 requirements: - build: - - ghostscript - - openjdk - - perl >=5.22 - - perl-cgi - - perl-algorithm-cluster - run: - ghostscript - openjdk diff --git a/recipes/trf/meta.yaml b/recipes/trf/meta.yaml index 2b035d447e911..3d11599330572 100644 --- a/recipes/trf/meta.yaml +++ b/recipes/trf/meta.yaml @@ -6,10 +6,10 @@ package: version: {{ version }} source: - url: https://tandem.bu.edu/trf/downloads/trf409.legacylinux64 # [linux] - url: https://tandem.bu.edu/trf/downloads/trf409.macosx # [osx] - md5: a88e4b47ddef4961c832a93a7cb6a35d # [linux] - md5: 14784824b6c2fae52f4b5c289ef67255 # [osx] + - url: https://tandem.bu.edu/trf/downloads/trf409.legacylinux64 # [linux] + md5: a88e4b47ddef4961c832a93a7cb6a35d # [linux] + - url: https://tandem.bu.edu/trf/downloads/trf409.macosx # [osx] + md5: 14784824b6c2fae52f4b5c289ef67255 # [osx] build: number: 1 @@ -31,3 +31,6 @@ about: extra: identifiers: - biotools:Trf + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/trim-galore/0.4.1/meta.yaml b/recipes/trim-galore/0.4.1/meta.yaml index 3b4243612abae..81dc53107c3fc 100644 --- a/recipes/trim-galore/0.4.1/meta.yaml +++ b/recipes/trim-galore/0.4.1/meta.yaml @@ -6,8 +6,8 @@ package: version: {{ version }} build: + noarch: generic number: 1 - skip: True # [osx] source: url: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v{{ version }}.zip diff --git a/recipes/trumicount/meta.yaml b/recipes/trumicount/meta.yaml index a70fd051c3ba5..98117c29a21cb 100644 --- a/recipes/trumicount/meta.yaml +++ b/recipes/trumicount/meta.yaml @@ -9,6 +9,7 @@ source: sha256: b606a465e364a4c2f16c6c4af97ef26cb051609b38ab083c016bdc7308e417b3 build: + noarch: generic number: 0 script: ./install.R --prefix $PREFIX diff --git a/recipes/truvari/meta.yaml b/recipes/truvari/meta.yaml index 6228894f9c14e..fa4881ccc4578 100644 --- a/recipes/truvari/meta.yaml +++ b/recipes/truvari/meta.yaml @@ -5,9 +5,10 @@ package: name: truvari version: {{ version }} + build: + noarch: generic number: 0 - skip: True # [not py27] source: url: https://github.com/spiralgenetics/truvari/archive/{{ revision }}.tar.gz @@ -16,11 +17,8 @@ source: - no_ref.patch requirements: - host: - - python - build: run: - - python + - python <3 - pyvcf - python-levenshtein - intervaltree diff --git a/recipes/ucsc-bedgraphtobigwig/357/meta.yaml b/recipes/ucsc-bedgraphtobigwig/357/meta.yaml index bc564b806307f..806a5c3b4a205 100644 --- a/recipes/ucsc-bedgraphtobigwig/357/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/357/meta.yaml @@ -51,4 +51,4 @@ extra: - doi:10.1093/bioinformatics/btq351 skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/ucsc-bedtobigbed/357/meta.yaml b/recipes/ucsc-bedtobigbed/357/meta.yaml index 5800582e5774b..c7d418def6b19 100644 --- a/recipes/ucsc-bedtobigbed/357/meta.yaml +++ b/recipes/ucsc-bedtobigbed/357/meta.yaml @@ -50,4 +50,4 @@ about: extra: skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/ucsc-fatotwobit/357/meta.yaml b/recipes/ucsc-fatotwobit/357/meta.yaml index e74f7bd725d14..0c9aefeb37e8b 100644 --- a/recipes/ucsc-fatotwobit/357/meta.yaml +++ b/recipes/ucsc-fatotwobit/357/meta.yaml @@ -49,4 +49,4 @@ about: extra: skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/ucsc-liftover/357/meta.yaml b/recipes/ucsc-liftover/357/meta.yaml index 9b8f7cbdecde9..6fbd7aedf63c1 100644 --- a/recipes/ucsc-liftover/357/meta.yaml +++ b/recipes/ucsc-liftover/357/meta.yaml @@ -48,4 +48,4 @@ about: extra: skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/ucsc-nibfrag/357/meta.yaml b/recipes/ucsc-nibfrag/357/meta.yaml index 37829c2ee265e..27f14e7039372 100644 --- a/recipes/ucsc-nibfrag/357/meta.yaml +++ b/recipes/ucsc-nibfrag/357/meta.yaml @@ -49,4 +49,4 @@ about: extra: skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/ucsc-twobittofa/357/meta.yaml b/recipes/ucsc-twobittofa/357/meta.yaml index c2bd29c727390..42237c4717a4d 100644 --- a/recipes/ucsc-twobittofa/357/meta.yaml +++ b/recipes/ucsc-twobittofa/357/meta.yaml @@ -48,4 +48,4 @@ about: extra: skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/ucsc-wigtobigwig/357/meta.yaml b/recipes/ucsc-wigtobigwig/357/meta.yaml index 8e6fb931c8486..a2fe39c79e867 100644 --- a/recipes/ucsc-wigtobigwig/357/meta.yaml +++ b/recipes/ucsc-wigtobigwig/357/meta.yaml @@ -48,4 +48,4 @@ about: extra: skip-lints: - missing_hash - + - should_not_be_noarch_source diff --git a/recipes/udocker/build.sh b/recipes/udocker/build.sh index d2d8804142ddc..809938c5425d1 100644 --- a/recipes/udocker/build.sh +++ b/recipes/udocker/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON -m pip install . --ignore-installed --no-deps -vv mv $PREFIX/bin/udocker $PREFIX/bin/udocker.py cat <$PREFIX/bin/udocker diff --git a/recipes/udocker/meta.yaml b/recipes/udocker/meta.yaml index 86f86fb6ffc38..101875db4f449 100644 --- a/recipes/udocker/meta.yaml +++ b/recipes/udocker/meta.yaml @@ -10,15 +10,15 @@ source: sha256: 682956e3a5a687fbe24354cd7befe515c191b9044f4304ea6bf255096eba45c9 build: + noarch: python number: 2 - skip: true # [not py27 or not linux] requirements: host: - - python - - pycurl + - python <3 + - pip run: - - python + - python <3 - proot - simplejson - pycurl diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index ad7e18a6ebd60..05c2fa6220915 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -22,7 +22,6 @@ requirements: - "click>=7.0" - pysam - regex - - cython - toolz - scipy test: diff --git a/recipes/umitools/meta.yaml b/recipes/umitools/meta.yaml index d9fe46d989f29..9507eced2088f 100644 --- a/recipes/umitools/meta.yaml +++ b/recipes/umitools/meta.yaml @@ -9,26 +9,22 @@ source: sha256: 43337b9b715495e69f2e46b8e5f997856407560ca9c0cd16a9ee55084ba63b48 build: + noarch: python 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 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " requirements: host: - - editdistance - - networkx - pip - - pysam - - python - + - python >=3 run: - - python + - python >=3 - pysam - editdistance - networkx diff --git a/recipes/unifrac/meta.yaml b/recipes/unifrac/meta.yaml index 41ef584abce02..ea03092f43ce5 100644 --- a/recipes/unifrac/meta.yaml +++ b/recipes/unifrac/meta.yaml @@ -14,15 +14,14 @@ build: requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} - host: - python - pip - h5py 2.9.0 - cython >=0.28.3 - numpy >=1.12.1 - run: - python - {{ pin_compatible('numpy') }} diff --git a/recipes/uniprot/build.sh b/recipes/uniprot/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/uniprot/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/uniprot/meta.yaml b/recipes/uniprot/meta.yaml index e7222b2139288..7a513805e0422 100644 --- a/recipes/uniprot/meta.yaml +++ b/recipes/uniprot/meta.yaml @@ -13,14 +13,12 @@ source: build: noarch: python number: 1 - skip: False + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - requests - + - pip run: - python - requests diff --git a/recipes/unitas/meta.yaml b/recipes/unitas/meta.yaml index 69fd858a17626..322019af24989 100644 --- a/recipes/unitas/meta.yaml +++ b/recipes/unitas/meta.yaml @@ -13,6 +13,7 @@ source: - perl_dos2unix.patch build: + noarch: generic number: 0 requirements: diff --git a/recipes/unitig-caller/meta.yaml b/recipes/unitig-caller/meta.yaml index 1f6c8ee1ce75a..5c3856b2b630d 100644 --- a/recipes/unitig-caller/meta.yaml +++ b/recipes/unitig-caller/meta.yaml @@ -49,5 +49,4 @@ about: extra: skip-lints: - - uses_git_url - uses_vcs_url diff --git a/recipes/unitig-counter/meta.yaml b/recipes/unitig-counter/meta.yaml index 08b29f4f7af3a..acc94396e41a0 100644 --- a/recipes/unitig-counter/meta.yaml +++ b/recipes/unitig-counter/meta.yaml @@ -41,6 +41,6 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url identifiers: - doi:10.1371/journal.pgen.1007758 diff --git a/recipes/ushuffle/build.sh b/recipes/ushuffle/build.sh index 9926073f6047c..4a3c8b8be8ee4 100644 --- a/recipes/ushuffle/build.sh +++ b/recipes/ushuffle/build.sh @@ -1,3 +1,3 @@ -python setup.py install -gcc -O3 -g -o ushuffle main.c ushuffle.c +$PYTHON -m pip install . --ignore-installed --no-deps -vv +$CC -O3 -g -o ushuffle main.c ushuffle.c install ushuffle $PREFIX/bin diff --git a/recipes/valet/meta.yaml b/recipes/valet/meta.yaml index 788c70043af1d..7ec00f79ec675 100644 --- a/recipes/valet/meta.yaml +++ b/recipes/valet/meta.yaml @@ -13,14 +13,12 @@ source: - valet.patch build: + noarch: generic number: 1 - skip: True # [py3k] requirements: - host: - - python run: - - python + - python <3 - bowtie2 - samtools - bedtools diff --git a/recipes/variantbam/meta.yaml b/recipes/variantbam/meta.yaml index 6d531e16c3859..35311ed42c8f2 100644 --- a/recipes/variantbam/meta.yaml +++ b/recipes/variantbam/meta.yaml @@ -38,4 +38,4 @@ about: extra: skip-lints: - - uses_git_url + - uses_vcs_url diff --git a/recipes/vcf-annotator/meta.yaml b/recipes/vcf-annotator/meta.yaml index 961b1c4fbd38a..3318ea3362a73 100644 --- a/recipes/vcf-annotator/meta.yaml +++ b/recipes/vcf-annotator/meta.yaml @@ -11,17 +11,12 @@ source: sha256: {{ sha256 }} build: + noarch: generic number: 0 - skip: True # [py27] requirements: - host: - - python - - pip - - biopython - - pyvcf run: - - python + - python >=3 - biopython - pyvcf diff --git a/recipes/vcf2db/meta.yaml b/recipes/vcf2db/meta.yaml index 8e4021e5af4a8..d3f95cde79bd4 100644 --- a/recipes/vcf2db/meta.yaml +++ b/recipes/vcf2db/meta.yaml @@ -3,8 +3,8 @@ package: version: '2018.10.26' build: + noarch: generic number: 0 - skip: True # [not py27] source: url: https://github.com/quinlan-lab/vcf2db/archive/03a31a6.tar.gz @@ -12,18 +12,9 @@ source: requirements: host: - - python - perl - - nomkl # [unix] - - snappy - - python-snappy - - sqlalchemy - - cyvcf2 - - numpy - - peddy >=0.2.9 - - geneimpacts >0.2.0 run: - - python + - python <3 - nomkl # [unix] - snappy - python-snappy diff --git a/recipes/vcf2maf/meta.yaml b/recipes/vcf2maf/meta.yaml index edec1658653a4..d32150cf89116 100644 --- a/recipes/vcf2maf/meta.yaml +++ b/recipes/vcf2maf/meta.yaml @@ -1,24 +1,19 @@ {% set version = "1.6.17" %} {% set sha256 = "c69c9c8a0b1a141a88d1f6facefc92013d0a740c63e1c1ae66037022dd00cb80" %} -build: - number: 0 - skip: true # [osx] since variant-effect-predictor is not there yet - package: name: vcf2maf version: '{{version}}' +build: + noarch: generic + number: 0 + source: url: https://github.com/mskcc/vcf2maf/archive/v{{ version }}.tar.gz sha256: c69c9c8a0b1a141a88d1f6facefc92013d0a740c63e1c1ae66037022dd00cb80 requirements: - host: - - perl - - variant-effect-predictor - - samtools - - htslib run: - perl - variant-effect-predictor diff --git a/recipes/vcfkit/meta.yaml b/recipes/vcfkit/meta.yaml index bc734a386d645..39efe96d590b2 100644 --- a/recipes/vcfkit/meta.yaml +++ b/recipes/vcfkit/meta.yaml @@ -8,12 +8,13 @@ source: build: number: 2 - skip: True # [not py27] preserve_egg_dir: True entry_points: - vk=vcfkit.vk:main requirements: + build: + - {{ compiler('c') }} host: - python - awesome-slugify @@ -39,7 +40,6 @@ requirements: - matplotlib - scipy - numpy - - cython - cyvcf2 >=0.1.9 - docopt - biopython diff --git a/recipes/vcflatten/meta.yaml b/recipes/vcflatten/meta.yaml index c55542480eaa7..627cbaa51171e 100644 --- a/recipes/vcflatten/meta.yaml +++ b/recipes/vcflatten/meta.yaml @@ -1,11 +1,11 @@ -build: - number: 2 - skip: True # [osx] - package: name: vcflatten version: "0.5.2" +build: + noarch: generic + number: 2 + source: url: https://github.com/downloads/innovativemedicine/vcfimp/vcflatten-0.5.2.zip md5: 69864df8a5a228a8fea73e0df5ddf394 diff --git a/recipes/vcfsamplecompare/meta.yaml b/recipes/vcfsamplecompare/meta.yaml index f0f0970d0919e..83cdca7c8334c 100644 --- a/recipes/vcfsamplecompare/meta.yaml +++ b/recipes/vcfsamplecompare/meta.yaml @@ -10,6 +10,7 @@ source: sha256: 6360ccae123099bdbbe7cc60d28aad7c62663bc127af16508e397c7acd07d775 build: + noarch: generic number: 0 requirements: diff --git a/recipes/virema/meta.yaml b/recipes/virema/meta.yaml index 5dd61a066b717..d0ae09d43b55b 100644 --- a/recipes/virema/meta.yaml +++ b/recipes/virema/meta.yaml @@ -9,13 +9,13 @@ source: - path.patch build: + noarch: generic number: 1 - skip: True # [py3k] requirements: host: run: - - python + - python <3 - bowtie <=1.0.0 test: diff --git a/recipes/vmatch/meta.yaml b/recipes/vmatch/meta.yaml index 56ef4d3641d57..d99413989980f 100644 --- a/recipes/vmatch/meta.yaml +++ b/recipes/vmatch/meta.yaml @@ -6,14 +6,14 @@ package: version: {{ version }} source: - url: http://www.vmatch.de/distributions/vmatch-{{ version }}-Linux_x86_64-64bit.tar.gz # [linux] - sha256: 5e18d0dddf04e86dad193fcdde6e48f3901365932634125602d8808f35acf979 # [linux] - url: http://www.vmatch.de/distributions/vmatch-{{ version }}-Darwin_i386-64bit.tar.gz # [osx] - sha256: 39695c7d20158446ff27656f9ba415097052570bcc67ed12efec376fc3b0b4c6 # [osx] - patches: - # Makefile in SELECT/ use gcc directly; this patch removes that so the compiler - # from the conda environment is used instead - - 0001-Remove-direct-call-to-GCC-in-Makefile.patch + - url: http://www.vmatch.de/distributions/vmatch-{{ version }}-Linux_x86_64-64bit.tar.gz # [linux] + sha256: 5e18d0dddf04e86dad193fcdde6e48f3901365932634125602d8808f35acf979 # [linux] + patches: # [linux] + - 0001-Remove-direct-call-to-GCC-in-Makefile.patch # [linux] + - url: http://www.vmatch.de/distributions/vmatch-{{ version }}-Darwin_i386-64bit.tar.gz # [osx] + sha256: 39695c7d20158446ff27656f9ba415097052570bcc67ed12efec376fc3b0b4c6 # [osx] + patches: # [osx] + - 0001-Remove-direct-call-to-GCC-in-Makefile.patch # [osx] build: number: 2 @@ -57,4 +57,3 @@ extra: - biotools:vmatch skip-lints: - should_not_be_noarch_source # we use platform specific sources but the recipe is valid on all platforms - - duplicate_key_in_meta_yaml diff --git a/recipes/vtools/meta.yaml b/recipes/vtools/meta.yaml index 3f4543f96ed4f..0932ce9e7d964 100644 --- a/recipes/vtools/meta.yaml +++ b/recipes/vtools/meta.yaml @@ -32,8 +32,6 @@ requirements: - tqdm run: - python >=3.6 - - setuptools - - cython - numpy - cyvcf2 - click diff --git a/recipes/weblogo/2.8.2/meta.yaml b/recipes/weblogo/2.8.2/meta.yaml index 296f797c043d6..9c96adb4ec193 100644 --- a/recipes/weblogo/2.8.2/meta.yaml +++ b/recipes/weblogo/2.8.2/meta.yaml @@ -3,6 +3,7 @@ package: version: 2.8.2 build: + noarch: generic number: 7 source: diff --git a/recipes/wes-service-client/meta.yaml b/recipes/wes-service-client/meta.yaml index 2ca3329c3dfac..b1f23fd024270 100644 --- a/recipes/wes-service-client/meta.yaml +++ b/recipes/wes-service-client/meta.yaml @@ -19,12 +19,8 @@ requirements: host: - python - setuptools - - future - - subprocess32 - - schema-salad >=2.6.20170927145003,<3.0 run: - python - - setuptools - future - subprocess32 - schema-salad >=2.6.20170927145003,<3.0 diff --git a/recipes/wgs2ncbi/meta.yaml b/recipes/wgs2ncbi/meta.yaml index 30199a9827df2..2df4c632f14d0 100644 --- a/recipes/wgs2ncbi/meta.yaml +++ b/recipes/wgs2ncbi/meta.yaml @@ -9,6 +9,7 @@ source: sha256: 778efdba148705981350e662e7700fb1148c9b7e723afd066f60dd5a577082fb build: + noarch: generic number: 0 requirements: @@ -16,9 +17,9 @@ requirements: - perl - perl-uri run: - - perl - - perl-uri - - tbl2asn + - perl + - perl-uri + - tbl2asn test: commands: diff --git a/recipes/wham/meta.yaml b/recipes/wham/meta.yaml index 15d6694e4ab9b..5ffd605f17d82 100644 --- a/recipes/wham/meta.yaml +++ b/recipes/wham/meta.yaml @@ -44,5 +44,5 @@ extra: - biotools:Wham6216 skip-lints: # This needs git for recursive checkouts - - uses_git_url + - uses_vcs_url - missing_hash diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index faec6f8efe84c..48f9678352c4c 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -21,7 +21,6 @@ requirements: - setuptools_scm run: - python - - setuptools - pysam >=0.15 - pyvcf - pyfaidx >=0.5.5.2 diff --git a/recipes/wisecondorX/meta.yaml b/recipes/wisecondorx/meta.yaml similarity index 100% rename from recipes/wisecondorX/meta.yaml rename to recipes/wisecondorx/meta.yaml diff --git a/recipes/workspace/build.sh b/recipes/workspace/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/workspace/build.sh +++ /dev/null @@ -1,9 +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/workspace/meta.yaml b/recipes/workspace/meta.yaml index 48bf160b1eeac..df9e905a8cac3 100644 --- a/recipes/workspace/meta.yaml +++ b/recipes/workspace/meta.yaml @@ -1,7 +1,3 @@ -build: - number: 2 - - package: name: workspace version: "0.3.1" @@ -10,12 +6,15 @@ source: url: https://pypi.python.org/packages/source/w/workspace/workspace-0.3.1.tar.gz md5: 643250e65bd836e3ed4810fe4cb86182 +build: + noarch: python + number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + requirements: host: - python - - setuptools - - sprinkles >=0.4.4 - + - pip run: - python - sprinkles >=0.4.4 @@ -26,23 +25,7 @@ test: - workspace - workspace.plugins - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called 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: http://an9.org/w/WorkspacePy license: MIT License summary: 'Workspace Overmind' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/wtforms-alchemy/meta.yaml b/recipes/wtforms-alchemy/meta.yaml index e60898b10ffb5..a59c99dadeea4 100644 --- a/recipes/wtforms-alchemy/meta.yaml +++ b/recipes/wtforms-alchemy/meta.yaml @@ -1,7 +1,3 @@ -build: - number: 0 - skip: True # [osx] - package: name: wtforms-alchemy version: "0.16.8" @@ -10,16 +6,14 @@ source: url: https://files.pythonhosted.org/packages/e9/b6/09d2306b53097d0ff2f1b8dc31b12411fc43f4afcfc0a828b1e2373b5b47/WTForms-Alchemy-0.16.8.tar.gz sha256: c6ed0b22096542fd3063c00329af56a9a338ba3d9b8656acc6404cfdd8085974 +build: + noarch: python + number: 0 + requirements: host: - python - - setuptools - - sqlalchemy >=0.8.0 - - wtforms >=1.0.4 - - wtforms-components >=0.9.2 - - sqlalchemy-utils >=0.30.0 - - six >=1.4.1 - + - pip run: - python - sqlalchemy >=0.8.0 diff --git a/recipes/wtforms-components/build.sh b/recipes/wtforms-components/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/wtforms-components/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/wtforms-components/meta.yaml b/recipes/wtforms-components/meta.yaml index 10eb9929fe442..4b4534ee0b0f9 100644 --- a/recipes/wtforms-components/meta.yaml +++ b/recipes/wtforms-components/meta.yaml @@ -11,18 +11,12 @@ source: build: number: 2 noarch: python - skip: False + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - - wtforms >=1.0.4 - - six >=1.4.1 - - validators >=0.5.0 - - intervals >=0.6.0 - - phonenumbers - + - pip run: - python - wtforms >=1.0.4 diff --git a/recipes/xmlbuilder/build.sh b/recipes/xmlbuilder/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/xmlbuilder/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/xmlbuilder/meta.yaml b/recipes/xmlbuilder/meta.yaml index 58a9a78c9da89..20bf409c5e7ac 100644 --- a/recipes/xmlbuilder/meta.yaml +++ b/recipes/xmlbuilder/meta.yaml @@ -3,7 +3,9 @@ package: version: "1.0" build: + noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/ab/50/7d5482347973e449432c7a09385a5d6769db63c95ef98590caa82d0792ae/xmlbuilder-1.0.tar.gz @@ -12,8 +14,7 @@ source: requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/xmltramp2/build.sh b/recipes/xmltramp2/build.sh deleted file mode 100644 index 3f50b74e1bff2..0000000000000 --- a/recipes/xmltramp2/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/xmltramp2/meta.yaml b/recipes/xmltramp2/meta.yaml index 63c958479a57a..f96b846890b1c 100644 --- a/recipes/xmltramp2/meta.yaml +++ b/recipes/xmltramp2/meta.yaml @@ -5,6 +5,7 @@ package: build: number: 1 noarch: python + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://pypi.python.org/packages/28/56/a8628b716378b67c8536989ad9347a003328e83a52f0a5c65407331e59d3/xmltramp2-3.1.1.tar.gz @@ -13,8 +14,7 @@ source: requirements: host: - python - - setuptools - - six + - pip run: - python - six diff --git a/recipes/xtail/meta.yaml b/recipes/xtail/meta.yaml index 01777dde1f71e..c90dead36346e 100644 --- a/recipes/xtail/meta.yaml +++ b/recipes/xtail/meta.yaml @@ -10,6 +10,7 @@ source: sha256: c653bf8b5898c5a52eb83b63738d6d1f085725560c943db1bbeecbef467f85d6 build: + noarch: generic number: 2 rpaths: - lib/R/lib/ diff --git a/recipes/xtermcolor/build.sh b/recipes/xtermcolor/build.sh deleted file mode 100644 index 8e25a1455f914..0000000000000 --- a/recipes/xtermcolor/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/xtermcolor/meta.yaml b/recipes/xtermcolor/meta.yaml index 22960af9a6d09..fddcd85feed29 100644 --- a/recipes/xtermcolor/meta.yaml +++ b/recipes/xtermcolor/meta.yaml @@ -8,14 +8,13 @@ source: build: noarch: python - skip: False number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - + - pip run: - python diff --git a/recipes/yaggo/meta.yaml b/recipes/yaggo/meta.yaml index f93c4e8a9550a..335fb1eff3534 100644 --- a/recipes/yaggo/meta.yaml +++ b/recipes/yaggo/meta.yaml @@ -6,6 +6,7 @@ package: version: '{{version}}' build: + noarch: generic number: 0 source: diff --git a/recipes/yahmm/build.sh b/recipes/yahmm/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/yahmm/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index 775bc63e7ec0b..8d2d976a7a1eb 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -8,19 +8,21 @@ source: build: number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - python + - pip - cython >=0.20.1 - numpy >=1.8.0 - scipy >=0.13.3 - networkx >=1.8.1 - matplotlib >=1.3.1 - run: - python - - cython >=0.20.1 - numpy >=1.8.0 - scipy >=0.13.3 - networkx >=1.8.1 diff --git a/recipes/yanagiba/build.sh b/recipes/yanagiba/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/yanagiba/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/yanagiba/meta.yaml b/recipes/yanagiba/meta.yaml index 44a3db42d2d4c..1d8710dbb9133 100644 --- a/recipes/yanagiba/meta.yaml +++ b/recipes/yanagiba/meta.yaml @@ -9,21 +9,18 @@ source: sha256: aa5a1be66267163cd7eebb10ea2c3e4339f8512f39c12374b85f23d4e606d854 build: - skip: True # [py27] + noarch: python entry_points: - yanagiba=yanagiba.cmd_line:main number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - - python - - setuptools - - nanomath >=0.13.0 - - pandas >=0.20.3 - - biopython >=1.70 - + - python >=3 + - pip run: - - python + - python >=3 - nanomath >=0.13.0 - pandas >=0.20.3 - biopython >=1.70 diff --git a/recipes/yanc/build.sh b/recipes/yanc/build.sh deleted file mode 100644 index 4d7fc032b8cbe..0000000000000 --- a/recipes/yanc/build.sh +++ /dev/null @@ -1,9 +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/yanc/meta.yaml b/recipes/yanc/meta.yaml index 7f85a12fb9b22..d73d39514dc96 100644 --- a/recipes/yanc/meta.yaml +++ b/recipes/yanc/meta.yaml @@ -10,15 +10,14 @@ build: noarch: python preserve_egg_dir: True number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools - + - pip run: - python - - setuptools test: # Python imports diff --git a/recipes/yara/meta.yaml b/recipes/yara/meta.yaml index 0e6c1c475107a..71b8196602b4f 100644 --- a/recipes/yara/meta.yaml +++ b/recipes/yara/meta.yaml @@ -1,28 +1,19 @@ {% set version="1.0.2" %} -build: - number: 1 - -about: - home: https://github.com/seqan/seqan/blob/develop/apps/yara/README.rst - license: https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE - summary: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. - license_family: BSD - package: name: yara version: {{ version }} +build: + number: 1 + source: - url: http://packages.seqan.de/yara/yara-{{ version }}-Mac-x86_64.zip # [osx] - sha256: d519e797c1c66252331146b63f0cb6edba9c1a6a9e7b342fd60e7344b29baf36 # [osx] - url: http://packages.seqan.de/yara/yara-{{ version }}-Linux-x86_64_sse4.tar.bz2 # [linux64] - sha256: 4f68552fbb4e4002fc4320bdd60b76c678e17d087bd3f893bf179387b1668b40 # [linux64] + - url: http://packages.seqan.de/yara/yara-{{ version }}-Mac-x86_64.zip # [osx] + sha256: d519e797c1c66252331146b63f0cb6edba9c1a6a9e7b342fd60e7344b29baf36 # [osx] + - url: http://packages.seqan.de/yara/yara-{{ version }}-Linux-x86_64_sse4.tar.bz2 # [linux] + sha256: 4f68552fbb4e4002fc4320bdd60b76c678e17d087bd3f893bf179387b1668b40 # [linux] requirements: - host: - - bzip2 - - zlib run: - bzip2 - zlib @@ -32,9 +23,18 @@ test: - yara_indexer --help 2>&1 > /dev/null - yara_mapper --help 2>&1 > /dev/null +about: + home: https://github.com/seqan/seqan/blob/develop/apps/yara/README.rst + license: https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE + summary: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + license_family: BSD + extra: identifiers: - biotools:yara - doi:10.1093/nar/gkt005 - maintainers: + recipe-maintainers: - eseiler + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source diff --git a/recipes/zifa/build.sh b/recipes/zifa/build.sh deleted file mode 100644 index 5a5aeeb48b45e..0000000000000 --- a/recipes/zifa/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install diff --git a/recipes/zifa/meta.yaml b/recipes/zifa/meta.yaml index f977ec537ee11..3919dfbd9823c 100644 --- a/recipes/zifa/meta.yaml +++ b/recipes/zifa/meta.yaml @@ -12,11 +12,12 @@ source: build: noarch: python number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python - - setuptools + - pip run: - python