Bulk updates for 040119 #12910

dpryan79 · 2019-01-04T12:29:49Z

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).

* 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…

* 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/_compare_reads.so): Needed DSO lib/libpython2.7.so.1.0 found in ['python'] WARNING (compare-reads,lib/python2.7/site-packages/compare_reads/_compare_reads.so): .. but ['python'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely) ``` * Update kipoi_veff to 0.2.2 (#13350) * shapeshifter recipe added (#13487) * added shapeshifter recipe * adding shapeshifter package, passed circleci tests * updating changes as requested in the review * fixed typo, items requested in review should be fixed * passed circleci locally, changes made as requested * Update sina to 1.5.0 (#13547) * Update sina to 1.5.0 * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * remove std=c++14 - won't work w/ boost * Dump test logs on failure * Add bc to host env * Rapid08 (#13666) * v0.8 update - added r-viridis package * r-viridis fix version * 0.8 viridis, plots CB friendly update * rapidv0.8_build_1 * Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230 * Creating v1.0 * Add new recipe for ataqv (#13665) * Bump umis to v1.0.3 with python3 support. (#13668) * Add recipe for fusioncatcher-seqtk (#13669) * moFF : Enforced python v3.4 or later as pymzml requires it. (#13541) * Enforced python v3.4 or later as pymzml requires it. * Increased build number * Update meta.yaml * Update meta.yaml * Update meta.yaml * Fixed reference to pymzml >=2.0.6 * Update meta.yaml * Update meta.yaml * add extra section * Avoiding dependency problem with Python 3.7 * WhatsHap 0.18 (#13670) * add python to run requirements (#13673) * fix mykrobe python package dependencies (#13672) * update mykrobe to v0.6.1 remove source fn add wget to build requirements add zlib to build requirements move zlib to host requirements specify zlib location specify zlib location move zlib to build requirements add c compiler add some more zlib related flags add some more zlib related flags add htslib to reqs add setuptools to reqs remove htslib to reqs try pip install instead try skipping py2 skip py27 and add imports test see if py27 works now remove py27 build create test script create test script add tests dir to test reqs add data dir to test reqs * Update meta.yaml * add wget to host * clean up build script. add test source files * add post-link script for downloading panel data * add prefix location specifier for mykrobe data dir * fix post-link script * switch to shasum for data download check. add wget to run reqs * use pip install * Delete build.sh * not sure why this has not failed before * Update meta.yaml * fix mccortex install * use default compiler for cxx * compile with -fPIC * remove hard-coded gcc in htslib Makefile. remove unncessary reqs * add python package reqs to run reqs and test * Tango (#13671) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * Bumped tango to version 0.3.0 * Update tango to version 0.3.1 * Updated shasum * Update meta.yaml * Update meta.yaml (#13674) :information_source: Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578). ---------------- * [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update scanpy (#13675) * Update meta.yaml * Delete build.sh * make noarch * Add recipe for fusioncatcher (#13676) * Add recipe for fusioncatcher * convert to noarch package (#13677) * convert to noarch package * Update meta.yaml * Update meta.yaml * add license file * VEP: bump subversion (#13681) * VEP: bump subversion * build -> host * Scanpy scripts pandas fix (#13678) * Prevent problematic pandas 0.24 * Bump build number * Bump anvio to 5.3.0 (#13682) * bump anvio * Fix file * Bump deepTools to 3.2.0 (#13683) * Bump deepTools to 3.2.0 * deepTools is now noarch: python * Update: simple_sv_annotation, up/down fixes + py3k (#13685) * update bioconda-utils to 0.15.8 (#13688) * digestiflow-cli v0.5.0 (#13689) * Fusioncatcher db file rename (#13690) * Rename download db file * Medaka (#13687) * First go at medaka * Building on linux, osx dying on docker * Add license_file to medaka/meta.yaml * Bump/scnic (#13691) * Update scnic to 0.6.0 * Add 0.6.0 new dependencies * Get rid of parallel dependency * Bump SCNIC version to 0.6.1 * Add igor_vdj (#13684) * Add igor_vdj * Odd, I didn't need automake locally * Not packaging the python module at this time. * Add autoconf * Use a standard jemalloc * Try not running configure in igor_src * What if we rerun autogen.sh * blah * blah * foo * sigh * Remove old build stuff, it was just a timestamp problem * Don't set -lrt on OSX * Update meta.yaml * pysradb: update to 0.7.1 (#13694) * pysradb: update to 0.7.1 * Now taking Genepop from a reproducible source (#13693) This uses a reproducible source for genepop (CRAN). ---------------- * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * tracy v0.5.2 (#13700) * Bump build (#13701) Trigger the build again for `bioconductor-flowtype`. * r-momr (#13703) * Mob suite 1.4.9.1 (#13697) * Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies * updated recipe to download from URL instead of github * build python version requirement defined (python >=3.4) * added build number * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added test statement (import) * added test statement (import) * added the new repository and py36 only compile * made requested corrections by daler. Corrected build number and package string * Small fixes * revert deleted row * New version, fixed sum bugs and improved stability * Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters * Updated to version 1.4.9 * Updated to version 1.4.9 * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * new db host * updated meta.yaml with resolved conficts from the head branch * build not more than python 3.6 * add a recipe for FastqPuri (#13679) * add a recipe for FastqPuri Changes to be committed: new file: recipes/fastqpuri/build.sh new file: recipes/fastqpuri/meta.yaml * fix issues in fastqpuri recipe Changes to be committed: modified: build.sh modified: meta.yaml * add neatfeatures track types + patch combotrackselector (xref https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/pull/5) (#13704) * Add new recipe for finestructure (#13707) * Version bump msstitch to 2.12 (#13705) * Bump CLARK (#13709) * Update fastp to 0.19.7. (#13714) * Update STAR to 2.7.0d, add 2.6.1d, as it doesn't require rebuilding the index (#13717) * update SURVIVOR to v1.0.6 (#13718) * Update cooler to v0.8.3 (#13712) * Update cooler to v0.8.3 * Update meta.yaml * Update UCSC templates to build under OSX * Update all UCSC recipes. * try fixing ucsc-overlapselect * Bump a bunch of packages for pinnings (#13960) * Upgrade cyvcf2 to v0.10.8 (#13726) Patch setup.py to use conda managed htslib * Update bcftools plot_vcfstats (#13721) * Python-tripal 3.2 and python-apollo (#13727) * update python-tripal * add python-apollo recipe * noarch * v0.1.4 February 2019 Release (#13720) * python3 and igv-reports (#13623) * python3 and igv-reports * changing test * adding ls * adding bin ls * print install path contents * run on python3 * proper test * Update meta.yaml (#13729) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * It looks like rJava has now been rebuilt. (#13728) * It looks like rJava has now been rebuilt. * r-rcdk is in conda-forge now * Remove the first batch from the blacklist * Update esATAC * Update CPAT to 1.2.4 (#13732) * Re-do an update undone by 3761102478f21107957c166e85ca843f9c3410b1 (#13733) * Gff3sort (#13731) * add gff3sort recipe * add new dep to sort gff3 files properly * lint * add perl-data-match (for Sort::Topological) * add dep * oh perl, I hate you so much * ...so much.... * take this perl-data-match * wrong path * rebuild with perl 5.26.2 for mac * Update PopPUNK to v1.1.4 (#13723) * Update PopPUNK to v1.1.4 * Add noarch Seems to be a py36 to py37 problem * Cannot have noarch as no python2 support * bump build numbers on dependencies needing rebuild * Update sharedmem recipe * Putting sharedmem build into meta.yaml * Correcting host/build in sharedmem meta for noarch * Make noarch and python>=3 * Remove redundancy in sharedmem meta.yaml * Update comet-ms to 2018014 (#13645) * Remove more rJava packages from the blacklist (#13734) * Remove more rJava packages from the blacklist * update * Sc3 scripts update (#13735) * Bump bioconductor-sc3-scripts package to 0.0.3 * Reset build counter * Add pychopper (#13738) * Add pychopper * build command * pb-falcon: 0.2.6 (#13740) * pbfalcon-0.2.6 * pb-falcon: Try openssl<1.1 * pb-assembly: update pb-falcon/openssl (#13575) * Remove the remainder of the rJava bioc packages from the blacklist (#13737) * Remove the remainder of the rJava bioc packages from the blacklist * Update * blacklist msgfgui * Add slivar 0.0.5. (#13741) * Add slivar 0.0.5. * Fix test. * Increment build number (#13743) * Update sevenbridges-python to 0.18.2 (#13746) * Bump to latest scanpy-scripts (#13747) * r-ldrtools (#13749) * Try to remove a few bioconductor packages from the blacklist (#13744) * Try to remove a few bioconductor packages from the blacklist * More updates * Yacrd add version 0.5.1 break compatibility with previous version (#13750) * Add version 0.5.0 break compatibility * up to version 0.5.1 * yacrd 0.5.1 correct error in sha256sum * r-mixkernel (#13745) * r-mixkernel * Spydrpick v1.1.1 (#13725) * Update SpydrPick to v1.1.0 * Update spydrpick v1.1.1; aprgrunt 0f34bdd80315e10b2234b5aae50b53102f04fbdd * Use SSE3 rather than AVX2 * With AVX guard around popcnt * PacBio: Update `ccs` to version 3.4.1 (#13755) * Remove a few more packages from the blacklist (#13753) * Remove a few more packages from the blacklist * a few updates * r-parallel is part of r-base * odd * Ready for OSX * needs gfortran it seems * Update PureCLIP to v1.3.0 (#13756) * updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers (#13757) updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers * try again (#13758) * Barcode splitter multi (#13663) * New directory for the barcode splitter recipe. * created using `conda skeleton pypi barcode_splitter_multi`. * created using `conda skeleton pypi barcode_splitter_multi`. * Added source files and tox. Files checked in: recipes/barcode_splitter_multi/meta.yaml * Re-wrote meta.yaml. The existing file was mostly wrong. Files checked in: recipes/barcode_splitter/meta.yaml * Change dirname. * Working out tests. Files checked in: * Addresses issues with conda build. Created a run_test.sh script to work around an issue with the exit code for --help and --version being 2 instead of 0. Added noarch: python to meta.yaml. Added "--single-version-externally-managed --record=record.txt" to the setup.py call in build.sh. Files checked in: recipes/barcode_splitter/build.sh recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Updated sandbox zenodo doi to real zenodo doi now that testing is done. Files checked in: recipes/barcode_splitter/meta.yaml * Removing pass of shell variable to echo. This is an attempt to address a warning from the remote circleci build that passing a variable as an argument generated from the output of the tool is a security risk. It might still complain due to the if conditional checking the variable too. I'll just have to see. Files checked in: recipes/barcode_splitter/run_test.sh * Removed eval of shell variable in if conditional. I suspect that this eval is still related to the security warning and subsequent failure of the test in the remote circleci build. Files checked in: recipes/barcode_splitter/run_test.sh * Updated to a release of barcode_splitter that exits with a status of 0 for --version. I could not get run_test.sh to pass mulled-build tests, so instead of work through that, I just worked around it by releasing the new version with the exit code fix. Files checked in: recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Reverted unintended changes. Files checked in: miniconda.sh .circleci/common.sh * Reverted another unintended change. Didn't realize the file was created instead of changed. Files checked in: .circleci/common.sh * Update meta.yaml * Delete build.sh * CPAT: Stricter python version requirement (#13742) * Stricter python version requirement In CPAT's code the version check for a python version that starts with 2.7 is hardcoded. * Correct license version It is incorrectly reported on PYPI. In the documentation of CPAT and in the project's license file it is mentioned that any later version of GPL is also allowed. * rdkit: remove blacklisted package - now at conda forge (#13759) * platypus update (#13494) * platypus update * added back buildPlatypus.sh * added new path to source * reset build number to 0 * this one needs a compiler isn't it? * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall (#13754) * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall - arvados: fix py3k support by avoiding subprocess32 on py3k - bcbio-variation-recall: fix platypus contig header generation. Fixes bcbio/bcbio-nextgen#2688 * Avoid py37 selectors, trying to fix py27 build * Try to avoid py37 errors with noarch * Fix python selectors * Avoid noarch linter errors, not sure why triggered * Avoid noarch linter errors, not sure why triggered * Pin arvados-python-client with py37 subprocess fix * Wasabi 1.0.0 (#13760) * UCSC blacklist (#13763) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1 (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicou…

* 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/_compare_reads.so): Needed DSO lib/libpython2.7.so.1.0 found in ['python'] WARNING (compare-reads,lib/python2.7/site-packages/compare_reads/_compare_reads.so): .. but ['python'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely) ``` * Update kipoi_veff to 0.2.2 (#13350) * shapeshifter recipe added (#13487) * added shapeshifter recipe * adding shapeshifter package, passed circleci tests * updating changes as requested in the review * fixed typo, items requested in review should be fixed * passed circleci locally, changes made as requested * Update sina to 1.5.0 (#13547) * Update sina to 1.5.0 * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * remove std=c++14 - won't work w/ boost * Dump test logs on failure * Add bc to host env * Rapid08 (#13666) * v0.8 update - added r-viridis package * r-viridis fix version * 0.8 viridis, plots CB friendly update * rapidv0.8_build_1 * Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230 * Creating v1.0 * Add new recipe for ataqv (#13665) * Bump umis to v1.0.3 with python3 support. (#13668) * Add recipe for fusioncatcher-seqtk (#13669) * moFF : Enforced python v3.4 or later as pymzml requires it. (#13541) * Enforced python v3.4 or later as pymzml requires it. * Increased build number * Update meta.yaml * Update meta.yaml * Update meta.yaml * Fixed reference to pymzml >=2.0.6 * Update meta.yaml * Update meta.yaml * add extra section * Avoiding dependency problem with Python 3.7 * WhatsHap 0.18 (#13670) * add python to run requirements (#13673) * fix mykrobe python package dependencies (#13672) * update mykrobe to v0.6.1 remove source fn add wget to build requirements add zlib to build requirements move zlib to host requirements specify zlib location specify zlib location move zlib to build requirements add c compiler add some more zlib related flags add some more zlib related flags add htslib to reqs add setuptools to reqs remove htslib to reqs try pip install instead try skipping py2 skip py27 and add imports test see if py27 works now remove py27 build create test script create test script add tests dir to test reqs add data dir to test reqs * Update meta.yaml * add wget to host * clean up build script. add test source files * add post-link script for downloading panel data * add prefix location specifier for mykrobe data dir * fix post-link script * switch to shasum for data download check. add wget to run reqs * use pip install * Delete build.sh * not sure why this has not failed before * Update meta.yaml * fix mccortex install * use default compiler for cxx * compile with -fPIC * remove hard-coded gcc in htslib Makefile. remove unncessary reqs * add python package reqs to run reqs and test * Tango (#13671) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * Bumped tango to version 0.3.0 * Update tango to version 0.3.1 * Updated shasum * Update meta.yaml * Update meta.yaml (#13674) :information_source: Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578). ---------------- * [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update scanpy (#13675) * Update meta.yaml * Delete build.sh * make noarch * Add recipe for fusioncatcher (#13676) * Add recipe for fusioncatcher * convert to noarch package (#13677) * convert to noarch package * Update meta.yaml * Update meta.yaml * add license file * VEP: bump subversion (#13681) * VEP: bump subversion * build -> host * Scanpy scripts pandas fix (#13678) * Prevent problematic pandas 0.24 * Bump build number * Bump anvio to 5.3.0 (#13682) * bump anvio * Fix file * Bump deepTools to 3.2.0 (#13683) * Bump deepTools to 3.2.0 * deepTools is now noarch: python * Update: simple_sv_annotation, up/down fixes + py3k (#13685) * update bioconda-utils to 0.15.8 (#13688) * digestiflow-cli v0.5.0 (#13689) * Fusioncatcher db file rename (#13690) * Rename download db file * Medaka (#13687) * First go at medaka * Building on linux, osx dying on docker * Add license_file to medaka/meta.yaml * Bump/scnic (#13691) * Update scnic to 0.6.0 * Add 0.6.0 new dependencies * Get rid of parallel dependency * Bump SCNIC version to 0.6.1 * Add igor_vdj (#13684) * Add igor_vdj * Odd, I didn't need automake locally * Not packaging the python module at this time. * Add autoconf * Use a standard jemalloc * Try not running configure in igor_src * What if we rerun autogen.sh * blah * blah * foo * sigh * Remove old build stuff, it was just a timestamp problem * Don't set -lrt on OSX * Update meta.yaml * pysradb: update to 0.7.1 (#13694) * pysradb: update to 0.7.1 * Now taking Genepop from a reproducible source (#13693) This uses a reproducible source for genepop (CRAN). ---------------- * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * tracy v0.5.2 (#13700) * Bump build (#13701) Trigger the build again for `bioconductor-flowtype`. * r-momr (#13703) * Mob suite 1.4.9.1 (#13697) * Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies * updated recipe to download from URL instead of github * build python version requirement defined (python >=3.4) * added build number * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added test statement (import) * added test statement (import) * added the new repository and py36 only compile * made requested corrections by daler. Corrected build number and package string * Small fixes * revert deleted row * New version, fixed sum bugs and improved stability * Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters * Updated to version 1.4.9 * Updated to version 1.4.9 * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * new db host * updated meta.yaml with resolved conficts from the head branch * build not more than python 3.6 * add a recipe for FastqPuri (#13679) * add a recipe for FastqPuri Changes to be committed: new file: recipes/fastqpuri/build.sh new file: recipes/fastqpuri/meta.yaml * fix issues in fastqpuri recipe Changes to be committed: modified: build.sh modified: meta.yaml * add neatfeatures track types + patch combotrackselector (xref https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/pull/5) (#13704) * Add new recipe for finestructure (#13707) * Version bump msstitch to 2.12 (#13705) * Bump CLARK (#13709) * Update fastp to 0.19.7. (#13714) * Update STAR to 2.7.0d, add 2.6.1d, as it doesn't require rebuilding the index (#13717) * update SURVIVOR to v1.0.6 (#13718) * Update cooler to v0.8.3 (#13712) * Update cooler to v0.8.3 * Update meta.yaml * Update UCSC templates to build under OSX * Update all UCSC recipes. * try fixing ucsc-overlapselect * Bump a bunch of packages for pinnings (#13960) * Upgrade cyvcf2 to v0.10.8 (#13726) Patch setup.py to use conda managed htslib * Update bcftools plot_vcfstats (#13721) * Python-tripal 3.2 and python-apollo (#13727) * update python-tripal * add python-apollo recipe * noarch * v0.1.4 February 2019 Release (#13720) * python3 and igv-reports (#13623) * python3 and igv-reports * changing test * adding ls * adding bin ls * print install path contents * run on python3 * proper test * Update meta.yaml (#13729) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * It looks like rJava has now been rebuilt. (#13728) * It looks like rJava has now been rebuilt. * r-rcdk is in conda-forge now * Remove the first batch from the blacklist * Update esATAC * Update CPAT to 1.2.4 (#13732) * Re-do an update undone by 3761102478f21107957c166e85ca843f9c3410b1 (#13733) * Gff3sort (#13731) * add gff3sort recipe * add new dep to sort gff3 files properly * lint * add perl-data-match (for Sort::Topological) * add dep * oh perl, I hate you so much * ...so much.... * take this perl-data-match * wrong path * rebuild with perl 5.26.2 for mac * Update PopPUNK to v1.1.4 (#13723) * Update PopPUNK to v1.1.4 * Add noarch Seems to be a py36 to py37 problem * Cannot have noarch as no python2 support * bump build numbers on dependencies needing rebuild * Update sharedmem recipe * Putting sharedmem build into meta.yaml * Correcting host/build in sharedmem meta for noarch * Make noarch and python>=3 * Remove redundancy in sharedmem meta.yaml * Update comet-ms to 2018014 (#13645) * Remove more rJava packages from the blacklist (#13734) * Remove more rJava packages from the blacklist * update * Sc3 scripts update (#13735) * Bump bioconductor-sc3-scripts package to 0.0.3 * Reset build counter * Add pychopper (#13738) * Add pychopper * build command * pb-falcon: 0.2.6 (#13740) * pbfalcon-0.2.6 * pb-falcon: Try openssl<1.1 * pb-assembly: update pb-falcon/openssl (#13575) * Remove the remainder of the rJava bioc packages from the blacklist (#13737) * Remove the remainder of the rJava bioc packages from the blacklist * Update * blacklist msgfgui * Add slivar 0.0.5. (#13741) * Add slivar 0.0.5. * Fix test. * Increment build number (#13743) * Update sevenbridges-python to 0.18.2 (#13746) * Bump to latest scanpy-scripts (#13747) * r-ldrtools (#13749) * Try to remove a few bioconductor packages from the blacklist (#13744) * Try to remove a few bioconductor packages from the blacklist * More updates * Yacrd add version 0.5.1 break compatibility with previous version (#13750) * Add version 0.5.0 break compatibility * up to version 0.5.1 * yacrd 0.5.1 correct error in sha256sum * r-mixkernel (#13745) * r-mixkernel * Spydrpick v1.1.1 (#13725) * Update SpydrPick to v1.1.0 * Update spydrpick v1.1.1; aprgrunt 0f34bdd80315e10b2234b5aae50b53102f04fbdd * Use SSE3 rather than AVX2 * With AVX guard around popcnt * PacBio: Update `ccs` to version 3.4.1 (#13755) * Remove a few more packages from the blacklist (#13753) * Remove a few more packages from the blacklist * a few updates * r-parallel is part of r-base * odd * Ready for OSX * needs gfortran it seems * Update PureCLIP to v1.3.0 (#13756) * updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers (#13757) updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers * try again (#13758) * Barcode splitter multi (#13663) * New directory for the barcode splitter recipe. * created using `conda skeleton pypi barcode_splitter_multi`. * created using `conda skeleton pypi barcode_splitter_multi`. * Added source files and tox. Files checked in: recipes/barcode_splitter_multi/meta.yaml * Re-wrote meta.yaml. The existing file was mostly wrong. Files checked in: recipes/barcode_splitter/meta.yaml * Change dirname. * Working out tests. Files checked in: * Addresses issues with conda build. Created a run_test.sh script to work around an issue with the exit code for --help and --version being 2 instead of 0. Added noarch: python to meta.yaml. Added "--single-version-externally-managed --record=record.txt" to the setup.py call in build.sh. Files checked in: recipes/barcode_splitter/build.sh recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Updated sandbox zenodo doi to real zenodo doi now that testing is done. Files checked in: recipes/barcode_splitter/meta.yaml * Removing pass of shell variable to echo. This is an attempt to address a warning from the remote circleci build that passing a variable as an argument generated from the output of the tool is a security risk. It might still complain due to the if conditional checking the variable too. I'll just have to see. Files checked in: recipes/barcode_splitter/run_test.sh * Removed eval of shell variable in if conditional. I suspect that this eval is still related to the security warning and subsequent failure of the test in the remote circleci build. Files checked in: recipes/barcode_splitter/run_test.sh * Updated to a release of barcode_splitter that exits with a status of 0 for --version. I could not get run_test.sh to pass mulled-build tests, so instead of work through that, I just worked around it by releasing the new version with the exit code fix. Files checked in: recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Reverted unintended changes. Files checked in: miniconda.sh .circleci/common.sh * Reverted another unintended change. Didn't realize the file was created instead of changed. Files checked in: .circleci/common.sh * Update meta.yaml * Delete build.sh * CPAT: Stricter python version requirement (#13742) * Stricter python version requirement In CPAT's code the version check for a python version that starts with 2.7 is hardcoded. * Correct license version It is incorrectly reported on PYPI. In the documentation of CPAT and in the project's license file it is mentioned that any later version of GPL is also allowed. * rdkit: remove blacklisted package - now at conda forge (#13759) * platypus update (#13494) * platypus update * added back buildPlatypus.sh * added new path to source * reset build number to 0 * this one needs a compiler isn't it? * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall (#13754) * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall - arvados: fix py3k support by avoiding subprocess32 on py3k - bcbio-variation-recall: fix platypus contig header generation. Fixes bcbio/bcbio-nextgen#2688 * Avoid py37 selectors, trying to fix py27 build * Try to avoid py37 errors with noarch * Fix python selectors * Avoid noarch linter errors, not sure why triggered * Avoid noarch linter errors, not sure why triggered * Pin arvados-python-client with py37 subprocess fix * Wasabi 1.0.0 (#13760) * UCSC blacklist (#13763) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1 (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipe…

* 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/_compare_reads.so): Needed DSO lib/libpython2.7.so.1.0 found in ['python'] WARNING (compare-reads,lib/python2.7/site-packages/compare_reads/_compare_reads.so): .. but ['python'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely) ``` * Update kipoi_veff to 0.2.2 (#13350) * shapeshifter recipe added (#13487) * added shapeshifter recipe * adding shapeshifter package, passed circleci tests * updating changes as requested in the review * fixed typo, items requested in review should be fixed * passed circleci locally, changes made as requested * Update sina to 1.5.0 (#13547) * Update sina to 1.5.0 * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * remove std=c++14 - won't work w/ boost * Dump test logs on failure * Add bc to host env * Rapid08 (#13666) * v0.8 update - added r-viridis package * r-viridis fix version * 0.8 viridis, plots CB friendly update * rapidv0.8_build_1 * Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230 * Creating v1.0 * Add new recipe for ataqv (#13665) * Bump umis to v1.0.3 with python3 support. (#13668) * Add recipe for fusioncatcher-seqtk (#13669) * moFF : Enforced python v3.4 or later as pymzml requires it. (#13541) * Enforced python v3.4 or later as pymzml requires it. * Increased build number * Update meta.yaml * Update meta.yaml * Update meta.yaml * Fixed reference to pymzml >=2.0.6 * Update meta.yaml * Update meta.yaml * add extra section * Avoiding dependency problem with Python 3.7 * WhatsHap 0.18 (#13670) * add python to run requirements (#13673) * fix mykrobe python package dependencies (#13672) * update mykrobe to v0.6.1 remove source fn add wget to build requirements add zlib to build requirements move zlib to host requirements specify zlib location specify zlib location move zlib to build requirements add c compiler add some more zlib related flags add some more zlib related flags add htslib to reqs add setuptools to reqs remove htslib to reqs try pip install instead try skipping py2 skip py27 and add imports test see if py27 works now remove py27 build create test script create test script add tests dir to test reqs add data dir to test reqs * Update meta.yaml * add wget to host * clean up build script. add test source files * add post-link script for downloading panel data * add prefix location specifier for mykrobe data dir * fix post-link script * switch to shasum for data download check. add wget to run reqs * use pip install * Delete build.sh * not sure why this has not failed before * Update meta.yaml * fix mccortex install * use default compiler for cxx * compile with -fPIC * remove hard-coded gcc in htslib Makefile. remove unncessary reqs * add python package reqs to run reqs and test * Tango (#13671) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * Bumped tango to version 0.3.0 * Update tango to version 0.3.1 * Updated shasum * Update meta.yaml * Update meta.yaml (#13674) :information_source: Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578). ---------------- * [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update scanpy (#13675) * Update meta.yaml * Delete build.sh * make noarch * Add recipe for fusioncatcher (#13676) * Add recipe for fusioncatcher * convert to noarch package (#13677) * convert to noarch package * Update meta.yaml * Update meta.yaml * add license file * VEP: bump subversion (#13681) * VEP: bump subversion * build -> host * Scanpy scripts pandas fix (#13678) * Prevent problematic pandas 0.24 * Bump build number * Bump anvio to 5.3.0 (#13682) * bump anvio * Fix file * Bump deepTools to 3.2.0 (#13683) * Bump deepTools to 3.2.0 * deepTools is now noarch: python * Update: simple_sv_annotation, up/down fixes + py3k (#13685) * update bioconda-utils to 0.15.8 (#13688) * digestiflow-cli v0.5.0 (#13689) * Fusioncatcher db file rename (#13690) * Rename download db file * Medaka (#13687) * First go at medaka * Building on linux, osx dying on docker * Add license_file to medaka/meta.yaml * Bump/scnic (#13691) * Update scnic to 0.6.0 * Add 0.6.0 new dependencies * Get rid of parallel dependency * Bump SCNIC version to 0.6.1 * Add igor_vdj (#13684) * Add igor_vdj * Odd, I didn't need automake locally * Not packaging the python module at this time. * Add autoconf * Use a standard jemalloc * Try not running configure in igor_src * What if we rerun autogen.sh * blah * blah * foo * sigh * Remove old build stuff, it was just a timestamp problem * Don't set -lrt on OSX * Update meta.yaml * pysradb: update to 0.7.1 (#13694) * pysradb: update to 0.7.1 * Now taking Genepop from a reproducible source (#13693) This uses a reproducible source for genepop (CRAN). ---------------- * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * tracy v0.5.2 (#13700) * Bump build (#13701) Trigger the build again for `bioconductor-flowtype`. * r-momr (#13703) * Mob suite 1.4.9.1 (#13697) * Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies * updated recipe to download from URL instead of github * build python version requirement defined (python >=3.4) * added build number * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added test statement (import) * added test statement (import) * added the new repository and py36 only compile * made requested corrections by daler. Corrected build number and package string * Small fixes * revert deleted row * New version, fixed sum bugs and improved stability * Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters * Updated to version 1.4.9 * Updated to version 1.4.9 * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * new db host * updated meta.yaml with resolved conficts from the head branch * build not more than python 3.6 * add a recipe for FastqPuri (#13679) * add a recipe for FastqPuri Changes to be committed: new file: recipes/fastqpuri/build.sh new file: recipes/fastqpuri/meta.yaml * fix issues in fastqpuri recipe Changes to be committed: modified: build.sh modified: meta.yaml * add neatfeatures track types + patch combotrackselector (xref https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/pull/5) (#13704) * Add new recipe for finestructure (#13707) * Version bump msstitch to 2.12 (#13705) * Bump CLARK (#13709) * Update fastp to 0.19.7. (#13714) * Update STAR to 2.7.0d, add 2.6.1d, as it doesn't require rebuilding the index (#13717) * update SURVIVOR to v1.0.6 (#13718) * Update cooler to v0.8.3 (#13712) * Update cooler to v0.8.3 * Update meta.yaml * Update UCSC templates to build under OSX * Update all UCSC recipes. * try fixing ucsc-overlapselect * Bump a bunch of packages for pinnings (#13960) * Upgrade cyvcf2 to v0.10.8 (#13726) Patch setup.py to use conda managed htslib * Update bcftools plot_vcfstats (#13721) * Python-tripal 3.2 and python-apollo (#13727) * update python-tripal * add python-apollo recipe * noarch * v0.1.4 February 2019 Release (#13720) * python3 and igv-reports (#13623) * python3 and igv-reports * changing test * adding ls * adding bin ls * print install path contents * run on python3 * proper test * Update meta.yaml (#13729) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * It looks like rJava has now been rebuilt. (#13728) * It looks like rJava has now been rebuilt. * r-rcdk is in conda-forge now * Remove the first batch from the blacklist * Update esATAC * Update CPAT to 1.2.4 (#13732) * Re-do an update undone by 3761102478f21107957c166e85ca843f9c3410b1 (#13733) * Gff3sort (#13731) * add gff3sort recipe * add new dep to sort gff3 files properly * lint * add perl-data-match (for Sort::Topological) * add dep * oh perl, I hate you so much * ...so much.... * take this perl-data-match * wrong path * rebuild with perl 5.26.2 for mac * Update PopPUNK to v1.1.4 (#13723) * Update PopPUNK to v1.1.4 * Add noarch Seems to be a py36 to py37 problem * Cannot have noarch as no python2 support * bump build numbers on dependencies needing rebuild * Update sharedmem recipe * Putting sharedmem build into meta.yaml * Correcting host/build in sharedmem meta for noarch * Make noarch and python>=3 * Remove redundancy in sharedmem meta.yaml * Update comet-ms to 2018014 (#13645) * Remove more rJava packages from the blacklist (#13734) * Remove more rJava packages from the blacklist * update * Sc3 scripts update (#13735) * Bump bioconductor-sc3-scripts package to 0.0.3 * Reset build counter * Add pychopper (#13738) * Add pychopper * build command * pb-falcon: 0.2.6 (#13740) * pbfalcon-0.2.6 * pb-falcon: Try openssl<1.1 * pb-assembly: update pb-falcon/openssl (#13575) * Remove the remainder of the rJava bioc packages from the blacklist (#13737) * Remove the remainder of the rJava bioc packages from the blacklist * Update * blacklist msgfgui * Add slivar 0.0.5. (#13741) * Add slivar 0.0.5. * Fix test. * Increment build number (#13743) * Update sevenbridges-python to 0.18.2 (#13746) * Bump to latest scanpy-scripts (#13747) * r-ldrtools (#13749) * Try to remove a few bioconductor packages from the blacklist (#13744) * Try to remove a few bioconductor packages from the blacklist * More updates * Yacrd add version 0.5.1 break compatibility with previous version (#13750) * Add version 0.5.0 break compatibility * up to version 0.5.1 * yacrd 0.5.1 correct error in sha256sum * r-mixkernel (#13745) * r-mixkernel * Spydrpick v1.1.1 (#13725) * Update SpydrPick to v1.1.0 * Update spydrpick v1.1.1; aprgrunt 0f34bdd80315e10b2234b5aae50b53102f04fbdd * Use SSE3 rather than AVX2 * With AVX guard around popcnt * PacBio: Update `ccs` to version 3.4.1 (#13755) * Remove a few more packages from the blacklist (#13753) * Remove a few more packages from the blacklist * a few updates * r-parallel is part of r-base * odd * Ready for OSX * needs gfortran it seems * Update PureCLIP to v1.3.0 (#13756) * updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers (#13757) updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers * try again (#13758) * Barcode splitter multi (#13663) * New directory for the barcode splitter recipe. * created using `conda skeleton pypi barcode_splitter_multi`. * created using `conda skeleton pypi barcode_splitter_multi`. * Added source files and tox. Files checked in: recipes/barcode_splitter_multi/meta.yaml * Re-wrote meta.yaml. The existing file was mostly wrong. Files checked in: recipes/barcode_splitter/meta.yaml * Change dirname. * Working out tests. Files checked in: * Addresses issues with conda build. Created a run_test.sh script to work around an issue with the exit code for --help and --version being 2 instead of 0. Added noarch: python to meta.yaml. Added "--single-version-externally-managed --record=record.txt" to the setup.py call in build.sh. Files checked in: recipes/barcode_splitter/build.sh recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Updated sandbox zenodo doi to real zenodo doi now that testing is done. Files checked in: recipes/barcode_splitter/meta.yaml * Removing pass of shell variable to echo. This is an attempt to address a warning from the remote circleci build that passing a variable as an argument generated from the output of the tool is a security risk. It might still complain due to the if conditional checking the variable too. I'll just have to see. Files checked in: recipes/barcode_splitter/run_test.sh * Removed eval of shell variable in if conditional. I suspect that this eval is still related to the security warning and subsequent failure of the test in the remote circleci build. Files checked in: recipes/barcode_splitter/run_test.sh * Updated to a release of barcode_splitter that exits with a status of 0 for --version. I could not get run_test.sh to pass mulled-build tests, so instead of work through that, I just worked around it by releasing the new version with the exit code fix. Files checked in: recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Reverted unintended changes. Files checked in: miniconda.sh .circleci/common.sh * Reverted another unintended change. Didn't realize the file was created instead of changed. Files checked in: .circleci/common.sh * Update meta.yaml * Delete build.sh * CPAT: Stricter python version requirement (#13742) * Stricter python version requirement In CPAT's code the version check for a python version that starts with 2.7 is hardcoded. * Correct license version It is incorrectly reported on PYPI. In the documentation of CPAT and in the project's license file it is mentioned that any later version of GPL is also allowed. * rdkit: remove blacklisted package - now at conda forge (#13759) * platypus update (#13494) * platypus update * added back buildPlatypus.sh * added new path to source * reset build number to 0 * this one needs a compiler isn't it? * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall (#13754) * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall - arvados: fix py3k support by avoiding subprocess32 on py3k - bcbio-variation-recall: fix platypus contig header generation. Fixes bcbio/bcbio-nextgen#2688 * Avoid py37 selectors, trying to fix py27 build * Try to avoid py37 errors with noarch * Fix python selectors * Avoid noarch linter errors, not sure why triggered * Avoid noarch linter errors, not sure why triggered * Pin arvados-python-client with py37 subprocess fix * Wasabi 1.0.0 (#13760) * UCSC blacklist (#13763) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1 (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN p…

* 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/_compare_reads.so): Needed DSO lib/libpython2.7.so.1.0 found in ['python'] WARNING (compare-reads,lib/python2.7/site-packages/compare_reads/_compare_reads.so): .. but ['python'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely) ``` * Update kipoi_veff to 0.2.2 (#13350) * shapeshifter recipe added (#13487) * added shapeshifter recipe * adding shapeshifter package, passed circleci tests * updating changes as requested in the review * fixed typo, items requested in review should be fixed * passed circleci locally, changes made as requested * Update sina to 1.5.0 (#13547) * Update sina to 1.5.0 * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * remove std=c++14 - won't work w/ boost * Dump test logs on failure * Add bc to host env * Rapid08 (#13666) * v0.8 update - added r-viridis package * r-viridis fix version * 0.8 viridis, plots CB friendly update * rapidv0.8_build_1 * Added pin to bowtie2 (v2.3.0) because of the issue: https://github.com/BenLangmead/bowtie2/issues/230 * Creating v1.0 * Add new recipe for ataqv (#13665) * Bump umis to v1.0.3 with python3 support. (#13668) * Add recipe for fusioncatcher-seqtk (#13669) * moFF : Enforced python v3.4 or later as pymzml requires it. (#13541) * Enforced python v3.4 or later as pymzml requires it. * Increased build number * Update meta.yaml * Update meta.yaml * Update meta.yaml * Fixed reference to pymzml >=2.0.6 * Update meta.yaml * Update meta.yaml * add extra section * Avoiding dependency problem with Python 3.7 * WhatsHap 0.18 (#13670) * add python to run requirements (#13673) * fix mykrobe python package dependencies (#13672) * update mykrobe to v0.6.1 remove source fn add wget to build requirements add zlib to build requirements move zlib to host requirements specify zlib location specify zlib location move zlib to build requirements add c compiler add some more zlib related flags add some more zlib related flags add htslib to reqs add setuptools to reqs remove htslib to reqs try pip install instead try skipping py2 skip py27 and add imports test see if py27 works now remove py27 build create test script create test script add tests dir to test reqs add data dir to test reqs * Update meta.yaml * add wget to host * clean up build script. add test source files * add post-link script for downloading panel data * add prefix location specifier for mykrobe data dir * fix post-link script * switch to shasum for data download check. add wget to run reqs * use pip install * Delete build.sh * not sure why this has not failed before * Update meta.yaml * fix mccortex install * use default compiler for cxx * compile with -fPIC * remove hard-coded gcc in htslib Makefile. remove unncessary reqs * add python package reqs to run reqs and test * Tango (#13671) * Initial commit for package tango * Update meta.yaml * use script * Delete build.sh * Bumped tango to version 0.3.0 * Update tango to version 0.3.1 * Updated shasum * Update meta.yaml * Update meta.yaml (#13674) :information_source: Bioconda has finished the [GCC7 migration](https://github.com/bioconda/bioconda-recipes/issues/13578). If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. [Bioconda utils - update-pinning](https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change) will assist you with that. If you have any questions please use [issue 13578](https://github.com/bioconda/bioconda-recipes/issues/13578). ---------------- * [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [ ] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * Update scanpy (#13675) * Update meta.yaml * Delete build.sh * make noarch * Add recipe for fusioncatcher (#13676) * Add recipe for fusioncatcher * convert to noarch package (#13677) * convert to noarch package * Update meta.yaml * Update meta.yaml * add license file * VEP: bump subversion (#13681) * VEP: bump subversion * build -> host * Scanpy scripts pandas fix (#13678) * Prevent problematic pandas 0.24 * Bump build number * Bump anvio to 5.3.0 (#13682) * bump anvio * Fix file * Bump deepTools to 3.2.0 (#13683) * Bump deepTools to 3.2.0 * deepTools is now noarch: python * Update: simple_sv_annotation, up/down fixes + py3k (#13685) * update bioconda-utils to 0.15.8 (#13688) * digestiflow-cli v0.5.0 (#13689) * Fusioncatcher db file rename (#13690) * Rename download db file * Medaka (#13687) * First go at medaka * Building on linux, osx dying on docker * Add license_file to medaka/meta.yaml * Bump/scnic (#13691) * Update scnic to 0.6.0 * Add 0.6.0 new dependencies * Get rid of parallel dependency * Bump SCNIC version to 0.6.1 * Add igor_vdj (#13684) * Add igor_vdj * Odd, I didn't need automake locally * Not packaging the python module at this time. * Add autoconf * Use a standard jemalloc * Try not running configure in igor_src * What if we rerun autogen.sh * blah * blah * foo * sigh * Remove old build stuff, it was just a timestamp problem * Don't set -lrt on OSX * Update meta.yaml * pysradb: update to 0.7.1 (#13694) * pysradb: update to 0.7.1 * Now taking Genepop from a reproducible source (#13693) This uses a reproducible source for genepop (CRAN). ---------------- * [X] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html). * [ ] This PR adds a new recipe. * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)). * [X] This PR updates an existing recipe. * [ ] This PR does something else (explain below). * tracy v0.5.2 (#13700) * Bump build (#13701) Trigger the build again for `bioconductor-flowtype`. * r-momr (#13703) * Mob suite 1.4.9.1 (#13697) * Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies * updated recipe to download from URL instead of github * build python version requirement defined (python >=3.4) * added build number * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added tests and noarch parameter * added test statement (import) * added test statement (import) * added the new repository and py36 only compile * made requested corrections by daler. Corrected build number and package string * Small fixes * revert deleted row * New version, fixed sum bugs and improved stability * Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters * Updated to version 1.4.9 * Updated to version 1.4.9 * Updated to version 1.4.9 * Downgraded to python >= 3.4 to accomodate lowandrew request * new build * no arch commit for python 3.4 * no arch conda package version * Set build number to 1 * new db host * updated meta.yaml with resolved conficts from the head branch * build not more than python 3.6 * add a recipe for FastqPuri (#13679) * add a recipe for FastqPuri Changes to be committed: new file: recipes/fastqpuri/build.sh new file: recipes/fastqpuri/meta.yaml * fix issues in fastqpuri recipe Changes to be committed: modified: build.sh modified: meta.yaml * add neatfeatures track types + patch combotrackselector (xref https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/pull/5) (#13704) * Add new recipe for finestructure (#13707) * Version bump msstitch to 2.12 (#13705) * Bump CLARK (#13709) * Update fastp to 0.19.7. (#13714) * Update STAR to 2.7.0d, add 2.6.1d, as it doesn't require rebuilding the index (#13717) * update SURVIVOR to v1.0.6 (#13718) * Update cooler to v0.8.3 (#13712) * Update cooler to v0.8.3 * Update meta.yaml * Update UCSC templates to build under OSX * Update all UCSC recipes. * try fixing ucsc-overlapselect * Bump a bunch of packages for pinnings (#13960) * Upgrade cyvcf2 to v0.10.8 (#13726) Patch setup.py to use conda managed htslib * Update bcftools plot_vcfstats (#13721) * Python-tripal 3.2 and python-apollo (#13727) * update python-tripal * add python-apollo recipe * noarch * v0.1.4 February 2019 Release (#13720) * python3 and igv-reports (#13623) * python3 and igv-reports * changing test * adding ls * adding bin ls * print install path contents * run on python3 * proper test * Update meta.yaml (#13729) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * It looks like rJava has now been rebuilt. (#13728) * It looks like rJava has now been rebuilt. * r-rcdk is in conda-forge now * Remove the first batch from the blacklist * Update esATAC * Update CPAT to 1.2.4 (#13732) * Re-do an update undone by 3761102478f21107957c166e85ca843f9c3410b1 (#13733) * Gff3sort (#13731) * add gff3sort recipe * add new dep to sort gff3 files properly * lint * add perl-data-match (for Sort::Topological) * add dep * oh perl, I hate you so much * ...so much.... * take this perl-data-match * wrong path * rebuild with perl 5.26.2 for mac * Update PopPUNK to v1.1.4 (#13723) * Update PopPUNK to v1.1.4 * Add noarch Seems to be a py36 to py37 problem * Cannot have noarch as no python2 support * bump build numbers on dependencies needing rebuild * Update sharedmem recipe * Putting sharedmem build into meta.yaml * Correcting host/build in sharedmem meta for noarch * Make noarch and python>=3 * Remove redundancy in sharedmem meta.yaml * Update comet-ms to 2018014 (#13645) * Remove more rJava packages from the blacklist (#13734) * Remove more rJava packages from the blacklist * update * Sc3 scripts update (#13735) * Bump bioconductor-sc3-scripts package to 0.0.3 * Reset build counter * Add pychopper (#13738) * Add pychopper * build command * pb-falcon: 0.2.6 (#13740) * pbfalcon-0.2.6 * pb-falcon: Try openssl<1.1 * pb-assembly: update pb-falcon/openssl (#13575) * Remove the remainder of the rJava bioc packages from the blacklist (#13737) * Remove the remainder of the rJava bioc packages from the blacklist * Update * blacklist msgfgui * Add slivar 0.0.5. (#13741) * Add slivar 0.0.5. * Fix test. * Increment build number (#13743) * Update sevenbridges-python to 0.18.2 (#13746) * Bump to latest scanpy-scripts (#13747) * r-ldrtools (#13749) * Try to remove a few bioconductor packages from the blacklist (#13744) * Try to remove a few bioconductor packages from the blacklist * More updates * Yacrd add version 0.5.1 break compatibility with previous version (#13750) * Add version 0.5.0 break compatibility * up to version 0.5.1 * yacrd 0.5.1 correct error in sha256sum * r-mixkernel (#13745) * r-mixkernel * Spydrpick v1.1.1 (#13725) * Update SpydrPick to v1.1.0 * Update spydrpick v1.1.1; aprgrunt 0f34bdd80315e10b2234b5aae50b53102f04fbdd * Use SSE3 rather than AVX2 * With AVX guard around popcnt * PacBio: Update `ccs` to version 3.4.1 (#13755) * Remove a few more packages from the blacklist (#13753) * Remove a few more packages from the blacklist * a few updates * r-parallel is part of r-base * odd * Ready for OSX * needs gfortran it seems * Update PureCLIP to v1.3.0 (#13756) * updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers (#13757) updating the recipe for the cromwell workflow manager to version 36.1, which should be used in preference to 37.0 until problems with that version are worked out, according to cromwell developers * try again (#13758) * Barcode splitter multi (#13663) * New directory for the barcode splitter recipe. * created using `conda skeleton pypi barcode_splitter_multi`. * created using `conda skeleton pypi barcode_splitter_multi`. * Added source files and tox. Files checked in: recipes/barcode_splitter_multi/meta.yaml * Re-wrote meta.yaml. The existing file was mostly wrong. Files checked in: recipes/barcode_splitter/meta.yaml * Change dirname. * Working out tests. Files checked in: * Addresses issues with conda build. Created a run_test.sh script to work around an issue with the exit code for --help and --version being 2 instead of 0. Added noarch: python to meta.yaml. Added "--single-version-externally-managed --record=record.txt" to the setup.py call in build.sh. Files checked in: recipes/barcode_splitter/build.sh recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Updated sandbox zenodo doi to real zenodo doi now that testing is done. Files checked in: recipes/barcode_splitter/meta.yaml * Removing pass of shell variable to echo. This is an attempt to address a warning from the remote circleci build that passing a variable as an argument generated from the output of the tool is a security risk. It might still complain due to the if conditional checking the variable too. I'll just have to see. Files checked in: recipes/barcode_splitter/run_test.sh * Removed eval of shell variable in if conditional. I suspect that this eval is still related to the security warning and subsequent failure of the test in the remote circleci build. Files checked in: recipes/barcode_splitter/run_test.sh * Updated to a release of barcode_splitter that exits with a status of 0 for --version. I could not get run_test.sh to pass mulled-build tests, so instead of work through that, I just worked around it by releasing the new version with the exit code fix. Files checked in: recipes/barcode_splitter/meta.yaml recipes/barcode_splitter/run_test.sh * Reverted unintended changes. Files checked in: miniconda.sh .circleci/common.sh * Reverted another unintended change. Didn't realize the file was created instead of changed. Files checked in: .circleci/common.sh * Update meta.yaml * Delete build.sh * CPAT: Stricter python version requirement (#13742) * Stricter python version requirement In CPAT's code the version check for a python version that starts with 2.7 is hardcoded. * Correct license version It is incorrectly reported on PYPI. In the documentation of CPAT and in the project's license file it is mentioned that any later version of GPL is also allowed. * rdkit: remove blacklisted package - now at conda forge (#13759) * platypus update (#13494) * platypus update * added back buildPlatypus.sh * added new path to source * reset build number to 0 * this one needs a compiler isn't it? * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall (#13754) * Update: arvados-python-client, arvados-cwl-runner, bcbio-variation-recall - arvados: fix py3k support by avoiding subprocess32 on py3k - bcbio-variation-recall: fix platypus contig header generation. Fixes bcbio/bcbio-nextgen#2688 * Avoid py37 selectors, trying to fix py27 build * Try to avoid py37 errors with noarch * Fix python selectors * Avoid noarch linter errors, not sure why triggered * Avoid noarch linter errors, not sure why triggered * Pin arvados-python-client with py37 subprocess fix * Wasabi 1.0.0 (#13760) * UCSC blacklist (#13763) * update mzr as a test * Begin building for R 3.5.1 (#11252) * Bump everything for R 3.5.1 * Fix most of the linting issues * Update blacklist * Revert "Fix most of the linting issues" This reverts commit a271e50f4b86f4ee76d1148bf78e6617da1b7cc5. * should_not_use_fn * More fixes * Fix incorrect yaml * Should really fix the linting blacklist stuff * Fix many recipes * Fix some linting * Fix r-wicket * Update derfinder * Pin to a given bioconductor release. * Add missing packages * Restore identifiers to bioconductor packages * Restore extra information to R packages * Update R bulk (#11283) * fixed incorrect doi of publication (#11175) * Added recipe for kinSimRiboswitch (#10838) Added recipe for kinSimRiboswitch, a pipeline for simulating the folding kinetics of RNA switches. * update multiqc-bcbio (#11187) * Add recipe for PopDel (#11181) * Add recipe for PopDel * Add clang and clangxx to build config * update seqbuster (#11190) * update seqbuster * fix build * fix test * Update pyseer to 1.1.2 (#11172) * bump sourmash (#11197) * Update BASIC to v1.4.1 (#11195) * Update BASIC to v1.4.1 * Trigger circleci * Fix build number * Update nf-core-1.2 (#11191) * Update nf-core-1.2 * Update build script * Update to InterMine 1.11.0 (#11182) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Add tinyfasta-0.1.0 (#11177) * Add tinyfasta * Update build script * Fix structure of build section * Bumping snippy (#11198) * Remove older version * Bump snippy * VEP: bump major version (#11201) * VEP: bump major version * VEP: bumped plugin major version * VEP: update plugin install Download and install all plugin modules, instead of just a selection * Update: PureCN to latest devel (1.11.13); wrapper scripts (#11200) * Update: PureCN to latest devel (1.11.13); wrapper scripts PureCN development (https://github.com/lima1/PureCN) has several improvements over the BioC 3.6 release for handling multiple VCF input types, and is back compatible with R 3.4.1 so still builds cleanly with two new dependencies. Also exposes PureCN wrapper scripts for running from the command line. Prefixes ambiguous scripts with PureCN_. * Try pinning to 3.4 to avoid 3.5.1 builds which we don't want yet * add cassiopee release 1.0.9 (#11168) * add cassiopee release 1.0.9 * update to conda build 3 * remove old version backup and use sha256 for source * Bump abeona version to 0.26.0 (#11202) * Bump abeona version to 0.24.0 * Bump abeona version to 0.26.0 * Update LexMapr to v0.1.2 (#11192) * Update LexMapr to v0.1.2 * Add rdflib dep * Update svtyper to 0.7.0 (#11196) * Update svtyper to 0.7.0 * Add recipe for perl-gtdbtk (#11194) * Add recipe for perl-gtdbtk * New recipe for RFMix (#11205) * New recipe for RFMix * updated version number information * updated version number information * updated version number information * initial purge_haplotigs commit (#11049) * initial purge_haplotigs commit * bioconda revisions, updating test commands to run the pipeline on the test dataset * rolling back test commands * Add recipe for fsm-lite (#11209) * Add recipe for fsm-lite * Add prefix to make * Remove v from version string * Updated reparation_blast to version v.1.0.7 (#11210) * Update sambamba to 0.6.8 (#11212) * Bump sambamba to 0.6.8 * It's somewhat annoying that missing_hash is thrown even if uses_git_url is specified. * Set some environment variables * The compiled binary is in a different place now * ldc provides some libraries that are linked against. * mtbseq: update recipe (#11110) * changed download location/add test * remove test * Confindr (#11217) * Update confindr to 0.4.2 * Fix typo in specifying version of pysam * Update Genenotebook to v0.1.4 (#11218) * genenotebook recipe * About * Package name * License * sha256sum * Update build.sh * Make bin dir * Change ln to cp * New symlink strategy * Build from prebundled tarball * genenotebook v0.1.2 * version fix * retry * fix * build number * genenotebook v0.1.3 * restore build procedure * Fix summary * updating to 0.1.3 (#11221) * sartools1.6.6 (#11222) * Perl bio automatedannotation (#11216) * Initial recipe for Bio-AutomatedAnnotation * Change URL * Run cpanm tests * Temporarily set HOME * Use cpan version instead * Add more depencencies * Set bioperl version * unset bioperl version, add bioperl-run * New release including version in modules * Remove comments * build -> host * Upgrade r-biodb to v1.1.2. (#11213) * Upgrade r-biodb to v1.1.2. * Remove old versions of r-biodb. * Comment out libgfortran. * PeptideShaker: updated to version 1.16.30 & SearchGUI: updated to version 3.3.5 (#11215) * PeptideShaker: updated to version 1.16.30 - Bugfix: HOME was still being used when folder with customised reports was specified. - Bugfix: Made it possible to use the MzidCLI options directly on the PeptideShakerCLI command line. * SearchGUI: updated to version 3.3.5. - BUG FIX: Cleanup of the temp path options when used as options for the other command lines. - FEATURE IMPROVEMENT: Updated Comet to 2018.01 rev. 2. - LIBRARY UPDATE: Updated utilities to version 4.12.8. * Update meta.yaml (#11227) * Svtools 0.4.0 (#11208) * Remove directories for old svtools versions * Update svtools to v0.4.0 * Move build number back to 0 * Anvio 52 (#11230) * Incrementing version to 5.2. Splitting out anvio-minimal package to just install the pip package. The anvio package will install it and all the most likely companion software. * Remove cgat-scripts from blacklist. (#11228) * Add new formula: bazam 1.0.1 (#11229) * Update gatk4 to 4.0.10.0 (#11224) * Add recipe for gtdbtk 0.1.3 (#11211) * Add recipe for gtdbtk * Added initial htstream recipe (#11113) * HTStream is a fast, quality control pipeline for Hight Throughput Sequencing data. The difference between HTStream and other pipelines is that HTStreams uses a tab delimited fastq format which allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data. * DeepTools 3.1.3 (#11226) * PacBio: Update `pbmm2` to version 0.10.0 (#11225) * fastqc: update to version 0.11.8 (#11214) * fastqc: update to version 0.11.8 * Update meta.yaml * Phame (#11223) * mac recipe and added bioperl * changing bill number * added no osx * adding new version * removed separate recipe for mac, dont need it * now running same recipe for mac and linux * fixed the way fasttrees version was being parsed * minor change test * adding detailed description * restaging the build number * new version * Make sure to use bioperl and perl 5.26 * Updated ngs-bits to version 2018_10 (#11235) * PacBio: Update `pbsv2` to version 2.0.2 (#11236) * Update VSEARCH to 2.8.5 (#11239) * Fix shorah recipe and remove from blacklist. (#11241) * Fix shorah recipe and remove from blacklist. * Fix blas variant. * Remove imports from tests. * unicycler 0.4.7 (#11240) * unicycler 0.4.7 * unicycler: Work around ValueError: invalid Unicycler thinks the terminal has 0 columns and produces this error: File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/textwrap.py", line 248, in _wrap_chunks raise ValueError("invalid width %r (must be > 0)" % self.width) ValueError: invalid width -5 (must be > 0) * Octopus: update to 0.5.1-beta (#11244) * New: PURPLE SV caller; Update: VarDictJava (1.5.6), PureCN (#11247) - PURPLE SV and heterogeneity caller for somatic tumor/normal samples. - VarDictJava -- 1.5.6 release with fixes for SV calling - PureCN -- add signature dependency and update with fixes for test samples. * Dinucleotide patterns analysis tools v1.0 (#11245) * Dinucleotide patterns analysis tools v1.0 * Lets try it, it seems to work locally for me. * Enable SpoTyping_plot.r (#11248) * rerun again (#11233) * rerun again * Update meta.yaml * Delete build.sh * Update segway dependency optbuild to 0.2 (#10459) * Update segway dependency optbuild to 0.2 * Update build and architecture requirements for optbuild 0.2 * Add six as a dependency to the optbuild recipe * Dinucleotide patterns analysis tools v1. / Add prefix dnp- to the package names (#11249) * Add prefix dnp- to the package names * Update build.sh * Update build.sh * Bump beast version to 1.10.2 (#11250) * add maxquant (#11253) * add mayquant * relax tests * PacBio: Update `pbmm2` to version 0.10.1 (#11256) * PacBio: Update `pbmm2` to version 0.10.1-1 (#11257) * remove xsv recipe (#11259) * add blast dependency (#11258) * Added riborex recipe (#11251) * Added riborex recipe * Relaxed version constraints * Pinned r-core for fdr tools * fixed the r-base stuff upstream * Update meta.yaml * fix graphprot (#11234) * increase build number * remove from blacklist * use cxx instead of c * move coreutoils to build section * set additional paths * patch makefile * blind try * update patch * explicitely copy from src_dir * update deprecated prefix variable * Revert "update deprecated prefix variable" This reverts commit 2559439a76ec60964f6bddd743b27171e8f91b4d. * update deprecated prefix variable * try moving to host section * Bump mash (#11264) * Add fmlrc (#11265) * Add fmlrc * add doi * PacBio: Update pb-falcon to 0.2.4. (#11266) * Add kopt recipe (#11269) * Genomepy 0.5.2 (#11267) * release 0.5.2 of genomepy * trigger new build * remove genomepy from blacklist * locale for osx * updated locale test * PacBio: Update pb-assembly to 0.0.2. Bumped the pinned version for pb-falcon. (#11275) * Update mmseqs2 recipe to new release 6-f5a1c (#11272) * Update yacrd to version 0.4.1 (#11273) * Add scprep (#11270) * Add scprep * All of these should not be needed as host dep * Metawrap preqs2 (#11242) * fixed issues * fixed issues * added tests * fixed tab * gemma 0.98 (#11254) * gemma 0.98 * gemma 0.98 Leave gsl and zlib out of runtime dependencies * Add DCA recipe (#11274) * Add DCA recipe * add noarch and doi * remove skip * Fix a bunch of packages that are actually in bioconductor and try to fix bioconductor-rhtslib * Various fixes for bulk and trigger a rebuild (#11313) * Various fixes, at least 4 packages (and their dependencies) should still fail (#11320) * A few fixes, remove a package from the blacklist since it prevents trumicounts from building. (#11336) * Fix various recipes (#11354) * Fix various recipes * Fix more recipes * Various CRAN package fixes, since they all lack license files (#11372) * Various CRAN package fixes, since they all lack license files * Fix the r-dartr recipe * There is a light at the end of the tunnel (#11381) * There is a light at the end of the tunnel * Licenses no longer exist * [BULK] Fixes for R/Bioconductor packages (#11406) * Require `r-base >=3.5` for some packages * Fix various CRAN packages lacking license file * Add missing libnetcdf requirement to bioconductor-mzr * Remove r-alakazam (moved to conda-forge) Fix linting issue: ``` recipes/r-alakazam in_other_channels {'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'} {'conda-forge'} consider deprecating ``` * [BULK] Many R 3.5 only packages (#11410) * [BULK] Bulk update 191018b (#11419) * update mzr as a test * B…

Bulk updates for 040119

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dpryan79 merged commit 363a330 into bulk Jan 4, 2019

dpryan79 deleted the bulk_update_040119a branch January 4, 2019 12:30

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Bulk updates for 040119 #12910

Bulk updates for 040119 #12910

dpryan79 commented Jan 4, 2019

Bulk updates for 040119 #12910

Bulk updates for 040119 #12910

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dpryan79 commented Jan 4, 2019