bump for alevin hotfix #10118
Merged
bump for alevin hotfix #10118
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Contributor
rob-p
commented
Jul 27, 2018
rob-p
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).
Put md5sum for the zip, not .tar.gz. Correct that.
asmariyaz23
pushed a commit
that referenced
this pull request
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.