Unblacklist 2 more perl #10166
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Unblacklist 2 more perl #10166
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druvus
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Jul 31, 2018
druvus
commented
- 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).
asmariyaz23
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Aug 14, 2018
* add convert_zero_one_based (#10001) * add convert_zero_one_based * remove unecessary tests * test import * Gembs (#10109) * gembs: passes a mulled build * correcting dependencies * gembs: passes a mulled build * correcting dependencies * pointing to the current gem3-mapper instead of a custom version * removing openssl * gembs: passes a mulled build * correcting dependencies * pointing to the current gem3-mapper instead of a custom version * removing openssl * starting build at 0 * Changing to the main repository instead of the testing fork * Update sevenbridges-python recipe to 0.15.0 (#10113) * update to new version (#10015) * update to new version the old version had a bug whereby some reads were dropped. See mourisl/Rcorrector#12 * remove recipe from blacklist * Update meta.yaml * try adding flags per comment from @jpuritz * fix makefile * bump for alevin hotfix (#10118) * bump for alevin hotfix * Update meta.yaml Put md5sum for the zip, not .tar.gz. Correct that. * Bump JBrowse version to 1.15.0 (#10116) Add missing dependency perl-io-uncompress-gunzip. Support osx. * Update krocus to v0.2.3 (#10115) * updating to ragout v2.1, should fix the problem with inconsistent ... (#10105) * updating to ragout v2.1, should fix the problem with inconsistent newick package versions * Dialign2 (#10098) * Started work on dialign2 * Fixing build/host * compiler * still compiler error * still * still working on compiler * should be fixed * Fixed typo * desperate measures * typo * whatever * Update meta.yaml * fix hash * freaky circleci, please run * working on paths and exports * still working on paths and exports * still working on paths * last fixes * verylast fixes * verylast fixes? * wtf circleci * wtf circleci aber echt * Fixing license * Working * env vars export * Working on postlink * Working on prelink * Working on env vars * Done? * skipping osx and done i hope * Added pre-unlink and added DOI * Fixing exports * Removed unnecessary scripts, added wrapper * Added patch and sed workaround for env var DIALIGN2_DIR * Fixing sed command * Fixing sed command again * I hate sed * fixed typo and eyecandy * Remove various packages from the blacklist (#10117) * Remove various packages from the blacklist * eqtlbma needs to always have openblas included * Patch mamotif so it uses matplotlib.use('Agg') early on * Skip eqtlbma on OSX due to openmp * Add r-bipartite (#10119) * Add r-bipartite * removed 2nd url * Add r-phylomeasures (#10120) * Add r-phylomeasures * removed 2nd url * Bump perl-file-path (#10123) * Bump perl-file-path * Small fixes * Fix 2 perl packages (#10124) * bump pysam (#10126) * Update primer3 to v2.4.0 (#10122) * Update primer3 to v2.4.0 * [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). Bump primer3 to `v2.4.0`. * Review fixups for Update primer3 to v2.4.0 * R phylosignal (#10128) * Add r-phylosignal * Removed fn: * removed all win * fixed meta.yaml; ade4 now updated to 1.7_11 * R coenocliner (#10127) * Add r-coenocliner * modified maintainers * add msisensor (#10092) * add msisensor * skip macos * change include and lib * fix ncurse * add tinfo * add cpath * add LIBRARY_PATH * Update to fastp v0.19.3 (#10131) This version provides a fix for possible deadlock on cloud-based docker env. * Add r-ggrasp (#10129) * Add r-ggrasp * trivial change to restart checks now the r-bgmm is on conda-forge * updated r-nodiv recipe; unblacklisted (#10132) * Blood moon blaclist changes (#10133) * remove a few things from the blacklist * Try something for osx * skip xatlas on osx * Fix two more perl (#10135) * Fix perl-image-size * Fix perl-aceperl * Add perl-cache-cache * Add perl-ipc-sharelite * Add perl-digest-sha1 * bumping to 0.7.1 (#10136) * Remove packages from the blacklist (#10134) * Remove packages from the blacklist * Fix fermi on osx I hope * Ah, only gnu assumes inline functions are static * preseq 2.0.3 includes the wrong header for proper building on newer OSX versions. Try to cxxflags around this. * Skip preseq on OSX, clang doesn't like the older headers * Added recipe prototype for pymisc-utils (#10139) * Added recipe prototype for pymisc-utils * Updated build dependencies * Updated repo url * Fixed copying of executables * Added dependency * Minor fix * Skip python 2 * Idr (#10112) * idr: push version to 2.0.4.2 * OMERO.py 5.4.7 (#10138) * OMERO.py 5.4.7 * Bump version in setup.py to 5.4.7 * Update EMA to v0.6.2 (#10141) * Add r-htssip (#10121) * Add r-htssip * converted r- to bioconductor- * trivial change to restart checks * Ragout 2.1.1 (#10144) * ragout 2.1.1 update (now as a Python package) * Riboseed updates (#10143) * [wip] riboseed add quast and networkx * update build number * bump version, remove dep on pyutilsnrw * [wip] remove quast (single tear), which isn't built for py3 on conda * bump version * bump version to fix cmdline args * updating cromwell to 0.34 (#10145) * updating cromwell to 0.34 * gembs, rebuild (#10140) removing restrictions on python beyond build-skip. matplotlib not needed for building * PacBio: bump lima to 1.7.0 (#10151) * gembs: adding missing runtime dependencies and moving build script to meta file (#10150) * Jcvi python module (#10152) * add jcvi recipe * fixes * update biokit to v0.4.4 (#10148) * update biokit to v0.4.4 * Jcvi is python 2 only (#10153) * jcvi is python 2 only * negation bug in my head * changed to 1.0.6 (#10157) * updated bbmap to 38.16 (#10159) * forgi: loosened the dependencies (#10156) * Grid6 (#10158) * changed to 1.0.6 * changed to veersion 1.0.6 * Update biohansel to v2.1.0 (#10160) * Update biohansel to v2.1.0 * Python 3.6 builds only * Update meta.yaml * Fixing perl-json-xs and deps (#10161) * Fix perl-common-sense * Fix perl-types-serialiser * Bump perl-canary-stability * Bump perl-json-xs * Unblacklist * Small fixes * Build perl-json-xs later * Unblacklist perl-json-xs (#10163) * PIPITS 2.2 update. (#10164) * Perl OS X fixes 20180731 (#10165) * Various perl OS X fixes. * Remove perl-parallel-forkmanager from blacklist. * Riboseed updates (#10162) * [wip] riboseed add quast and networkx * update build number * bump version, remove dep on pyutilsnrw * [wip] remove quast (single tear), which isn't built for py3 on conda * bump version * bump version to fix cmdline args * bump version * Update meta.yaml * Unblacklist 2 more perl (#10166) * Unblacklist 2 perl * Unblacklisting * Fix typo * alfred v0.1.8 (#10168) * bump build numbers for htslib dependent recipes. * PacBio: Update `pbcommand` to 1.1.1 (#10172) * PacBio: Update `pbcore` to 1.5.1 (#10173) * Remove obsolete build script. * PacBio: Remove `pbcommand` from build-fail-blacklist (#10176) * PacBio: Initial addition of `pbcoretools` (#10169) * bump htslib to get libdeflate pinning * 2.1.3 update (#10180) * updated bbmap to 38.18 (#10178) * snakemake 5.2.2 (#10179) * snakemake 5.2.2 * add python as run dependency. * Chado tools (#9991) * bioconda recipe for chado-tools * use meta.yaml created by skeleton * set source to github * remove build script section * remove import section * restore import section * correction * noarch: python * Update mob_suite to 1.4.6 (#10088) * Update mob_suite to 1.4.6 * Update sha256 * added recipe for itsxpress 1.6.4 (#10099) * Enable python3.6 build (#10101) This recipe should not skip py36, as version 4.0.3 of RGI primarily supports Python3. This change will enable rgi to work in Python3 environments. * bump phyluce to 1.6.6 (#10114) * bump phyluce to 1.6.6 * adding DOI * Update breseq to v0.33.0 (#10175) * Update breseq to v0.33.0 * add disable-compiler-version-check.patch * Update meta.yaml * Dropseq tools (#10170) * first attempt * package name now lowercase * test command gave an exit 1 * another try * try.. * missed a slash * wrong test to test * qutoe * finalizing recipe before push * last test * add a test on help * added test for each command * Add deepsvr (#10167) * add deepsvr * switch install to pip * test cli entry point in build * update sha * update sha * update sha * Test help command * Remove command test * Add command test * Perl OS X fixes 20180801 (#10184) * More perl fixes for OS X. * Remove unneeded dependency. * Update schema-salad to 2.7.20180731120629 (#10195) * Update gatk4 to 4.0.7.0 (#10191) * Update toulligqc to v0.10 (#10192) * Update gridss to v1.8.0 (#10193) * Update dxpy to v0.257.3 (#10197) * Update anndata to 0.6.6 (#10186) * Update anndata to 0.6.6 * python >=3 * require python >=3.5 * Update isatools to v0.10.2 (#10190) * Update chado-tools to v0.0.4 (#10189) * enabled jni; bumped version to 38.19 . (#10185) * enabled jni; bumped version to 38.19 . * construct test file on the fly * use already-installed resource file for testing * added nodisk to avoid creating leftover files after test * changed tests to what blast does * fixed filenames * another filename fix * dropped pipefail * Update mglex to v0.2.1 (#10188) * Update mglex to v0.2.1 * update meta.yaml * New: wes-service client only (#10200) Provides a client for Workflow Execution Service (WES) endpoints, part of the GA4GH initiative. * Riboseed updates (#10202) * [wip] riboseed add quast and networkx * update build number * bump version, remove dep on pyutilsnrw * [wip] remove quast (single tear), which isn't built for py3 on conda * bump version * bump version to fix cmdline args * bump version * bump version * 2.1.4 release (#10204) * trigger rebuild * Trinotate: fix error in Build_Trinotate_Boilerplate_SQLite_db.pl (#10205) * fix path error in Build_Trinotate_Boilerplate_SQLite_db.pl * patch trinotate_report_summary.pl too * Move PyVCF to conda-forge (#9979) * Add recipe for hotspot3d 0.6.0. (#10209) * Fasttreecondbuild3 (#10177) * remove FastMP test * add SRC_DIR and filename to build script and move MP into linux-specific build * remove fasttree from blacklist * update older versions as well * trigger rebuild * bump build versions * change the tests so that they end * Update WGCNA to 1.63 (#10203) * phantompeakqualtools first commit (#10171) * phantompeakqualtools first commit * add in r-spp dependency * correcting dependencies * Updated ont-tombo to version 1.4. (#10182) * Updated ont-tombo to version 1.4. * Removed setuptools from run requirements. * Added extra identifier to the bioarxiv pre-print. * Update meta.yaml * Update pycoqc to 1.1.alpha3 (#10198) * Update pycoqc to 1.1.alpha3 * add noarch: python * remove universal binaries for ViennaRNA (#10043) * remove universal binaries for ViennaRNA * the flag in configure causes a 1.33-2.00x slowdown (docs say it interferes with some link-time optimizations) * the flag is unnecessary since its intent was to bind with Apple's stock python distribution (rather than conda) echo 'GCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA' | time RNAcofold --noPS -p RNAcofold --noPS -p 0.02s user 0.00s system 89% cpu 0.030 total RNAcofold --noPS -p 0.01s user 0.00s system 74% cpu 0.022 tota * bump buildno to trigger build * Bump libsequence to 1.9.4. Update dependencies, which are build-only! (#10210) * Bump libsequence to 1.9.4. Update dependencies, which are build-only! Compiler and run unit tests after build. * skip os x for now. the case-sensitivity of the file system makes building impossible until we get closer to libseq 2.0 * Unblacklist perl-file-find-rule (#10218) * unblacklist perl-file-find-rule * workaround from conda/conda-build#2824 * Fix python dependency for Stacks 2.1 and remove Stacks dependency from dDocent (#10213) * remove python spec * remove python * remove python * remove stacks dependency from dDocent * Update meta.yaml * Add deepbinner. (#10111) * Add deepbinner. * overwrite numpy pinning because tensorflow needs a newer version. * rebuild htslib in the hope that libdeflate pinning is now included on linux as well. * add suport for centroid rna package (#9647) * add suport for centroid rna package * add suport for centroid rna package * linting fail - fix by removing fn name * Change test from python to sh script. * Change test from python to sh script. * skiping osx, reintroducing python based test (simple check of output code not reliable) * add doi identifiers doi iderntifiers directly related to programs contained in package * run test from meta with grep instead of run_test.py add py2k to skip per request adding py2k to skip * suppress output of the test commands * unblacklist perl-dbi (#10236) * unblacklist perl-dbi * permission problem with fix_shebang * chmod again * Update r-wgcna build * Update build number * Fix macs2 recipe (#10232) * New recipe: Slamdunk (#10199) * Slamdunk recipe setup. * No fixed java version. * Java-jdk -> Openjdk. * PREFIX removed from recipe. * wget dependency added. * conda build checking. * path extensions. * Only py2.7 requirement. * Win skip removed. * lka * lkal * pip install switch * samtools dependencies added * senf * senf1 * recent * satool * sha * shaupdate * freaky * testy * testz * Slamdunk v0.3.1 bioconda build 0. * SHA256 updated. * Skipping py3 build. Using pip. * Python3 builds not skipped - otherwise package will not be built at all. * OSX build deactivated. * Skip py3k. OSX activated. * OSX deactivated for good. * .buildkite restored. Skip merged into one-liner. * Unblacklist perl-dbd-sqlite (#10239) * Unblacklist perl-dbd-sqlite * permission problem * Update treetime to v0.4.1 (#10229) * Update nglview to v1.1.5 (#10217) * Unblacklist trinotate recipe (#10206) * unblacklist trinotate * this module needs to be rebuilt * fix broken recipe * fix find command * rebuild * permission problem * Update build.sh * python-chado 2.1.5 (#10246) * Add recipe for connectome-workbench 1.3.1. (#10248) * Add recipe for connectome-workbench 1.3.1. * Use extended container. * Update: wes-service-client, bcbio-variation-recall, bcbio (#10249) - bcbio-variation-recall: Avoid use of gatk-framework. Fixes bcbio/bcbio-nextgen#2412 - wes-service-client: python2/3 fixes - bcbio: RNA-seq CWL improvements * Support osx. (#10251) zlib not needed. * Change compiler from c to cxx and bump build number. (#9900) * Change compiler from c to cxx and bump build number. * fix older recipes and remove fwdpp from blacklist * reset build number * blacklist old versions of fwdpp * remove fwdpy11 from blacklist * bump fwdpp to 0.6.1 * try not defining any environment variables related to compilation * pull build fail blacklist from master * include C compiler, too * Update vt to 0.57721 (#10253) * Trimmomatic update (#10257) * update trimmomatic * Update and rename trimmomatic.sh to trimmomatic.py * Update build.sh * Update meta.yaml * Update trimmomatic.py * remove old trimmomatic pkg * Pairtools v0.2.0 (#10252) * pairtools v0.2.0 * MultiQC version 1.6 release (#10254) * MultiQC version 1.6 release * Update meta.yaml * Update meta.yaml * bump version (#10258) * adding recipe for lordfast (#10255) * adding recipe lordfast * adding c++ compiler * Perl fix 11 (#10259) * Bump perl-array-compare * Fix perl-unicode-map * Unblacklist * Perl fix 12 (#10261) * Add perl-module-loaded * Add perl-graphics-colornames * Fix perl-graphics-colorobject * skesa 2.2-2 (#10262) * Update shovill to 1.0.0 (#10256) * Fastqe (#10245) * Add fastqe * Fix whitespace in description and noarch lint skip [lint skip should_be_noarch for recipes/fastqe] * Add GeneNoteBook recipe (#10089) * genenotebook recipe * Build from prebundled tarball * Bump perl-gd and add new dependency (#10260) * Add perl-test-fork * Bump perl-gd * Revert extra deps * NovaSplice (#10250) * attempt #1 to add novasplice recipe * novasplice * Update meta.yaml * Perl fix 13 (#10265) * Bump perl-file-fetch * Bump perl-file-sharedir-install * Bump perl-file-sharedir * Bump perl-html-tree * Unblacklist * Build perl-file-sharedir later * Unblacklist perl-file-sharedir (#10267) * Perl fix 14 (#10266) * Add perl-padwalker * Add perl-devel-cycle/ * Add perl-test-memory-cycle * Fix perl-font-ttf * Unblacklist * Correct build numbe * Correct build numbe * Unblacklist perl-pdf-api2 (#10268) * Fix perl-pdf-api2 * Unblacklist * Remove various packages from the blacklist (#10269) * Remove various packages from the blacklist * graphmap uses openmp, which is problematic with clang * Update bpipe to 0.9.9.6 (#10240) * Update bpipe to 0.9.9.6 * Update meta.yaml * add new commit to retrigger test * use http instead of ftp (friendlier with travis) (#10272) * gmap 2014.12.28 (#10181) * gmap 2014.12.28 * added host section * Update meta.yaml * Add -ldeflate to gqt compile command. Add missing limit macro defintion to pindel compile command. * Update: bcbio, bcbio-vm with WES support (#10274) * ensure SIZE_MAX is defined. * Fix flags. * try setting variable as make argument * set generic flags. * Update sleuth to 0.30.0. (#10278) * upgrade rscape (#10208) * upgrade rscape * glib * clean then compile * Update meta.yaml * debug info * relax plot version * simplify test * minor fix * older versions * older test * even older * even older * no clean * orig test * bump version * grep test * working version * bump working version * Create conda_build_config.yaml * clean then build * v0.7.3 * upgrade rscape * glib * clean then compile * Update meta.yaml * debug info * relax plot version * simplify test * minor fix * older versions * older test * even older * even older * no clean * orig test * bump version * grep test * working version * bump working version * Create conda_build_config.yaml * clean then build * v0.7.3 * Update conda_build_config.yaml * fix R2R makefile * gxx config * minor cleanup * skip mac * rnachipintegrator 1.1.0 (#10276) * rnachipintegrator: update to version 1.1.0. * Update meta.yaml * Dialign fix, again (#10279) * Fixing patch * Increased build number * Delete patchdialign.txt * Clinker (#10244) * Add clinker with wrapper * Add full test * Remove test data test as per guidelines * Updated minimap2 to v2.12 (#10282) * delly: update to fix boost linker error (#10283) Trying to fix: ``` delly: symbol lookup error: delly: undefined symbol: _ZN5boost15program_options3argE ``` and seems like it might need a re-build after being unblacklisted. * Unblacklist a few perl packages (#10275) * unblacklist a few perl packages * add back to blacklist temporarily * add back temporarily * another one * trigger new test * mac permissions * reset build number [ci skip] * mac permissions * try to rebuild mac packages maybe * damn, typo * mac perms * trigger new test * trigger new test * trigger * Update mlst to 2.11 (#10263) * Remove various packages from the blacklist (#10280) * Remove various packages from the blacklist * Tepid gave a rather tepid response * update gubbins to a new version (#10289) * Slamdunk package fix (#10290) * Slamdunk recipe setup. * No fixed java version. * Java-jdk -> Openjdk. * PREFIX removed from recipe. * wget dependency added. * conda build checking. * path extensions. * Only py2.7 requirement. * Win skip removed. * lka * lkal * pip install switch * samtools dependencies added * senf * senf1 * recent * satool * sha * shaupdate * freaky * testy * testz * Slamdunk v0.3.1 bioconda build 0. * SHA256 updated. * Skipping py3 build. Using pip. * Python3 builds not skipped - otherwise package will not be built at all. * OSX build deactivated. * Skip py3k. OSX activated. * OSX deactivated for good. * .buildkite restored. Skip merged into one-liner. * slamdunk v0.3.1 -> slamdunk v0.3.2 (Softlink fix). * Update confindr to v0.3.3 (#10224) * Update confindr to v0.3.3 * Update meta.yaml * Delete build.sh * Adding recipe for XHMM (#10183) * Remove strainest, starseqr, strudel, and svtools from the blacklist (#10291) * Build number updated. sha256 updated. (#10292) * updates bwameth to 0.2.2 (#10293) * Add setuptools as run dependency (needed by some helper). Add python as a host dependency, to work around problems with the metapackage. (#10294) * adding recipe for hulk (#10295) * nextflow 0.31.1 (#10296) * nextflow 0.31.1 * reset build number * Perl fix 15 (#10298) * Fix perl-forks * Fix perl-acme-damn * Unblacklist * Remove a few more perl recipes from blacklist (#10287) * remove a few more perl recipes from blacklist * temp disable * we need perl-cgi on mac * tab * mac fixes * various mac fixes * fix lint missing_tests * test * modified the wrong recipe * some broken perl osx packages * Needed by perl-soap-lite * perl-xml-twig dep problem * damn... forgot this * add back to blacklist until next batch * mac permission * mac rebuild * fix hang * perm problem * blacklist for now * Perl fix 16 (#10301) * bump perl-excel-writer-xlsx * Bump perl-archive-zip * Unblacklist * Bump perl-graphviz (#10303) * Bump perl-test-inter (#10306) * NanoSim-H 1.1.0.4 (#10307) * NanoSim-H 1.1.0.4 * Update sha256 * Reset build nb * flye 2.3.5 (#10309) * Faqcs (#10300) * adding recipe for FaQCs software * update test command for R * build change to number 1 * change R to r-base * test for no R --version * test redirect STDERR to STDOUT * add R testing * provide precomplied binary for MacOSX * build number 1 -> 0 * make OPENMP="" * nim-falcon (#10312) * Update nasp to v1.1.2 (#10308) * Update nasp to v1.1.2 * lint doi and skip noarch * build linux only * Update meta.yaml * add recipe-maintainers * update bbmap to 38.20; add doi for bbmerge; misc meta.yaml cleanup. (#10310) * Rebuild older perl-json-xs (#10313) * Rebuild older perl-json-xs * fix permission on mac * Unblacklist perl-lwp-protocol-https (#10304) * unblacklist perl-lwp-protocol-https * bump version * requirement * lint * experimental patch * disable tests * fix * perl-lwp-protocol-https fix (#10317) * Update cyvcf2 to 0.10.0 (#10314) * Update cyvcf2 to 0.10.0 * cyvcf2: add libcurl dependency * PacBio: Update `lima` to 1.7.1 (#10318) * PacBio: Update `isoseq3` to 3.0.0 (#10319) * Perl: more unblacklisting (#10305) * more unblacklisting * graphviz * fix * mac build * mac build * perm * rebuild on macos * no need to rebuild this version (see #10313) * mac perms * rebuild * rebuild * PacBio: Initial addition of `pbsv` (#10320) * Remove r-biclust in favour of the conda-forge one. (#10322) * Unblacklist perl-soap-lite (#10324) * unblacklist perl-soap-lite * rebuild mac * mac perms * Bt2 build (#10328) * Changes for building bowtie 2 static binaries * Blank out LDFLAGS * Update seven-bridges-python to 0.15.2 (#10330) * Update CrossMap version (0.2.7 -> 0.2.8) (#10327) * Update python-cluster to v1.4.1.post1 (#10222) * Update python-cluster to v1.4.1.post1 * use pip * Update loompy to 2.0.10 (#10214) * Update loompy to 2.0.10 * Update meta.yaml * noarch: python * remove loompy from build-fail-blacklist * Update meta.yaml * Update gridss to v1.8.1 (#10331) * Update catch to v1.1.0 (#10225) * Update catch to v1.1.0 * add noarch and use pip * Build cdbtools for osx (#10329) * Update nanopolish recipe for 0.10.1 release (#10333) * fixed flye build error (due to zlib) - package removed from blacklist (#10335) * fixes #10336 (#10337) * fixes 10336 * increase build number and add test * Update meta.yaml * tcoffee 11.00.8cbe486 (#10130) * tcoffee 11.00.8cbe486 * Revert meta.yaml * Update folder name * add DOI [ci skip] * Fixing test * Added t-coffee required runtime deps * Exclude poa from MacOS build * Add poa dependency * Update nglview to v1.1.6 (#10339) * lumpy: trying to fix skipped build (#10338) * lumpy: use python version restriction instead of selector * lumpy: pass on compiler/linker flags to make * lumpy: add C(PLUS)?_INCLUDE_PATH exports again because the world ain't perfect * lumpy-sv: also export LIBRARY_PATH... * lumpy-sv: fix extractSplitReads_BwaMem path * mac os rebuild (#10347) * pb-dazzler-0.0.0 (#10348) * Unblacklist bioperl (#10325) * fix build * add missing deps * update bioperl version * 3 modules which were moved out of bioperl-run in the latest version * fix cyclic dep * move out bio-coordinate + adapt tests everywhere * unblacklist * break the (vicious) cycle * fix tests * missing dep * fix versions * disable temporarily * disable temporarily * typos * fix * disable this too for now * disable temp * good old mac permission problem * rebuild this one too * another one * bump * bump * bump * another one * bump * bump * bump * bump * Update vcftools to 0.1.16. (#10345) * unblacklist (#10349) * Unblacklist perl-bio-samtools (#10350) * Unblacklist perl-bio-samtools * mac perms * Unblacklist perl-bio-asn1-entrezgene (#10351) * Unblacklist perl-bioperl-run (#10352) * increase build number * updated scvi to v0.1.6 (#10346) * scvi v0.1.4 * fix pytorch and python version * fix noarch * remove fn * add scvi v0.1.6 * Nglview v1.1.6 (#10343) * Update nglview to v1.1.6 * remove nglview from blacklist * Update hyphy to 2.3.14 (#10342) * Update hyphy to 2.3.14 * disable extended-base * Create conda_build_config.yaml * Update meta.yaml * Update isatools to v0.10.3 (#10340) * Unblacklist perl-bio-tools-* (#10353) * Unblacklist perl-bio-tools-* * trigger new test * add missing dep * we need this one on mac * need this too on mac * conda is confused between python and perl, it tries to import the module in perl while it's a python one * mac perm * t_coffee is too complicated (for me) to isntall on mac * Update solvebio to v2.6.1 (#10220) * Unblacklist more bioperl (#10354) * Unblacklist more bioperl * fixes + add extutils-makemaker * remove obsolete checks * Unblacklist some other perl-bio-* (#10358) * Unblacklist some other perl-bio-* * disable for now * mac perm * Update bioconda-utils to v0.14.2 (#10360) * Update bioconda-utils to v0.14.2 * noarch: python * Update PureCLIP recipe to v1.1.1 (#10361) * Update beast to v1.10.1 (#10362) * Add tandem-genotypes (#10286) * Add tandem-genotypes * Add tandem-genotypes license * Add tandem-genotypes noarch * Add tandem-genotypes host * Update helperlibs to release-0-1-9 (#10223) * Update helperlibs to release-0-1-9 * use pip * Update binsanity to 0.2.6.3 (#10363) * Update binsanity to 0.2.6.3 * add noarch * update bioconvert to v0.2.0 (#10316) * update bioconvert to v0.2.0 * vep: bumped major version (#10366) * Update treetime to v0.5.0 (#10370) * new jbrowse release (#10371) * Unblacklist a few recipes (#10364) * unblacklist * lint * bump * typo * force version * fix augustus 3.2.3 * bump * bump more * disable repeatmasker until prl package removed from bioconda * mac perms * thanks @bgruening :) * mac fix * mac fix * max fix * mac fix * typo * typo * trigger new test * delay repeatmasker * mac perms * Fixing some perl (#10375) * Fix perl-date-manip * Fix perl-env-path * Unblacklist * Fix perl-json-parse * Unblacklist * Remove older perl-json-parse * fix build number * Rebuild perl-file-slurp (#10376) * Update mob suite to version 1.4.8 (#10377) * 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 * new version should reset the build number to 0 * nanopolish out of blacklist (#10368) * nanopolish outof blacklist * openmp * cxx compiler * config for build * compiler mess * skip linting for compilers to accept the hack * Update meta.yaml * of course old style needs libgcc * Dpryan79 fixes 090818 1 (#10378) * Remove various recipes from the black list * apoc needs fortran * skip OSX with agg * Add bioconductor-zinbwave (#10142) * Add r-softimpute * Add bioconductor-zinbwave * Fixed errors detected during linting * Added the 'extras' section * Removed Windows-specific lines from the r-softimpute recipe * Forgot to remove some Windows-specific lines * Fixed r-softimpute build.sh * Fix source url * Remove r-softimpute * Add gsl dependency * Fix gsl version * skip macOS build * trigger rebuild * Remove barrnap, bfc and bgt from the black list (#10380) * Update snippy to 4.0.0 (#10315) * Adding a recipe for ksw (#10382) * Adding a recipe for ksw * lint? * use tag as PCK_VERSION * more * one commit to rule them all * cromwell uses find during runtime. With a normal conda installation it can fall back on the host installation, but when running in a biocontainer it only has access to the busybox version which lacks some necessary options. (#10383) * Perl fix 17 (#10379) * Fix perl-text-nsp * Fix perl-image-exiftool * Fix perl-test-output * Unblacklist * Fix shebang * rebuild flowtools (#10385) * flowtools * Update meta.yaml * skip noarch linting * Fix typo (#10386) * Bump perl-vcftools-vcf (#10387) * Perl parse yapp fix (#10388) * Bump perl-parse-yapp * Fix typo * Enable ensembl-vep from blacklist (#10394) perl-bioperl now available, pin to updated version to get all dependencies in sync. Fixes #10366 * Biobb common (#10397) * First version of biobb_common package recipe * Adding build noarch section and removing fn section * Modification in no arch section * Deleting build.sh * Ngsplotdb bugfixes (#10396) * Fix installation for hg19 * Fix hg38 * Fix mm10 * Better syntax * bioconda release for Trinity v2.8.1 * bioconda updates for v2.8.1
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