Merge bioconductor packages back into master #16953
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* Use quotes when extending PATH env var, in order to handle potential space characters.
* 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
* A few updates * update blacklist * Fix biocsklearn * seems to needs gsl
* 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
* A few fixes * remove all bld.bat files
[BULK] Bulk update 241218
* Update atacseqqc * another fix * fix r-exomedepth * update blacklist
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Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the
please review & mergelabel so other members of the bioconda community can have a look at your PR and either make suggestions or merge it. Note that if you are not already a member of the bioconda project (meaning that you can't add this label), please ping@bioconda/coreso that your PR can be reviewed and merged (please note if you'd like to be added to the bioconda project). Please see #15332 for more details.