t-coffee 12.00.7fb08c2 #12594

pditommaso · 2018-12-12T14:57:26Z

I have read the guidelines for bioconda recipes.
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).
This PR updates an existing recipe.
This PR does something else (explain below).

SchwarzMarek · 2018-12-12T15:00:41Z

Would you consider to add viennarna package to deps (it would allow -mode rcoffee to run)?

pditommaso · 2018-12-12T15:02:24Z

All the ones in this list are welcome.

Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run.

This commit adds vienna packages and remove TMalign copy command

Adding TMalign

apeltzer · 2018-12-12T18:51:49Z

Nice and thanks @pditommaso !

@druvus

* Update intarna to 2.3.1 (#12367) * Update agfusion to 1.231 (#12366) * Update bioconda-utils to 0.15.0 (#12359) * Update mapdamage2 to 2.0.9 (#12358) * Update scanpy to 1.3.4 (#12357) * Update goatools to 0.8.11 (#12361) * Update perl-math-random-mt-auto to 6.23 (#12362) * Update kipoi to 0.6.3 (#12374) * Update kipoi_veff to 0.2.1 (#12364) * Update perl-object-insideout to 4.05 (#12380) * Update sevenbridges-python to 0.17.1 (#12379) * Update nanosv to 1.2.3 (#12378) * Update starfish to 0.0.30 (#12368) * Update clust to 1.8.10 (#12356) * Update pypairs to 2.0.6 (#12381) * Update khmer to 3.0.0a2 (#12360) * Update flashlfq to 0.1.110 (#12385) * Update perl-algorithm-cluster to 1.57 (#12384) * Update arvados-python-client to 1.2.0.20181121194423 (#12382) * Update avro-cwl to 1.8.9 (#12355) * Update avro-cwl to 1.8.9 * Set noarch: python * r-breakaway (#12386) * R sads (#12388) * Update python-sortedcontainers to 2.1.0 (#12383) * r-ebimetagenomics (#12339) * pin armadilo on major version (#12389) * IgDiscover version 0.11 (#12351) * IgDiscover version 0.11 * IgDiscover requires Python 3.6 * Fix build on macOS with a small patch * Remove unneeded host dependencies * Update goatools to 0.8.12 (#12391) * Update bioconda-utils to 0.15.1 (#12390) * R ebimetagenomics (#12393) * Add dimspy recipes for reference purposes (#12387) * Add dimspy recipes for reference purposes * Remove filename * remove from blacklist * Update build-fail-blacklist * Added BioExcel_SeqQC to bioconda-recipes (#12276) * PacBio: Update pbalign to 0.3.2 (#12396) * PacBio: Update pbalign to 0.3.2 Closes: PacificBiosciences/pbbioconda#39 * add bgreat to bioconda (#12350) * bgreat addition * zlib in build should not be needed * btrim integration to conda (#12395) * Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399) * PacBio: Update `pbsv2` to version 2.1.0 (#12400) * Genenotebook v0.1.11 (#12398) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * prosolo: new package version 0.6.0 (#12397) * Update sevenbridges-python to 0.17.2 (#12404) * Add recipe for ICED (#12406) * Downgrade version for iced (#12409) * Update recipe for libstatgen 1.0.5 (#12348) * Add recipe for libstatgen-1.0.5 * Update iced to 0.5.0 (#12411) * Update perl-test2-suite to 0.000116 (#12412) * fix compatibility with other tools (#12415) * Restore dexseq python helper scripts (#12352) * Restore dexseq python helper scripts * Add python requirement for helper scripts * Add python noarch to build section * pin it to python2k * Add htseq requirement, support only python <3 for now * Genenotebook v0.1.12 (#12418) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * added medpy recipe (#12417) * added medpy recipe * removed osx from build * Update meta.yaml * Update meta.yaml * add boost and a compiler * Update meta.yaml * Update meta.yaml * add itk * Updated ddrage to version 1.6.1. (#12421) * Add r-mcpcounter recipe. (#12261) * Add MCPcounter recipe. * fix lint: remove 'fn' * fix license_file, version number and doi * Update DEXSeq requirements to force compatible HTSeq version (#12423) * ARB: Pin glib (#11782) * Pin glib * Update meta.yaml * Update meta.yaml * Work around CB3 issues * Work around bioconda-utils lint false positive * Disable lint check should_not_be_noarch * Can't reference other packages built in recipe from anything but run * Move perl to host section. Maybe that helps. * constraining interpreter version breaks with CB3? * disable perl version constraint :( * Update meta.yaml (#12426) * stacks: fix for fix 'fixing' @ in exe_path (#12420) * stacks: fix for fix 'fixing' @ in exe_path the previous fix #11580 tried to solve the problem with the @ in the exe_path by setting this variable empty. But the perl scripts - append a / to the empty string and (i.e. the bin path gets /binary) - check for file presence (problem: neither binary nor /binary are present) Now I quote the @ in the exe_path. * stacks: add refmap bugfix * Genenotebook v0.1.13 (#12424) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * v0.1.13 * metaQuantome (#12413) replaces metaquant, which is now deprecated. * New MMseqs2 release 7-4e23d (#12432) New mmseqs2 release 7-4e23d * update spades to 3.13.0 (#12408) * update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure * Update Crossmap to 0.3.1 (#12439) * Update Crossmap to 0.3.1 * Make metaquantome dependencies more specific (#12442) * less stringent deps * bump build * pin goatools * test extra pins * integration of bcool to bioconda (#12422) * Update hifive to 1.5.7 (#12433) * Update scvi to 0.2.3 (#12434) * Update Subread from 1.6.2 to 1.6.3. (#12425) * Update Subread from 1.6.2 to 1.6.3. * Subread executable coverageCount has been removed. https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ * UCSC Cell Browser 0.4.23 (#12347) * Starting files for ucsc-cell-browser * Customised recipe for ucsc-cell-browser * meta update for ucsc-cell-browser * Changes cbTrackHub to cbHub * Point to static release * Moves to 0.25 * Updates sha hash for ucsc-browser * Reverts to 0.1.9 * At ebi * Update meta.yaml * pins numpy to last know working version * Back to 0.25, no numpy pinning. * Remove git, pin python and numpy. Add build section. * Update meta.yaml * Update meta.yaml * Move to 0.4.20 without skeleton on provisional commit * Typo on executable name * Moves to release version and adds dependencies for converters * Update libstatgen to 1.0.14 (#12437) * Update arvados-python-client to 1.2.1 (#12438) * Update tirmite to 1.1.3 (#12435) * Bump metaquantome (#12449) * less stringent deps * bump build * pin goatools * test extra pins * bump metaquantome to 0.99.3 * Update ADAM to 0.25.0 (#12445) * Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453) * update rgi4.2.2 recipe (#12282) * update to enforce python3.6 and load card.json * remove lines from build.sh * update build number * make PR comment changes * add test to verify db is loaded * update build script * update build script * fix lint errors * fix linting errors * fix liniting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * revert test change * Add CRAN R package leapp. (#12428) * Bump DECIPHER to Bioconductor 3.7 (#12463) * Bump DECIPHER to Bioconductor 3.7 * Change r-rsqlite version dependency * Update meta.yaml * updated scVI to 0.2.3 (#12429) * Add recipe for PyAAVF 0.1.0 (#12451) * Add recipe for PyAAVF 0.1.0 * Fix linting error * seqkit 0.9.3 (#12455) * HTSeq - Pin numpy version (#12467) * update eigensoft to 7.2.1 (#12469) * Update scnic to 0.6.0 (#12436) * Update scnic to 0.6.0 * Work around fastspar insufficient armadillo pin * fix pin * GimmeMotifs 0.13.1 (#12471) * Bumped version to newest, with introspective text (#12461) * Update Segway 2.0.2 recipe to use older depedencies (#11803) * Update Segway 2.0.2 recipe to use older depedencies * Update maximum genomedata version supported * Update build number * Fix missing older dependency information * Update meta.yaml * updating dependencies for reparation_blast (#12443) * updating dependencies for reparation_blast * changed dependency of pysam * Added DropletUtils package (#12448) * Create recipe for SVIM (#12272) * add svim recipe * fix bugs in svim recipe * replace source file * remove license file * Lowercase biopython * upgrade to svim 0.4.1 * add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency * fix python version * try to fix lint error * replace "skip: True" with "noarch: python" * Update bioconductor-biocgenerics (#12477) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Irida sistr results 0.6.0 (#12478) * Update irida-sistr-results to 0.6.0 * Fixed dependency string * Adding recipe for clinvar-tsv v0.1.0. (#12481) * no fixed boost version (#12483) * New recipe: pysradb (#12470) * Pyseer 1.2.0 (#12444) * Update pyseer to 1.1.2 * Update pyseer to 1.2.0 * Update pyseer to 1.2.0 Update pyseer to 1.2.0 Update pyseer to 1.2.0 (fixed) * Final touches to pyseer 1.2.0 * Additional update to pyseer recipe * sentieon: minor version bump to 201808.01 (#12480) * adding java to mutations recipe (#12485) * Update ncrf to 1.00.06 (#12369) * Update ncrf to 1.00.06 * Update test string * Bump umitools (#12486) * Mob suite version 1.4.9 no arch build number 2 (#12479) * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * Update r-goeveg to 0.4.2 (#12375) * Update r-goeveg to 0.4.2 * Add r-hmisc as dependency * Removes r-seurat-scripts from blacklisting (#12489) * Removes r-seurat-scripts from blacklisting * Unblacklist some non bioconductor packages * For VarDict-Java, install utility scripts. (#12488) * For VarDict-Java, install utility scripts. Utility script that were previously only shipped with VarDict are not part of VarDict-Java as well, making installation of both packages unnecessary. * Bump build. * Improve variable name. * Make vardict depend on vardict-java for utility scripts. * Pin compatible numpy for older HTSEQ versions (#12490) * Pin compatible numpy for older HTSEQ versions This is required to keep older versions of HTSEQ functional * HTSeq - update old versions to build properly with new build system * HTSeq 0.6.1 - Increment build number * add recipe for r-epic (#12473) * Add new recipe - RVTESTS (#12465) * Add rvtests * Update pre-req * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create LICENSE * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Create run_test.sh * Update meta.yaml * Delete run_test.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Adding recipe for var-agg v0.1.0 (#12482) * Adding recipe for var-agg v0.1.0 * runtime deps do have run-exports defined * move rust into the host section * Adding dependency to clangdev * Adding var-agg v0.1.1. (#12495) * [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441) Salmon v0.12.0 --- version bump and fix OSX build * Considerable updates in terms of features and fixes (check release notes). * Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX). * Performancean alytics (#12498) * Add bioconductor package RNASeqR * Add performanceanalytics * Performancean alytics (#12499) * Add bioconductor package RNASeqR * Add performanceanalytics * Move recipes/r-performanceanalytics and add r-rafalib * Move r-performanceanalytics/ to recipes * Update recipes/r-performanceanalytics * Update r-rafalib * Remove recipes/r-performanceanalytics/bld.bat * Remove recipes/r-performanceanalytics * Update r-performanceanalytics/ * Update r-performanceanalytics/ * Add r-performanceanalytics/ * remove r-performanceanalytics * Add performanceanalytics * Remove r-performanceanalytics * Update Picard to 2.18.20. (#12501) * Update vsearch to 2.10.0. (#12504) * Update Purge Haplotigs to v1.0.4 (#12497) * Update duphold to 0.1.1 (#12516) * Update starfish to 0.0.31 (#12515) * Update perl-term-app-roles to 0.02 (#12512) * Update perl-dbd-sqlite to 1.60 (#12511) * Update perl-json to 4.00 (#12509) * Update kipoi to 0.6.5 (#12508) * Update illumina-interop to 1.1.8 (#12507) * Update beagle-lib to 3.1.2 (#12523) * Update pysradb to 0.3.0 (#12522) * Update bioconda-utils to 0.15.2 (#12525) * Update perl-json-pp to 4.0 (#12524) * Update perl-term-table to 0.013 (#12529) * Update abyss to 2.1.5 (#12528) * Update perl-test2-suite to 0.000117 (#12527) * Update wtforms-alchemy to 0.16.8 (#12505) * Update perl-carp-clan to 6.07 (#12518) * Update perl-date-manip to 6.75 (#12519) * Update: seq2c, multiqc-bcbio (#12533) * tracy v0.3.7 (#12534) * Version bump 2.10 (#12535) * Version bump 2.10 * Copy paste error forgot the https * Missing deps for ucsc-cell-browser 0.4.23 (#12537) * Missing deps for ucsc-cell-browser * Bumps build nuber * Update vsearch to 2.10.1 (#12540) * New recipe for MicroHapDB 0.2 (#12531) * New recipe for MicroHapDB 0.2 * Troubleshoot config * Successful build locally! * Clean up recipe * Update moff to 2.0.2 (#12539) * Update PopDel to version 1.0.5 (#12502) * Update PopDel to version 1.0.5 * Remove Makefile.patch Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead. * Automatically get version from PKG_VERSION * Update to teloclip v0.0.3 (#12542) * Update biolite to 1.2.0 (#12544) * Update kneaddata to 0.7.2 (#12543) * snakemake 5.3.1 (#12500) * snakemake 5.3.1 * fix jinja variables * only warn if git not present in tests * use explicit jinja for version again. Conda seems to have lost the ability to use PKG_VERSION in meta.yaml. * try masking env var * try defining env var before command * nextflow: pin openjdk=8 to solve java version parsing issue (#12493) * Pin openjdk=8 * Alllow openjdk 8 or 9 * Update bioconda-utils to 0.15.3 (#12546) * Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 (#12549) * Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 * Update install patch for 0.2.4 * Match nim release version 0.19.0 * Scanpy scripts (#12551) * Bump version * Fix scanpy version requirement to v1.3.2 * Update to v0.0.4 * Update nanosim to 2.2.0 (#12517) * Update nanosim to 2.2.0 * Add sklearn as dependency * Recipe for kma (#12554) * PacBio: Update `pbsv2` to version 2.1.1 (#12556) * Add counterr (#12541) * Add counterr * Fix typo * Use tagged release * Updated ddRAGE to version 1.6.3 (#12557) * Add recipe for SNVer 0.5.3 (#12265) * Add recipe for SNVer 0.5.3 * Add CRAN R package cate. (#12562) * r-seurat-scripts: Fixed DimPlots() issues, addressed libpng issue for OSX (#12563) * Fixed DimPlots() issues, addressed libpng issue for OSX * Correction: removed testing line in source package * Update scanpy to 1.3.5 (#12571) * Update vsearch to 2.10.2 (#12579) * Update mentalist to 0.2.4 (#12578) * Update krakenuniq to 0.5.5 (#12575) * Update mlst to 2.16 (#12572) * Update transit to 2.3.3 (#12570) * Update anndata to 0.6.14 (#12568) * Update svim to 0.4.2 (#12566) * Update perl-test-cleannamespaces to 0.24 (#12569) * uptdate mlst to 2.16.1 (#12582) * Update jcvi to 0.8.12 (#12574) * add cromwell-tools (CLI and API for Cromwell workflow manager). (#12564) * added cromwell-tools * point to stable docs rather than latest * Remove noarch to make os-specifics work (#12583) * prosolo: update to v0.6.1 (#12584) * integration to bioconda (#12456) * Recipe for sparcc (#12459) * Recipe for SparCC * Remove maintainers lines * Add license info * Mention pull request for patch * Fix lint * Build noarch * Update: bcbio (v1.1.2), bcbio-vm (GCP support) (#12585) * t-coffee 12.00.7fb08c2 (#12594) * t-coffee 12.00.7fb08c2 * add viennarna to deps Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run. * t-coffee 12.00.7fb08c2 (2) This commit adds vienna packages and remove TMalign copy command * t-coffee 12.00.7fb08c2 (4) Adding TMalign * Nf core V 1.4 (#12599) * Need to update SHA256 once release is out! * Update to release 1.4 * Sleuth unblacklist (#12591) * remove sleuth from blacklist * Remove obsolete dependency. * Bump spectra-cluster-cli (#12598) * Update gseapy to 0.9.9 (#12530) * Update gseapy to 0.9.9 * Add scipy * Add bioservices as dependency * added recipe perl-bio-viennangs 0.19.2 (#12596) * Add SVMlight (#12595) * Add SVMlight * Update meta yaml * Update SHA256 sum * Update build script to copy executables * Update meta.yaml * Fix o-umlaut * Fix test stalls svm_learn -? displays a pager, waiting for keyboard input * rhdf5 2.26 and rhdf5lib 1.4 (#12597) * rhdf5 2.26 and rhdf5lib 1.4 * force C99 mode * set CFLAGS in Makevars * Add recipe for hiddenDomains (#12614) * bump pysradb 0.3.0 -> 0.4.0 (#12612) * bump pysradb 0.3.0 -> 0.4.0 * Fix imports * Add extras * Update slicedimage to 1.0.2 (#12609) * Update perl-module-scandeps to 1.26 (#12608) * Update scanpy to 1.3.6 (#12605) * Update abeona to 0.40.2 (#12602) * Update confindr to 0.4.8 (#12607) * Update anndata to 0.6.15 (#12606) * tmaling (#12588) Add tmalign recipe * pysvmlight added (#12617) * Add fontconfig / ttf-dejavu to fastqc recipe (#12616) * pdate adVNTR to 1.2.0 (#12613) * add adVNTR * fix linux error for adVNTR * add numpy to adVNTR requirements * add numpy include dirs for cythonize * Update advntr to 1.1.0 * Update advntr to 1.1.0 * update advntr to 1.1.1 * update adVNTR to 1.2.0 * update sha256 for adVNTR-1.2.0 * fix build script for adVNTR-1.2.0 * fix adVNTR-1.2.0 * PeptideShaker v1.16.36 & SearchGUI v3.3.10 (#12620) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 * PeptideShaker version updated to 1.16.36 SearchGUI version updated to 3.3.10 * New recipe (refinem: 0.0.24) (#12628) * Replace sha256 and bump build num (#12629) * Update galaxy-parsec to 1.0.6 (#12634) * Add recipe for SeqMap (#12615) * Add recipe for SeqMap * Change cp Change cp * Updated concoct to version 1.0.0 (#12600) * Updated concoct to version 1.0.0 * Skip build for macosx at this point * New build number * Reset build number to 0, thanks @druvus * Update deepvariant to 0.7.2 (#12638) * Update abeona to 0.41.1 (#12637) * Update shmlast to 1.3 (#12636) * Update krakenuniq to 0.5.6 (#12633) * Update selene-sdk to 0.2.0 (#12632) * Update comet-ms to 2018013 (#12555) * Update with selene-sdk v0.2.0 (#12631) * update with selene-0.2.0 * Update meta.yaml * add self to recipe maintainers * Cat updated version (#12587) * v 4.3.1 * Pin BLAST+ version to >= 2.2, < 2.4 (#12639) * Shmlast v1.4 (#12645) * Bump shmlast to v1.4 * Update PopDel to version 1.0.6 (#12644) * Update PopDel to version 1.0.6 * Adapt tests * Remove test for correct version number Redirection seems to cause error in circleci: ".Passing program arguments as a string may be a security hazard if combined with untrusted input" * Concoct add samtools as a dependency (#12642) * Updated concoct to version 1.0.0 * Skip build for macosx at this point * New build number * Reset build number to 0, thanks @druvus * Samtools new requirement for concoct v1.0.0 * Bump topas (#12618) * Bump spectra-cluster-cli * Bump topas * Use ${PKG_VERSION} * Small tweaks * No recursion * pasta-1.7.8-build-2 (#12641) * pasta-1.7.8-build-2 * Relax requirements * Rebuild pasta (#12648) * Bump spectra-cluster-cli * Delete old pasta * Rebuild pasta * Unblacklist pasta * Revert dendropy version * Correct build number * Use openjdk * Rebuild perl-pod-coverage (#12652) * Rebuild perl-pod-coverage * Unblacklist * tracy v0.3.8 (#12651) * Kalign (#12647) * add kalign This recipe adds kalign * fix for osx * fix for osx #2 * Rebuild perl-test-pod-coverage (#12654) * Rebuild perl-test-pod-coverage * Unblacklist * Update: bcbio (1.1.3a) Fixes bcbio/bcbio-nextgen#2594 (#12655) * Rebuild perl-test-file-contents (#12649) * Bump spectra-cluster-cli * Rebuild perl-test-file-contents * Kleborate 0.3.0 (#12657) * Adding recipe for >> kleborate << * Rebuild perl-params-coerce (#12660) * Upgrade biodb to version 1.2.0b. (#12663) * Add recipe for unitas (#12658) * Add recipe for unitas * Rebuild perl-file-share (#12661) * Update sevenbridges-python to 0.17.3 (#12667) * Update slicedimage to 1.0.3 (#12666) * Update cat to 4.3.3 (#12665) * Update crossmap to 0.3.2 (#12664) * Update: deepvariant 0.7.2 model and dependencies (#12672) - Requires tensorflow 1.12 - Update model data for 0.7.2 - Remove requirement for --regions in dv_make_examples.py wrapper. Fixes #12560 * unblacklist perl-bio-viennangs (#12643) * unblacklist perl-bio-viennangs * fix version string; remove 0.19 recipe * remove all perl version strings * increased build nr * Add pysvmlight (#12673) * Remove the mess I created in the main repository (#12674) * Add missing dependencies and bump version for FRED2 (#12621) * Add missing dependencies and bump version for FRED2 * Bump version to force rebuild * Update meraculous to 2.2.6 (#12254) * Update meraculous to 2.2.6 * Remove perl pinning * Update BioExcel_SeqQC to 0.6 (#12604) * Update BioExcel_SeqQC to 0.6 * Fix name * Update anndata to 0.6.16 (#12676) * Update pysradb to 0.4.2 (#12675) * version 3.0.3 (#12678) * Add perl-math-utils (#12681) * Add perl-math-utils * Remove fn * Rebuild perl-extutils-makemaker (#12680) * Update perl-html-formatter to 2.16 (#12225) * Update perl-html-formatter to 2.16 * Fix deps * Update perl-readonly to 2.05 (#12153) * Update perl-readonly to 2.05 * Fix deps * Update perl-html-tidy to 1.60 (#12187) * Update perl-html-tidy to 1.60 * Update deps * Update meta.yaml * Update perl-libwww-perl to 6.36 (#12180) * Update perl-libwww-perl to 6.36 * Update deps * Update meta.yaml * Add perl-html-parser as dep * Add back perl-ntlm * Update PopDel to version 1.0.7 (#12685) * Use quotes when extending PATH. (#12662) * Use quotes when extending PATH env var, in order to handle potential space characters. * Update perl-math-derivative to 1.01 (#12158) * Update perl-math-derivative to 1.01 * Update dependency * Update perl-data-dumper to 2.173 (#12224) * Update perl-parallel-forkmanager to 2.02 (#12170) * Update perl-parallel-forkmanager to 2.02 * Update deps * Update bioblend to 0.12.0 (#12687) * Update abeona to 0.42.0 (#12686) * blacklist r-rbamtools

* add gsl * try to build mzr * add sklearn as deps * Various updates (#12677) * remove mzr dependent packages from blacklist * add extended base image * update version * add openblas * Use quotes when extending PATH. (#12662) * Use quotes when extending PATH env var, in order to handle potential space characters. * trigger * [BULK] Fix bulk (#12695) * Update intarna to 2.3.1 (#12367) * Update agfusion to 1.231 (#12366) * Update bioconda-utils to 0.15.0 (#12359) * Update mapdamage2 to 2.0.9 (#12358) * Update scanpy to 1.3.4 (#12357) * Update goatools to 0.8.11 (#12361) * Update perl-math-random-mt-auto to 6.23 (#12362) * Update kipoi to 0.6.3 (#12374) * Update kipoi_veff to 0.2.1 (#12364) * Update perl-object-insideout to 4.05 (#12380) * Update sevenbridges-python to 0.17.1 (#12379) * Update nanosv to 1.2.3 (#12378) * Update starfish to 0.0.30 (#12368) * Update clust to 1.8.10 (#12356) * Update pypairs to 2.0.6 (#12381) * Update khmer to 3.0.0a2 (#12360) * Update flashlfq to 0.1.110 (#12385) * Update perl-algorithm-cluster to 1.57 (#12384) * Update arvados-python-client to 1.2.0.20181121194423 (#12382) * Update avro-cwl to 1.8.9 (#12355) * Update avro-cwl to 1.8.9 * Set noarch: python * r-breakaway (#12386) * R sads (#12388) * Update python-sortedcontainers to 2.1.0 (#12383) * r-ebimetagenomics (#12339) * pin armadilo on major version (#12389) * IgDiscover version 0.11 (#12351) * IgDiscover version 0.11 * IgDiscover requires Python 3.6 * Fix build on macOS with a small patch * Remove unneeded host dependencies * Update goatools to 0.8.12 (#12391) * Update bioconda-utils to 0.15.1 (#12390) * R ebimetagenomics (#12393) * Add dimspy recipes for reference purposes (#12387) * Add dimspy recipes for reference purposes * Remove filename * remove from blacklist * Update build-fail-blacklist * Added BioExcel_SeqQC to bioconda-recipes (#12276) * PacBio: Update pbalign to 0.3.2 (#12396) * PacBio: Update pbalign to 0.3.2 Closes: PacificBiosciences/pbbioconda#39 * add bgreat to bioconda (#12350) * bgreat addition * zlib in build should not be needed * btrim integration to conda (#12395) * Format sleuth recipe. Trigger rebuild because latest version was never uploaded for some reason. (#12399) * PacBio: Update `pbsv2` to version 2.1.0 (#12400) * Genenotebook v0.1.11 (#12398) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * prosolo: new package version 0.6.0 (#12397) * Update sevenbridges-python to 0.17.2 (#12404) * Add recipe for ICED (#12406) * Downgrade version for iced (#12409) * Update recipe for libstatgen 1.0.5 (#12348) * Add recipe for libstatgen-1.0.5 * Update iced to 0.5.0 (#12411) * Update perl-test2-suite to 0.000116 (#12412) * fix compatibility with other tools (#12415) * Restore dexseq python helper scripts (#12352) * Restore dexseq python helper scripts * Add python requirement for helper scripts * Add python noarch to build section * pin it to python2k * Add htseq requirement, support only python <3 for now * Genenotebook v0.1.12 (#12418) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * added medpy recipe (#12417) * added medpy recipe * removed osx from build * Update meta.yaml * Update meta.yaml * add boost and a compiler * Update meta.yaml * Update meta.yaml * add itk * Updated ddrage to version 1.6.1. (#12421) * Add r-mcpcounter recipe. (#12261) * Add MCPcounter recipe. * fix lint: remove 'fn' * fix license_file, version number and doi * Update DEXSeq requirements to force compatible HTSeq version (#12423) * ARB: Pin glib (#11782) * Pin glib * Update meta.yaml * Update meta.yaml * Work around CB3 issues * Work around bioconda-utils lint false positive * Disable lint check should_not_be_noarch * Can't reference other packages built in recipe from anything but run * Move perl to host section. Maybe that helps. * constraining interpreter version breaks with CB3? * disable perl version constraint :( * Update meta.yaml (#12426) * stacks: fix for fix 'fixing' @ in exe_path (#12420) * stacks: fix for fix 'fixing' @ in exe_path the previous fix https://github.com/bioconda/bioconda-recipes/pull/11580 tried to solve the problem with the @ in the exe_path by setting this variable empty. But the perl scripts - append a / to the empty string and (i.e. the bin path gets /binary) - check for file presence (problem: neither binary nor /binary are present) Now I quote the @ in the exe_path. * stacks: add refmap bugfix * Genenotebook v0.1.13 (#12424) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * genenotebook v0.1.3 * new build procedure * change run dependencies * build * restore build procedure * Fix summary * dependency versions * v0.1.5 * version fix * v0.1.6 * reset build number * build number * genenotebook v0.1.7 * v0.1.8 * v0.1.9 * v0.1.10 * v0.1.11 * v0.1.12 * updated source * v0.1.13 * metaQuantome (#12413) replaces metaquant, which is now deprecated. * New MMseqs2 release 7-4e23d (#12432) New mmseqs2 release 7-4e23d * update spades to 3.13.0 (#12408) * update spades to 3.13.0 * spades: removed dipspades; added 3.12.0 recipe in subdir * bumped build number for 3.11.1 due to CI failure * Update Crossmap to 0.3.1 (#12439) * Update Crossmap to 0.3.1 * Make metaquantome dependencies more specific (#12442) * less stringent deps * bump build * pin goatools * test extra pins * integration of bcool to bioconda (#12422) * Update hifive to 1.5.7 (#12433) * Update scvi to 0.2.3 (#12434) * Update Subread from 1.6.2 to 1.6.3. (#12425) * Update Subread from 1.6.2 to 1.6.3. * Subread executable coverageCount has been removed. https://groups.google.com/d/msg/subread/Au1CpKGAXaA/KndhDbrfAwAJ * UCSC Cell Browser 0.4.23 (#12347) * Starting files for ucsc-cell-browser * Customised recipe for ucsc-cell-browser * meta update for ucsc-cell-browser * Changes cbTrackHub to cbHub * Point to static release * Moves to 0.25 * Updates sha hash for ucsc-browser * Reverts to 0.1.9 * At ebi * Update meta.yaml * pins numpy to last know working version * Back to 0.25, no numpy pinning. * Remove git, pin python and numpy. Add build section. * Update meta.yaml * Update meta.yaml * Move to 0.4.20 without skeleton on provisional commit * Typo on executable name * Moves to release version and adds dependencies for converters * Update libstatgen to 1.0.14 (#12437) * Update arvados-python-client to 1.2.1 (#12438) * Update tirmite to 1.1.3 (#12435) * Bump metaquantome (#12449) * less stringent deps * bump build * pin goatools * test extra pins * bump metaquantome to 0.99.3 * Update ADAM to 0.25.0 (#12445) * Update: bcbio, bcbio-vm with viral QC, Docker fixes (#12453) * update rgi4.2.2 recipe (#12282) * update to enforce python3.6 and load card.json * remove lines from build.sh * update build number * make PR comment changes * add test to verify db is loaded * update build script * update build script * fix lint errors * fix linting errors * fix liniting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * fix linting errors * revert test change * Add CRAN R package leapp. (#12428) * Bump DECIPHER to Bioconductor 3.7 (#12463) * Bump DECIPHER to Bioconductor 3.7 * Change r-rsqlite version dependency * Update meta.yaml * updated scVI to 0.2.3 (#12429) * Add recipe for PyAAVF 0.1.0 (#12451) * Add recipe for PyAAVF 0.1.0 * Fix linting error * seqkit 0.9.3 (#12455) * HTSeq - Pin numpy version (#12467) * update eigensoft to 7.2.1 (#12469) * Update scnic to 0.6.0 (#12436) * Update scnic to 0.6.0 * Work around fastspar insufficient armadillo pin * fix pin * GimmeMotifs 0.13.1 (#12471) * Bumped version to newest, with introspective text (#12461) * Update Segway 2.0.2 recipe to use older depedencies (#11803) * Update Segway 2.0.2 recipe to use older depedencies * Update maximum genomedata version supported * Update build number * Fix missing older dependency information * Update meta.yaml * updating dependencies for reparation_blast (#12443) * updating dependencies for reparation_blast * changed dependency of pysam * Added DropletUtils package (#12448) * Create recipe for SVIM (#12272) * add svim recipe * fix bugs in svim recipe * replace source file * remove license file * Lowercase biopython * upgrade to svim 0.4.1 * add GPL LICENSE file, allow python 3.6.* patch releases, add minimap2 dependency * fix python version * try to fix lint error * replace "skip: True" with "noarch: python" * Update bioconductor-biocgenerics (#12477) * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Irida sistr results 0.6.0 (#12478) * Update irida-sistr-results to 0.6.0 * Fixed dependency string * Adding recipe for clinvar-tsv v0.1.0. (#12481) * no fixed boost version (#12483) * New recipe: pysradb (#12470) * Pyseer 1.2.0 (#12444) * Update pyseer to 1.1.2 * Update pyseer to 1.2.0 * Update pyseer to 1.2.0 Update pyseer to 1.2.0 Update pyseer to 1.2.0 (fixed) * Final touches to pyseer 1.2.0 * Additional update to pyseer recipe * sentieon: minor version bump to 201808.01 (#12480) * adding java to mutations recipe (#12485) * Update ncrf to 1.00.06 (#12369) * Update ncrf to 1.00.06 * Update test string * Bump umitools (#12486) * Mob suite version 1.4.9 no arch build number 2 (#12479) * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * Update r-goeveg to 0.4.2 (#12375) * Update r-goeveg to 0.4.2 * Add r-hmisc as dependency * Removes r-seurat-scripts from blacklisting (#12489) * Removes r-seurat-scripts from blacklisting * Unblacklist some non bioconductor packages * For VarDict-Java, install utility scripts. (#12488) * For VarDict-Java, install utility scripts. Utility script that were previously only shipped with VarDict are not part of VarDict-Java as well, making installation of both packages unnecessary. * Bump build. * Improve variable name. * Make vardict depend on vardict-java for utility scripts. * Pin compatible numpy for older HTSEQ versions (#12490) * Pin compatible numpy for older HTSEQ versions This is required to keep older versions of HTSEQ functional * HTSeq - update old versions to build properly with new build system * HTSeq 0.6.1 - Increment build number * add recipe for r-epic (#12473) * Add new recipe - RVTESTS (#12465) * Add rvtests * Update pre-req * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create LICENSE * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Create run_test.sh * Update meta.yaml * Delete run_test.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Adding recipe for var-agg v0.1.0 (#12482) * Adding recipe for var-agg v0.1.0 * runtime deps do have run-exports defined * move rust into the host section * Adding dependency to clangdev * Adding var-agg v0.1.1. (#12495) * [WIP] Salmon v0.12.0 --- try to fix OSX build for real (#12441) Salmon v0.12.0 --- version bump and fix OSX build * Considerable updates in terms of features and fixes (check release notes). * Fix OSX build that would compile, but segfault in quant (but only when built on "old" OSX). * Performancean alytics (#12498) * Add bioconductor package RNASeqR * Add performanceanalytics * Performancean alytics (#12499) * Add bioconductor package RNASeqR * Add performanceanalytics * Move recipes/r-performanceanalytics and add r-rafalib * Move r-performanceanalytics/ to recipes * Update recipes/r-performanceanalytics * Update r-rafalib * Remove recipes/r-performanceanalytics/bld.bat * Remove recipes/r-performanceanalytics * Update r-performanceanalytics/ * Update r-performanceanalytics/ * Add r-performanceanalytics/ * remove r-performanceanalytics * Add performanceanalytics * Remove r-performanceanalytics * Update Picard to 2.18.20. (#12501) * Update vsearch to 2.10.0. (#12504) * Update Purge Haplotigs to v1.0.4 (#12497) * Update duphold to 0.1.1 (#12516) * Update starfish to 0.0.31 (#12515) * Update perl-term-app-roles to 0.02 (#12512) * Update perl-dbd-sqlite to 1.60 (#12511) * Update perl-json to 4.00 (#12509) * Update kipoi to 0.6.5 (#12508) * Update illumina-interop to 1.1.8 (#12507) * Update beagle-lib to 3.1.2 (#12523) * Update pysradb to 0.3.0 (#12522) * Update bioconda-utils to 0.15.2 (#12525) * Update perl-json-pp to 4.0 (#12524) * Update perl-term-table to 0.013 (#12529) * Update abyss to 2.1.5 (#12528) * Update perl-test2-suite to 0.000117 (#12527) * Update wtforms-alchemy to 0.16.8 (#12505) * Update perl-carp-clan to 6.07 (#12518) * Update perl-date-manip to 6.75 (#12519) * Update: seq2c, multiqc-bcbio (#12533) * tracy v0.3.7 (#12534) * Version bump 2.10 (#12535) * Version bump 2.10 * Copy paste error forgot the https * Missing deps for ucsc-cell-browser 0.4.23 (#12537) * Missing deps for ucsc-cell-browser * Bumps build nuber * Update vsearch to 2.10.1 (#12540) * New recipe for MicroHapDB 0.2 (#12531) * New recipe for MicroHapDB 0.2 * Troubleshoot config * Successful build locally! * Clean up recipe * Update moff to 2.0.2 (#12539) * Update PopDel to version 1.0.5 (#12502) * Update PopDel to version 1.0.5 * Remove Makefile.patch Remove Makefile.patch and adapt build.sh to set the correct version, date and CXX-path in its stead. * Automatically get version from PKG_VERSION * Update to teloclip v0.0.3 (#12542) * Update biolite to 1.2.0 (#12544) * Update kneaddata to 0.7.2 (#12543) * snakemake 5.3.1 (#12500) * snakemake 5.3.1 * fix jinja variables * only warn if git not present in tests * use explicit jinja for version again. Conda seems to have lost the ability to use PKG_VERSION in meta.yaml. * try masking env var * try defining env var before command * nextflow: pin openjdk=8 to solve java version parsing issue (#12493) * Pin openjdk=8 * Alllow openjdk 8 or 9 * Update bioconda-utils to 0.15.3 (#12546) * Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 (#12549) * Update: mosdepth (0.2.4) bcbio/bcbio-nextgen#2590 * Update install patch for 0.2.4 * Match nim release version 0.19.0 * Scanpy scripts (#12551) * Bump version * Fix scanpy version requirement to v1.3.2 * Update to v0.0.4 * Update nanosim to 2.2.0 (#12517) * Update nanosim to 2.2.0 * Add sklearn as dependency * Recipe for kma (#12554) * PacBio: Update `pbsv2` to version 2.1.1 (#12556) * Add counterr (#12541) * Add counterr * Fix typo * Use tagged release * Updated ddRAGE to version 1.6.3 (#12557) * Add recipe for SNVer 0.5.3 (#12265) * Add recipe for SNVer 0.5.3 * Add CRAN R package cate. (#12562) * r-seurat-scripts: Fixed DimPlots() issues, addressed libpng issue for OSX (#12563) * Fixed DimPlots() issues, addressed libpng issue for OSX * Correction: removed testing line in source package * Update scanpy to 1.3.5 (#12571) * Update vsearch to 2.10.2 (#12579) * Update mentalist to 0.2.4 (#12578) * Update krakenuniq to 0.5.5 (#12575) * Update mlst to 2.16 (#12572) * Update transit to 2.3.3 (#12570) * Update anndata to 0.6.14 (#12568) * Update svim to 0.4.2 (#12566) * Update perl-test-cleannamespaces to 0.24 (#12569) * uptdate mlst to 2.16.1 (#12582) * Update jcvi to 0.8.12 (#12574) * add cromwell-tools (CLI and API for Cromwell workflow manager). (#12564) * added cromwell-tools * point to stable docs rather than latest * Remove noarch to make os-specifics work (#12583) * prosolo: update to v0.6.1 (#12584) * integration to bioconda (#12456) * Recipe for sparcc (#12459) * Recipe for SparCC * Remove maintainers lines * Add license info * Mention pull request for patch * Fix lint * Build noarch * Update: bcbio (v1.1.2), bcbio-vm (GCP support) (#12585) * t-coffee 12.00.7fb08c2 (#12594) * t-coffee 12.00.7fb08c2 * add viennarna to deps Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run. * t-coffee 12.00.7fb08c2 (2) This commit adds vienna packages and remove TMalign copy command * t-coffee 12.00.7fb08c2 (4) Adding TMalign * Nf core V 1.4 (#12599) * Need to update SHA256 once release is out! * Update to release 1.4 * Sleuth unblacklist (#12591) * remove sleuth from blacklist * Remove obsolete dependency. * Bump spectra-cluster-cli (#12598) * Update gseapy to 0.9.9 (#12530) * Update gseapy to 0.9.9 * Add scipy * Add bioservices as dependency * added recipe perl-bio-viennangs 0.19.2 (#12596) * Add SVMlight (#12595) * Add SVMlight * Update meta yaml * Update SHA256 sum * Update build script to copy executables * Update meta.yaml * Fix o-umlaut * Fix test stalls svm_learn -? displays a pager, waiting for keyboard input * rhdf5 2.26 and rhdf5lib 1.4 (#12597) * rhdf5 2.26 and rhdf5lib 1.4 * force C99 mode * set CFLAGS in Makevars * Add recipe for hiddenDomains (#12614) * bump pysradb 0.3.0 -> 0.4.0 (#12612) * bump pysradb 0.3.0 -> 0.4.0 * Fix imports * Add extras * Update slicedimage to 1.0.2 (#12609) * Update perl-module-scandeps to 1.26 (#12608) * Update scanpy to 1.3.6 (#12605) * Update abeona to 0.40.2 (#12602) * Update confindr to 0.4.8 (#12607) * Update anndata to 0.6.15 (#12606) * tmaling (#12588) Add tmalign recipe * pysvmlight added (#12617) * Add fontconfig / ttf-dejavu to fastqc recipe (#12616) * pdate adVNTR to 1.2.0 (#12613) * add adVNTR * fix linux error for adVNTR * add numpy to adVNTR requirements * add numpy include dirs for cythonize * Update advntr to 1.1.0 * Update advntr to 1.1.0 * update advntr to 1.1.1 * update adVNTR to 1.2.0 * update sha256 for adVNTR-1.2.0 * fix build script for adVNTR-1.2.0 * fix adVNTR-1.2.0 * PeptideShaker v1.16.36 & SearchGUI v3.3.10 (#12620) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 * PeptideShaker version updated to 1.16.36 SearchGUI version updated to 3.3.10 * New recipe (refinem: 0.0.24) (#12628) * Replace sha256 and bump build num (#12629) * Update galaxy-parsec to 1.0.6 (#12634) * Add recipe for SeqMap (#12615) * Add recipe for SeqMap * Change cp Change cp * Updated concoct to version 1.0.0 (#12600) * Updated concoct to version 1.0.0 * Skip build for macosx at this point * New build number * Reset build number to 0, thanks @druvus * Update deepvariant to 0.7.2 (#12638) * Update abeona to 0.41.1 (#12637) * Update shmlast to 1.3 (#12636) * Update krakenuniq to 0.5.6 (#12633) * Update selene-sdk to 0.2.0 (#12632) * Update comet-ms to 2018013 (#12555) * Update with selene-sdk v0.2.0 (#12631) * update with selene-0.2.0 * Update meta.yaml * add self to recipe maintainers * Cat updated version (#12587) * v 4.3.1 * Pin BLAST+ version to >= 2.2, < 2.4 (#12639) * Shmlast v1.4 (#12645) * Bump shmlast to v1.4 * Update PopDel to version 1.0.6 (#12644) * Update PopDel to version 1.0.6 * Adapt tests * Remove test for correct version number Redirection seems to cause error in circleci: ".Passing program arguments as a string may be a security hazard if combined with untrusted input" * Concoct add samtools as a dependency (#12642) * Updated concoct to version 1.0.0 * Skip build for macosx at this point * New build number * Reset build number to 0, thanks @druvus * Samtools new requirement for concoct v1.0.0 * Bump topas (#12618) * Bump spectra-cluster-cli * Bump topas * Use ${PKG_VERSION} * Small tweaks * No recursion * pasta-1.7.8-build-2 (#12641) * pasta-1.7.8-build-2 * Relax requirements * Rebuild pasta (#12648) * Bump spectra-cluster-cli * Delete old pasta * Rebuild pasta * Unblacklist pasta * Revert dendropy version * Correct build number * Use openjdk * Rebuild perl-pod-coverage (#12652) * Rebuild perl-pod-coverage * Unblacklist * tracy v0.3.8 (#12651) * Kalign (#12647) * add kalign This recipe adds kalign * fix for osx * fix for osx #2 * Rebuild perl-test-pod-coverage (#12654) * Rebuild perl-test-pod-coverage * Unblacklist * Update: bcbio (1.1.3a) Fixes bcbio/bcbio-nextgen#2594 (#12655) * Rebuild perl-test-file-contents (#12649) * Bump spectra-cluster-cli * Rebuild perl-test-file-contents * Kleborate 0.3.0 (#12657) * Adding recipe for >> kleborate << * Rebuild perl-params-coerce (#12660) * Upgrade biodb to version 1.2.0b. (#12663) * Add recipe for unitas (#12658) * Add recipe for unitas * Rebuild perl-file-share (#12661) * Update sevenbridges-python to 0.17.3 (#12667) * Update slicedimage to 1.0.3 (#12666) * Update cat to 4.3.3 (#12665) * Update crossmap to 0.3.2 (#12664) * Update: deepvariant 0.7.2 model and dependencies (#12672) - Requires tensorflow 1.12 - Update model data for 0.7.2 - Remove requirement for --regions in dv_make_examples.py wrapper. Fixes #12560 * unblacklist perl-bio-viennangs (#12643) * unblacklist perl-bio-viennangs * fix version string; remove 0.19 recipe * remove all perl version strings * increased build nr * Add pysvmlight (#12673) * Remove the mess I created in the main repository (#12674) * Add missing dependencies and bump version for FRED2 (#12621) * Add missing dependencies and bump version for FRED2 * Bump version to force rebuild * Update meraculous to 2.2.6 (#12254) * Update meraculous to 2.2.6 * Remove perl pinning * Update BioExcel_SeqQC to 0.6 (#12604) * Update BioExcel_SeqQC to 0.6 * Fix name * Update anndata to 0.6.16 (#12676) * Update pysradb to 0.4.2 (#12675) * version 3.0.3 (#12678) * Add perl-math-utils (#12681) * Add perl-math-utils * Remove fn * Rebuild perl-extutils-makemaker (#12680) * Update perl-html-formatter to 2.16 (#12225) * Update perl-html-formatter to 2.16 * Fix deps * Update perl-readonly to 2.05 (#12153) * Update perl-readonly to 2.05 * Fix deps * Update perl-html-tidy to 1.60 (#12187) * Update perl-html-tidy to 1.60 * Update deps * Update meta.yaml * Update perl-libwww-perl to 6.36 (#12180) * Update perl-libwww-perl to 6.36 * Update deps * Update meta.yaml * Add perl-html-parser as dep * Add back perl-ntlm * Update PopDel to version 1.0.7 (#12685) * Use quotes when extending PATH. (#12662) * Use quotes when extending PATH env var, in order to handle potential space characters. * Update perl-math-derivative to 1.01 (#12158) * Update perl-math-derivative to 1.01 * Update dependency * Update perl-data-dumper to 2.173 (#12224) * Update perl-parallel-forkmanager to 2.02 (#12170) * Update perl-parallel-forkmanager to 2.02 * Update deps * Update bioblend to 0.12.0 (#12687) * Update abeona to 0.42.0 (#12686) * blacklist r-rbamtools * just skip the check for now * [BULK] Bulk update 191218 (#12731) * A few updates * update blacklist * Fix biocsklearn * seems to needs gsl * fix a few recipes (#12785) * Fixes (#12787) * fix a few recipes * fix recipes * add new blacklisted recipes * remove old recipes * remove old recipes * add jackstraw * add orqa * add isogene * Fixes for bulk (#12788) * fix a few recipes * fix recipes * add new blacklisted recipes * remove old recipes * remove old recipes * add jackstraw * add orqa * add isogene * add r-grain * add r-pcalg * fix recipes * fix more r-* recipes * quick fix for bulk (#12789) * try linking the shared object * fix dependency * [BULK] A few fixes (#12792) * A few fixes * remove all bld.bat files * build bumps * Bulk update 241218 (#12795) [BULK] Bulk update 241218 * increase build numbers * bump build number * bump * blacklist a few more * Bump karyoploteR as seen in https://github.com/bioconda/bioconda-recipes/pull/12732, thanks @dpryan79 and @bgruening. (#12800) * Bulk update 271218 (#12820) * Update atacseqqc * another fix * fix r-exomedepth * update blacklist * Fix r-loose.rock * increase build number * add recipes/r-rcdk to the blacklist * various bulk fixes (#12858) * bbn * update the blacklist (#12862) * various bulk updates (#12863) * fix gviz (#12864) * a few updates, modify blacklist (#12865) * a few updates (#12866) * Add a few CRAN recipes (#12867) * Last updates for the year (#12881) * Guten Rutsch (#12882) * add r-diffcorr and update blacklist (#12883) * updates for bulk (#12884) * update and add recipes (#12885) * Fix r-htscluster real quick * bulk updates (#12887) * more updates (#12888) * more updates * update mageckflute * Bulk update 030119a (#12896) * bulk updates * a couple more updates * Bulk updates for 040119 (#12910) * Bulk update 040119b (#12916) * Bulk updates for 040119 * update blacklist * update champ * fix license string * bumb build number * a few updates (#12923) * a few updates * Remove bld.bat * bumb build-numbers and keep bulk busy * bumb build-numbers and keep bulk busy (#12924) * 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…

t-coffee 12.00.7fb08c2

1c5655b

pditommaso mentioned this pull request Dec 12, 2018

Bioconda has two (redundant) T-COFFEE packages #10614

Closed

SchwarzMarek and others added 3 commits December 12, 2018 16:06

add viennarna to deps

eb54e12

Adding viennarna to runtime dependencies will include RNAplfold thus allowing -mode rcoffee to run.

t-coffee 12.00.7fb08c2 (2)

cffdebc

This commit adds vienna packages and remove TMalign copy command

t-coffee 12.00.7fb08c2 (4)

5aff296

Adding TMalign

apeltzer merged commit 2096759 into bioconda:master Dec 12, 2018

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t-coffee 12.00.7fb08c2 #12594

t-coffee 12.00.7fb08c2 #12594

pditommaso commented Dec 12, 2018

SchwarzMarek commented Dec 12, 2018 •

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pditommaso commented Dec 12, 2018 •

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apeltzer commented Dec 12, 2018

t-coffee 12.00.7fb08c2 #12594

t-coffee 12.00.7fb08c2 #12594

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pditommaso commented Dec 12, 2018

SchwarzMarek commented Dec 12, 2018 • edited Loading

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apeltzer commented Dec 12, 2018

SchwarzMarek commented Dec 12, 2018 •

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pditommaso commented Dec 12, 2018 •

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