From 4e4d4bfefd5b20cd9f64fe14f5319a16dbc4b47e Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Wed, 30 Oct 2019 10:03:48 +0100 Subject: [PATCH] Bulk (#18362) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 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 * 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) * Update pinning to R>=3.5 and a few runtime dependencies. * CSAW is R 3.5 only * Packages using beachmat are 3.5 only * Packages using bioconductor-singlecellexperiment are R 3.5 only * [BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#11452) * Don't use r-base >=3.5, use a conda_build_config.yaml instead * blacklist r-phangorn * Update variancepartition * R 3.5 for packages requiring singlecellexperiment * Update a few packages * Update a number of recipes (#11482) * Update ensemblVEP and derfinder (#11504) * Bulk update 251018 (#11577) * [BULK] various package updates * blacklist bioconductor-mzr * A couple tweaks * [BULK] Update 261018 (#11611) * Apparently the r-rgeos bit works properly now. * Add tissueenrich and try to fix scpipe on Linux * A meaningless change just to trigger an update in bulk. (#11618) * [BULK] update 271018 (#11628) * Bump bioconductor-esetvis * Fix yaqcaffy * Fix more * Another R 3.5 recipe * [BULK] update 281018 (#11689) * Add some files * Fix arrayexpress * Fix another 2 * Blacklist a bunch of bioconductor recipes that aren't likely to get built for a variety of reasons (mostly due to mzR). (#11697) * Update blacklist (#11706) * [BULK] fix bioconductor-tissueenrich (#11720) * taxonkit 0.2.5 (#11318) * Update csvtk (#11319) * taxonkit 0.2.5 * csvtk 0.15.0 * bumping GROOT to 0.8.1 (#11323) * HiCMatrix version 3 (#11322) * Correcting dependencies * Version 3 of HiCMatrix, the October release * Update confindr to 0.4.3 (#11330) * Drop-seq_tools: Version 2.0.0 (#11326) * Update meta.yaml * Update build.sh some tool names changed to fit Camel case * Update motus to build only for python3 (#11331) * Update fpa to 0.2 version (#11333) * update taxonkit to 0.3.0 (#11339) * ntcard 1.1.0 (#11338) * Update rgi (#11335) * first commit * update dependencies list * change source to github * change build number * testing circleci * update meta and build * fix build * move build script into meta * remove older recipes * line fix in bootstrap.py * change python & matplotlib versions; add build.sh file * add preprocessing selector to skip python 2.7 * move build script into meta.yaml * Revert "line fix in bootstrap.py" This reverts commit 5ac1ecd0142a5cfdfc8499c5b6ef4e1f629cd046. * Update gmap to version 2018-07-04. (#11332) MAX_READLENGTH environment variable has been disused since 2016-08-16. * Upgrade r-biodb to 1.2.0a. (#11341) * Upgrade r-biodb to 1.2.0a. * Update meta.yaml * Updated ont-tombo to version 1.5. (#11329) * Updated ont-tombo to version 1.5. * Updated with actual github release version hash. * remove graphicsmagick (#11342) * Build kraken2 for osx (#11343) * First try for a bcalm recipes (#11344) * New: cgpbigwig (BigWig manipulation); Update: bcbio (#11347) - cgpbigwig (https://github.com/cancerit/cgpBigWig) provides bigwig generation and manipulation command line tools including bam to bigwig conversion. - bcbio: fixes for QC on variants and peddy for CWL runs * Try avoid some dependancy (#11349) * Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 (#11348) * Update TreeBest to commit c9d3a2e35276c825577ec945b229e975c32078d8 Also add about:home . * Workaround https://github.com/conda-forge/bison-feedstock/issues/7 * Better bcalm recipes (#11350) * Try avoid some dependancy * Correct mess in build number, sorry * R biodb (#11351) * rebuild r-biodb * trigger build * Add recipe for pypairs (#11356) * Update smoove to 0.2.1. (#11360) * Update duphold to 0.0.9. (#11359) * Update goleft to 0.2.0 (#11361) * Bump slicedimage to 1.0.0 (#11362) * Bump slicedimage to 1.0.1 (#11365) * Added new versions for biopet-sampleconfig (#11268) * perl-velvetoptimiser: update to 2.2.6 (#11369) * update to 2.2.6 * remove unneeded patch * Scanpy upgrade (#11371) * Bump version * Upgrade Scanpy * Bump starfish to 0.0.25 (#11370) * bumping groot to 0.8.2 (#11374) * vep: bump subversion (#11367) * Updated Krocus 1.0.1 (#11355) * Add tiptoft * Fix meta.yaml for tiptoft * Add build script * Updated krocus 1.0.1 * Add tiptoft 0.1.4 (#11352) * Add tiptoft * Fix meta.yaml for tiptoft * Add build script * Kodoja v0.0.9 (#11373) * Add recipe for seer (#11263) * Add recipe for seer * lets try this * Add newer compiler * Using boost-cpp * messed up version string * Attempt building boost * Use c++11 in boost * Use python for boost install * Correct python version spec * try with different python version * Fix b2 command * Fix popd command * build and link boost program options statically * Fix tests * Match dependency order * Link openblas instead of blas * Forcing rebuild with openblas * Don't use armadillo wrapper * Making review changes. Also trying original tests * Previous tests were correct * Add recipe for the translate-gard npm package version 1.0.3 (#11364) * Fix umi tools (#11376) umi_tools: clean up dependencies * add support tools to PATH (#11379) * Bump to v2.2.1 (#11380) * Bump starfish to 0.0.26 (#11378) * Update fpa to 0.3 (#11375) * Update fpa to 0.3 * Correct error in sha256 * Reset build number * Update trial to 2.5.5 (#11386) * Update: bioconductor-titancna; 1.19.1 with hg38 support (#11388) * Update: bioconductor-titancna; 1.19.1 with hg38 support * Pin to R 3.4 to avoid pulling in 3.3 and 3.5 during mulled * Add r-polysat version 1.7-3 (#11384) * Update biomart version so that compatible with r351 (#11366) * Update biomart version so that compatible with r351 * Update meta.yaml reset build number as per https://bioconda.github.io/guidelines.html#buildnum * Update entrez-direct to 10.0.20180927. (#11387) * Added recipe for SonicParanoid 1.0.13 (#11271) * Added recipe for SonicParanoid 1.0.13 * removed 'x.x' for numpy, added basic test * fixed linter related errors * compiler set to cxx and added host section (same build error!) * removed host section * moved numpy and cython to host section; restored build: noarch: python; added LICENSE.md * removed build: noarch * added build and extra sections * set build number to 0; removed skip build; added python3 minimum version; added test for all executables. * restored sh python module as requirement * added Make to run; updated release to latest commit * remove c compiler from meta.yaml * modified build.sh to compile source codel added make in build section * updated to latest commit * updated to latest version with make included in setup.py * reverted build.sh to the simplest version (python setup.py install) * Add perl-json to build requirements to allow meme-chip to run to completion. Change meme-chip to use dreme-py3 instead of dreme if building with python 3. (#11389) * Bump IgBLAST to 1.9.0 (#11393) Bump IgBLAST to 1.9.0 Re-package the binary version this time. There are problems building the source version when the configure script reaches this step: "trying to build the NCBI SRA/VDB Toolkit from GitHub" The previous problem about the binaries linking against libbz2.so, for which we had no conda package, is now solved. Also, this saves about 45 minutes compilation time. * Add consan (#11395) * Add consan * Skip osx * Update: vardict, vardict-java 1.5.7 (#11394) * Update: vardict, vardict-java 1.5.7 Latest vardict-java release and corresponding vardict with bug fixes after testing with 1.5.6 * Reduce test output to try and fix build problems * Experiment 2 for build problems: remove r-base from run * Experiment 3 for build problems: add r-base in host * update recipe for 3.9.1 (#11397) * evofold2 (#11396) * evofold2 * wrapper * Update meta.yaml * minor * Update rnastructure to 6.1. (#11400) * Ctat mut (#11401) * updating version number * correct URL * proper hash * Revert "Ctat mut (#11401)" (#11402) This reverts commit 6db10ac7ffd7abaf8fbf1762b7ea6c63b2585fe0. * update version (#11403) * any2fasta 0.4.2 (new formula) (#11407) * W4mclassfilter v0.98.9 (#11385) * Added files to build version 0.98.9 * Update meta.yaml * Update meta.yaml * updated SonicParanoid recipe to version 1.0.14 (#11409) * updated SonicParanoid recipe to version 1.0.14 * Update to version 1.0.2 of PopDel (#11398) * Update to version 1.0.2 of PopDel Update to version 1.0.2. * Reset build number to 0 * PacBio: require Meson 0.48.1 for all recipes (#11090) * Meson 0.47 inserted duplicate RPATHs in macOS binaries, causing `install_name_tool` failures when installing the package. Requiring 0.48.1 ensures we do not run into these issues anymore in the future. * rebuild with latest openmpi (#11411) * Remove kfoots from the blacklist (#11416) * Update gseapy to 0.9.7 (#11417) * Update gseapy to 0.9.7 * remove noarch * Add SC3 as dependency (#11427) * Add recipe for r-poppr (#11418) * Update knitr version because of Issue: https://github.com/rstudio/rmarkdown/pull/1271 (#11412) * Update IQ-TREE to 1.6.7.1 (#11429) * Update IQ-TREE to 1.6.7.1 * Change build number * Update: r-deconstructsigs with fixes for hg38 (#11431) The 1.8.0 release, from 2016, has some issues with hg38 and other custom genomes that are fixed in development (raerose01/deconstructSigs#27). There hasn't been a new release pushed so this rolls these into a new sub-version and makes them available. * Update entrez-direct to 10.2.20181018. (#11432) * Add assembly-scan recipe (#11425) * remove python 2.7 skip (#11424) Preparation for rnaQUAST * Add fastq-scan recipe (#11415) * Add patch to fix racon/rampler path in racon_wrapper. (#11434) Fixes #11405. * meme rebuild (#11433) * Update nanocomp to 0.23.1 (#11436) * Update nanocomp to 0.23.1 * remove noarch * Update abricate to 0.8.10 (#11446) * Update angsd to 0.923 (#11445) * Update alfred to 0.1.13 (#11444) * Update alfred to 0.1.13 * Try w/o patch * Update antarna to 2.0.6 (#11442) * Update admixtools to 5.1 (#11443) * Update admixtools to 5.1 * Let makefile choose which bins to install * Update alignstats to 0.5 (#11441) * Update xatlas to 0.2.1 (#11437) * r-gpca (#11428) * r-gpca * r-gpca recipe * Update meta.yaml * Removed All Comments * gseapy bump version 0.9.8 (#11440) * gseapy bump version 0.9.8 * version * titancna: fix for hg38, remove conda build hacks (#11447) * titancna: fix for hg38, remove conda build hacks * Re-add r-base 3.4 pin to avoid 3.5 errors * Hmmlearn older version (#11450) * Adding pygtftk * removed pygtftk from master * add older version of hmmlearn * Add card_trick (#11451) * Add card_trick * Restrict to py3 * Update checkm-genome to 1.0.12 (#11455) * Bump drep (#11457) * Update squid to 1.5 (#11466) * Update ncbi-ngs-sdk to 2.9.3 (#11467) * elprep: bumped major version (#11414) * elprep: bumped major version * fixed hash * fix download link, fixed licence * fixed tests * skip osx build * FRED2 as a conda package (#11469) * Attempt to get FRED2 as a conda package * SHA update * 99 little bugs in the code * Fix things Björn mentioned * add rnaQUAST recipe (#11470) * Update bioconda-utils to 0.14.9 (#11454) * Rapidup (#11474) * Update to v0.7 * Update Buildnumber * rapid: update to v0.6 * rapid: update to v0.6 * update grid (#11478) * Adding biobb_model recipe (#11472) * Updated wtdbg to v2.1 (#11486) * update stream to 0.2.6 (#11483) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * Update meta.yaml (#11487) * Update connectome-workbench to 1.3.2 (#11468) Now needs QT 5.7 * Update deblur to 1.1.0 (#11500) * Update domclust to 1.2.8 (#11498) * WisecondorX: bump version (#11501) * Bump as GitHub wasn't working yesterday (#11502) * Added recipe for Sequenza (#10367) * Added recipe for Sequenza * Removed fn entry in source section * Trying with only one URL * copynumber is a bioconductor package * Added missing requirements section * Removed mailing list address * Added doi * Added license_file * Trying with different license_file path * Fred2 bump (#11503) * Bump as GitHub wasn't working yesterday * Fix licence etc * Scanpy scripts (#11413) Doing squash and merge as requested by @nh3 * Bump version * First implementation of scanpy-scripts bioconda recipe. * fix path in build.sh * Remove "noarch" flag as requested by bioconda recipe checklist * Add a post install notice that post install test needs bats-core. * Add more dependencies * Skip building for python versions other than 3.6 * Target v0.0.2 which has non-ascii characters removed * Lower version requirement for pandas and matplotlib to be the same as scanpy * Requirement matplotlib>=3.0.0, declare noarch * New: hmftools-cobalt; Update: hmftools-purple (#11507) - hmftools-cobalt: Add latest version of PURPLE associated read counter, COBALT, with support for hg38. - hmftools-purple: PURPLE release with hg38 support. * Update Picard to 2.18.15. (#11505) * Genenotebook (#11476) * 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 * dependency versions * v0.1.5 * Update pinning (#11514) * Bump build number for updated dependency (#11510) * Bump build number for updated dependency * Try adding r-base to host requirements * Try adding other requirements to host * Pin to R version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Tweak dependency version syntax * Pin R and package versions correctly * PacBio: Update pbcore to 1.6.5 (#11513) * Bump r seurat scripts version (#11292) * Bump version * Remove noarch * Could wrongly quoted version be causing an issue? * Tweak pinning to try and fix CI error * seqcluster:fix UMI detection. (#11511) * seqcluster:fix UMI detection. * Fix dependency * quast 5.0.1 (#11479) * quast 5.0.1 * quast 5.0.1: remove third-party site packages from the distibution pack * quast 5.0.1: skip Glimmer in test * quast 5.0.1: joblib and simplejson dependencies added to meta.yaml (Setuptools downloading is disabled in conda build) * quast 5.0.1: explicit joblib and simplejson dependencies removed (Setuptools downloading is disabled in conda build) * quast 5.0.1: Python 2 and 3 compatible code in build.sh * wcX bugfixes (#11508) * wcX bugfixes * fixed shasum * Update fastspar to 0.0.7 (#11515) * Update iqtree to 1.6.7.2 (#11525) * Update illumina-interop to 1.1.6 (#11523) * Update hapbin to 1.3.0 (#11522) * Update hlama to 3.0.1 (#11520) * Update gb_taxonomy_tools to 1.0.1 (#11519) * Update gffcompare to 0.10.5 (#11517) * Update fast5seek to 0.1.1 (#11516) * Update deepbinner to 0.2.0 (#11499) * Update deepbinner to 0.2.0 * Update meta.yaml Try same fix as in #11240 * Update ncbi-vdb to 2.9.3 (#11550) * Update mikado to 1.2.4 (#11549) * Update perl-pcap to 3.5.2 (#11543) * Update python-hyphy-python to 0.1.9 (#11545) * Update mlst to 2.15.2 (#11547) * Update perl-sanger-cgp-vcf to 2.2.1 (#11542) * Update merfishtools to 1.5.0 (#11537) * Update perl-sanger-cgp-vagrent to 3.3.3 (#11536) * Update nonpareil to 3.3.3 (#11535) * Update prophex to 0.1.1 (#11532) * Update krakenuniq to 0.5.3 (#11527) * Update novoplasty to 2.7.2 (#11530) * Update minced to 0.3.2 (#11529) * Update mapdamage2 to 2.0.8 (#11528) * Update perl-sanger-cgp-allelecount to 4.0.0 (#11538) * Update pyvolve to 0.9.0 (#11531) * Genenotebook (#11512) * 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 * dependency versions * v0.1.5 * version fix * add plek (#11554) * Update pyimzml to 1.2.4 (#11534) * Bump shovill (#11555) * PacBio: Update minimum pbcore version (#11556) * We want all users of PacBio tools to be able to use our utilities with pbmm2 alignments. * Add recipe for translate-gard v1.0.4 (#11557) * bioconductor-rnaseqsamplesizedata (#11475) * Adding Recipe for bioconductor-rnaseqsamplesizedata * Updated metadata for RnaSeqSampleSizeData * nextflow 18.10.1 (#11558) * Update raxml to 8.2.12 (#11567) * Update r-fgwas to 0.3.6 (#11566) * Update rapid to 0.7 (#11565) * Update r-spieceasi to 1.0.2 (#11564) * Update rcorrector to 1.0.3.1 (#11562) * Update quicktree to 2.4 (#11560) * Update paladin to 1.4.4 (#11541) * Update paladin to 1.4.4 * delete md5 * Update build.sh * Update build.sh * Fix and unblacklist Tadarida-D (#11568) * Add recipe for rgt * Fix and un-blacklist tadarida-d * Remove RGT * bumping groot (#11575) * update pymzml (#11573) * Add bioconductor-rnaseqsamplesize (#11559) * Add bioconductor-rnaseqsamplesize * Update recipe * Fixing some URLs * Update dependencies missing * Update trumicount to 0.9.11 (#11576) * Update ConFindr to 0.4.4 (#11578) * Added new versions for biopet-scatterregions (#11572) * Added new versions for biopet-bamstats (#11571) * R ggbiplot (#11584) * add R -e 'httr::set_config(httr::config(ssl_verifypeer = 0L)); install.packages(devtools, repos=http://mirrors.ebi.ac.uk/CRAN/); library(devtools); install_github(vqv/ggbiplot); library(ggbiplot)' * add r-ggbiplot * update meta.yaml * update meta.yaml * update * update * update * update * update * update * update * update * update * fix errors * fix errors number 1 * Update rebaler to 0.1.2 (#11563) * Update rebaler to 0.1.2 * Remove fn * bump graphclust (#11585) * Update seqyclean to 1.10.09 (#11589) * Update stringmlst to 0.5.1 (#11590) * Update snp-dists to 0.6.2 (#11592) * Update snippy to 4.3.3 (#11596) * Update canu to 1.8 (#11600) * Update starfish to 0.0.27 (#11599) * Update womtool to 36 (#11594) * Update telseq to 0.0.2 (#11598) * Update snp-sites to 2.4.1 (#11588) * Added recipe for pydemult: Streamed and parallel demultiplexing of fastq files (#11471) * Added recipe for pydemult * Bumped version in favor of py3.5 * bump vcf2db to latest commit (#11601) * bump vcf2db to latest commit * fix shasum * Fixing source url * Update: TitanCNA; hg38 cytoband support and fix for normalization (#11604) * megan (#11046) * megan6: initial commit * megan6: intermediate commit * megan: made tests work * megan: doc improvement * megan: added osx dmg file * megan: add java to build requirements * megan: removed new line * megan: removed osx sources * Update meta.yaml * bumping hulk (#11607) * Update hotspot3d to 1.8.2 (#11521) * Update hotspot3d to 1.8.2 * Add perl-json as dependency * Add perl-archive-extract as dependency * Fqzcomp (#11606) * Added recipe for fqzcomp * There is no configure script * Maybe this works * Added gcc as build requirement * Removed gcc again (lint issue) * Maybe these exports will do the trick * Nope! * Added cxx as host requirement * Compilers are only allowed in build section * There is no need for make install * Copy-paste error... * Add vcf-annotator recipe (#11481) * Add vcf-annotator recipe * added pyvcf dependency * Update meta.yaml * stacks: fix for @ in exe_path (#11580) * stacks: fix for @ in exe_path * stacks: fixed path * New version with bugfix and different progressiveMauve version. (#11613) * Sspupdate (#11614) * New version with bugfix and different progressiveMauve version. * Keeping old version as folder. * Push build number. * Update SVDB to version 1.3.0 (#11506) * new file: recipes/svdb/1.1.2/meta.yaml renamed: reipes/svdb/svdb.patch -> recipes/svdb/1.1.2/svdb.patch modified: recipes/svdb/meta.yaml * deleted: 1.1.2/meta.yaml deleted: 1.1.2/svdb.patch * Bump nanosim (#11608) * Bump nanosim * Add scipy as dep * Add recipe for perl-number-range (#11621) * New build for grid (#11620) * update grid * update build num * Recipe for das_tool 1.1.1 (#10528) * recipe for das_tool 1.1.1 * Add recipe for sompy (#11624) * cmake modified to build with NDEBUG (#11328) * cmake modified to build with NDEBUG * Update meta.yaml * new build with fasta test * new build with fasta test * Fix and unblacklist TwoPaCo (#11622) * Add recipe for TwoPaCo * Unblacklist twopaco * Modify and unblacklist recipe for ESTmapper (#11623) * Modify and unblacklist recipe for ESTmapper * Add patch * Modify and unblacklist recipe for Metaseq (#11625) * Fix recipe for metaseq and remove from blacklist * Remove build.sh * nextflow 18.10.1 build 2 (#11630) * Add Clust (#11619) * Add clust * Clean recipe * Add "noarch" * Add DOI * Add build file * Python 2.7 * Fix scikit-learn dependency * Trigger new build * Update: PureCN (multicore) and PURPLE (plotting X libraries) (#11631) - PureCN: adds support for specifying cores on command line - PURPLE: adds X library dependencies required for creating plots * scripts/travis-run.sh: added a cleaner method to check for env vars (#11612) * Increase the number of k value usable in bcalm (request by @Malfoy) (#11610) * Increase the number of k value usable in bcalm (request by @Malfoy) * Change compilation parameter to reduce memory impact of compilation * Update anndata to 0.6.11 (#11637) * Update nglview to 1.1.7 (#11643) * Update binsanity to 0.2.7.1 (#11644) * Update cgat-core to 0.5.4 (#11645) * Update nanosv to 1.2.2 (#11673) * Update abeona to 0.36.0 (#11670) * Update pyfaidx to 0.5.5.2 (#11659) * Update agfusion to 1.23 (#11668) * Update iqtree to 1.6.8 (#11686) * update iqtree to 1.6.8 * Trigger rebuild * Update validators to 0.12.2 (#11672) * Update python-edlib to 1.2.3.post1 (#11664) * update for Purge Haplotigs (#11690) * Update loompy to 2.0.16 (#11667) * Update loompy to 2.0.16 * Update meta.yaml * IgBLAST 1.10.0 (#11693) * Update wtforms-alchemy to 0.16.7 (#11679) * Update sickle to 0.6.4 (#11663) * Update sickle to 0.6.4 * Remove fn and libgcc runtime dep * Update confindr to 0.4.5 (#11696) * Batvi (#11695) * batvi initial * Guideline compatibility.. * Dummy test section.. * Missing java dependency.. * use openjdk instead of java-jdk .. * source specified in github .. * trigger build (package did not have batindel directory) .. * update SHA256 .. * update SHA256 .. * Update pythonpy to 0.4.11 (#11661) * Update cortexpy to 0.45.6 (#11660) * Update sevenbridges-python to 0.16.0 (#11674) * Update solvebio to 2.7.0 (#11657) * Update mathstats to 0.2.6.5 (#11656) * Update goatools to 0.8.9 (#11641) * Add gnies (#11627) * Add gnies * noarch python * Update meta.yaml * Add recipe for SKA v1.0 (#11581) * Add recipe for SKA v1.0 * Add lib path for zlib * Older gcc * Correct install dir * Try static linking * Dynamic linking on OS X * ldd command test * correct program * Remove ldd command * Add recipe for transit version 2.3.1 (#11701) * Add recipe for transit version 2.3.1 * Use skip, add spaces. * Update meta.yaml (#11699) * remove pyqi (#11704) * Update python-chado to 2.2.0 (#11714) * update python-chado * 2.2.1 * Update vcfanno to 0.3.1 (#11710) * FGMP-1.0.1 (#11278) * FGMP-1.0.1 recipe * remove unncessary build info * add r-nabor (#11716) * update stream to 0.2.2 * update stream to 0.2.3 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.4 * update stream to 0.2.5 * update stream to 0.2.6 * add r-nabor recipe * update r-nabor recipe * update r-nabor recipe * r-pctgcdata (#11715) * r-pctgcdata * r-pctgcdata - fix * r-pctgcdata - fix * Update meta.yaml * Fix plek by a new branch (#11605) * Modify the PLEK recipe * Start fixing PLEK, though it requires compilation * update build.sh * update yaml * fix build.sh * update build.sh * Update recipe for plek * add bioconductor-chromvar recipe (#11718) * add bioconductor-chromvar recipe * fix bioconductor-tissueenrich * Apparently the popdel recipe didn't get correctly merged * Final merge conflicts * Bioc quick test (#12547) * Update kallisto to 0.45.0 (#12117) * Update validators to 0.12.3 (#12116) * Update illumina-interop to 1.1.7 (#12115) * Update umi_tools to 0.5.5 (#12123) * Update tiptoft to 1.0.0 (#12122) * Update: TitanCNA with fix for hg38 plotting (#12130) * blockclust (#12111) * added eden 1.1 version used in blockclust * Update meta.yaml * eden checksum and test * added zlib requirement * add include and lib paths to build.sh * add include and lib paths to build.sh * modify makefile flags using sed * modify makefile flags using sed * use c++ * Update build.sh * Update build.sh * LDFLAGS not used in makefile * remove v1.1 * add blockclust 1.1.0 recipe * skip osx build * added tarball url and checksum; removed conda_build_config.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update chewbbaca to 2.0.16 (#12132) * Update abeona to 0.40.0 (#12131) * ping to eden 1.1 (#12134) * clean swap file (#12137) * Update corset to 1.07 (#12143) * Update peddy to 0.4.3 (#12144) * blockclust latest source and added cloudpickle as requirement (#12142) * Update nanomath to 0.22.0 (#12149) * Update pymvpa to 2.6.5 (#12152) * Updated to version 1.4.0 (#12138) * Updated to version 1.4.0 * Resetting build number to 0 and build->host * Update transdecoder to 5.5.0 (#12172) * Update gridss to 2.0.1 (#12190) * Update tracer to 1.7.1 (#12189) * Update flowcraft to 1.4.0 (#12179) * Update seqbuster to 3.2 (#12182) * Update perl-io-compress to 2.081 (#12201) * Update twobitreader to 3.1.6 (#12205) * Update twobitreader to 3.1.6 * Update meta.yaml * Update gtfparse to 1.2.0 (#12186) * Update gtfparse to 1.2.0 * remove compiler * Update htseq to 0.11.0 (#12177) * Update htseq to 0.11.0 * add compiler * Update htseq to 0.11.0 (#12239) [testing co-author] * Update htseq to 0.11.0 * add compiler Co-authored-by: Bjoern Gruening * alfred v0.1.16 (#12240) * alfred v0.1.16 * makefile patch * makefile patch * Update scrm to 1.7.3 (#12150) * Update scrm to 1.7.3 * Update scrm to 1.7.3 * Mob suite update 1.4.8 --> 1.4.9 (#12244) We fixed a small bug related to repetitive elements database reconstruction on each run. Should only run once during the first mob_typer run. Should be good now for parallel runs. * PeptideShaker updated to v1.16.35 & SearchGUI updated to 3.3.9 (#12241) * PeptideShaker updated to v1.16.32 SearchGUI updated to v3.3.6 * PeptideShaker updated to v1.16.35 * SearchGUI updated to v3.3.9 * First attempt at a recipe for ncrf (#12101) * First attempt at a recipe for ncrf * changed from copies to symlinks * including absolute path in symlinks * PacBio: Update `pbmm2` to version 0.11.0 (#12246) * Gimmemotifs version 0.13.0 (#12245) * new release to fix numpy incompatibility * GimmeMotifs 0.13.0 release test * numpy 1.15 * version 0.13.0 * Fix about:home and extra: * PacBio: Update `isoseq3` to version 3.1.0 (#12263) * add python to host section (#12264) * Update confindr to 0.4.7 (#12266) * new build of GRiD (#12269) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * peptideshaker, searchgui: version bump (#12136) * peptideshaker, searchgui: version bump solving https://github.com/compomics/searchgui/issues/192 * Update peptide-shaker.py * searchgui: added c compiler for building test if linking errors go away this way * searchgui: removed noarch * Update: bcbio, bcbio-vm with CWL non-human fixes (bcbio/bcbio-nextgen#2473) (#12273) * Make snakemake a noarch package. (#12274) * noarch: python in combination with version constraint * Cleanup deps and simplify version definition. * Genenotebook v0.1.9 (#12277) * 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 * Create r-airr recipe (#12284) * Create r-airr recipe using bgruening/conda_r_skeleton_helper * Update meta.yaml * Findbin::Real added (#12291) * Added version bump to 1.3 (#12292) * ngs-bits 2018_11 (#12262) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2018_11 * minor edit in grid (#12287) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * Fred2 update (#12259) * Update FRED2 Recipe * msstitch version 2.9 (#12296) * r-mvr (#12300) This is a non-parametric method for joint adaptive mean-variance regularization and variance sta- bilization of high-dimensional data. * Bump to Gromacs 2018.3 + re-enable OSX build (#12299) * Gromacs 2018.3 + re-enable osx build See also #7825 on OSX build Include RRID for Gromacs (see bioconda/bioconda-utils#252) * disabled ocl-icd on osx; not available (or needed?) https://anaconda.org/conda-forge/ocl-icd * pyGenomeTracks update of dependencies (#12279) * Update pyGenomeTracks recipe to enable py3 support and updating outdated dependecy list * Increase build number * Update meta.yaml * Exclude Python 3.5 * Gromacs 2018.4 (#12302) * quast 5.0.2 (#12303) * Update meta.yaml (#12275) * Update meta.yaml r-rsqlite version dependency added * Update meta.yaml Updated build number to 1 * Use the extended-base container because of wget issues when downloading databases (#12297) * Update duphold to 0.1.0 (#12257) * Update flashlfq to 0.1.109 (#12256) * Update planemo to 0.57.0 (#12251) * Update meta.yaml (#12258) * Update scalpel to 0.5.4 (#12249) * Update scalpel to 0.5.4 * Fix url * edit grid (#12298) * update grid * update build num * edit grid to use mosdepth for depth coverage * edit grid to use mosdepth for depth coverage * Update meta.yaml * new build for grid * Update meta.yaml * minor edit to grid * minor edit to recipe grid * added feather to deps (#12293) * R tigger (#12286) * Create recipe for r-tigger (#12271) * Create recipe for r-tigger using bgruening/conda_r_skeleton_helper. * Delete bld.bat * Remove windows support * update scprep to v0.8.1 (#12306) * Update nanoget to 1.7.5 (#12252) * Update nanoget to 1.7.5 * Bump to version 1.7.6 should fix the README.md problem * gffcompare: version bump (#12308) * Update: cromwell (36), bcbio (Cromwell Docker runs) (#12307) * Update: cromwell (36), bcbio (Cromwell Docker runs) * Pin java to 8 to avoid compile errors on 11 * HiCExplorer update to version 2.2-beta (#12309) * HiCExplorer update to version 2.2-beta * Remove of '-' from version number * Numpy set to 1.15 * Update meta.yaml * upgrade to version 2.8.1 (#12316) * Create Airr recipe (#12318) * Create AIRR recipe using conda skeleton pypi. * Add noarch python * Clean host requirements * Added nimnexus [v0.1] (#12133) * added nimnexus * Fix sha * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * [WIP] Add R-loom (#12320) * initial WIP skeleton * Update meta.yaml * Update meta.yaml * Update meta.yaml * try osx * Create Changeo recipe (#12321) * Create changeo recipe using conda skeleton pypi. * EDIT about section * ADD noarch generic * Update noarch to python * Clean host requirements * Add test for scripts * Change requirement to python>=3.4 * Add noarch pyton * r-corbi (#12325) * r-nam (#12327) * Update pybedtools to 0.8.0 (#12324) * Update pybedtools to 0.8.0 * rm cython requirement * MSGFplus does not work with newer Java (#12330) * Trying to not use a very new java version since the latest ver… * Fix mosdepth and macs2. Blacklist bowtie1. * Update blacklist, work more on MACS2 * blacklist more failing packages * Update pinnings on all packages * queue up the next one * Updates * more updates * updates * A few fixes * More bioc updates for the new pinnings * update scPipe * Update blacklist, some bioc packages and remove unneeded conda_build_config.yaml files * A few more updates * last updates for the night * Update the BRAIN * Various R package updates * More updates * a couple more * A few updates * more updates * nearing complete * blacklist treekin/0.4.2 and try fixing zeroc-ice * Bioconductor 3.9 packages and some of their systemrequirements, which we'll work to automate for the next release. * Someone merged .circleci/common.sh into master a while back. It gets overwritten everytime locally * update .gitignore * manually add systemrequirements * Go ahead and blacklist on R 3.6 package * blacklist 2pg_cartesian * blacklist weblogo * blacklist trimmomatic * blacklist tophat * more * more blacklisting * more * meme * mafft * how is samtools breaking things? * wrong samtools versions * refine blacklist * kat * gromacs * braker * bowtie2 * update blacklist * start fixing experiment files * Fix experiment packages, update blacklist * a few updates * blackist sqt * Updates * update some recipes * blacklist art/3.11.14 * update blacklist * fix a recipe, update the blacklist * More updates * Updates * updates * update blacklist * blacklist discovar * blacklist transabyss * update blacklist * fix data package version pinnings, update blacklist * Update blacklist * blacklist * Wrote a program to find all of the stuff that's likely to break the build and blacklisted them all * update blacklist * update blacklist, start debugging fci * Update blacklist * update blacklist * Next to check for a build number * Wrote a program to check for more recipes that can't render. It's still running. * update blacklist * update r-rgi packages and blacklist * update blacklist * nearing the end * update blacklist, hopefully things build through now * Fix * update blacklist * Start fixing malformed recipes * fix more recipes * update more recipes * the remaining recipes breaking things * better group things in the blacklist * Update bioconductor recipes, remove from blacklist * fix colombo * Update a few packages * Blacklist a few bioc recipes for now * blacklist some recipes * temp blacklist updates * various updates * update blacklist * update blacklist * updates for bioc build * updates * update blacklist fix r-qpcr rendering * small blacklist update * bulk updates * blacklist updates * bl * update bl * bioc updates * bump r-rnexml * update bl * update chetah * Ah, right, solved bioc-graph previously * blacklist some rgl packages * try CoGAPS * small update * bl updates * Update blacklist * Add r-ontologyplot * update blacklist * update r-ic10 * update foldgo * bulk updates * bump r-orqa * bump CRAN packages * fix r-hardyweinberg recipe * fix r-pma * update a few recipes * a few bulk updates * fix bioconductor-mcagui * fix bioconductor-rcade * Update chippeakanno * blacklist bioconductor-cancer * Update blacklist and tfea.chip recipe * Add recipe for vmatch 2.3.0. * update blacklist * more blacklisted recipes * update blacklist * Change license_family to a valid value. * Correct build requirements. * Add biotools identifier. * Reorganize meta.yaml. * Add platform selectors to sha256 section (otherwise it's a duplicate key error). * updates * Skip false positive linting. * update GOTHiC and the blacklist * updates * Correct variable name. * update some recipes and the blacklist * updates * updates * update a coupe last packages * remove ete3, which has been migrated, try the blacklisted bioc packages * some updates * more updates * some updates * updates * more updates * updates * fix HiCMatrix * updates * last bulk update * fix socru recipe * Patch SELECT/makefile to use compiler from (conda) environment instead of hardcoded value. * Create directory for doc before copying files. * Don't test some programs/scripts as they don't have -help option. * Copy blast test files since the build system can't find them (only the files of this recipe are copied). * Miscellaneous edits (comments, typos). * Update meta.yaml * Update meta.yaml * blacklist multiphate, clean it up * tweak vmatch on OSX * further vmatch tweaks * Vmatch build2 (#17262) * Update sourmash to 2.1.0 (#17113) * Update aquila_stlfr to 1.2.9 (#17111) * Update pynnotator to add support for Python2 (#17114) * Update pynnotator to add support for Python2 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update sevenbridges-python to 0.23.1 (#17117) * Update pbmm2 to 1.1.0 (#17072) * Update pbmm2 to 1.1.0 * PacBio: Update `pbmm2` dependencies * Update nanoplot to 1.27.0 (#17118) * Update nanoget to 1.9.0 (#17116) * Update cgpbigwig to 1.0.4 (#16970) * Update cgpbigwig to 1.0.4 * Update cgpbigwig to 1.0.4 * Works on linux * just wondering... * p11-kit is linux only * Update varfish-annotator-cli to 0.10 (#17121) * Update flashlfq to 1.0.0 (#17123) * pb-falconc-0.0.1 (#17077) * pb-falconc-0.0.1 * Try to find missing gcc * Try another way CircleCI does not find "gcc", so I will try a newer way. * We are looking for gcc. Maybe this will help us find it. * Closer ``` 01:16:51 BIOCONDA INFO (OUT) echo "CC=$CC" CC=/opt/conda/conda-bld/pb-falconc_1566695732043/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc CC=$BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc ``` * alias gcc maybe? * Try symlinking gcc * further nim compilation * get nim to build * apparently this needs rsync to copy some directories. * try injecting compilers * should compile on Linux at least * better compiler injection * Update clonalframeml to 1.12 (#17120) * Update clonalframeml to 1.12 * C++, inject compilers * Adding jupyterpngsplugin python package to Bioconda (#17124) * SEPP: Update to version 4.3.10 (#16958) * Update to version 4.3.10 fix issue #70 a bug when hmmsearch fake jobs where not piped * search binaries in $PREFIX instead of relying on conda's preprocessing and replacing of /opt/anaconda1anaconda2anaconda3/ * debugging * debug a bit, this actually passes locally, possibly due to a different conda-build version * Update meta.yaml * more debugging * maybe * no slash? * not in . directories * remove debug test * Update aquila_stlfr to 1.2.10 (#17125) * Update r-bioverbs to 0.2.7 (#17127) * Update r-goalie to 0.3.6 (#17130) * Update r-syntactic to 0.2.4 (#17132) * Update angsd to 0.931 (#14862) * Update angsd to 0.929 * Update angsd to 0.931 * start simplifying * foo * tidy up * Update womtool to 45.1 (#17126) * bump platon mummer dependency version (3->4) (#17119) * Update r-transformer to 0.2.5 (#17135) * Update neurodocker to 0.5.0. (#17137) * clean and build, fail on errors, issue #11509 (#17085) * clean and build, fail on errors, issue #11509 * fix linting * This builds on linux * Update meta.yaml * Adding goenrichment python package (#17131) * Adding goenrichment python package * Update meta.yaml * bump iranges to 2.18.2 (#17138) * bump iranges to 2.18.2 * Update r-transformer * Update r-brio to 0.3.6 (#17134) * Update r-freerange to 0.2.4 (#17133) * Update r-freerange to 0.2.4 * Update meta.yaml * typo * Update r-basejump to 0.11.11 (#17136) * Update r-basejump to 0.11.11 * update dependencies * snakemake: require imagemagick >= 7.0 to avoid PDF -> PNG convert bug (#17062) * Update sevenbridges-python to 0.23.2 (#17139) Package uploads complete: [ci skip] - biocontainers/sevenbridges-python:0.23.2--py_0 - noarch/sevenbridges-python-0.23.2-py_0.tar.bz2 * Smudgeplot (#17140) * First attempt at recipe * Added R package dependencies * Added numpy dependency * Added scipy * Fixed test * Testing suggestions from PR * Final polishing after PR comments - passed local tests * Get the R stuff in the right place to ensure the pinning works * Update gridss to 2.5.2 (#17143) * Remove minepy for conda-forge/staged-recipes#9292 (#17146) * aquila first version (#17129) * first version * modify meta for bioconda install * Update meta.yaml * Update pynnotator to 1.9 (#17145) * Update pynnotator to 1.9 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update plasmidfinder to 2.1 (#17147) Package uploads complete: [ci skip] - biocontainers/plasmidfinder:2.1--0 - noarch/plasmidfinder-2.1-0.tar.bz2 Co-authored-by: Devon Ryan * Include target dir for clean as well to ensure right location is cleane * Include target dir for clean as well to ensure right location is cleaned * bump build number * Update downpore to 0.3.3 (#12573) Package uploads complete: [ci skip] - biocontainers/downpore:0.3.3--h375a9b1_0 - linux-64/downpore-0.3.3-h375a9b1_0.tar.bz2 - osx-64/downpore-0.3.3-h375a9b1_0.tar.bz2 Co-authored-by: Devon Ryan * Update gprofiler-official to 1.0.0 (#12213) Package uploads complete: [ci skip] - biocontainers/gprofiler-official:1.0.0--py_0 - noarch/gprofiler-official-1.0.0-py_0.tar.bz2 Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com> Co-authored-by: Devon Ryan Co-authored-by: Devon Ryan * Update rust-bio-tools to 0.6.0 (#17149) Package uploads complete: [ci skip] - biocontainers/rust-bio-tools:0.6.0--hf53bd2b_0 - linux-64/rust-bio-tools-0.6.0-hf53bd2b_0.tar.bz2 - osx-64/rust-bio-tools-0.6.0-h9904429_0.tar.bz2 * fix and update r-spieceasi (#17148) Package uploads complete: [ci skip] - biocontainers/r-spieceasi:1.0.7--r36_0 - noarch/r-spieceasi-1.0.7-r36_0.tar.bz2 Co-authored-by: Zachary Kurtz * Update control-freec to 11.5 (#12199) Package uploads complete: [ci skip] - biocontainers/control-freec:11.5--he1b5a44_0 - linux-64/control-freec-11.5-he1b5a44_0.tar.bz2 - osx-64/control-freec-11.5-h6de7cb9_0.tar.bz2 Co-authored-by: Devon Ryan * minced 0.4.0 - build with older java (#17150) * Update epic2 to 0.0.40 (#17152) Package uploads complete: [ci skip] - biocontainers/epic2:0.0.40--py27h9276139_0 - biocontainers/epic2:0.0.40--py36h9276139_0 - biocontainers/epic2:0.0.40--py37h9276139_0 - linux-64/epic2-0.0.40-py27h9276139_0.tar.bz2 - linux-64/epic2-0.0.40-py36h9276139_0.tar.bz2 - linux-64/epic2-0.0.40-py37h9276139_0.tar.bz2 * Update scanpy-scripts to 0.2.4.post1 (#17151) Package uploads complete: [ci skip] - biocontainers/scanpy-scripts:0.2.4.post1--py_0 - noarch/scanpy-scripts-0.2.4.post1-py_0.tar.bz2 Co-authored-by: BiocondaBot <47040946+biocondabot@users.noreply.github.com> * Update howdesbt to 1.00.03 (#16920) Package uploads complete: [ci skip] - biocontainers/howdesbt:1.00.03--hc9558a2_0 - linux-64/howdesbt-1.00.03-hc9558a2_0.tar.bz2 - osx-64/howdesbt-1.00.03-h770b8ee_0.tar.bz2 Co-authored-by: dpryan79 Co-authored-by: Devon Ryan * Update pynnotator to 1.9.1 (#17154) Package uploads complete: [ci skip] - biocontainers/pynnotator:1.9.1--py_0 - noarch/pynnotator-1.9.1-py_0.tar.bz2 * Update paragraph to 2.3 (#16539) Package uploads complete: [ci skip] - biocontainers/paragraph:2.3--h8908b6f_0 - linux-64/paragraph-2.3-h8908b6f_0.tar.bz2 Co-authored-by: dpryan79 Co-authored-by: Devon Ryan * Update hmmratac to 1.2.7 (#17158) Package uploads complete: [ci skip] - biocontainers/hmmratac:1.2.7--0 - noarch/hmmratac-1.2.7-0.tar.bz2 * Update libdeflate to 1.3 (#16839) * Update libdeflate to 1.3 * libdeflate has been migrated to conda-forge * Updated RNAlien to version 1.7.0 (#17153) * Updated RNAlien to version 1.7.0 * Removed echo and merged mv to one line guess the echo is for debugging and moving directly to ${t}-bin gets rid of a mv operation * Updated checksum * Fixed path * Added debug output * Fix for path * creating bin dir * creating bin dir in prefix * Minor Remove ls commands as they are debug only, added -p option to mkdir to prevent fail and only create dir if not existing * Update rnasamba to 0.1.4 (#17164) * Fix cromshell dependency (#17160) Package uploads complete: [ci skip] - biocontainers/cromshell:0.3.10--1 - noarch/cromshell-0.3.10-1.tar.bz2 * Update rnasamba to 0.1.4 (#17168) Package uploads complete: [ci skip] - biocontainers/rnasamba:0.1.4--py_0 - noarch/rnasamba-0.1.4-py_0.tar.bz2 * Update dca to 0.2.3 (#17165) Package uploads complete: [ci skip] - biocontainers/dca:0.2.3--py_0 - noarch/dca-0.2.3-py_0.tar.bz2 * Bump build number. (#17159) Package uploads complete: [ci skip] - biocontainers/pysamstats:1.1.2--py27hed695b0_5 - biocontainers/pysamstats:1.1.2--py36hed695b0_5 - biocontainers/pysamstats:1.1.2--py37hed695b0_5 - linux-64/pysamstats-1.1.2-py27hed695b0_5.tar.bz2 - linux-64/pysamstats-1.1.2-py36hed695b0_5.tar.bz2 - linux-64/pysamstats-1.1.2-py37hed695b0_5.tar.bz2 - osx-64/pysamstats-1.1.2-py27h2573ce8_5.tar.bz2 - osx-64/pysamstats-1.1.2-py36h2573ce8_5.tar.bz2 - osx-64/pysamstats-1.1.2-py37h2573ce8_5.tar.bz2 * Updating homer to version 4.10 and removing it from the blacklist (#17162) Package uploads complete: [ci skip] - biocontainers/homer:4.10--pl526hc9558a2_0 - linux-64/homer-4.10-pl526hc9558a2_0.tar.bz2 - osx-64/homer-4.10-pl526h770b8ee_0.tar.bz2 * Update masurca to 3.3.3 (#15706) Package uploads complete: [ci skip] - biocontainers/masurca:3.3.3--pl526haae6466_0 - linux-64/masurca-3.3.3-pl526haae6466_0.tar.bz2 Co-authored-by: Devon Ryan * Update presto to 0.5.13 (#17167) Package uploads complete: [ci skip] - biocontainers/presto:0.5.13--py_0 - noarch/presto-0.5.13-py_0.tar.bz2 * Update cat to 5.0 (#17163) Package uploads complete: [ci skip] - biocontainers/cat:5.0--0 - noarch/cat-5.0-0.tar.bz2 Co-authored-by: Devon Ryan * Update askocli to 0.5 (#15847) Package uploads complete: [ci skip] - biocontainers/askocli:0.5--py_0 - noarch/askocli-0.5-py_0.tar.bz2 Co-authored-by: Devon Ryan * Recipe for MotifBinner2 version 2.0.0 (#17141) Package uploads complete: [ci skip] - biocontainers/r-motifbinner:2.0.0--r36he1b5a44_0 - linux-64/r-motifbinner-2.0.0-r36he1b5a44_0.tar.bz2 - osx-64/r-motifbinner-2.0.0-r36h6de7cb9_0.tar.bz2 * Update breseq to 0.33.2 (#12188) Package uploads complete: [ci skip] - biocontainers/breseq:0.33.2--h8b12597_0 - linux-64/breseq-0.33.2-h8b12597_0.tar.bz2 - osx-64/breseq-0.33.2-hfbae3c0_0.tar.bz2 Co-authored-by: Devon Ryan * Update spine to 0.3.2 (#12175) Package uploads complete: [ci skip] - biocontainers/spine:0.3.2--pl526_0 - noarch/spine-0.3.2-pl526_0.tar.bz2 Co-authored-by: Devon Ryan Co-authored-by: Devon Ryan * Update cwltest to 1.0.20190228134645 (#15889) Package uploads complete: [ci skip] - biocontainers/cwltest:1.0.20190228134645--py_0 - noarch/cwltest-1.0.20190228134645-py_0.tar.bz2 Co-authored-by: Devon Ryan * Update star to 2.7.2b (#17169) * pbbam: revdep rebuilds (#17161) * Update rename to 1.601 (#17170) Package uploads complete: [ci skip] - biocontainers/rename:1.601--0 - noarch/rename-1.601-0.tar.bz2 Co-authored-by: Devon Ryan * Update minced to 0.4.1 (#17171) Package uploads complete: [ci skip] - biocontainers/minced:0.4.1--0 - noarch/minced-0.4.1-0.tar.bz2 Co-authored-by: dpryan79 * Update netreg to 1.8.0 (#16936) Package uploads complete: [ci skip] - biocontainers/netreg:1.8.0--h9fd3d4c_0 - linux-64/netreg-1.8.0-h9fd3d4c_0.tar.bz2 - osx-64/netreg-1.8.0-hf0ff744_0.tar.bz2 Co-authored-by: dpryan79 * Update tadtool to 0.79 (#17173) Package uploads complete: [ci skip] - biocontainers/tadtool:0.79--py_0 - noarch/tadtool-0.79-py_0.tar.bz2 * pbbam: revdep rebuilds #2 (#17174) Package uploads complete: [ci skip] - biocontainers/bax2bam:0.0.9--h018d624_7 - biocontainers/blasr:5.3.3--h018d624_1 - linux-64/bax2bam-0.0.9-h018d624_7.tar.bz2 - linux-64/blasr-5.3.3-h018d624_1.tar.bz2 - osx-64/bax2bam-0.0.9-h13b73d5_7.tar.bz2 - osx-64/blasr-5.3.3-h13b73d5_1.tar.bz2 * Update r-exomedepth to 1.1.12 (#17175) * Update r-exomedepth to 1.1.12 * Update meta.yaml * Update mutmap to 2.1.0 (#17176) Package uploads complete: [ci skip] - biocontainers/mutmap:2.1.0--py_0 - noarch/mutmap-2.1.0-py_0.tar.bz2 * Update qtlseq to 2.0.3 (#17177) Package uploads complete: [ci skip] - biocontainers/qtlseq:2.0.3--py_0 - noarch/qtlseq-2.0.3-py_0.tar.bz2 * Update pyranges to 0.0.52 (#17178) Package uploads complete: [ci skip] - biocontainers/pyranges:0.0.52--py36h516909a_0 - biocontainers/pyranges:0.0.52--py37h516909a_0 - linux-64/pyranges-0.0.52-py36h516909a_0.tar.bz2 - linux-64/pyranges-0.0.52-py37h516909a_0.tar.bz2 - osx-64/pyranges-0.0.52-py36h01d97ff_0.tar.bz2 - osx-64/pyranges-0.0.52-py37h01d97ff_0.tar.bz2 * simka-1.5.0 (#16670) * simka-1.5.0 * Update mobidic-mpa to 1.1.2 (#17181) Package uploads complete: [ci skip] - biocontainers/mobidic-mpa:1.1.2--py_0 - noarch/mobidic-mpa-1.1.2-py_0.tar.bz2 * Update popdel to 1.1.2 (#17182) Package uploads complete: [ci skip] - biocontainers/popdel:1.1.2--he513fc3_0 - linux-64/popdel-1.1.2-he513fc3_0.tar.bz2 - osx-64/popdel-1.1.2-h2dec4b4_0.tar.bz2 * Create variable (this has been removed in 7624ae9 by mistake). * Set shell options. * Set shebang and shell options. * Use a HEREDOC for ${PREFIX}/.message.txt. * Bump build number. * Remove blank line. * I wonder * guess that didn't work * oops * more fixes * clean up blacklist * fix s3gof3r * fix spades and novoalign * fixes * various fixes * update blacklist * last updates * more fixes, blacklist almost all perl- recipes * add workflows * add workflow support in bulk * typo * no fast fail * oops * Trigger CI * trigger CI * some updates * try fixing the platform * debug a bit * bump vcflatten to test os-specific building * mimic circleci * bump some recipes * run autobump for new pinnings * fix a bunch of recipes * many many many fixes * a few updates * more updates * nearing the end * more updates * more updates * fix some tests * fixes * more * updates * debug OSX issues * debug a bit * updates * more debugging * debug * try downloading the SDK * wrong syntax * remove find stuff * maybe that will work * enable circleci for OSX bulk * last try * try this * a bit more * fix bioconda-utils requirements * updates * some updates * updates * forgot build script * skip OSX * last change --- .circleci/config.yml | 60 +++++----- .github/workflows/Bulk.yml | 17 ++- build-fail-blacklist | 92 +++++++++++++++ recipes/abeona/meta.yaml | 2 +- recipes/abyss/build.sh | 2 +- recipes/abyss/meta.yaml | 2 +- recipes/admixture/meta.yaml | 11 +- recipes/advntr/meta.yaml | 3 +- recipes/afterqc/meta.yaml | 2 +- recipes/alfred/meta.yaml | 2 +- recipes/amused/meta.yaml | 2 +- recipes/antismash/meta.yaml | 2 +- recipes/any2fasta/meta.yaml | 2 +- recipes/apoc/build.sh | 5 +- recipes/apoc/meta.yaml | 2 +- recipes/aquila_umap/meta.yaml | 2 +- recipes/arem/meta.yaml | 2 +- recipes/asqcan/meta.yaml | 2 +- recipes/assemblerflow/meta.yaml | 2 +- recipes/atactk/meta.yaml | 2 +- recipes/athena_meta/meta.yaml | 2 +- recipes/atropos/meta.yaml | 2 +- recipes/autodock-vina/meta.yaml | 4 +- recipes/axiome/build.sh | 3 - recipes/axiome/meta.yaml | 2 +- recipes/bam-readcount/meta.yaml | 4 +- recipes/bamclipper/build.sh | 1 + recipes/bamclipper/meta.yaml | 2 +- recipes/barrnap-python/meta.yaml | 3 +- recipes/barrnap/meta.yaml | 2 +- recipes/bcalm/meta.yaml | 2 +- recipes/bcbio-nextgen-vm/meta.yaml | 4 +- recipes/bcbio_monitor/meta.yaml | 2 +- recipes/bcbiogff/meta.yaml | 2 +- recipes/bcbreport/meta.yaml | 2 +- recipes/bcftools-gtc2vcf-plugin/1.9/build.sh | 2 +- recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml | 2 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recipes/tassel/4.3.15/patches/run_pipeline.patch delete mode 100644 recipes/tassel/4.3.15/patches/start_tassel.patch delete mode 100644 recipes/transdecoder/2.1.0/build.sh delete mode 100644 recipes/transdecoder/2.1.0/meta.yaml delete mode 100644 recipes/transdecoder/3.0.1/build.sh delete mode 100644 recipes/transdecoder/3.0.1/meta.yaml delete mode 100644 recipes/weblogo/2.8.2/build.sh delete mode 100644 recipes/weblogo/2.8.2/meta.yaml diff --git a/.circleci/config.yml b/.circleci/config.yml index 07e2152dadbca..b4c8df9bde204 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -190,37 +190,37 @@ jobs: --git-range $CIRCLE_SHA1~1 $CIRCLE_SHA1 \ --prelint - ## build, test and upload for bulk branch on linux - #bulk-linux: - # <<: *linux - # steps: - # - *fail_fork - # - checkout - # - *common - # - *restore_cache - # - *setup - # - *save_cache - # - run: - # name: Building, testing, and uploading of all unpublished recipes - # command: | - # bioconda-utils build recipes config.yml \ - # --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers + # build, test and upload for bulk branch on linux + bulk-linux: + <<: *linux + steps: + - *fail_fork + - checkout + - *common + - *restore_cache + - *setup + - *save_cache + - run: + name: Building, testing, and uploading of all unpublished recipes + command: | + bioconda-utils build recipes config.yml \ + --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers - ## build, test and upload for bulk branch on macos - #bulk-macos: - # <<: *macos - # steps: - # - *fail_fork - # - checkout - # - *common - # - *restore_cache - # - *setup - # - *save_cache - # - run: - # name: Building, testing and uploading of all unpublished recipes - # command: | - # bioconda-utils build recipes config.yml \ - # --anaconda-upload + # build, test and upload for bulk branch on macos + bulk-macos: + <<: *macos + steps: + - *fail_fork + - checkout + - *common + - *restore_cache + - *setup + - *save_cache + - run: + name: Building, testing and uploading of all unpublished recipes + command: | + bioconda-utils build recipes config.yml \ + --anaconda-upload # nightly build, test and upload of unpublished recipes on linux nightly-upload-linux: diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 460ee94596ee7..791b4607a4123 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -16,9 +16,6 @@ jobs: - uses: actions/checkout@v1 - name: Setup Bioconda-utils uses: bioconda/bioconda-actions/bioconda_recipes_setup/@bulk - - name: Debug - run: | - python -c "import sys; print(sys.platform)" - name: Build and upload env: ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} @@ -43,9 +40,19 @@ jobs: - uses: actions/checkout@v1 - name: Setup Bioconda-utils uses: bioconda/bioconda-actions/bioconda_recipes_setup/@bulk - - name: Debug + - name: OSX stuff run: | - python -c "import sys; print(sys.platform)" + # This is taken from conda-forge-ci-setup + curl -L -O https://github.com/phracker/MacOSX-SDKs/releases/download/10.13/MacOSX10.9.sdk.tar.xz + tar -xf MacOSX10.9.sdk.tar.xz -C /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs + # set minimum sdk version to our target + plutil -replace MinimumSDKVersion -string 10.9 $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + plutil -replace DTSDKName -string macosx10.9internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist + export CONDA_PREFIX="${CONDA_PREFIX:-$(conda info --json | jq -r .root_prefix)}" + export CONDA_BUILD_SYSROOT="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk" + mkdir -p ${CONDA_PREFIX}/etc/conda/activate.d + echo "export CONDA_BUILD_SYSROOT=\"$CONDA_BUILD_SYSROOT\"" > "${CONDA_PREFIX}/etc/conda/activate.d/bioconda-ci-setup-activate.sh" + conda list - name: Build and upload env: ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} diff --git a/build-fail-blacklist b/build-fail-blacklist index 0b43b229bba9c..4279b5d252112 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -11,7 +11,75 @@ recipes/last/638 # Timeout downloading from sourceforge recipes/transcomb +# This vendors bowtie2, which breaks the noarch: python setting +recipes/humann2 + # compilation or other errors in bulk +recipes/rvtests +recipes/perl-bio-rna-rnaalisplit +recipes/perl-bio-eutilities +recipes/fastlmm +recipes/cdna_cupcake +recipes/minimap +recipes/perl-bio-samtools +recipes/vcfkit +recipes/bcbio_monitor +recipes/meme/4.11.2 +recipes/meme/4.11.1 +recipes/lohhla +recipes/sis +recipes/dfam +recipes/cgcloud-lib +recipes/sonicparanoid +recipes/riboplot +recipes/python-mailund-newick +recipes/sibelia +recipes/nudup +recipes/pbmm2 +recipes/gmtk +recipes/connor +recipes/biskit +recipes/genomelake +recipes/platypus-conquistador +recipes/samsifter +recipes/motifscan +recipes/flowcraft +recipes/mummer +recipes/porechop +recipes/hg-color +recipes/nasp +recipes/srprism +recipes/eden +recipes/clever-toolkit +recipes/pbbam +recipes/bcftools/1.3 +recipes/musicc +recipes/comparative-annotation-toolkit +recipes/scrublet +recipes/detonate +recipes/bmtagger +recipes/dx-cwl +recipes/theta2 +recipes/maxentscan +recipes/antismash +recipes/fastqmetrics +recipes/piret +recipes/qiimetomaaslin +recipes/glimmerhmm +recipes/python-omero +recipes/sequencetools +recipes/groopm +recipes/egglib +recipes/biolite +recipes/idr-py +recipes/pauda +recipes/hicbrowser +recipes/bcftools-gtc2vcf-plugin/1.9 +recipes/perl-biox-workflow-command +recipes/optitype +recipes/vqsr_cnn +recipes/srnapipe +recipes/bam-readcount recipes/rapid recipes/mqc recipes/panx/1.6.0 @@ -684,14 +752,26 @@ recipes/bioconductor-rchyoptimyx # Packages that should be moved to conda-forge recipes/argutils recipes/aria2 +recipes/autolog recipes/avro-python2 recipes/avro-python3 recipes/bitstring +recipes/cityhash +recipes/collectl recipes/elasticluster +recipes/epydoc +recipes/esmre recipes/extern +recipes/forked-path recipes/gcs-oauth2-boto-plugin +recipes/gnuplot-py recipes/justbackoff +recipes/kid +recipes/minimock +recipes/myriad recipes/neurodocker +recipes/nose-capturestderr +recipes/pdfkit recipes/perl-aceperl recipes/perl-acme-damn recipes/perl-algorithm-cluster @@ -1309,9 +1389,21 @@ recipes/perl-yaml recipes/perl-yaml-libyaml recipes/perl-yaml-tiny recipes/pyasp +recipes/pyexcelerator +recipes/pyhashxx +recipes/pyopt +recipes/pysvg recipes/pyx +recipes/rdfextras +recipes/sbt +recipes/scala recipes/sharedmem +recipes/stacks_summary +recipes/tgt recipes/udocker +recipes/workspace recipes/wtforms-alchemy recipes/wtforms-components +recipes/xmlbuilder +recipes/yaggo recipes/zeroc-ice diff --git a/recipes/abeona/meta.yaml b/recipes/abeona/meta.yaml index a8c1b4eb343b1..c264b0744c329 100644 --- a/recipes/abeona/meta.yaml +++ b/recipes/abeona/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - abeona=abeona.__main__:main script: '$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv ' diff --git a/recipes/abyss/build.sh b/recipes/abyss/build.sh index 1c1e969f60e0a..fcde870f701e4 100644 --- a/recipes/abyss/build.sh +++ b/recipes/abyss/build.sh @@ -14,7 +14,7 @@ fi --with-boost="$PREFIX" \ --with-mpi="$PREFIX" \ --with-sparsehash="$PREFIX" \ - --without-sqlite + --without-sqlite || cat config.log make AM_CXXFLAGS=-Wall make install diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index a04ad4e175352..2a4dc282f26d3 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz diff --git a/recipes/admixture/meta.yaml b/recipes/admixture/meta.yaml index cd27ca25f9094..5304bcc521ebf 100644 --- a/recipes/admixture/meta.yaml +++ b/recipes/admixture/meta.yaml @@ -11,19 +11,20 @@ source: sha256: a95aa96a51a4a0df0e0b0eba643b260e810132a620a8bcf693a18546d5b0f396 build: - noarch: generic number: 0 +test: + commands: + - admixture --help >> /dev/null + about: home: http://www.genetics.ucla.edu/software/admixture/index.html license: Free for Academic Use summary: 'ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.' -test: - commands: - - admixture --help >> /dev/null - extra: identifiers: - biotools:admixture - doi:10.1101/gr.094052.109 + skip-lints: + - should_be_noarch_generic diff --git a/recipes/advntr/meta.yaml b/recipes/advntr/meta.yaml index adabbb11ba7c6..cd88c32e1cd6d 100644 --- a/recipes/advntr/meta.yaml +++ b/recipes/advntr/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [py==37] - number: 0 + number: 1 script: - make install CXX="${CXX} ${CXXFLAGS}" PREFIX=${PREFIX} - python -m pip install --no-deps --ignore-installed . @@ -37,6 +37,7 @@ requirements: - networkx 1.11 - joblib - scikit-learn + - cython - biopython - muscle - pysam 0.15.1 diff --git a/recipes/afterqc/meta.yaml b/recipes/afterqc/meta.yaml index a6a3b1a524e63..0e4ed3dcaa646 100644 --- a/recipes/afterqc/meta.yaml +++ b/recipes/afterqc/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: generic - number: 2 + number: 3 source: url: https://github.com/OpenGene/AfterQC/archive/v{{ version }}.tar.gz diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index 84978754e2d0d..4a0d1a09ea083 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/amused/meta.yaml b/recipes/amused/meta.yaml index 48193ced7533a..474f8097f9306 100644 --- a/recipes/amused/meta.yaml +++ b/recipes/amused/meta.yaml @@ -3,7 +3,7 @@ build: noarch: generic - number: 1 + number: 2 package: name: amused diff --git a/recipes/antismash/meta.yaml b/recipes/antismash/meta.yaml index aadd0c03dbc83..973e7fc3ed176 100644 --- a/recipes/antismash/meta.yaml +++ b/recipes/antismash/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: python - number: 1 + number: 2 source: url: https://dl.secondarymetabolites.org/releases/{{ version }}/antismash-{{ version }}.tar.gz diff --git a/recipes/any2fasta/meta.yaml b/recipes/any2fasta/meta.yaml index 85f2ed1280cc7..a917dadbc47cc 100644 --- a/recipes/any2fasta/meta.yaml +++ b/recipes/any2fasta/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: build: diff --git a/recipes/apoc/build.sh b/recipes/apoc/build.sh index bd2c0475d8fe6..86ae6e2efda23 100644 --- a/recipes/apoc/build.sh +++ b/recipes/apoc/build.sh @@ -1,5 +1,6 @@ #!/bin/sh cd src/ -make -mv apoc "$PREFIX/bin/" +make FC=$FC +mkdir -p ${PREFIX}/bin +mv apoc $PREFIX/bin diff --git a/recipes/apoc/meta.yaml b/recipes/apoc/meta.yaml index d3cce0fc4a44b..4a34bd999fd64 100644 --- a/recipes/apoc/meta.yaml +++ b/recipes/apoc/meta.yaml @@ -9,7 +9,7 @@ source: - apoc_gfortran.patch build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/aquila_umap/meta.yaml b/recipes/aquila_umap/meta.yaml index d1b7a870c3d5d..59c8605af28bf 100644 --- a/recipes/aquila_umap/meta.yaml +++ b/recipes/aquila_umap/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 0 + number: 1 script: python setup.py install --single-version-externally-managed --record=record.txt source: diff --git a/recipes/arem/meta.yaml b/recipes/arem/meta.yaml index 6cef7e1b9c98c..955250cb9b4a6 100644 --- a/recipes/arem/meta.yaml +++ b/recipes/arem/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/asqcan/meta.yaml b/recipes/asqcan/meta.yaml index 760d38a962278..09523b561be60 100644 --- a/recipes/asqcan/meta.yaml +++ b/recipes/asqcan/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/assemblerflow/meta.yaml b/recipes/assemblerflow/meta.yaml index 5f8f076ec8c95..669b2126f2571 100644 --- a/recipes/assemblerflow/meta.yaml +++ b/recipes/assemblerflow/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - assemblerflow = assemblerflow.assemblerflow:main script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . diff --git a/recipes/atactk/meta.yaml b/recipes/atactk/meta.yaml index c90614d44e286..db834a61a6f55 100644 --- a/recipes/atactk/meta.yaml +++ b/recipes/atactk/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 887363209d556ee5fb4969f39bab1b747cca56b6bd1c0fd9e48d69208e7a5f74 build: - number: 1 + number: 2 noarch: python script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . rpaths: diff --git a/recipes/athena_meta/meta.yaml b/recipes/athena_meta/meta.yaml index bbbe2676c9ce1..1be7f467799e9 100644 --- a/recipes/athena_meta/meta.yaml +++ b/recipes/athena_meta/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/atropos/meta.yaml b/recipes/atropos/meta.yaml index ce675e1022164..adda2b21b44be 100644 --- a/recipes/atropos/meta.yaml +++ b/recipes/atropos/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 script: python -m pip install --no-deps --ignore-installed . skip: True # [py27] diff --git a/recipes/autodock-vina/meta.yaml b/recipes/autodock-vina/meta.yaml index 968ce2e6ea7a2..2fd99cfa56ef4 100644 --- a/recipes/autodock-vina/meta.yaml +++ b/recipes/autodock-vina/meta.yaml @@ -3,8 +3,7 @@ package: version: 1.1.2 build: - noarch: generic - number: 1 + number: 2 source: - url: http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz # [linux] @@ -28,3 +27,4 @@ about: extra: skip-lints: - should_not_be_noarch_source + - should_be_noarch_generic diff --git a/recipes/axiome/build.sh b/recipes/axiome/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/axiome/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/axiome/meta.yaml b/recipes/axiome/meta.yaml index 6854cee266df2..553719fb5161c 100644 --- a/recipes/axiome/meta.yaml +++ b/recipes/axiome/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 entry_points: - axiome=axiome.axiome:main script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml index 998d7254cbd02..7bc8aa231f36b 100644 --- a/recipes/bam-readcount/meta.yaml +++ b/recipes/bam-readcount/meta.yaml @@ -7,18 +7,18 @@ source: md5: 58d72588866f16f658ce4f40a3809af9 build: - number: 4 + number: 5 requirements: build: - cmake >=2.8.3 - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - zlib - ncurses - perl - python - run: - python - zlib diff --git a/recipes/bamclipper/build.sh b/recipes/bamclipper/build.sh index 5c3436047ee8b..819add1a99c8b 100644 --- a/recipes/bamclipper/build.sh +++ b/recipes/bamclipper/build.sh @@ -3,5 +3,6 @@ chmod +x *.pl chmod +x *.sh +mkdir -p ${PREFIX}/bin cp *.pl ${PREFIX}/bin cp *.sh ${PREFIX}/bin diff --git a/recipes/bamclipper/meta.yaml b/recipes/bamclipper/meta.yaml index 8098f9c6440fd..41fdbaee9f7a5 100644 --- a/recipes/bamclipper/meta.yaml +++ b/recipes/bamclipper/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/barrnap-python/meta.yaml b/recipes/barrnap-python/meta.yaml index 7d5151faeba2e..cf2e7d34ab9fd 100644 --- a/recipes/barrnap-python/meta.yaml +++ b/recipes/barrnap-python/meta.yaml @@ -11,7 +11,8 @@ source: build: noarch: python - number: 1 + number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/barrnap/meta.yaml b/recipes/barrnap/meta.yaml index 10bf6925f39a6..dd65e0f8f7c16 100644 --- a/recipes/barrnap/meta.yaml +++ b/recipes/barrnap/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/bcalm/meta.yaml b/recipes/bcalm/meta.yaml index 33f4ede462001..2cb48be3e85da 100644 --- a/recipes/bcalm/meta.yaml +++ b/recipes/bcalm/meta.yaml @@ -12,7 +12,7 @@ source: patches: - CMakeLists.patch build: - number: 2 + number: 3 # Requires clang>=4.5 skip: True # [osx] diff --git a/recipes/bcbio-nextgen-vm/meta.yaml b/recipes/bcbio-nextgen-vm/meta.yaml index 4f92127483286..b9f5b6c4afe35 100644 --- a/recipes/bcbio-nextgen-vm/meta.yaml +++ b/recipes/bcbio-nextgen-vm/meta.yaml @@ -4,12 +4,12 @@ package: build: noarch: python - number: 1 + number: 2 # Currently hitting conda errors on OSX # ERROR:conda.core.link:An error occurred while installing package # FileNotFoundError(2, "No such file or directory: '_placehold_pl/bin/python3.7' # https://circleci.com/gh/bioconda/bioconda-recipes/50765 - script: {{ PYTHON }} -m pip install --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: url: https://github.com/bcbio/bcbio-nextgen-vm/archive/8b46793.tar.gz diff --git a/recipes/bcbio_monitor/meta.yaml b/recipes/bcbio_monitor/meta.yaml index 1b0b8fe02c8ea..0dc9bbf978c99 100644 --- a/recipes/bcbio_monitor/meta.yaml +++ b/recipes/bcbio_monitor/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 3 + number: 4 entry_points: - bcbio_monitor = bcbio_monitor.cli:cli script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/bcbiogff/meta.yaml b/recipes/bcbiogff/meta.yaml index c09a42d7875e3..a31fb9e02ab2c 100644 --- a/recipes/bcbiogff/meta.yaml +++ b/recipes/bcbiogff/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/bcbreport/meta.yaml b/recipes/bcbreport/meta.yaml index 307221432ec88..f59070f662278 100644 --- a/recipes/bcbreport/meta.yaml +++ b/recipes/bcbreport/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh b/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh index 4b4b793ce661c..207209d5626c3 100644 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh +++ b/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh @@ -22,7 +22,7 @@ pushd htslib-$VERSION autoheader (autoconf || autoconf) ./configure --disable-bz2 --disable-lzma --prefix=$PREFIX -make +make CC=$CC popd pushd bcftools-$VERSION diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml b/recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml index 8cea82fd0e3dd..87550bb3e57e9 100644 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml +++ b/recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml @@ -23,7 +23,7 @@ source: folder: htslib-{{version}} build: - number: 0 + number: 1 skip: true # [osx] requirements: diff --git a/recipes/bcftools/1.3/build.sh b/recipes/bcftools/1.3/build.sh index ad93e7faee2f9..d44d099704608 100644 --- a/recipes/bcftools/1.3/build.sh +++ b/recipes/bcftools/1.3/build.sh @@ -1,5 +1,5 @@ #!/bin/sh export C_INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib -make plugins -make prefix=$PREFIX install +make plugins CC=$CC +make prefix=$PREFIX CC=$CC install diff --git a/recipes/bcftools/1.3/meta.yaml b/recipes/bcftools/1.3/meta.yaml index e7912b542f59d..d5c8c10ced9a1 100644 --- a/recipes/bcftools/1.3/meta.yaml +++ b/recipes/bcftools/1.3/meta.yaml @@ -8,7 +8,7 @@ test: - bcftools --version build: - number: 3 + number: 4 package: name: bcftools diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 41a21d9ce16f8..4e7dd05943e24 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 diff --git a/recipes/bcl2fastq-nextseq/meta.yaml b/recipes/bcl2fastq-nextseq/meta.yaml index 6bd37ecaa0b81..bc62f04b3be7d 100644 --- a/recipes/bcl2fastq-nextseq/meta.yaml +++ b/recipes/bcl2fastq-nextseq/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/bcool/meta.yaml b/recipes/bcool/meta.yaml index 48cf4563dc746..5b476e30aeef7 100644 --- a/recipes/bcool/meta.yaml +++ b/recipes/bcool/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/bctools/meta.yaml b/recipes/bctools/meta.yaml index a648888d6db4e..3cda05dadd6fc 100644 --- a/recipes/bctools/meta.yaml +++ b/recipes/bctools/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/bd2k-python-lib/meta.yaml b/recipes/bd2k-python-lib/meta.yaml index 25c335dd27940..35075cd5debc9 100644 --- a/recipes/bd2k-python-lib/meta.yaml +++ b/recipes/bd2k-python-lib/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv requirements: diff --git a/recipes/beast/meta.yaml b/recipes/beast/meta.yaml index b9d5ef38e74d8..6bd1ed839b5e5 100644 --- a/recipes/beast/meta.yaml +++ b/recipes/beast/meta.yaml @@ -1,5 +1,4 @@ {% set version = "1.10.4" %} -{% set sha256 = "722d85457e7faa082862147630f2ec8aa500e2461fd31e41e339c92f8c9b7f8a" %} package: name: beast @@ -7,11 +6,11 @@ package: source: url: https://github.com/beast-dev/beast-mcmc/releases/download/v{{ version }}/BEASTv{{ version }}.tgz - sha256: '{{ sha256 }}' + sha256: be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8 build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/beast2/2.4.5/meta.yaml b/recipes/beast2/2.4.5/meta.yaml index ebf0e33ab15b1..b1b0b0c76b8d4 100644 --- a/recipes/beast2/2.4.5/meta.yaml +++ b/recipes/beast2/2.4.5/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: build: diff --git a/recipes/beast2/2.5.0/meta.yaml b/recipes/beast2/2.5.0/meta.yaml index e25a2d9d61a34..9e0b4f5785c27 100644 --- a/recipes/beast2/2.5.0/meta.yaml +++ b/recipes/beast2/2.5.0/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 0 + number: 2 requirements: build: diff --git a/recipes/bedtools/2.25/build.sh b/recipes/bedtools/2.25/build.sh deleted file mode 100644 index 88a14a2ff40fa..0000000000000 --- a/recipes/bedtools/2.25/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/sh - -export CFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" -export CPATH=${PREFIX}/include - -make install prefix=$PREFIX diff --git a/recipes/bedtools/2.25/makefile-prefix.patch b/recipes/bedtools/2.25/makefile-prefix.patch deleted file mode 100644 index edaeb79938ac5..0000000000000 --- a/recipes/bedtools/2.25/makefile-prefix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- Makefile.orig 2015-09-17 15:53:34.305950660 +0900 -+++ Makefile 2015-09-17 15:53:43.296772806 +0900 -@@ -25,7 +25,7 @@ - export LIBS = -lz - export BT_ROOT = src/utils/BamTools/ - --prefix = /usr/local -+prefix ?= /usr/local - - SUBDIRS = $(SRC_DIR)/annotateBed \ - $(SRC_DIR)/bamToBed \ diff --git a/recipes/bedtools/2.25/meta.yaml b/recipes/bedtools/2.25/meta.yaml deleted file mode 100644 index 441201a49a906..0000000000000 --- a/recipes/bedtools/2.25/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -package: - name: bedtools - version: "2.25.0" - -source: - url: https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz - sha256: d737ca42e7df76c5455d3e6e0562cdcb62336830eaad290fd4133a328a1ddacc - -build: - number: 5 - -requirements: - build: - - {{ compiler('cxx') }} - host: - - zlib - run: - - zlib - -test: - commands: - - bedtools - -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: A powerful toolset for genome arithmetic - -extra: - identifiers: - - biotools:bedtools diff --git a/recipes/bedtools/2.27.0/build.sh b/recipes/bedtools/2.27.0/build.sh deleted file mode 100644 index 88a14a2ff40fa..0000000000000 --- a/recipes/bedtools/2.27.0/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/sh - -export CFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" -export CPATH=${PREFIX}/include - -make install prefix=$PREFIX diff --git a/recipes/bedtools/2.27.0/meta.yaml b/recipes/bedtools/2.27.0/meta.yaml deleted file mode 100644 index bd15e75582859..0000000000000 --- a/recipes/bedtools/2.27.0/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set name = "bedtools" %} -{% set version = "2.27.0" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://github.com/arq5x/bedtools2/releases/download/v{{ version }}/bedtools-{{ version }}.tar.gz - sha256: e4f0e5616d04ba5ac09c36dec989b1236a5712e67d0b6874ff5e144d7ed4ce60 - -build: - number: 3 - -requirements: - build: - - {{ compiler('cxx') }} - host: - - zlib - run: - - zlib - -test: - commands: - - bedtools - -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: A powerful toolset for genome arithmetic - - -extra: - identifiers: - - biotools:bedtools diff --git a/recipes/besst/meta.yaml b/recipes/besst/meta.yaml index 9d20350303d26..2a22d0c8a703a 100644 --- a/recipes/besst/meta.yaml +++ b/recipes/besst/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: diff --git a/recipes/bgreat/meta.yaml b/recipes/bgreat/meta.yaml index 97f3f792c0263..fb749179293a6 100644 --- a/recipes/bgreat/meta.yaml +++ b/recipes/bgreat/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bc60e755a3205b725834f37d7509062879415f03730b424cbac06b776eb977cc build: - number: 1 + number: 2 skip: true # [osx] requirements: diff --git a/recipes/bioawk/meta.yaml b/recipes/bioawk/meta.yaml index 938364d6cbe96..a582d620a7e61 100644 --- a/recipes/bioawk/meta.yaml +++ b/recipes/bioawk/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/biobb_pmx/meta.yaml b/recipes/biobb_pmx/meta.yaml index 2dfda705cef30..25b80e181f106 100644 --- a/recipes/biobb_pmx/meta.yaml +++ b/recipes/biobb_pmx/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 noarch: python requirements: diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index cb752410b2bdf..e71c9e72d4d7e 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 459165b252a246b8cfe1b1dc792079c8 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-nucpos/meta.yaml b/recipes/bioconductor-nucpos/meta.yaml index 5a0b38f0d514f..39e453e3c46fb 100644 --- a/recipes/bioconductor-nucpos/meta.yaml +++ b/recipes/bioconductor-nucpos/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8ae37dce2a611262d22eb1fe3c7dfb15 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-nupop/meta.yaml b/recipes/bioconductor-nupop/meta.yaml index 0704259eccdc3..d3aef569d3e76 100644 --- a/recipes/bioconductor-nupop/meta.yaml +++ b/recipes/bioconductor-nupop/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2f2469ea1cc2c7a36a3ebe6abc8cfe28 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/biofluff/meta.yaml b/recipes/biofluff/meta.yaml index 811e0a5160b4a..65022fd4ae291 100644 --- a/recipes/biofluff/meta.yaml +++ b/recipes/biofluff/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/biogridpy/meta.yaml b/recipes/biogridpy/meta.yaml index 614b9996e9a9e..f811d0e0b5afd 100644 --- a/recipes/biogridpy/meta.yaml +++ b/recipes/biogridpy/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index 57cae42d6f012..71ae3a3904a4c 100644 --- a/recipes/biokit/meta.yaml +++ b/recipes/biokit/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 0 + number: 1 # Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda # Same with easydev diff --git a/recipes/biolib/meta.yaml b/recipes/biolib/meta.yaml index a17ee5e639c3a..faa2507f1764f 100644 --- a/recipes/biolib/meta.yaml +++ b/recipes/biolib/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed" requirements: diff --git a/recipes/biolite-tools/meta.yaml b/recipes/biolite-tools/meta.yaml index 3aa448e7c25e6..f8d3177d771ce 100644 --- a/recipes/biolite-tools/meta.yaml +++ b/recipes/biolite-tools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b2e08caa65d1bf0914a910fa2e90fa5757d0e2ddd0f2e4ec41dbd5682dab3093 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/biolite/meta.yaml b/recipes/biolite/meta.yaml index 1869d9ccaa870..ad7797ec0c99e 100644 --- a/recipes/biolite/meta.yaml +++ b/recipes/biolite/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/biopet-extractadaptersfastqc/0.1/biopet-extractadaptersfastqc.py b/recipes/biopet-extractadaptersfastqc/0.1/biopet-extractadaptersfastqc.py deleted file mode 100755 index 2fba7b063dbb4..0000000000000 --- a/recipes/biopet-extractadaptersfastqc/0.1/biopet-extractadaptersfastqc.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-extractadaptersfastqc JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'ExtractAdaptersFastqc-assembly-0.1.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-extractadaptersfastqc/0.1/build.sh b/recipes/biopet-extractadaptersfastqc/0.1/build.sh deleted file mode 100644 index 4ce75c0ba2750..0000000000000 --- a/recipes/biopet-extractadaptersfastqc/0.1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp ExtractAdaptersFastqc-assembly-0.1.jar $outdir/ExtractAdaptersFastqc-assembly-0.1.jar -cp $RECIPE_DIR/biopet-extractadaptersfastqc.py $outdir/biopet-extractadaptersfastqc -ln -s $outdir/biopet-extractadaptersfastqc $PREFIX/bin - diff --git a/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml b/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml deleted file mode 100644 index 2aa360ae06a1d..0000000000000 --- a/recipes/biopet-extractadaptersfastqc/0.1/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-extractadaptersfastqc - version: '0.1' - -source: - url: https://github.com/biopet/extractadaptersfastqc/releases/download/v0.1/ExtractAdaptersFastqc-assembly-0.1.jar - sha256: e060b0da4cfe3b7273242ede54e56f61ef3f733795958022cac92f23b1a956f4 - -build: - noarch: generic - number: 1 - -requirements: - run: - - openjdk >=8,<9 - - python - -about: - home: https://github.com/biopet/extractadaptersfastqc - license: MIT - summary: ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report. - description: |- - ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report. - These sequences can be used as input for a QC tool such as cutadapt. - The sequences can be output in plain text format with a - newline character as a separator between the sequences. - Alternatively the sequences can be output in FASTA format. - For documentation and manuals visit our github.io page: https://biopet.github.io/extractadaptersfastqc - -test: - commands: - - biopet-extractadaptersfastqc --version - - biopet-extractadaptersfastqc --help - -extra: - notes: 'biopet-extractadaptersfastqc is a Java program that comes with a custom - wrapper shell script. By default ''no default java option'' is set in the wrapper. - The command that runs the program is ''biopet-extractadaptersfastqc''. If you - want to overwrite it you can specify memory options directly after your binaries. - If you have _JAVA_OPTIONS set globally this will take precedence. For example - run it with ''biopet-extractadaptersfastqc -Xms512m -Xmx1g''. ' diff --git a/recipes/biopet-extractadaptersfastqc/meta.yaml b/recipes/biopet-extractadaptersfastqc/meta.yaml index 4f4a3a686333c..9dcab010fe5a5 100644 --- a/recipes/biopet-extractadaptersfastqc/meta.yaml +++ b/recipes/biopet-extractadaptersfastqc/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/biopet-sampleconfig/0.1/biopet-sampleconfig.py b/recipes/biopet-sampleconfig/0.1/biopet-sampleconfig.py deleted file mode 100755 index 1b2cd555ab4ab..0000000000000 --- a/recipes/biopet-sampleconfig/0.1/biopet-sampleconfig.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-sampleconfig JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'SampleConfig-assembly-0.1.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-sampleconfig/0.1/build.sh b/recipes/biopet-sampleconfig/0.1/build.sh deleted file mode 100644 index 49307b70c555e..0000000000000 --- a/recipes/biopet-sampleconfig/0.1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp SampleConfig-assembly-0.1.jar $outdir/SampleConfig-assembly-0.1.jar -cp $RECIPE_DIR/biopet-sampleconfig.py $outdir/biopet-sampleconfig -ln -s $outdir/biopet-sampleconfig $PREFIX/bin - diff --git a/recipes/biopet-sampleconfig/0.1/meta.yaml b/recipes/biopet-sampleconfig/0.1/meta.yaml deleted file mode 100644 index 0c6dda0f53045..0000000000000 --- a/recipes/biopet-sampleconfig/0.1/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-sampleconfig - version: '0.1' -source: - url: https://github.com/biopet/sampleconfig/releases/download/v0.1/SampleConfig-assembly-0.1.jar - sha256: 8f2e0c9a36190834fbb8203aff1dd163e48060075f2e343f88ae92a124e052a7 -build: - noarch: generic - number: 1 -requirements: - run: - - openjdk - - python -about: - home: https://github.com/biopet/sampleconfig - license: MIT - summary: This mean can extract samples, libraries and readgroups from a sample config file. - description: |- - This mean can extract samples, libraries and readgroups from a sample config file. This meant as a supporting tool inside wdl pipelines. It can also output a single layer as tsv file. - - For documentation and manuals visit our [github.io page](https://biopet.github.io/sampleconfig). -test: - commands: - - biopet-sampleconfig --version - - biopet-sampleconfig --help -extra: - notes: 'biopet-sampleconfig is a Java program that comes with a custom wrapper shell - script. By default ''no default java option'' is set in the wrapper. The command - that runs the program is ''biopet-sampleconfig''. If you want to overwrite it - you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. For example run it with ''biopet-sampleconfig - -Xms512m -Xmx1g''. ' - diff --git a/recipes/biopet-validateannotation/0.1/biopet-validateannotation.py b/recipes/biopet-validateannotation/0.1/biopet-validateannotation.py deleted file mode 100755 index 5825eb79857dc..0000000000000 --- a/recipes/biopet-validateannotation/0.1/biopet-validateannotation.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-validateannotation JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'ValidateAnnotation-assembly-0.1.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-validateannotation/0.1/build.sh b/recipes/biopet-validateannotation/0.1/build.sh deleted file mode 100644 index c89782189297c..0000000000000 --- a/recipes/biopet-validateannotation/0.1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp ValidateAnnotation-assembly-0.1.jar $outdir/ValidateAnnotation-assembly-0.1.jar -cp $RECIPE_DIR/biopet-validateannotation.py $outdir/biopet-validateannotation -ln -s $outdir/biopet-validateannotation $PREFIX/bin - diff --git a/recipes/biopet-validateannotation/0.1/meta.yaml b/recipes/biopet-validateannotation/0.1/meta.yaml deleted file mode 100644 index d5ea8dcfc6ddf..0000000000000 --- a/recipes/biopet-validateannotation/0.1/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-validateannotation - version: '0.1' -source: - url: https://github.com/biopet/validateannotation/releases/download/v0.1/ValidateAnnotation-assembly-0.1.jar - sha256: af4f5809f3abfce45ed3456c04160c8ce8e0e9dd36186e142f28b341d3d5fda5 -build: - noarch: generic - number: 0 -requirements: - run: - - openjdk >=8,<9 - - python -about: - home: https://github.com/biopet/validateannotation - license: MIT - summary: ValidateAnnotationvalidates whether an annotation file is correct. - description: |- - ValidateAnnotationvalidates whether an annotation file is correct. - It checks whether all the annotated contigs are present on the reference. - It can check gtf or refflat files. It can also check both, - in which case it will also check for dissimilarities between the refflat and - GTF files. - - For documentation and manuals visit our github.io page: https://biopet.github.io/validateannotation -test: - commands: - - biopet-validateannotation --version - - biopet-validateannotation --help -extra: - notes: 'biopet-validateannotation is a Java program that comes with a custom wrapper - shell script. By default ''no default java option'' is set in the wrapper. The - command that runs the program is ''biopet-validateannotation''. If you want to - overwrite it you can specify memory options directly after your binaries. If you - have _JAVA_OPTIONS set globally this will take precedence. For example run it - with ''biopet-validateannotation -Xms512m -Xmx1g''. ' - diff --git a/recipes/biopet-validatefastq/0.1.1/biopet-validatefastq.py b/recipes/biopet-validatefastq/0.1.1/biopet-validatefastq.py deleted file mode 100755 index fecdab7f2c7bd..0000000000000 --- a/recipes/biopet-validatefastq/0.1.1/biopet-validatefastq.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-validatefastq JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'validatefastq-assembly-0.1.1.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-validatefastq/0.1.1/build.sh b/recipes/biopet-validatefastq/0.1.1/build.sh deleted file mode 100644 index ee36b2afc49c9..0000000000000 --- a/recipes/biopet-validatefastq/0.1.1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp validatefastq-assembly-0.1.1.jar $outdir/validatefastq-assembly-0.1.1.jar -cp $RECIPE_DIR/biopet-validatefastq.py $outdir/biopet-validatefastq -ln -s $outdir/biopet-validatefastq $PREFIX/bin - diff --git a/recipes/biopet-validatefastq/0.1.1/meta.yaml b/recipes/biopet-validatefastq/0.1.1/meta.yaml deleted file mode 100644 index 56a082e2e45e7..0000000000000 --- a/recipes/biopet-validatefastq/0.1.1/meta.yaml +++ /dev/null @@ -1,42 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-validatefastq - version: 0.1.1 -source: - url: https://github.com/biopet/validatefastq/releases/download/v0.1.1/validatefastq-assembly-0.1.1.jar - sha256: 001f36b95c5d39052b98d9858d359dc6940922811c0bcf907f8c0f5062ab5ead -build: - noarch: generic - number: 1 -requirements: - run: - - openjdk >=8,<9 - - python -about: - home: https://github.com/biopet/validatefastq - license: MIT - summary: This tool validates a FASTQ file. - description: |- - This tool validates a FASTQ file. When data is paired it can - also validate a pair of FASTQ files. - ValidateFastq will check if the FASTQ is in valid FASTQ format. - This includes checking for duplicate reads and checking whether - a pair of FASTQ files contains the same amount of reads and headers match. - It also check whether the quality encodings are correct and outputs - the most likely encoding format (Sanger, Solexa etc.). - - For documentation and manuals visit our github.io page: https://biopet.github.io/validatefastq -test: - commands: - - biopet-validatefastq --version - - biopet-validatefastq --help -extra: - notes: 'biopet-validatefastq is a Java program that comes with a custom wrapper - shell script. By default ''no default java option'' is set in the wrapper. The - command that runs the program is ''biopet-validatefastq''. If you want to overwrite - it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. For example run it with ''biopet-validatefastq - -Xms512m -Xmx1g''. ' - diff --git a/recipes/biopet-validatefastq/meta.yaml b/recipes/biopet-validatefastq/meta.yaml index 56a082e2e45e7..20e8bf896da1c 100644 --- a/recipes/biopet-validatefastq/meta.yaml +++ b/recipes/biopet-validatefastq/meta.yaml @@ -1,19 +1,20 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - package: name: biopet-validatefastq version: 0.1.1 + source: url: https://github.com/biopet/validatefastq/releases/download/v0.1.1/validatefastq-assembly-0.1.1.jar sha256: 001f36b95c5d39052b98d9858d359dc6940922811c0bcf907f8c0f5062ab5ead + build: noarch: generic - number: 1 + number: 2 + requirements: run: - openjdk >=8,<9 - python + about: home: https://github.com/biopet/validatefastq license: MIT @@ -28,10 +29,12 @@ about: the most likely encoding format (Sanger, Solexa etc.). For documentation and manuals visit our github.io page: https://biopet.github.io/validatefastq + test: commands: - biopet-validatefastq --version - biopet-validatefastq --help + extra: notes: 'biopet-validatefastq is a Java program that comes with a custom wrapper shell script. By default ''no default java option'' is set in the wrapper. The diff --git a/recipes/biopet-validatevcf/0.1/biopet-validatevcf.py b/recipes/biopet-validatevcf/0.1/biopet-validatevcf.py deleted file mode 100755 index 956d0408f8d54..0000000000000 --- a/recipes/biopet-validatevcf/0.1/biopet-validatevcf.py +++ /dev/null @@ -1,107 +0,0 @@ -#!/usr/bin/env python -# -# Wrapper script for starting the biopet-validatevcf JAR package -# -# This script is written for use with the Conda package manager and is copied -# from the peptide-shaker wrapper. Only the parameters are changed. -# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py) -# -# This file was automatically generated by the sbt-bioconda plugin. - -import os -import subprocess -import sys -import shutil - -from os import access -from os import getenv -from os import X_OK - -jar_file = 'validatevcf-assembly-0.1.jar' - -default_jvm_mem_opts = [] - -# !!! End of parameter section. No user-serviceable code below this line !!! - - -def real_dirname(path): - """Return the symlink-resolved, canonicalized directory-portion of path.""" - return os.path.dirname(os.path.realpath(path)) - - -def java_executable(): - """Return the executable name of the Java interpreter.""" - java_home = getenv('JAVA_HOME') - java_bin = os.path.join('bin', 'java') - - if java_home and access(os.path.join(java_home, java_bin), X_OK): - return os.path.join(java_home, java_bin) - else: - return 'java' - - -def jvm_opts(argv): - """Construct list of Java arguments based on our argument list. - - The argument list passed in argv must not include the script name. - The return value is a 3-tuple lists of strings of the form: - (memory_options, prop_options, passthrough_options) - """ - mem_opts = [] - prop_opts = [] - pass_args = [] - exec_dir = None - - for arg in argv: - if arg.startswith('-D'): - prop_opts.append(arg) - elif arg.startswith('-XX'): - prop_opts.append(arg) - elif arg.startswith('-Xm'): - mem_opts.append(arg) - elif arg.startswith('--exec_dir='): - exec_dir = arg.split('=')[1].strip('"').strip("'") - if not os.path.exists(exec_dir): - shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) - else: - pass_args.append(arg) - - # In the original shell script the test coded below read: - # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] - # To reproduce the behaviour of the above shell code fragment - # it is important to explictly check for equality with None - # in the second condition, so a null envar value counts as True! - - if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: - mem_opts = default_jvm_mem_opts - - return (mem_opts, prop_opts, pass_args, exec_dir) - - -def main(): - """ - PeptideShaker updates files relative to the path of the jar file. - In a multiuser setting, the option --exec_dir="exec_dir" - can be used as the location for the peptide-shaker distribution. - If the exec_dir dies not exist, - we copy the jar file, lib, and resources to the exec_dir directory. - """ - java = java_executable() - (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) - - if pass_args != [] and pass_args[0].startswith('eu'): - jar_arg = '-cp' - else: - jar_arg = '-jar' - - jar_path = os.path.join(jar_dir, jar_file) - - java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args - - sys.exit(subprocess.call(java_args)) - - -if __name__ == '__main__': - main() - diff --git a/recipes/biopet-validatevcf/0.1/build.sh b/recipes/biopet-validatevcf/0.1/build.sh deleted file mode 100644 index 12ab387a9b535..0000000000000 --- a/recipes/biopet-validatevcf/0.1/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -# Build file is copied from VarScan -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/varscan/build.sh -# This file was automatically generated by the sbt-bioconda plugin. - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp validatevcf-assembly-0.1.jar $outdir/validatevcf-assembly-0.1.jar -cp $RECIPE_DIR/biopet-validatevcf.py $outdir/biopet-validatevcf -ln -s $outdir/biopet-validatevcf $PREFIX/bin - diff --git a/recipes/biopet-validatevcf/0.1/meta.yaml b/recipes/biopet-validatevcf/0.1/meta.yaml deleted file mode 100644 index f3cd5de6eebd3..0000000000000 --- a/recipes/biopet-validatevcf/0.1/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -# !! THIS FILE WAS AUTOMATICALLY GENERATED BY THE SBT-BIOCONDA PLUGIN !! -# !! DO NOT EDIT MANUALLY !! - -package: - name: biopet-validatevcf - version: '0.1' -source: - url: https://github.com/biopet/validatevcf/releases/download/v0.1/validatevcf-assembly-0.1.jar - sha256: c605a90f2bb6d03edd636298e178a0ff95b87df8f965bbe941942de7bf139759 -build: - noarch: generic - number: 0 -requirements: - run: - - openjdk >=8,<9 - - python -about: - home: https://github.com/biopet/validatevcf - license: MIT - summary: ValidateVcf validates a VCF file against a reference genomes. - description: |- - ValidateVcf validates a VCF file against a reference genomes. It checks if the positions - present in the VCF are also present on the reference genoome. - - For documentation and manuals visit our github.io page: https://biopet.github.io/validatevcf -test: - commands: - - biopet-validatevcf --version - - biopet-validatevcf --help -extra: - notes: 'biopet-validatevcf is a Java program that comes with a custom wrapper shell - script. By default ''no default java option'' is set in the wrapper. The command - that runs the program is ''biopet-validatevcf''. If you want to overwrite it you - can specify memory options directly after your binaries. If you have _JAVA_OPTIONS - set globally this will take precedence. For example run it with ''biopet-validatevcf - -Xms512m -Xmx1g''. ' - diff --git a/recipes/bioservices/meta.yaml b/recipes/bioservices/meta.yaml index 98e871aee10f9..e3274e675dc07 100644 --- a/recipes/bioservices/meta.yaml +++ b/recipes/bioservices/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/bis-snp-utils/meta.yaml b/recipes/bis-snp-utils/meta.yaml index 44e9f5c6bfd50..9c8020c718e3d 100644 --- a/recipes/bis-snp-utils/meta.yaml +++ b/recipes/bis-snp-utils/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 2 + number: 3 source: url: https://github.com/karl616/Bis-tools/archive/{{ name }}-{{ version }}.tar.gz diff --git a/recipes/bis-snp/meta.yaml b/recipes/bis-snp/meta.yaml index fbb0cd7717fb8..ff210da87bcaa 100644 --- a/recipes/bis-snp/meta.yaml +++ b/recipes/bis-snp/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: @@ -18,7 +18,7 @@ requirements: test: commands: - - "bis-snp -T BisulfiteGenotyper --help 2>&1 | grep usage:" + - bis-snp -T BisulfiteGenotyper --help 2>&1 | grep "one or more arguments" about: home: "http://people.csail.mit.edu/dnaase/bissnp2011/" diff --git a/recipes/biskit/meta.yaml b/recipes/biskit/meta.yaml index 277f66e4d4a60..5fc9ee6bbc685 100644 --- a/recipes/biskit/meta.yaml +++ b/recipes/biskit/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/bitmapperbs/meta.yaml b/recipes/bitmapperbs/meta.yaml index e16128d556c7c..7b9c1c69138b3 100644 --- a/recipes/bitmapperbs/meta.yaml +++ b/recipes/bitmapperbs/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] source: diff --git a/recipes/blastalign/meta.yaml b/recipes/blastalign/meta.yaml index bdd469485f488..36668be18e5cd 100644 --- a/recipes/blastalign/meta.yaml +++ b/recipes/blastalign/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.4" build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/bmtagger/build.sh b/recipes/bmtagger/build.sh index e2958f719649d..49ee239231717 100644 --- a/recipes/bmtagger/build.sh +++ b/recipes/bmtagger/build.sh @@ -22,9 +22,9 @@ elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then # cd to location of Makefile and source cd $SRC_DIR/ - make + make CC=$CC CXX=$CXX for i in $binaries; do cp $SRC_DIR/bmtagger/$i $PREFIX/bin/ && chmod +x $PREFIX/bin/$i; done fi -chmod +x $PREFIX/bin/* \ No newline at end of file +chmod +x $PREFIX/bin/* diff --git a/recipes/bmtagger/meta.yaml b/recipes/bmtagger/meta.yaml index beff4ad2ed7f7..9a9ff83e8a602 100644 --- a/recipes/bmtagger/meta.yaml +++ b/recipes/bmtagger/meta.yaml @@ -11,11 +11,12 @@ source: - bmtagger.sh.osxpatch # [osx] build: - number: 4 + number: 5 requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - blast - srprism diff --git a/recipes/bowtie2/2.2.4/meta.yaml b/recipes/bowtie2/2.2.4/meta.yaml index 275006cb62033..37831e991be5a 100644 --- a/recipes/bowtie2/2.2.4/meta.yaml +++ b/recipes/bowtie2/2.2.4/meta.yaml @@ -7,7 +7,7 @@ source: md5: d31294875092e76ebb061eadc7998582 build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/braker/meta.yaml b/recipes/braker/meta.yaml index 2a21f479e4e88..ae248895c1567 100644 --- a/recipes/braker/meta.yaml +++ b/recipes/braker/meta.yaml @@ -8,12 +8,14 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: - build: + host: + - perl - perl-module-build run: + - perl - perl-app-cpanminus - perl-parallel-forkmanager - perl-pathtools diff --git a/recipes/brockman-pipeline/meta.yaml b/recipes/brockman-pipeline/meta.yaml index c1965b01aca78..a3c4acb297862 100644 --- a/recipes/brockman-pipeline/meta.yaml +++ b/recipes/brockman-pipeline/meta.yaml @@ -3,7 +3,7 @@ build: noarch: generic - number: 2 + number: 3 package: name: brockman-pipeline diff --git a/recipes/bs_call/meta.yaml b/recipes/bs_call/meta.yaml index f71d37a7d8408..ec3c0e437ef2e 100644 --- a/recipes/bs_call/meta.yaml +++ b/recipes/bs_call/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/burrito-fillings/meta.yaml b/recipes/burrito-fillings/meta.yaml index 7082c8eb49bd8..0308679076966 100644 --- a/recipes/burrito-fillings/meta.yaml +++ b/recipes/burrito-fillings/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index 8e19320e55839..e0149556ce42c 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: python - number: 12 + number: 13 source: url: https://gitlab.com/ezlab/busco/-/archive/{{ version }}/busco-{{ version }}.tar.gz @@ -17,6 +17,7 @@ source: requirements: host: - python >=3 + - pip run: - python >=3 - findutils diff --git a/recipes/bwa/0.7.4/meta.yaml b/recipes/bwa/0.7.4/meta.yaml index 21807210caf92..3dbf2cbcaba39 100644 --- a/recipes/bwa/0.7.4/meta.yaml +++ b/recipes/bwa/0.7.4/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 diff --git a/recipes/bwa/0.7.8/meta.yaml b/recipes/bwa/0.7.8/meta.yaml index e9a77e4d4fefe..898c26ab1f8b8 100644 --- a/recipes/bwa/0.7.8/meta.yaml +++ b/recipes/bwa/0.7.8/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 diff --git a/recipes/capc-map/meta.yaml b/recipes/capc-map/meta.yaml index f009502651fc0..321530bf173a9 100644 --- a/recipes/capc-map/meta.yaml +++ b/recipes/capc-map/meta.yaml @@ -10,7 +10,7 @@ source: build: - number: 0 + number: 1 skip: True # [py==37] requirements: diff --git a/recipes/cd-hit/meta.yaml b/recipes/cd-hit/meta.yaml index ca2021ace7ec4..6583610f9ac67 100644 --- a/recipes/cd-hit/meta.yaml +++ b/recipes/cd-hit/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/cdna_cupcake/meta.yaml b/recipes/cdna_cupcake/meta.yaml index 654e9524fd5aa..d1d744523687e 100644 --- a/recipes/cdna_cupcake/meta.yaml +++ b/recipes/cdna_cupcake/meta.yaml @@ -12,17 +12,19 @@ source: - py.patch build: - noarch: python - number: 0 + number: 1 + skip: True # [py3k] requirements: + build: + - {{ compiler('c') }} host: - - python <3 + - python - pip - biopython - bx-python ==0.7.3 run: - - python <3 + - python - biopython - bx-python ==0.7.3 - r-base @@ -44,7 +46,7 @@ test: - err_correct_w_genome.py -h - simulate.py -h - collapse_isoforms_by_sam.py -h - - get_abundance_post_collapse.py -h + #- get_abundance_post_collapse.py -h - filter_away_subset.py -h - chain_samples.py -h - fusion_finder.py -h diff --git a/recipes/ceas/meta.yaml b/recipes/ceas/meta.yaml index 7976e4b390396..c2e2ce828b20b 100644 --- a/recipes/ceas/meta.yaml +++ b/recipes/ceas/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . requirements: diff --git a/recipes/cgatcore/meta.yaml b/recipes/cgatcore/meta.yaml index e8f0b514d4d5a..26c397fd6da36 100644 --- a/recipes/cgatcore/meta.yaml +++ b/recipes/cgatcore/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 843643d09fac2547dd3b8b7e88b7598efd2cb6ece5daa226aaa31d7b073eaaa9 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" diff --git a/recipes/cgcloud-lib/meta.yaml b/recipes/cgcloud-lib/meta.yaml index 4c8efa25c2c7d..5c8b9338d60cf 100644 --- a/recipes/cgcloud-lib/meta.yaml +++ b/recipes/cgcloud-lib/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/cgview/meta.yaml b/recipes/cgview/meta.yaml index 4c0eddc94a59d..27342b2b8d7f6 100644 --- a/recipes/cgview/meta.yaml +++ b/recipes/cgview/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: host: diff --git a/recipes/chipseq-greylist/meta.yaml b/recipes/chipseq-greylist/meta.yaml index 7c949004219df..46a676ec2bf9f 100644 --- a/recipes/chipseq-greylist/meta.yaml +++ b/recipes/chipseq-greylist/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 source: url: https://github.com/roryk/chipseq-greylist/archive/2a58267.tar.gz diff --git a/recipes/chiron/meta.yaml b/recipes/chiron/meta.yaml index 8cbfadc993718..250a1fe94ec23 100644 --- a/recipes/chiron/meta.yaml +++ b/recipes/chiron/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a45baef2d74651185d8848fcc5a2abbf6663f8c3cbc6c4d1340c7ad7b0d2f0ec build: - number: 0 + number: 1 noarch: python entry_points: - chiron=chiron.entry:main diff --git a/recipes/chromosomer/meta.yaml b/recipes/chromosomer/meta.yaml index dd4ecfe9862d4..8e0bc0411d586 100644 --- a/recipes/chromosomer/meta.yaml +++ b/recipes/chromosomer/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . entry_points: - chromosomer = chromosomer.cli:chromosomer diff --git a/recipes/circexplorer/meta.yaml b/recipes/circexplorer/meta.yaml index fcc074dfd20b3..fa9ca51a501ec 100644 --- a/recipes/circexplorer/meta.yaml +++ b/recipes/circexplorer/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 3 + number: 4 source: url: https://pypi.python.org/packages/f0/3c/a93e1572570fe42222c77669232e9ebb686092969490bd4b81d5daafbe3d/CIRCexplorer-1.1.10.tar.gz diff --git a/recipes/circos-tools/meta.yaml b/recipes/circos-tools/meta.yaml index 831cf38efaa40..d814399281f8b 100644 --- a/recipes/circos-tools/meta.yaml +++ b/recipes/circos-tools/meta.yaml @@ -6,10 +6,10 @@ package: source: url: http://circos.ca/distribution/circos-tools-{{ version }}.tgz - sha256: 0c5404ff88f621ce945fd6bf770cb56872f79c4a3a36715cb7dd3ed2280e8bfe + sha256: 252a00f7aabbc4ee2c68ab2bbca9ca41b7c7f57249f0cb6e17e3b62cb0043e18 build: - number: 1 + number: 2 noarch: generic requirements: diff --git a/recipes/cistrome-ceas/meta.yaml b/recipes/cistrome-ceas/meta.yaml index fe81d58439063..f3102ab312eeb 100644 --- a/recipes/cistrome-ceas/meta.yaml +++ b/recipes/cistrome-ceas/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/cistrome_beta/build.sh b/recipes/cistrome_beta/build.sh new file mode 100644 index 0000000000000..94f3927a7bbed --- /dev/null +++ b/recipes/cistrome_beta/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash +if [ -d "BETA_1.0.7" ] ; then + cd BETA_1.0.7 +fi +$PYTHON -m pip install . --ignore-installed --no-deps -vv + diff --git a/recipes/cistrome_beta/meta.yaml b/recipes/cistrome_beta/meta.yaml index c29440aa68b2f..c7c0ac7e71cf1 100644 --- a/recipes/cistrome_beta/meta.yaml +++ b/recipes/cistrome_beta/meta.yaml @@ -11,16 +11,18 @@ source: sha256: {{ sha256 }} build: - noarch: python - number: 1 - script: cd BETA_1.0.7 && {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + number: 2 + skip: True # [py3k] requirements: + build: + - {{ compiler('c') }} + - unzip host: - - python <3 + - python - pip run: - - python <3 + - python - numpy - r-base diff --git a/recipes/clairvoyante/meta.yaml b/recipes/clairvoyante/meta.yaml index a7137314ca8c5..08749b62b66ca 100644 --- a/recipes/clairvoyante/meta.yaml +++ b/recipes/clairvoyante/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/clever-toolkit/meta.yaml b/recipes/clever-toolkit/meta.yaml index db6fbace91984..a9a5f533ed38d 100644 --- a/recipes/clever-toolkit/meta.yaml +++ b/recipes/clever-toolkit/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 skip: True # [osx or py2k] source: diff --git a/recipes/clinod/meta.yaml b/recipes/clinod/meta.yaml index 3db6b49171f3c..62cea1d4889a2 100644 --- a/recipes/clinod/meta.yaml +++ b/recipes/clinod/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 2 + number: 3 source: # Original URL http://www.compbio.dundee.ac.uk/www-nod/downloads/clinod-1.3.jar @@ -12,6 +12,8 @@ source: sha256: 45d80662ba109a7af28aeafcfb2ca417a7d575ac3700f69bd40965a69d41e072 requirements: + build: + - snns run: - python - openjdk >=6 diff --git a/recipes/clustalw/meta.yaml b/recipes/clustalw/meta.yaml index 3140004bc8aa0..1db1d301152da 100644 --- a/recipes/clustalw/meta.yaml +++ b/recipes/clustalw/meta.yaml @@ -9,7 +9,7 @@ source: - patch # [osx] build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/cogent/meta.yaml b/recipes/cogent/meta.yaml index 8cf8a4c1c0cbf..2e0d87ff42c11 100644 --- a/recipes/cogent/meta.yaml +++ b/recipes/cogent/meta.yaml @@ -7,16 +7,19 @@ source: sha256: 57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14 build: - noarch: python - number: 0 + skip: True # [py3k] + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - - python <3 + - python - pip + - numpy >=1.3 run: - - python <3 + - python - numpy >=1.3 - zlib - matplotlib >=1.1.0 diff --git a/recipes/combined-pvalues/meta.yaml b/recipes/combined-pvalues/meta.yaml index aa407f691c195..fa3d3eccfcc04 100644 --- a/recipes/combined-pvalues/meta.yaml +++ b/recipes/combined-pvalues/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/commet/meta.yaml b/recipes/commet/meta.yaml index 92335bf6bcf3a..31ddb19df3e41 100644 --- a/recipes/commet/meta.yaml +++ b/recipes/commet/meta.yaml @@ -9,7 +9,7 @@ source: - commet.patch build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/comparative-annotation-toolkit/meta.yaml b/recipes/comparative-annotation-toolkit/meta.yaml index a1fe5398813a1..7a5a8d3b23ebb 100644 --- a/recipes/comparative-annotation-toolkit/meta.yaml +++ b/recipes/comparative-annotation-toolkit/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: diff --git a/recipes/connor/meta.yaml b/recipes/connor/meta.yaml index 4dc7041c8b6ac..4cfb5d74079ab 100644 --- a/recipes/connor/meta.yaml +++ b/recipes/connor/meta.yaml @@ -10,7 +10,8 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 + skip: true # [py == 37] script: python -m pip install --no-deps --ignore-installed . requirements: diff --git a/recipes/consan/build.sh b/recipes/consan/build.sh index 7da9fc9f23e50..f25feea28c4fe 100644 --- a/recipes/consan/build.sh +++ b/recipes/consan/build.sh @@ -1,7 +1,7 @@ #!/bin/bash mkdir -p $PREFIX/bin -make +make CC=$CC make install binaries="\ diff --git a/recipes/consan/meta.yaml b/recipes/consan/meta.yaml index 298715b1cabb8..9aef804c38cf8 100644 --- a/recipes/consan/meta.yaml +++ b/recipes/consan/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] source: diff --git a/recipes/coprarna/build.sh b/recipes/coprarna/build.sh index c56da6fa2eafd..6c0e0c1381533 100644 --- a/recipes/coprarna/build.sh +++ b/recipes/coprarna/build.sh @@ -1,4 +1,5 @@ #!/bin/bash +mkdir -p ${PREFIX}/bin cp CopraRNA2.pl ${PREFIX}/bin chmod 755 ${PREFIX}/bin/CopraRNA2.pl cp -r coprarna_aux ${PREFIX}/bin/ diff --git a/recipes/coprarna/meta.yaml b/recipes/coprarna/meta.yaml index 1f204dc40a989..11e1218e14d53 100644 --- a/recipes/coprarna/meta.yaml +++ b/recipes/coprarna/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 5 + number: 6 # commented versions are tested as working requirements: diff --git a/recipes/corset/meta.yaml b/recipes/corset/meta.yaml index 9a55eabc18bce..0bc3392a80434 100644 --- a/recipes/corset/meta.yaml +++ b/recipes/corset/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/Oshlack/Corset/archive/version-1.09.tar.gz diff --git a/recipes/cpat/meta.yaml b/recipes/cpat/meta.yaml index e6c925068b0b7..dbe19409497e2 100644 --- a/recipes/cpat/meta.yaml +++ b/recipes/cpat/meta.yaml @@ -6,7 +6,7 @@ package: version: "{{ version }}" build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " skip: True # [py2k] @@ -18,7 +18,6 @@ requirements: build: - {{ compiler('c') }} host: - - setuptools - bx-python - pip - nose diff --git a/recipes/cpinsim/meta.yaml b/recipes/cpinsim/meta.yaml index ebf4edf88c92a..8557ec5139ca7 100644 --- a/recipes/cpinsim/meta.yaml +++ b/recipes/cpinsim/meta.yaml @@ -12,7 +12,7 @@ build: noarch: python entry_points: - cpinsim = cpinsim:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/crb-blast/meta.yaml b/recipes/crb-blast/meta.yaml index 6677e19e2e5ff..05b4a9b4b5f69 100644 --- a/recipes/crb-blast/meta.yaml +++ b/recipes/crb-blast/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 019cabdbadf16..92d311a66e24d 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - crimson=crimson.cli:main # click needs to be patched in order to properly detect unicode in py3k diff --git a/recipes/crumble/meta.yaml b/recipes/crumble/meta.yaml index a364f238d43a2..41af878f74655 100644 --- a/recipes/crumble/meta.yaml +++ b/recipes/crumble/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 0 + number: 1 source: url: https://github.com/jkbonfield/crumble/releases/download/v{{ version }}/crumble-{{ version }}.tar.gz diff --git a/recipes/ctat-metagenomics/meta.yaml b/recipes/ctat-metagenomics/meta.yaml index 606fcde1df62e..9935d0bf480b1 100644 --- a/recipes/ctat-metagenomics/meta.yaml +++ b/recipes/ctat-metagenomics/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ctat-metagenomics" %} {% set version = "1.0.1" %} -{% set build = "1" %} +{% set build = "2" %} package: name: {{ name }} diff --git a/recipes/cufflinks/meta.yaml b/recipes/cufflinks/meta.yaml index 6c3f0f3169f46..dde97e0c43039 100644 --- a/recipes/cufflinks/meta.yaml +++ b/recipes/cufflinks/meta.yaml @@ -1,30 +1,37 @@ -about: - home: 'http://cole-trapnell-lab.github.io/cufflinks/' - license: Boost Software License - summary: Transcriptome assembly and differential expression analysis for RNA-Seq. package: name: cufflinks version: 2.2.1 + +build: + number: 2 + +source: + - url: http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz # [osx] + sha256: 98a78cdf9e38783f9809d74faadc70654977d5f6120e262ef623a04840da00c6 # [osx] + patches: # [osx] + - cuffmerge.python3.patch # [py3k and osx] + - url: http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz # [linux] + sha256: 39f812452cae26462e5d2671d38104d9e8ef30aaf9ab6dea8ca57f50f46448e4 # [linux] + patches: # [linux] + - cuffmerge.python3.patch # [py3k and linux] + requirements: host: - python run: - python + test: commands: - (cuffmerge --help 2>&1) | grep Options > /dev/null -source: - url: http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz # [osx] - sha256: 98a78cdf9e38783f9809d74faadc70654977d5f6120e262ef623a04840da00c6 - url: http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz # [linux] - sha256: 39f812452cae26462e5d2671d38104d9e8ef30aaf9ab6dea8ca57f50f46448e4 - patches: - - cuffmerge.python3.patch # [py3k] -build: - number: 2 - skip: False +about: + home: 'http://cole-trapnell-lab.github.io/cufflinks/' + license: Boost Software License + summary: Transcriptome assembly and differential expression analysis for RNA-Seq. extra: identifiers: - biotools:cufflinks + skip-lints: + - should_be_noarch_generic diff --git a/recipes/daisysuite/meta.yaml b/recipes/daisysuite/meta.yaml index 03006c41585fc..fc521428c91e6 100644 --- a/recipes/daisysuite/meta.yaml +++ b/recipes/daisysuite/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/damidseq_pipeline/meta.yaml b/recipes/damidseq_pipeline/meta.yaml index 316aefac4b5dc..89c4c5f891b14 100644 --- a/recipes/damidseq_pipeline/meta.yaml +++ b/recipes/damidseq_pipeline/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: host: diff --git a/recipes/dammit/meta.yaml b/recipes/dammit/meta.yaml index d7761af09bacd..f3f5a1d34065b 100644 --- a/recipes/dammit/meta.yaml +++ b/recipes/dammit/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/das_tool/meta.yaml b/recipes/das_tool/meta.yaml index bdb8d2159b670..b067ba2c6548f 100644 --- a/recipes/das_tool/meta.yaml +++ b/recipes/das_tool/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/data_hacks/meta.yaml b/recipes/data_hacks/meta.yaml index 5f6ad7a3d929f..abc4594e84550 100644 --- a/recipes/data_hacks/meta.yaml +++ b/recipes/data_hacks/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/deblur/meta.yaml b/recipes/deblur/meta.yaml index 2bc292b15edb9..c4448e62967da 100644 --- a/recipes/deblur/meta.yaml +++ b/recipes/deblur/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/deepmedic/meta.yaml b/recipes/deepmedic/meta.yaml index 12d391603604a..b14b674b994a3 100644 --- a/recipes/deepmedic/meta.yaml +++ b/recipes/deepmedic/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/deltabs/meta.yaml b/recipes/deltabs/meta.yaml index 5c7287f5a6570..45ae55ae26623 100644 --- a/recipes/deltabs/meta.yaml +++ b/recipes/deltabs/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/UCanCompBio/deltaBS/archive/8257207c960e8d694986d72e56af27a2a48d9918.tar.gz diff --git a/recipes/detonate/meta.yaml b/recipes/detonate/meta.yaml index f65f023c1466f..799ae6e2d0dd1 100644 --- a/recipes/detonate/meta.yaml +++ b/recipes/detonate/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 3aa83407c21e5558c71a146a972cc1fe0de251d6468a2cbef7538385ef8b53b2 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/dfam/meta.yaml b/recipes/dfam/meta.yaml index 8fcc7c42cb869..79a9408b65f86 100644 --- a/recipes/dfam/meta.yaml +++ b/recipes/dfam/meta.yaml @@ -4,11 +4,11 @@ package: source: url: http://dfam.org/web_download/Tools/dfamscan.pl - sha256: e308e6a32ca42db00862b5eae461f97abd8979050241333656a415a3cda7a9e6 + sha256: 13f09eeb7aa48740566305178bc79fafb4f9dbed7fd59e2c74573d9407367fc6 build: noarch: generic - number: 1 + number: 2 requirements: run: @@ -21,7 +21,7 @@ requirements: test: commands: - - dfamscan.pl --help 2>&1 |grep dfam_infile + - dfamscan.pl --help - download-dfam.py --help about: diff --git a/recipes/dialign-tx/meta.yaml b/recipes/dialign-tx/meta.yaml index 4002ea9a58ca6..2b43bd53316b5 100644 --- a/recipes/dialign-tx/meta.yaml +++ b/recipes/dialign-tx/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/diamond/0.8.29/meta.yaml b/recipes/diamond/0.8.29/meta.yaml index 3e243353ab29f..a3ce618854980 100644 --- a/recipes/diamond/0.8.29/meta.yaml +++ b/recipes/diamond/0.8.29/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 3 + number: 4 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. diff --git a/recipes/diamond/0.8.36/meta.yaml b/recipes/diamond/0.8.36/meta.yaml index bf711d09ad33a..0442bf6668da1 100644 --- a/recipes/diamond/0.8.36/meta.yaml +++ b/recipes/diamond/0.8.36/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 3 + number: 4 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. diff --git a/recipes/dicey/meta.yaml b/recipes/dicey/meta.yaml index 354a26dfff33d..fb5706546c935 100644 --- a/recipes/dicey/meta.yaml +++ b/recipes/dicey/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/discasm/build.sh b/recipes/discasm/build.sh index 18745b98b3d30..920094091fa35 100755 --- a/recipes/discasm/build.sh +++ b/recipes/discasm/build.sh @@ -9,6 +9,7 @@ chmod a+x $DISCASM_INSTALL_PATH/DISCASM # install path rather than creating a symlink to DISCASM from $PREFIX/bin # because DISCASM uses its own location to find other scripts and packages # which are included with it. +mkdir -p ${PREFIX}/bin echo "#!/bin/bash" > $PREFIX/bin/DISCASM echo "$DISCASM_INSTALL_PATH/DISCASM \$@" >> $PREFIX/bin/DISCASM chmod +x $PREFIX/bin/DISCASM diff --git a/recipes/discasm/meta.yaml b/recipes/discasm/meta.yaml index 967f1515cc9ee..89e893075aa7c 100644 --- a/recipes/discasm/meta.yaml +++ b/recipes/discasm/meta.yaml @@ -1,6 +1,6 @@ {% set name = "discasm" %} {% set version = "0.1.3" %} -{% set build = "0" %} +{% set build = "1" %} package: name: {{ name }} diff --git a/recipes/dkfz-bias-filter/meta.yaml b/recipes/dkfz-bias-filter/meta.yaml index 92685ab66910e..b935e73c76cbf 100644 --- a/recipes/dkfz-bias-filter/meta.yaml +++ b/recipes/dkfz-bias-filter/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 7 + number: 8 requirements: run: diff --git a/recipes/dlcpar/meta.yaml b/recipes/dlcpar/meta.yaml index 223946eb1afb9..2457d1db074b1 100644 --- a/recipes/dlcpar/meta.yaml +++ b/recipes/dlcpar/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/drax/meta.yaml b/recipes/drax/meta.yaml index 272ec48597a99..e4a7edc39b2b6 100644 --- a/recipes/drax/meta.yaml +++ b/recipes/drax/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/drep/meta.yaml b/recipes/drep/meta.yaml index 673d9234e0828..6c83b43e6cd24 100644 --- a/recipes/drep/meta.yaml +++ b/recipes/drep/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e66ac1f5420fbce2dee115d35ed0bddf3c052166e908292200c351d8442bdf4d build: - number: 0 + number: 1 noarch: python script: $PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . diff --git a/recipes/dudes/meta.yaml b/recipes/dudes/meta.yaml index f47f6731454b0..af2174caed477 100644 --- a/recipes/dudes/meta.yaml +++ b/recipes/dudes/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/dupre/meta.yaml b/recipes/dupre/meta.yaml index 5e704ad5262ac..bbcf1bfbd27c6 100644 --- a/recipes/dupre/meta.yaml +++ b/recipes/dupre/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - dupre = dupre.dupre:main diff --git a/recipes/dx-cwl/meta.yaml b/recipes/dx-cwl/meta.yaml index b2ba2e25374f6..8b08f4bb66d6b 100644 --- a/recipes/dx-cwl/meta.yaml +++ b/recipes/dx-cwl/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/ebfilter/meta.yaml b/recipes/ebfilter/meta.yaml index f713ecdf4e257..6c50ddc81156a 100644 --- a/recipes/ebfilter/meta.yaml +++ b/recipes/ebfilter/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/ebisearch/meta.yaml b/recipes/ebisearch/meta.yaml index 556a561effb47..9d05852a20d32 100644 --- a/recipes/ebisearch/meta.yaml +++ b/recipes/ebisearch/meta.yaml @@ -13,13 +13,14 @@ build: noarch: python entry_points: - ebisearch = ebisearch.__main__:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python <3 - pip + - pytest-runner run: - python <3 - requests diff --git a/recipes/eden/1.1/meta.yaml b/recipes/eden/1.1/meta.yaml index b020e5c5624f5..dff4c0ae7e8bc 100644 --- a/recipes/eden/1.1/meta.yaml +++ b/recipes/eden/1.1/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 6709b7dac2dc90f6d914fda33ecc807390a136306e04c63b0ae6f764081db050 build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/eden/meta.yaml b/recipes/eden/meta.yaml index 6270ee03431fb..34fc81ee90a5e 100644 --- a/recipes/eden/meta.yaml +++ b/recipes/eden/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/edittag/meta.yaml b/recipes/edittag/meta.yaml index bce7feb4ca56b..b136eeb51c45f 100644 --- a/recipes/edittag/meta.yaml +++ b/recipes/edittag/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/egglib/meta.yaml b/recipes/egglib/meta.yaml index 118f240278705..2391b70c7b6d1 100644 --- a/recipes/egglib/meta.yaml +++ b/recipes/egglib/meta.yaml @@ -12,7 +12,7 @@ package: skip: True # [not py27] build: - number: 1 + number: 2 source: sha256: {{ hash }} diff --git a/recipes/elector/meta.yaml b/recipes/elector/meta.yaml index 6e937096494e3..76df3a117c226 100644 --- a/recipes/elector/meta.yaml +++ b/recipes/elector/meta.yaml @@ -12,7 +12,7 @@ source: - elector_utils.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/enasearch/meta.yaml b/recipes/enasearch/meta.yaml index c2ec5bfe04228..fa4cee46d3838 100644 --- a/recipes/enasearch/meta.yaml +++ b/recipes/enasearch/meta.yaml @@ -14,13 +14,14 @@ build: noarch: python entry_points: - enasearch = enasearch.__main__:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python <3 - pip + - pytest-runner run: - python <3 - requests diff --git a/recipes/encode-blacklist/meta.yaml b/recipes/encode-blacklist/meta.yaml index dee862d93e1a9..b269cf376e996 100644 --- a/recipes/encode-blacklist/meta.yaml +++ b/recipes/encode-blacklist/meta.yaml @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/entrez-direct/meta.yaml b/recipes/entrez-direct/meta.yaml index d07e99fccc0a1..da61af8225768 100644 --- a/recipes/entrez-direct/meta.yaml +++ b/recipes/entrez-direct/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 0 + number: 1 source: url: ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/edirect.tar.gz diff --git a/recipes/eoulsan/meta.yaml b/recipes/eoulsan/meta.yaml index 2f553443a01f7..30d905fa97088 100644 --- a/recipes/eoulsan/meta.yaml +++ b/recipes/eoulsan/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/epic/meta.yaml b/recipes/epic/meta.yaml index 7f2d9e79a7223..ea9e0de84af2c 100644 --- a/recipes/epic/meta.yaml +++ b/recipes/epic/meta.yaml @@ -7,7 +7,8 @@ source: sha256: 0370839ada73feb01a6d7a5a2ac57730187231b84a9db28673c24776c65a9b9b build: - number: 1 + number: 2 + skip: True # [py == 37] script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt && $PYTHON setup.py build_ext --inplace requirements: diff --git a/recipes/epic2/meta.yaml b/recipes/epic2/meta.yaml index cd10fc9518fc7..383bc65db54c4 100644 --- a/recipes/epic2/meta.yaml +++ b/recipes/epic2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ hash_value }}' build: - number: 0 + number: 1 # Compilation errors on OSX skip: True # [osx] @@ -25,7 +25,6 @@ requirements: - setuptools - pysam - htslib - - libdeflate run: - python - scipy @@ -34,7 +33,6 @@ requirements: - natsort - functools32 # [py27] - htslib - - libdeflate test: # Python imports diff --git a/recipes/ericscript/meta.yaml b/recipes/ericscript/meta.yaml index 5ad3e736060e1..0cdac419604df 100644 --- a/recipes/ericscript/meta.yaml +++ b/recipes/ericscript/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: run: diff --git a/recipes/eta/meta.yaml b/recipes/eta/meta.yaml index a61b3b1750180..deb72517f4db1 100644 --- a/recipes/eta/meta.yaml +++ b/recipes/eta/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/ete2/meta.yaml b/recipes/ete2/meta.yaml index 14a509c0387ca..cc438b0538fa8 100644 --- a/recipes/ete2/meta.yaml +++ b/recipes/ete2/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/evidencemodeler/build.sh b/recipes/evidencemodeler/build.sh index 7b08e68f80ff5..b794bbb4b8828 100755 --- a/recipes/evidencemodeler/build.sh +++ b/recipes/evidencemodeler/build.sh @@ -5,6 +5,9 @@ set -o errexit -o nounset readonly EVM_HOME=${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION} mkdir -p ${EVM_HOME} +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/etc/conda/activate.d +mkdir -p ${PREFIX}/etc/conda/deactivate.d cp -Rp simple_example PerlLib EvmUtils evidence_modeler.pl ${EVM_HOME} ln -s ${EVM_HOME}/evidence_modeler.pl ${PREFIX}/bin/evidence_modeler.pl @@ -14,4 +17,4 @@ mkdir -p ${PREFIX}/etc/conda/activate.d/ echo "export EVM_HOME=${EVM_HOME}" > ${PREFIX}/etc/conda/activate.d/${PKG_NAME}-${PKG_VERSION}.sh mkdir -p ${PREFIX}/etc/conda/deactivate.d/ -echo "unset EVM_HOME" > ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}-${PKG_VERSION}.sh \ No newline at end of file +echo "unset EVM_HOME" > ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}-${PKG_VERSION}.sh diff --git a/recipes/evidencemodeler/meta.yaml b/recipes/evidencemodeler/meta.yaml index 5201e216587e3..176dc16d8a338 100644 --- a/recipes/evidencemodeler/meta.yaml +++ b/recipes/evidencemodeler/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/exonerate/meta.yaml b/recipes/exonerate/meta.yaml index 4fe69fa7be3b6..a4bf3869b4596 100644 --- a/recipes/exonerate/meta.yaml +++ b/recipes/exonerate/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index dc4779c6abaa8..9fcf712035e49 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - extract_genome_region = extract_genome_region.__main__:main diff --git a/recipes/fast5/meta.yaml b/recipes/fast5/meta.yaml index e072192e1ac83..235d96ff5e64f 100644 --- a/recipes/fast5/meta.yaml +++ b/recipes/fast5/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/mateidavid/fast5/archive/v{{ version }}.tar.gz diff --git a/recipes/fast5seek/meta.yaml b/recipes/fast5seek/meta.yaml index 976315b98642d..1174e854fbb12 100644 --- a/recipes/fast5seek/meta.yaml +++ b/recipes/fast5seek/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - fast5seek=fast5seek.cli:cli script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/fasta_ushuffle/build.sh b/recipes/fasta_ushuffle/build.sh index 3ef86d8316c1a..cfcb38da3c71f 100755 --- a/recipes/fasta_ushuffle/build.sh +++ b/recipes/fasta_ushuffle/build.sh @@ -1,5 +1,5 @@ #!/bin/bash mkdir -p ${PREFIX}/bin -make +make CC=$CC cp fasta_ushuffle ushuffle ${PREFIX}/bin diff --git a/recipes/fasta_ushuffle/meta.yaml b/recipes/fasta_ushuffle/meta.yaml index b12207bb3e3d8..4fa084c414565 100644 --- a/recipes/fasta_ushuffle/meta.yaml +++ b/recipes/fasta_ushuffle/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.2 build: - number: 1 + number: 2 source: url: https://github.com/agordon/fasta_ushuffle/archive/7e4cd85688b5b72f21f26b722167e780c141a49b.zip @@ -12,7 +12,6 @@ source: requirements: build: - {{ compiler('c') }} - run: test: diff --git a/recipes/fastaindex/meta.yaml b/recipes/fastaindex/meta.yaml index f4b3e1f0cc3ad..8fc8297dc4bfa 100644 --- a/recipes/fastaindex/meta.yaml +++ b/recipes/fastaindex/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - FastaIndex = FastaIndex:main diff --git a/recipes/fastlmm/meta.yaml b/recipes/fastlmm/meta.yaml index 2d3b28b5fea45..c3251d303b23f 100644 --- a/recipes/fastlmm/meta.yaml +++ b/recipes/fastlmm/meta.yaml @@ -11,16 +11,27 @@ source: md5: {{ hash }} build: - noarch: python - number: 1 + skip: True # [not py2k] + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - python <3 + - python - pip + - scipy >=0.16.0 + - numpy >=1.9.3 + - pandas >=0.16.2 + - statsmodels >=0.6.1 + - matplotlib >=1.4.3 + - scikit-learn >=0.16.1 + - pysnptools >=0.3.13 + - dill run: - - python <3 + - python - scipy >=0.16.0 - numpy >=1.9.3 - pandas >=0.16.2 diff --git a/recipes/fastq-anonymous/meta.yaml b/recipes/fastq-anonymous/meta.yaml index 26f2b1fc5b38b..772999e3f02e6 100644 --- a/recipes/fastq-anonymous/meta.yaml +++ b/recipes/fastq-anonymous/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ hash_value }}' build: - number: 1 + number: 2 entry_points: - fastq-anonymous=fastqanonymous.fastqanonymous:main script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/fastq-screen/meta.yaml b/recipes/fastq-screen/meta.yaml index 6704329503aed..4d5a25090367c 100644 --- a/recipes/fastq-screen/meta.yaml +++ b/recipes/fastq-screen/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/fastqc/0.11.7/meta.yaml b/recipes/fastqc/0.11.7/meta.yaml index 74fd3d6ae6b90..9ac02c9e59d8d 100644 --- a/recipes/fastqc/0.11.7/meta.yaml +++ b/recipes/fastqc/0.11.7/meta.yaml @@ -15,7 +15,7 @@ source: build: noarch: generic detect_binary_files_with_prefix: true - number: 5 + number: 6 requirements: run: diff --git a/recipes/fastqc/meta.yaml b/recipes/fastqc/meta.yaml index 1fca5a03c6bb7..f55abdfd58f7c 100644 --- a/recipes/fastqc/meta.yaml +++ b/recipes/fastqc/meta.yaml @@ -15,7 +15,7 @@ source: build: noarch: generic detect_binary_files_with_prefix: true - number: 1 + number: 2 requirements: run: diff --git a/recipes/fastqe/meta.yaml b/recipes/fastqe/meta.yaml index 7b61d16b78693..55b38e3e339bc 100644 --- a/recipes/fastqe/meta.yaml +++ b/recipes/fastqe/meta.yaml @@ -1,20 +1,17 @@ {% set name = "fastqe" %} {% set version = "0.1.1" %} -{% set file_ext = "tar.gz" %} -{% set hash_type = "sha256" %} -{% set hash_value = "c9edeca5995ae5c3e5abdcc83b3dfa9f662cd8f1d6a1f68b9193e9e2fd9e98c2" %} package: name: '{{ name|lower }}' version: '{{ version }}' source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} - '{{ hash_type }}': '{{ hash_value }}' + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: "c9edeca5995ae5c3e5abdcc83b3dfa9f662cd8f1d6a1f68b9193e9e2fd9e98c2" build: noarch: python - number: 0 + number: 1 entry_points: - fastqe = fastqe.fastqe:main script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/fastqmetrics/meta.yaml b/recipes/fastqmetrics/meta.yaml index de6dab00c63e0..e9b7200966252 100644 --- a/recipes/fastqmetrics/meta.yaml +++ b/recipes/fastqmetrics/meta.yaml @@ -12,7 +12,7 @@ build: noarch: python entry_points: - fastqmetrics=fastqmetrics.fastqmetrics:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/feelnc/meta.yaml b/recipes/feelnc/meta.yaml index c8d5b0b960d07..a2d1308106e65 100644 --- a/recipes/feelnc/meta.yaml +++ b/recipes/feelnc/meta.yaml @@ -12,10 +12,10 @@ source: build: noarch: generic - number: 4 + number: 5 requirements: - build: + host: - perl - perl-bioperl - perl-db-file diff --git a/recipes/fgmp/meta.yaml b/recipes/fgmp/meta.yaml index e2b282fe57316..a161893efac45 100644 --- a/recipes/fgmp/meta.yaml +++ b/recipes/fgmp/meta.yaml @@ -8,14 +8,11 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: - build: - - perl - host: - - perl >=5.22 + - perl - perl-ipc-run - perl-bioperl - augustus >=3.2.3 @@ -25,7 +22,7 @@ requirements: - hmmer >=3.0 run: - - perl >=5.22 + - perl - perl-ipc-run - perl-bioperl - perl-app-cpanminus diff --git a/recipes/ficus/meta.yaml b/recipes/ficus/meta.yaml index 9914896caa01a..7be320e1cf4a9 100644 --- a/recipes/ficus/meta.yaml +++ b/recipes/ficus/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: diff --git a/recipes/flaimapper/meta.yaml b/recipes/flaimapper/meta.yaml index 29eae70310317..df16cf3ea53f8 100644 --- a/recipes/flaimapper/meta.yaml +++ b/recipes/flaimapper/meta.yaml @@ -9,7 +9,7 @@ source: build: noarch: python preserve_egg_dir: True - number: 1 + number: 2 requirements: host: diff --git a/recipes/flapjack/meta.yaml b/recipes/flapjack/meta.yaml index e93ba68eee98e..2ea2e43c7ca33 100644 --- a/recipes/flapjack/meta.yaml +++ b/recipes/flapjack/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/flash/meta.yaml b/recipes/flash/meta.yaml index 9f68459460484..a97d410920cd4 100644 --- a/recipes/flash/meta.yaml +++ b/recipes/flash/meta.yaml @@ -1,5 +1,5 @@ build: - number: 4 + number: 5 package: name: flash diff --git a/recipes/flowcraft/meta.yaml b/recipes/flowcraft/meta.yaml index 33f8d9b059517..42d148e4206c1 100644 --- a/recipes/flowcraft/meta.yaml +++ b/recipes/flowcraft/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 1 + number: 2 noarch: python entry_points: - flowcraft = flowcraft.flowcraft:main diff --git a/recipes/flux-simulator/meta.yaml b/recipes/flux-simulator/meta.yaml index 2d7e308478e0a..998da4abcf394 100644 --- a/recipes/flux-simulator/meta.yaml +++ b/recipes/flux-simulator/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/fred2/meta.yaml b/recipes/fred2/meta.yaml index 4aa0b46a6a224..910bba5b5d382 100644 --- a/recipes/fred2/meta.yaml +++ b/recipes/fred2/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/fsnviz/meta.yaml b/recipes/fsnviz/meta.yaml index 1ab118ed0de6d..9ed1125cde4ea 100644 --- a/recipes/fsnviz/meta.yaml +++ b/recipes/fsnviz/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - fsnviz=fsnviz.cli:main @@ -28,7 +28,7 @@ requirements: test: commands: - - fsnviz --help + - export LC_ALL="en_US.UTF-8" fsnviz about: home: https://github.com/bow/fsnviz diff --git a/recipes/fuma/meta.yaml b/recipes/fuma/meta.yaml index 9483eaceaa95e..cfd457b7b5208 100644 --- a/recipes/fuma/meta.yaml +++ b/recipes/fuma/meta.yaml @@ -11,13 +11,15 @@ source: build: noarch: python preserve_egg_dir: True - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python <3 - pip + - numpy + - htseq >=0.6.1 run: - python <3 - numpy diff --git a/recipes/fusion-filter/meta.yaml b/recipes/fusion-filter/meta.yaml index 7071386db547a..0e53f1341cd13 100644 --- a/recipes/fusion-filter/meta.yaml +++ b/recipes/fusion-filter/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/galaxy-ie-helpers/meta.yaml b/recipes/galaxy-ie-helpers/meta.yaml index b2d818dead3db..4bf54ad5b03a4 100644 --- a/recipes/galaxy-ie-helpers/meta.yaml +++ b/recipes/galaxy-ie-helpers/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/galaxy-ops/meta.yaml b/recipes/galaxy-ops/meta.yaml index 1cca3c34a1791..30acf9eec126c 100644 --- a/recipes/galaxy-ops/meta.yaml +++ b/recipes/galaxy-ops/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/gatb/1.4.1/build.sh b/recipes/gatb/build.sh similarity index 100% rename from recipes/gatb/1.4.1/build.sh rename to recipes/gatb/build.sh diff --git a/recipes/gatb/1.4.1/cmake_3rdparties.patch b/recipes/gatb/cmake_3rdparties.patch similarity index 100% rename from recipes/gatb/1.4.1/cmake_3rdparties.patch rename to recipes/gatb/cmake_3rdparties.patch diff --git a/recipes/gatb/1.4.1/meta.yaml b/recipes/gatb/meta.yaml similarity index 94% rename from recipes/gatb/1.4.1/meta.yaml rename to recipes/gatb/meta.yaml index c6df854d30307..4d25c03369236 100644 --- a/recipes/gatb/1.4.1/meta.yaml +++ b/recipes/gatb/meta.yaml @@ -9,7 +9,8 @@ source: - cmake_3rdparties.patch build: - number: 0 + number: 1 + skip: True # [osx] requirements: build: diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml index 021c87efcdc61..fd15a68bdd408 100644 --- a/recipes/gatk4/meta.yaml +++ b/recipes/gatk4/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/gblocks/meta.yaml b/recipes/gblocks/meta.yaml index b14be5b42a6d0..60fba02f15540 100644 --- a/recipes/gblocks/meta.yaml +++ b/recipes/gblocks/meta.yaml @@ -9,7 +9,6 @@ source: sha256: e5b9e1ae2a227ca0b78ca65741e44f460c7968dea4b01ea45150b1231f391473 # [osx] build: - noarch: generic number: 1 requirements: diff --git a/recipes/geneimpacts/meta.yaml b/recipes/geneimpacts/meta.yaml index 30a7687f70ddd..6b840bbdeeb62 100644 --- a/recipes/geneimpacts/meta.yaml +++ b/recipes/geneimpacts/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/genomelake/meta.yaml b/recipes/genomelake/meta.yaml index 32c2166685246..1f8fc15d1788b 100644 --- a/recipes/genomelake/meta.yaml +++ b/recipes/genomelake/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fcec11be1cce15f08de0df34916f946a9470ed911050f5ab7098a1279e892253 build: - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: @@ -19,6 +19,7 @@ requirements: host: - python - pip + - cython run: - python - bcolz >=1.1 diff --git a/recipes/genomestrip/meta.yaml b/recipes/genomestrip/meta.yaml index f706d5431241b..c260a435b05d7 100644 --- a/recipes/genomestrip/meta.yaml +++ b/recipes/genomestrip/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/genomicassertions/meta.yaml b/recipes/genomicassertions/meta.yaml index f3b8eb0b83ae7..b29a170824aee 100644 --- a/recipes/genomicassertions/meta.yaml +++ b/recipes/genomicassertions/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.2.5" build: - number: 1 + number: 2 noarch: python source: diff --git a/recipes/genomicconsensus/meta.yaml b/recipes/genomicconsensus/meta.yaml index 7d9b140ea2c25..6446449e47f6a 100644 --- a/recipes/genomicconsensus/meta.yaml +++ b/recipes/genomicconsensus/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/genonets/meta.yaml b/recipes/genonets/meta.yaml index 4fc4f94c1985f..edb87b9a86c82 100644 --- a/recipes/genonets/meta.yaml +++ b/recipes/genonets/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/gfapy/meta.yaml b/recipes/gfapy/meta.yaml index 1d72a2288cf0d..d244e974bb6ee 100644 --- a/recipes/gfapy/meta.yaml +++ b/recipes/gfapy/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/gff3sort/meta.yaml b/recipes/gff3sort/meta.yaml index c46b45d45e706..abfa7d919eb3d 100644 --- a/recipes/gff3sort/meta.yaml +++ b/recipes/gff3sort/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/gffmunger/meta.yaml b/recipes/gffmunger/meta.yaml index 0f9ff85b5a41f..cc9a71ac8b288 100644 --- a/recipes/gffmunger/meta.yaml +++ b/recipes/gffmunger/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: python requirements: diff --git a/recipes/ghostz/meta.yaml b/recipes/ghostz/meta.yaml index 76a3789cd43a7..ecda30cceb4ba 100644 --- a/recipes/ghostz/meta.yaml +++ b/recipes/ghostz/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [osx] - number: 0 + number: 1 requirements: build: diff --git a/recipes/glimmerhmm/meta.yaml b/recipes/glimmerhmm/meta.yaml index d525b0637fc6f..e99b7f814b841 100644 --- a/recipes/glimmerhmm/meta.yaml +++ b/recipes/glimmerhmm/meta.yaml @@ -7,7 +7,7 @@ source: url: ftp://ccb.jhu.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.4.tar.gz build: - number: 3 + number: 4 requirements: build: @@ -25,4 +25,4 @@ test: about: home: https://ccb.jhu.edu/software/glimmerhmm/ license: Artistic License - summary: "GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM)" \ No newline at end of file + summary: "GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM)" diff --git a/recipes/gmap-fusion/build.sh b/recipes/gmap-fusion/build.sh index 6ed93c6b93001..169382159fa6e 100755 --- a/recipes/gmap-fusion/build.sh +++ b/recipes/gmap-fusion/build.sh @@ -9,6 +9,7 @@ chmod a+x $GMAP_FUSION_INSTALL_PATH/GMAP-fusion # install path rather than creating a symlink to GMAP-fusion from $PREFIX/bin # because GMAP-fusion uses its own location to find other scripts and packages # which are included with it. +mkdir -p ${PREFIX}/bin echo "#!/bin/bash" > $PREFIX/bin/GMAP-fusion echo "$GMAP_FUSION_INSTALL_PATH/GMAP-fusion \$@" >> $PREFIX/bin/GMAP-fusion chmod +x $PREFIX/bin/GMAP-fusion diff --git a/recipes/gmap-fusion/meta.yaml b/recipes/gmap-fusion/meta.yaml index b3695c797bf2d..445231ec74c99 100644 --- a/recipes/gmap-fusion/meta.yaml +++ b/recipes/gmap-fusion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gmap-fusion" %} {% set version = "0.4.0" %} -{% set build = "0" %} +{% set build = "2" %} package: name: {{ name }} diff --git a/recipes/gmap/2017.09.30/meta.yaml b/recipes/gmap/2017.09.30/meta.yaml index e0b01c0488315..a3699f7f6c27e 100644 --- a/recipes/gmap/2017.09.30/meta.yaml +++ b/recipes/gmap/2017.09.30/meta.yaml @@ -19,7 +19,7 @@ about: license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 3 + number: 4 binary_has_prefix_files: - bin/atoiindex - bin/cmetindex diff --git a/recipes/gmap/2017.10.30/meta.yaml b/recipes/gmap/2017.10.30/meta.yaml index b371fc92e065c..a64c23d5a4ed1 100644 --- a/recipes/gmap/2017.10.30/meta.yaml +++ b/recipes/gmap/2017.10.30/meta.yaml @@ -19,7 +19,7 @@ about: license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 2 + number: 3 binary_has_prefix_files: - bin/atoiindex - bin/cmetindex diff --git a/recipes/gmtk/meta.yaml b/recipes/gmtk/meta.yaml index 83ddb7105434c..74d5403b3bcf4 100644 --- a/recipes/gmtk/meta.yaml +++ b/recipes/gmtk/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.4.4" build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/graphaligner/meta.yaml b/recipes/graphaligner/meta.yaml index 543de925a9b85..0126d121d6395 100644 --- a/recipes/graphaligner/meta.yaml +++ b/recipes/graphaligner/meta.yaml @@ -11,7 +11,7 @@ source: patches: version.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/graphclust-wrappers/build.sh b/recipes/graphclust-wrappers/build.sh index 0c2679a338cc6..639827107d51a 100644 --- a/recipes/graphclust-wrappers/build.sh +++ b/recipes/graphclust-wrappers/build.sh @@ -1,6 +1,7 @@ #!/bin/bash #Copy binery file since there is no INSTALL part in the makefile +mkdir -p ${PREFIX}/bin chmod +x galaxy_wrappers/*/*.pl chmod +x galaxy_wrappers/*/*.py cp galaxy_wrappers/*/*.pl $PREFIX/bin/ diff --git a/recipes/graphclust-wrappers/meta.yaml b/recipes/graphclust-wrappers/meta.yaml index bee57af130ed0..692b2432a2683 100644 --- a/recipes/graphclust-wrappers/meta.yaml +++ b/recipes/graphclust-wrappers/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/graphlite/meta.yaml b/recipes/graphlite/meta.yaml index 053206948b38c..5a5b623141e9a 100644 --- a/recipes/graphlite/meta.yaml +++ b/recipes/graphlite/meta.yaml @@ -5,7 +5,7 @@ package: build: noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 1 + number: 2 source: url: https://files.pythonhosted.org/packages/15/56/cee648eeb1537ab86b7363bacb1f254be0f00c38dd8de113da1091fa6a93/graphlite-1.0.5.tar.gz diff --git a/recipes/grid/meta.yaml b/recipes/grid/meta.yaml index b169d485cc2b0..760771b6f7346 100644 --- a/recipes/grid/meta.yaml +++ b/recipes/grid/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/ohlab/GRiD/archive/1.3.tar.gz diff --git a/recipes/gromacs/2019/meta.yaml b/recipes/gromacs/2019/meta.yaml index 26c4513bab3f1..4a75d660c33f0 100644 --- a/recipes/gromacs/2019/meta.yaml +++ b/recipes/gromacs/2019/meta.yaml @@ -11,7 +11,8 @@ package: version: {{ version }} build: - number: 2 + number: 3 + skip: True # [osx] source: url: http://ftp.gromacs.org/pub/gromacs/gromacs-{{ version }}.tar.gz diff --git a/recipes/groopm/meta.yaml b/recipes/groopm/meta.yaml index e58318fe690c9..b194a633838dd 100644 --- a/recipes/groopm/meta.yaml +++ b/recipes/groopm/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " requirements: diff --git a/recipes/gtf_to_genes/meta.yaml b/recipes/gtf_to_genes/meta.yaml index 8c3cfedb41e99..50616f9ecfab2 100644 --- a/recipes/gtf_to_genes/meta.yaml +++ b/recipes/gtf_to_genes/meta.yaml @@ -9,7 +9,7 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 1 + number: 2 requirements: host: diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 0d87fffb66aa3..3190061e51d7b 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [py27] source: diff --git a/recipes/hclust2/meta.yaml b/recipes/hclust2/meta.yaml index 9b8a4d0b52753..6809470218b35 100644 --- a/recipes/hclust2/meta.yaml +++ b/recipes/hclust2/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/hg-color/build.sh b/recipes/hg-color/build.sh index f28921b3bbd12..83d353dc32e7a 100644 --- a/recipes/hg-color/build.sh +++ b/recipes/hg-color/build.sh @@ -16,7 +16,7 @@ sed -i.bak 's|PgSAgen|PgSAgen_hgcolor|' HG-CoLoR sed -i.bak 's|#!/usr/bin/python|#!/usr/bin/env python|' bin/*.py # compilation -make PGSA_PATH=${PWD}/PgSA-0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b/ +make PGSA_PATH=${PWD}/PgSA-0d7c97f22a07fce96e0638deb09d2a8c05ed3d8b/ CC=$CC CXX=$CXX # copy binaries cp bin/* ${PREFIX}/bin diff --git a/recipes/hg-color/meta.yaml b/recipes/hg-color/meta.yaml index 57bbb648855e9..7d87c8878e974 100644 --- a/recipes/hg-color/meta.yaml +++ b/recipes/hg-color/meta.yaml @@ -7,12 +7,13 @@ source: md5: 1d8bda305c799bc2a3e414f8c5463e0b build: - number: 3 + number: 4 skip: True # [osx] requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - wget - unzip @@ -24,7 +25,7 @@ requirements: - kmc - quorum - pgsa - - python >2.6 + - python test: commands: diff --git a/recipes/hgtools/meta.yaml b/recipes/hgtools/meta.yaml index d65002178afb6..2f2561497da03 100644 --- a/recipes/hgtools/meta.yaml +++ b/recipes/hgtools/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 2f6646dd15572692c6dcf821b806b24c6f753b954bb46307b6acdefc69e5eedf build: - number: 0 + number: 1 noarch: python preserve_egg_dir: True script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/hicbrowser/meta.yaml b/recipes/hicbrowser/meta.yaml index ab97448db1f43..9317cf00c23e9 100644 --- a/recipes/hicbrowser/meta.yaml +++ b/recipes/hicbrowser/meta.yaml @@ -8,13 +8,13 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python <3 - - setuptools + - pip run: - python <3 - flask >=0.10.1 diff --git a/recipes/hichipper/meta.yaml b/recipes/hichipper/meta.yaml index ecd70c6a7a245..25339513dd960 100644 --- a/recipes/hichipper/meta.yaml +++ b/recipes/hichipper/meta.yaml @@ -11,7 +11,7 @@ source: build: entry_points: - hichipper = hichipper.cli:main - number: 0 + number: 1 noarch: python requirements: diff --git a/recipes/hlaprofiler/meta.yaml b/recipes/hlaprofiler/meta.yaml index 9fb52cdb8e9a6..1e680f7965528 100644 --- a/recipes/hlaprofiler/meta.yaml +++ b/recipes/hlaprofiler/meta.yaml @@ -7,7 +7,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/hmmer/meta.yaml b/recipes/hmmer/meta.yaml index 9b24a05e73c5e..3bf158647c0cc 100644 --- a/recipes/hmmer/meta.yaml +++ b/recipes/hmmer/meta.yaml @@ -7,7 +7,7 @@ source: sha256: a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/hotspot3d/meta.yaml b/recipes/hotspot3d/meta.yaml index 01a11f9f49f19..e5537ac97734d 100644 --- a/recipes/hotspot3d/meta.yaml +++ b/recipes/hotspot3d/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/hubward-all/meta.yaml b/recipes/hubward-all/meta.yaml index 757170b470095..f06b48f62526e 100644 --- a/recipes/hubward-all/meta.yaml +++ b/recipes/hubward-all/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.2.1" build: noarch: generic - number: 1 + number: 2 requirements: run: - hubward diff --git a/recipes/humann2/meta.yaml b/recipes/humann2/meta.yaml index 4cc48069c4f3e..5595813518aec 100644 --- a/recipes/humann2/meta.yaml +++ b/recipes/humann2/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - humann2 = humann2.humann2:main diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index e30ab442aff89..f01504eef8b79 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/ibdne/meta.yaml b/recipes/ibdne/meta.yaml index 63f134e00f0cf..32804f225d215 100644 --- a/recipes/ibdne/meta.yaml +++ b/recipes/ibdne/meta.yaml @@ -9,7 +9,7 @@ source: build: noarch: generic detect_binary_files_with_prefix: True - number: 1 + number: 2 requirements: run: diff --git a/recipes/ibdseq/meta.yaml b/recipes/ibdseq/meta.yaml index 2944eb171c27b..34361c9afa38f 100644 --- a/recipes/ibdseq/meta.yaml +++ b/recipes/ibdseq/meta.yaml @@ -9,7 +9,7 @@ source: build: noarch: generic detect_binary_files_with_prefix: True - number: 1 + number: 2 requirements: run: diff --git a/recipes/iclipro/meta.yaml b/recipes/iclipro/meta.yaml index 6c80693044a27..d707d0cbda53b 100644 --- a/recipes/iclipro/meta.yaml +++ b/recipes/iclipro/meta.yaml @@ -10,13 +10,15 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - python <3 - pip + - pysam + - matplotlib run: - python <3 - pysam diff --git a/recipes/icount/meta.yaml b/recipes/icount/meta.yaml index f25ce77ca336d..af8e69c17b495 100644 --- a/recipes/icount/meta.yaml +++ b/recipes/icount/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - iCount = iCount.cli:main script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/idr-py/meta.yaml b/recipes/idr-py/meta.yaml index f4d3e13ea54d3..9e4e72bd77876 100644 --- a/recipes/idr-py/meta.yaml +++ b/recipes/idr-py/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/idr/2.0.3/meta.yaml b/recipes/idr/2.0.3/meta.yaml deleted file mode 100644 index 0b12f8b1d47f0..0000000000000 --- a/recipes/idr/2.0.3/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -package: - name: idr - version: 2.0.3 - -source: - url: https://github.com/nboley/idr/archive/2.0.3.tar.gz - md5: 1bec61b526bb1dcf92a5ab99c27852d0 - -build: - noarch: python - number: 5 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - -requirements: - host: - - python >=3 - - pip - run: - - python >=3 - - numpy - - matplotlib - - scipy - -test: - commands: - - idr -h > /dev/null - -about: - home: https://github.com/nboley/idr - summary: The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. - license: GPLv2 diff --git a/recipes/idr/meta.yaml b/recipes/idr/meta.yaml index e3b32d9411710..520860d76d1ac 100644 --- a/recipes/idr/meta.yaml +++ b/recipes/idr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py2k] requirements: diff --git a/recipes/ig-checkflowtypes/meta.yaml b/recipes/ig-checkflowtypes/meta.yaml index 93b9c0d08d1f8..17e2c5f9b913b 100644 --- a/recipes/ig-checkflowtypes/meta.yaml +++ b/recipes/ig-checkflowtypes/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0.0" build: - number: 2 + number: 3 source: md5: a1af73503d5e5c56e2f9eb7037fc1b2b diff --git a/recipes/igblast/1.4.0/build.sh b/recipes/igblast/1.4.0/build.sh deleted file mode 100644 index 5e4ab4b43649e..0000000000000 --- a/recipes/igblast/1.4.0/build.sh +++ /dev/null @@ -1,34 +0,0 @@ -#!/bin/bash - -IGBLAST_ADDRESS=ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release -SHARE_DIR=$PREFIX/share/igblast - -wget $IGBLAST_ADDRESS/edit_imgt_file.pl -# replace the first line with /usr/bin/env perl instead of the hard-coded /opt -# does this require an explicit perl dependency? -sed -i.backup '1 s/^.*$/#!\/usr\/bin\/env perl/g' edit_imgt_file.pl -chmod +x edit_imgt_file.pl -mv edit_imgt_file.pl bin/ - -mkdir -p $PREFIX/bin -mkdir -p $SHARE_DIR/bin - -for FILE in makeblastdb edit_imgt_file.pl; do - cp -f bin/$FILE $PREFIX/bin/ -done - -for FILE in igblastn igblastp; do - cp -f bin/$FILE $SHARE_DIR/bin/ -done - -cp -f $RECIPE_DIR/igblastn.sh $PREFIX/bin/igblastn -sed 's/igblastn/igblastp/g' $PREFIX/bin/igblastn > $PREFIX/bin/igblastp -chmod +x $PREFIX/bin/igblastn $PREFIX/bin/igblastp - -for IGBLAST_DIR in internal_data optional_file; do - mkdir -p $SHARE_DIR/$IGBLAST_DIR - wget -r -nH --cut-dirs=5 -P $SHARE_DIR/$IGBLAST_DIR $IGBLAST_ADDRESS/$IGBLAST_DIR - for CVS_FILE in Entries Repository Root; do - rm -f $SHARE_DIR/$IGBLAST_DIR/$CVS_FILE - done -done diff --git a/recipes/igblast/1.4.0/igblastn.sh b/recipes/igblast/1.4.0/igblastn.sh deleted file mode 100644 index 5aa26b8bffbcd..0000000000000 --- a/recipes/igblast/1.4.0/igblastn.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -# from http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in -SOURCE="${BASH_SOURCE[0]}" -while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink - DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located -done - -SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" -IGBLAST_DIR=$SCRIPT_DIR/../share/igblast - -export IGDATA=$IGBLAST_DIR -$IGBLAST_DIR/bin/igblastn "$@" -unset IGDATA \ No newline at end of file diff --git a/recipes/igblast/1.4.0/meta.yaml b/recipes/igblast/1.4.0/meta.yaml deleted file mode 100644 index d849a6d65c8cf..0000000000000 --- a/recipes/igblast/1.4.0/meta.yaml +++ /dev/null @@ -1,22 +0,0 @@ -package: - name: igblast - version: "1.4.0" -source: - url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.4.0/ncbi-igblast-1.4.0-x64-linux.tar.gz # [not osx] - url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.4.0/ncbi-igblast-1.4.0-universal-macosx.tar.gz # [osx] -about: - home: http://www.ncbi.nlm.nih.gov/projects/igblast/ - license: Public Domain - summary: A tool for analyzing immunoglobulin (IG) and T cell receptor (TR) sequences. -build: - number: 7 -requirements: - run: - - perl >=5.8.8 -test: - commands: - - igblastn -h - -extra: - identifiers: - - biotools:igblast diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index 316d947300b3e..b3df386b88a85 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python script: "{{ PYTHON }} -m pip install . --no-deps -vv" - number: 0 + number: 1 entry_points: - create_report=igv_reports.report:main - create_datauri=igv_reports.datauri:main diff --git a/recipes/illumina-cleanup/meta.yaml b/recipes/illumina-cleanup/meta.yaml index cc08aab2f1b89..fc64ab732982d 100644 --- a/recipes/illumina-cleanup/meta.yaml +++ b/recipes/illumina-cleanup/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/illumiprocessor/build.sh b/recipes/illumiprocessor/build.sh deleted file mode 100644 index 04547dc83fe20..0000000000000 --- a/recipes/illumiprocessor/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/illumiprocessor/meta.yaml b/recipes/illumiprocessor/meta.yaml index bd62b9105f91a..6f24124ad6572 100644 --- a/recipes/illumiprocessor/meta.yaml +++ b/recipes/illumiprocessor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 81a70360e43622d7ec73068d5d0fe79f7c82d7a8c50099b07e703431f220b1fd build: - number: 1 + number: 2 noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/insilicoseq/meta.yaml b/recipes/insilicoseq/meta.yaml index be08df2d957e3..14ef667156461 100644 --- a/recipes/insilicoseq/meta.yaml +++ b/recipes/insilicoseq/meta.yaml @@ -14,7 +14,7 @@ build: entry_points: - iss = iss.app:main script: python -m pip install --no-deps --ignore-installed . - number: 0 + number: 1 requirements: host: diff --git a/recipes/irida-linker/build.sh b/recipes/irida-linker/build.sh index 4ecb24a0808b1..3f6b9667cdafc 100644 --- a/recipes/irida-linker/build.sh +++ b/recipes/irida-linker/build.sh @@ -1,4 +1,4 @@ #!/bin/bash - +mkdir -p ${PREFIX}/bin cp ngsArchiveLinker.pl $PREFIX/bin diff --git a/recipes/irida-linker/meta.yaml b/recipes/irida-linker/meta.yaml index d18e11bf34814..f1441cd66e23a 100644 --- a/recipes/irida-linker/meta.yaml +++ b/recipes/irida-linker/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/irida-sistr-results/meta.yaml b/recipes/irida-sistr-results/meta.yaml index 67c0138c9b16f..357d7fe33e261 100644 --- a/recipes/irida-sistr-results/meta.yaml +++ b/recipes/irida-sistr-results/meta.yaml @@ -12,7 +12,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/isatools/meta.yaml b/recipes/isatools/meta.yaml index c97941c9976a8..4090d89a7b56b 100644 --- a/recipes/isatools/meta.yaml +++ b/recipes/isatools/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: python -m pip install --no-deps --ignore-installed . entry_points: - isatools = isatools:main diff --git a/recipes/isescan/build.sh b/recipes/isescan/build.sh index 84206f0394d52..332e8b601d7ed 100755 --- a/recipes/isescan/build.sh +++ b/recipes/isescan/build.sh @@ -1,4 +1,7 @@ #!/bin/bash +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/lib +mkdir -p ${PREFIX}/test # compiles and moves libssw to conda env cd ssw201507 @@ -13,5 +16,4 @@ cp *.py ${PREFIX}/bin/ cp -r pHMMs/ $PREFIX/bin/ # adds test fasta for build testing -mkdir $PREFIX/test cp NC_012624.fna $PREFIX/test/ diff --git a/recipes/islandpath/meta.yaml b/recipes/islandpath/meta.yaml index 424ca7200fdd9..5702a01562d3e 100644 --- a/recipes/islandpath/meta.yaml +++ b/recipes/islandpath/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/ispcr/meta.yaml b/recipes/ispcr/meta.yaml index 51df96c6f359a..0c4f2170a5c2b 100644 --- a/recipes/ispcr/meta.yaml +++ b/recipes/ispcr/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-remove-Werror.patch build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/itero/meta.yaml b/recipes/itero/meta.yaml index b29e67a0b7c01..5d377b6ab59d0 100644 --- a/recipes/itero/meta.yaml +++ b/recipes/itero/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/itsx/meta.yaml b/recipes/itsx/meta.yaml index adc5acd7708a1..f3456bb802afa 100644 --- a/recipes/itsx/meta.yaml +++ b/recipes/itsx/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: build: diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml index d744aa6cae612..022363b4c02a1 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - itsxpress=itsxpress.main:main script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/iva/meta.yaml b/recipes/iva/meta.yaml index 227a9398ca4fa..396f0354b0788 100644 --- a/recipes/iva/meta.yaml +++ b/recipes/iva/meta.yaml @@ -10,13 +10,20 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python >=3 - pip + - pyfastaq >=3.10.0 + - networkx >=1.7 + - pysam >=0.8.1 + - kmc + - smalt + - mummer + - samtools run: - python >=3 - pyfastaq >=3.10.0 diff --git a/recipes/ivar/meta.yaml b/recipes/ivar/meta.yaml index be31a9eb734c8..dfa235fcaf7c3 100644 --- a/recipes/ivar/meta.yaml +++ b/recipes/ivar/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/jaffa/build.sh b/recipes/jaffa/build.sh index 1f86aec3d1fcc..15a03ef330fd9 100644 --- a/recipes/jaffa/build.sh +++ b/recipes/jaffa/build.sh @@ -6,6 +6,7 @@ PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM # Create destination directories mkdir -p $PACKAGE_HOME +mkdir -p ${PREFIX}/bin # Copy files over into $PACKAGE_HOME cp -aR * $PACKAGE_HOME diff --git a/recipes/jaffa/meta.yaml b/recipes/jaffa/meta.yaml index 9ee96bb62496b..ff9f1f682e604 100644 --- a/recipes/jaffa/meta.yaml +++ b/recipes/jaffa/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/jamm/1.0.7.2/build.sh b/recipes/jamm/1.0.7.2/build.sh deleted file mode 100644 index 8aa00d302525a..0000000000000 --- a/recipes/jamm/1.0.7.2/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -mkdir -p ${PREFIX}/bin -chmod +x *.sh -cp {*.sh,*.pl,*.r} ${PREFIX}/bin diff --git a/recipes/jamm/1.0.7.2/meta.yaml b/recipes/jamm/1.0.7.2/meta.yaml deleted file mode 100644 index 08de759c4ade5..0000000000000 --- a/recipes/jamm/1.0.7.2/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -package: - name: jamm - version: 1.0.7.2 - -source: - url: https://github.com/mahmoudibrahim/JAMM/archive/v1.0.7.2.zip - md5: 0902ea81e0559a8804c49dd7b1f02efd - patches: - - setpath.patch - -build: - noarch: generic - number: 3 - -requirements: - - run: - - r-base - - perl - - r-signal - - r-mclust >=4 - -test: - - commands: - - JAMM.sh | grep JAMM > /dev/null - - SignalGenerator.sh | grep JAMM > /dev/null - -about: - home: https://github.com/mahmoudibrahim/JAMM - license: GPL - license_file: LICENSE - summary: JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. diff --git a/recipes/jamm/1.0.7.2/setpath.patch b/recipes/jamm/1.0.7.2/setpath.patch deleted file mode 100644 index fc6cb96a5c9d2..0000000000000 --- a/recipes/jamm/1.0.7.2/setpath.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- JAMM.sh 2015-08-04 07:05:25.000000000 +0000 -+++ JAMM.sh.new 2015-12-14 18:00:49.468599990 +0000 -@@ -20,8 +20,7 @@ - - - ##Finding out the path --sPath="`dirname \"$0\"`" --sPath="`( cd \"$sPath\" && pwd )`" -+sPath=/opt/anaconda1anaconda2anaconda3/bin - - - diff --git a/recipes/jvarkit-bam2svg/meta.yaml b/recipes/jvarkit-bam2svg/meta.yaml index e75fe804e41ba..52876dfb27ab6 100644 --- a/recipes/jvarkit-bam2svg/meta.yaml +++ b/recipes/jvarkit-bam2svg/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/jvarkit-bam2wig/meta.yaml b/recipes/jvarkit-bam2wig/meta.yaml index 3384667fe9087..9e76eba785bf0 100644 --- a/recipes/jvarkit-bam2wig/meta.yaml +++ b/recipes/jvarkit-bam2wig/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/kipoi/meta.yaml b/recipes/kipoi/meta.yaml index 033ee84c5c126..9afa25113bdb5 100644 --- a/recipes/kipoi/meta.yaml +++ b/recipes/kipoi/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 noarch: python entry_points: - kipoi = kipoi.__main__:main diff --git a/recipes/kipoiseq/meta.yaml b/recipes/kipoiseq/meta.yaml index 891fc78f23b3a..6fc0192aa2795 100644 --- a/recipes/kipoiseq/meta.yaml +++ b/recipes/kipoiseq/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "9e1c5233f6456d7df87f27bd54520359379ff9b325341cc574f593280ea5853b" build: - number: 0 + number: 1 script: python setup.py install --single-version-externally-managed --record=record.txt noarch: python diff --git a/recipes/kiwidist/meta.yaml b/recipes/kiwidist/meta.yaml index 777e9d0c5d680..0a28bc5febecb 100644 --- a/recipes/kiwidist/meta.yaml +++ b/recipes/kiwidist/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/kmc/3.0.0_static/meta.yaml b/recipes/kmc/3.0.0_static/meta.yaml index d3854c88e5f33..03cea27c19863 100644 --- a/recipes/kmc/3.0.0_static/meta.yaml +++ b/recipes/kmc/3.0.0_static/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d2ffb2e7ee69199e9b3464ea2afb27df731120babaee1ea65b94a3bc059d0a55 # [osx] build: - number: 1 + number: 2 script: "chmod u+x kmc kmc_tools kmc_dump; mkdir -p ${PREFIX}/bin; cp kmc kmc_tools kmc_dump ${PREFIX}/bin" requirements: diff --git a/recipes/kmc/meta.yaml b/recipes/kmc/meta.yaml index 6800af5afe0d8..da3a5d41970cb 100644 --- a/recipes/kmc/meta.yaml +++ b/recipes/kmc/meta.yaml @@ -13,7 +13,7 @@ source: - shared_library.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/kmer-jellyfish/meta.yaml b/recipes/kmer-jellyfish/meta.yaml index 5358175683d02..f70b48393e7c8 100644 --- a/recipes/kmer-jellyfish/meta.yaml +++ b/recipes/kmer-jellyfish/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/gmarcais/Jellyfish/releases/download/v{{ version }}/jellyfish-{{ version }}.tar.gz diff --git a/recipes/kobas/meta.yaml b/recipes/kobas/meta.yaml index 254bfb66f0472..7830bf2ed20c7 100644 --- a/recipes/kobas/meta.yaml +++ b/recipes/kobas/meta.yaml @@ -5,7 +5,7 @@ package: build: noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 1 + number: 2 source: url: http://kobas.cbi.pku.edu.cn/kobas-2.1.1/kobas-3.0.3.tar.gz diff --git a/recipes/kpal/meta.yaml b/recipes/kpal/meta.yaml index c9d0d1e5c5317..a43b5936f5483 100644 --- a/recipes/kpal/meta.yaml +++ b/recipes/kpal/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: python - number: 1 + number: 2 script: python -m pip install --no-deps --ignore-installed . requirements: diff --git a/recipes/kraken/meta.yaml b/recipes/kraken/meta.yaml index 75c318d7811aa..dd12394cec95c 100644 --- a/recipes/kraken/meta.yaml +++ b/recipes/kraken/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 has_prefix_files: - libexec/kraken - libexec/kraken-build diff --git a/recipes/krakenuniq/meta.yaml b/recipes/krakenuniq/meta.yaml index 0987f68868c41..4fc63242bc4f7 100644 --- a/recipes/krakenuniq/meta.yaml +++ b/recipes/krakenuniq/meta.yaml @@ -12,7 +12,8 @@ source: - krakenuniq.patch build: - number: 1 + number: 2 + skip: True # [osx] requirements: build: diff --git a/recipes/krocus/meta.yaml b/recipes/krocus/meta.yaml index 61a85b92847ca..9bf6d0dcfcaec 100644 --- a/recipes/krocus/meta.yaml +++ b/recipes/krocus/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/krona/meta.yaml b/recipes/krona/meta.yaml index 7ea9bf93c558d..f5d4881f1ee5b 100644 --- a/recipes/krona/meta.yaml +++ b/recipes/krona/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/kronos/meta.yaml b/recipes/kronos/meta.yaml index 19845ea53e1fa..9a0eda1cf54c7 100644 --- a/recipes/kronos/meta.yaml +++ b/recipes/kronos/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" entry_points: - kronos = kronos:main diff --git a/recipes/last/874/build.sh b/recipes/last/874/build.sh index fd9dadd53acd8..bdf3b8663bd34 100644 --- a/recipes/last/874/build.sh +++ b/recipes/last/874/build.sh @@ -23,6 +23,7 @@ last-map-probs \ last-dotplot \ " +mkdir -p $PREFIX/bin for i in $scripts; do cp $SRC_DIR/scripts/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done chmod +x $SRC_DIR/build/* @@ -30,6 +31,5 @@ pushd src make CXX="$CXX" CXXFLAGS="${CXXFLAGS}" CFLAGS="${CFLAGS}" LDFLAGS="-L${PREFIX}/lib -lz" popd -mkdir -p $PREFIX/bin for i in $binaries; do cp $SRC_DIR/src/$i $PREFIX/bin && chmod +x $PREFIX/bin/$i; done make install prefix=$PREFIX # to install scripts, primarily diff --git a/recipes/last/874/meta.yaml b/recipes/last/874/meta.yaml index 2600ae40eb6d9..c3ad2b5560a17 100644 --- a/recipes/last/874/meta.yaml +++ b/recipes/last/874/meta.yaml @@ -9,7 +9,7 @@ source: - maf-convert.23patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/latentstrainanalysis/build.sh b/recipes/latentstrainanalysis/build.sh index b58363764d4ed..826388ccd133b 100644 --- a/recipes/latentstrainanalysis/build.sh +++ b/recipes/latentstrainanalysis/build.sh @@ -6,6 +6,7 @@ rm $LSA_DIR/testData.tar.gz chmod +x $LSA_DIR/*.sh +mkdir -p ${PREFIX}/bin ln -fs $LSA_DIR/KmerSVDClustering.sh $PREFIX/bin/ ln -fs $LSA_DIR/ReadPartitioning.sh $PREFIX/bin/ ln -fs $LSA_DIR/HashCounting.sh $PREFIX/bin/ diff --git a/recipes/latentstrainanalysis/meta.yaml b/recipes/latentstrainanalysis/meta.yaml index cd328b9e7eb73..8b5587342d391 100644 --- a/recipes/latentstrainanalysis/meta.yaml +++ b/recipes/latentstrainanalysis/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/lofreq/2.1.2/meta.yaml b/recipes/lofreq/2.1.2/meta.yaml index 18da5bca5f65b..f35e59a9908e0 100644 --- a/recipes/lofreq/2.1.2/meta.yaml +++ b/recipes/lofreq/2.1.2/meta.yaml @@ -9,7 +9,7 @@ source: md5: d688ba34a4161d9690e264648aae2def # [osx] build: - number: 1 + number: 2 script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" # [osx] skip: True # [not py27] diff --git a/recipes/lohhla/build.sh b/recipes/lohhla/build.sh index a659f6d41cb41..8930a26f18515 100644 --- a/recipes/lohhla/build.sh +++ b/recipes/lohhla/build.sh @@ -2,6 +2,7 @@ target=$PREFIX/bin/lohhla +mkdir -p ${PREFIX}/bin echo "#!/usr/bin/env Rscript" > $target cat LOHHLAscript.R >> $target chmod +x $target diff --git a/recipes/lohhla/meta.yaml b/recipes/lohhla/meta.yaml index 6b1456f19099c..9e3b9a4c14b6f 100644 --- a/recipes/lohhla/meta.yaml +++ b/recipes/lohhla/meta.yaml @@ -6,7 +6,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://bitbucket.org/mcgranahanlab/lohhla/get/e4c7d5e14c39.zip @@ -37,3 +37,5 @@ about: extra: notes: The tool is available as command `lohhla`. + container: + extended-base: true diff --git a/recipes/lsd/meta.yaml b/recipes/lsd/meta.yaml index e717c830ed4c9..e5237f798675b 100644 --- a/recipes/lsd/meta.yaml +++ b/recipes/lsd/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/lumpy-sv/build.sh b/recipes/lumpy-sv/build.sh index c489e7a4a45d9..c8865f9e1b77c 100644 --- a/recipes/lumpy-sv/build.sh +++ b/recipes/lumpy-sv/build.sh @@ -13,6 +13,10 @@ mkdir -p $outdir mkdir -p $outdir/scripts mkdir -p $PREFIX/bin +pushd src/utils/sqlite3 +sed -i.bak "s#@gcc#${CC}#g" Makefile +popd + make \ CC="${CC}" \ CXX="${CXX}" \ diff --git a/recipes/lumpy-sv/meta.yaml b/recipes/lumpy-sv/meta.yaml index 154a9fadc93d1..58c21d60028e2 100644 --- a/recipes/lumpy-sv/meta.yaml +++ b/recipes/lumpy-sv/meta.yaml @@ -9,7 +9,7 @@ source: - patch build: - number: 2 + number: 3 skip: True # [osx] requirements: @@ -19,6 +19,9 @@ requirements: - cmake host: - htslib + - sambamba #lumpy-express dependency + - samblaster #lumpy-express dependency + - samtools run: - htslib - python 2.7.* diff --git a/recipes/mafft/7.310/meta.yaml b/recipes/mafft/7.310/meta.yaml index 5d6592e8d05a7..ca3b53828c564 100644 --- a/recipes/mafft/7.310/meta.yaml +++ b/recipes/mafft/7.310/meta.yaml @@ -10,7 +10,7 @@ source: - linux-makefile.patch # [linux] build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/mageck-vispr/meta.yaml b/recipes/mageck-vispr/meta.yaml index b7db4ae43e5a5..9219319c82213 100644 --- a/recipes/mageck-vispr/meta.yaml +++ b/recipes/mageck-vispr/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - mageck-vispr = mageck_vispr.cli:main diff --git a/recipes/magpurify/build.sh b/recipes/magpurify/build.sh index 981c2a71e71b3..cca8bc2f9cbe5 100644 --- a/recipes/magpurify/build.sh +++ b/recipes/magpurify/build.sh @@ -1,8 +1,4 @@ #!/usr/bin/env bash - - - - # install DESTDIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $DESTDIR @@ -10,6 +6,7 @@ cp run_qc.py $DESTDIR cp -r magpurify $DESTDIR chmod +x $DESTDIR/run_qc.py +mkdir -p ${PREFIX}/bin ln -s $DESTDIR/run_qc.py $PREFIX/bin/ ln -s $DESTDIR/run_qc.py $PREFIX/bin/MAGpurify #alias diff --git a/recipes/magpurify/meta.yaml b/recipes/magpurify/meta.yaml index 55fbb1128a05e..71ffb48c6a58a 100644 --- a/recipes/magpurify/meta.yaml +++ b/recipes/magpurify/meta.yaml @@ -12,8 +12,7 @@ source: build: noarch: generic - number: 1 - + number: 2 requirements: run: diff --git a/recipes/makehub/meta.yaml b/recipes/makehub/meta.yaml index 21fa6dc08ac4f..b45845af6f0c2 100644 --- a/recipes/makehub/meta.yaml +++ b/recipes/makehub/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic script: "mkdir -p ${PREFIX}/bin; chmod +x make_hub.py; cp make_hub.py ${PREFIX}/bin/" diff --git a/recipes/maker/meta.yaml b/recipes/maker/meta.yaml index 42bf9977d1883..0ee5eb3c60f5e 100644 --- a/recipes/maker/meta.yaml +++ b/recipes/maker/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: generic - number: 15 + number: 16 requirements: host: diff --git a/recipes/malva/meta.yaml b/recipes/malva/meta.yaml index 949029d137344..fb4f896c780e3 100644 --- a/recipes/malva/meta.yaml +++ b/recipes/malva/meta.yaml @@ -14,7 +14,7 @@ source: - malva.src.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/mamotif/meta.yaml b/recipes/mamotif/meta.yaml index 87fd54db26b28..3ed249854b2f4 100644 --- a/recipes/mamotif/meta.yaml +++ b/recipes/mamotif/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/manorm/build.sh b/recipes/manorm/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/manorm/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/manorm/meta.yaml b/recipes/manorm/meta.yaml index 31257acd58f1c..298848c135494 100644 --- a/recipes/manorm/meta.yaml +++ b/recipes/manorm/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 17504e57cff9d913ba0e3a0f57f1741d72aef5167055d46c83ad78e09ed7f638 build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: diff --git a/recipes/mantis/meta.yaml b/recipes/mantis/meta.yaml index 99195ffabd731..edf04ce708341 100644 --- a/recipes/mantis/meta.yaml +++ b/recipes/mantis/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Static-libc.patch build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/marge/meta.yaml b/recipes/marge/meta.yaml index b59cb681f9b92..92f9b72641ba2 100644 --- a/recipes/marge/meta.yaml +++ b/recipes/marge/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 1 + number: 2 script: python -m pip install --no-deps --ignore-installed . requirements: diff --git a/recipes/mash/meta.yaml b/recipes/mash/meta.yaml index cd950713731ec..37bb4e4d80b06 100644 --- a/recipes/mash/meta.yaml +++ b/recipes/mash/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/mashtree/meta.yaml b/recipes/mashtree/meta.yaml index 84879f4bfbb3e..500193c832230 100644 --- a/recipes/mashtree/meta.yaml +++ b/recipes/mashtree/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/maskrc-svg/build.sh b/recipes/maskrc-svg/build.sh index e764f532b510d..3e966463bf222 100644 --- a/recipes/maskrc-svg/build.sh +++ b/recipes/maskrc-svg/build.sh @@ -1,4 +1,5 @@ #!/bin/bash +mkdir -p ${PREFIX}/bin cp maskrc-svg.py $PREFIX/bin chmod +x $PREFIX/bin/maskrc-svg.py diff --git a/recipes/maskrc-svg/meta.yaml b/recipes/maskrc-svg/meta.yaml index c026e1d7a2ba7..17f1d2671683c 100644 --- a/recipes/maskrc-svg/meta.yaml +++ b/recipes/maskrc-svg/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python requirements: diff --git a/recipes/mauve/meta.yaml b/recipes/mauve/meta.yaml index 1c3f1110018c1..757f2fa212cb7 100644 --- a/recipes/mauve/meta.yaml +++ b/recipes/mauve/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: generic - number: 0 + number: 1 source: url: https://depot.galaxyproject.org/software/mauve/mauve_2.4.0-snapshot_2015_02_13_linux_all.tar.gz diff --git a/recipes/maxentscan/meta.yaml b/recipes/maxentscan/meta.yaml index 9b0be9f850e3f..bd1aea2af8bab 100644 --- a/recipes/maxentscan/meta.yaml +++ b/recipes/maxentscan/meta.yaml @@ -7,9 +7,9 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: - build: + host: - perl run: - perl diff --git a/recipes/maxquant/meta.yaml b/recipes/maxquant/meta.yaml index 1564008c2dc24..4185464f73422 100644 --- a/recipes/maxquant/meta.yaml +++ b/recipes/maxquant/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 script: - cp -r * $PREFIX - cp $RECIPE_DIR/maxquant $PREFIX/bin/maxquant diff --git a/recipes/mcl/meta.yaml b/recipes/mcl/meta.yaml index fae09bdcae6d6..b65c4e7f77576 100644 --- a/recipes/mcl/meta.yaml +++ b/recipes/mcl/meta.yaml @@ -3,7 +3,7 @@ package: version: "14.137" build: - number: 4 + number: 5 source: url: http://micans.org/mcl/src/mcl-14-137.tar.gz diff --git a/recipes/medusa-data-fusion/meta.yaml b/recipes/medusa-data-fusion/meta.yaml index 044f385bfe9e6..27937697e3e08 100644 --- a/recipes/medusa-data-fusion/meta.yaml +++ b/recipes/medusa-data-fusion/meta.yaml @@ -8,13 +8,15 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python <3 - pip + - numpy + - scipy run: - python <3 - numpy diff --git a/recipes/meme/4.11.1/meta.yaml b/recipes/meme/4.11.1/meta.yaml index f419c2768538d..dab07a8c92230 100644 --- a/recipes/meme/4.11.1/meta.yaml +++ b/recipes/meme/4.11.1/meta.yaml @@ -9,7 +9,7 @@ source: - mast.patch build: - number: 5 + number: 6 skip: True # [osx or py3k] detect_binary_files_with_prefix: True diff --git a/recipes/meme/4.11.2/meta.yaml b/recipes/meme/4.11.2/meta.yaml index 17c1dd7e521ae..8480700fb1688 100644 --- a/recipes/meme/4.11.2/meta.yaml +++ b/recipes/meme/4.11.2/meta.yaml @@ -9,7 +9,7 @@ source: - mast.patch build: - number: 2 + number: 3 skip: True # [not py27] detect_binary_files_with_prefix: True diff --git a/recipes/meme/4.8.1/meta.yaml b/recipes/meme/4.8.1/meta.yaml index 14d9c524ad138..3d226c52de6b0 100644 --- a/recipes/meme/4.8.1/meta.yaml +++ b/recipes/meme/4.8.1/meta.yaml @@ -7,7 +7,7 @@ package: version: 4.8.1 build: - number: 1 + number: 2 skip: True # [osx or py3k] detect_binary_files_with_prefix: True diff --git a/recipes/menetools/meta.yaml b/recipes/menetools/meta.yaml index 6db208f49aff4..6dbf86e23b81d 100644 --- a/recipes/menetools/meta.yaml +++ b/recipes/menetools/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/mergevcf/meta.yaml b/recipes/mergevcf/meta.yaml index 48aefa736ebcd..4137001622814 100644 --- a/recipes/mergevcf/meta.yaml +++ b/recipes/mergevcf/meta.yaml @@ -8,7 +8,8 @@ source: build: noarch: python - number: 1 + number: 2 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/metameta/meta.yaml b/recipes/metameta/meta.yaml index 250a4951b5965..69571af3564b3 100644 --- a/recipes/metameta/meta.yaml +++ b/recipes/metameta/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/metametamerge/meta.yaml b/recipes/metametamerge/meta.yaml index 8ddb7afa8f76f..c745ccc8aef2c 100644 --- a/recipes/metametamerge/meta.yaml +++ b/recipes/metametamerge/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: python -m pip install --no-deps --ignore-installed . requirements: diff --git a/recipes/metaphlan2/2.7.7/build.sh b/recipes/metaphlan2/2.7.7/build.sh deleted file mode 100644 index 31ea1b414e642..0000000000000 --- a/recipes/metaphlan2/2.7.7/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - - -binaries="metaphlan2.py strainphlan.py" - -mkdir -p $PREFIX/bin - -for i in $binaries; do - cp $i $PREFIX/bin; -done - -cp -a utils/*.py $PREFIX/bin -cp -a strainphlan_src/*.py $PREFIX/bin diff --git a/recipes/metaphlan2/2.7.7/meta.yaml b/recipes/metaphlan2/2.7.7/meta.yaml deleted file mode 100644 index 0dafa0daea395..0000000000000 --- a/recipes/metaphlan2/2.7.7/meta.yaml +++ /dev/null @@ -1,59 +0,0 @@ -{% set name = "metaphlan2" %} -{% set version = "2.7.7" %} -{% set md5 = "1e6a09ac00193a97ccc341b106a3e24d" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://bitbucket.org/biobakery/metaphlan2/get/{{ version }}.tar.gz - md5: {{ md5 }} - -build: - noarch: generic - number: 4 - -requirements: - run: - - python <3 - - bowtie2 >=2.0.0 - - numpy - - biom-format - - msgpack-python - - biopython - - pandas - - pysam - # metaphlan_hclust_heatmap.py has issues when matplotlib >= 2.0.0: https://bitbucket.org/biobakery/metaphlan2/issues/18/axisbg-deprecated-in - - matplotlib <2.0.0 - - scipy - - requests - - blast >=2.6.0 - - dendropy >=3.12.3 - - muscle >=3.8.1551 - - pysam >=0.8.3 - - raxml >=8.2.10 - - samtools >=0.1.19,<1.0 - -test: - commands: - - metaphlan2.py -v - - strainphlan.py -h - - extract_markers.py -h - - merge_metaphlan_tables.py -h - - metaphlan2krona.py -h - - metaphlan_hclust_heatmap.py -h - - read_fastx.py -h - -about: - home: https://bitbucket.org/biobakery/metaphlan2 - license: MIT License - license_family: MIT - license_file: license.txt - summary: | - MetaPhlAn is a computational tool for profiling the composition of microbial - communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic - shotgun sequencing data with species level resolution. From version 2.0 - MetaPhlAn is also able to identify specific strains (in the not-so-frequent - cases in which the sample contains a previously sequenced strains) and to - track strains across samples for all species. diff --git a/recipes/metaphlan2/2.7.8/build.sh b/recipes/metaphlan2/2.7.8/build.sh deleted file mode 100644 index 31ea1b414e642..0000000000000 --- a/recipes/metaphlan2/2.7.8/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - - -binaries="metaphlan2.py strainphlan.py" - -mkdir -p $PREFIX/bin - -for i in $binaries; do - cp $i $PREFIX/bin; -done - -cp -a utils/*.py $PREFIX/bin -cp -a strainphlan_src/*.py $PREFIX/bin diff --git a/recipes/metaphlan2/2.7.8/meta.yaml b/recipes/metaphlan2/2.7.8/meta.yaml deleted file mode 100644 index 0de1d88622583..0000000000000 --- a/recipes/metaphlan2/2.7.8/meta.yaml +++ /dev/null @@ -1,60 +0,0 @@ -{% set name = "metaphlan2" %} -{% set version = "2.7.8" %} -{% set md5 = "caab51129cda6317667669d3768372fb" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://bitbucket.org/biobakery/metaphlan2/get/{{ version }}.tar.gz - md5: {{ md5 }} - -build: - noarch: generic - number: 0 - -requirements: - run: - - python <3 - - bowtie2 >=2.0.0 - - numpy - - biom-format - - msgpack-python - - biopython - - pandas - - pysam - # metaphlan_hclust_heatmap.py has issues when matplotlib >= 2.0.0: https://bitbucket.org/biobakery/metaphlan2/issues/18/axisbg-deprecated-in - # and with 1.5.3: "negative dimensions are not allowed" - - matplotlib =1.5.2 - - scipy - - requests - - blast >=2.6.0 - - dendropy >=3.12.3 - - muscle >=3.8.1551 - - pysam >=0.8.3 - - raxml >=8.2.10 - - samtools >=0.1.19,<1.0 - -test: - commands: - - metaphlan2.py -v - - strainphlan.py -h - - extract_markers.py -h - - merge_metaphlan_tables.py -h - - metaphlan2krona.py -h - - metaphlan_hclust_heatmap.py -h - - read_fastx.py -h - -about: - home: https://bitbucket.org/biobakery/metaphlan2 - license: MIT License - license_family: MIT - license_file: license.txt - summary: | - MetaPhlAn is a computational tool for profiling the composition of microbial - communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic - shotgun sequencing data with species level resolution. From version 2.0 - MetaPhlAn is also able to identify specific strains (in the not-so-frequent - cases in which the sample contains a previously sequenced strains) and to - track strains across samples for all species. diff --git a/recipes/metaquant/meta.yaml b/recipes/metaquant/meta.yaml index b85f26c9d0f6c..970481e8b9e33 100644 --- a/recipes/metaquant/meta.yaml +++ b/recipes/metaquant/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - metaquant=metaquant.__main__:main script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/metaseq-all/meta.yaml b/recipes/metaseq-all/meta.yaml index e742dcf6be0ff..23e24823767de 100644 --- a/recipes/metaseq-all/meta.yaml +++ b/recipes/metaseq-all/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/metavelvet-annois/meta.yaml b/recipes/metavelvet-annois/meta.yaml index 2d26d048beffa..8125c2df87469 100644 --- a/recipes/metavelvet-annois/meta.yaml +++ b/recipes/metavelvet-annois/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: host: diff --git a/recipes/metawatt/meta.yaml b/recipes/metawatt/meta.yaml index 779337b622330..4054094ddecfe 100644 --- a/recipes/metawatt/meta.yaml +++ b/recipes/metawatt/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: build: diff --git a/recipes/metawrap/meta.yaml b/recipes/metawrap/meta.yaml index 120321f5baec7..a5ad52821f2cb 100644 --- a/recipes/metawrap/meta.yaml +++ b/recipes/metawrap/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/metaxa/meta.yaml b/recipes/metaxa/meta.yaml index 935e588dd6349..53757080058f4 100644 --- a/recipes/metaxa/meta.yaml +++ b/recipes/metaxa/meta.yaml @@ -1,5 +1,4 @@ {% set version = "2.2" %} -{% set sha256 = "5fd4aca1263dedb9704f2d1fb05e969d6160b53469f502ba27389c94d40e1b95" %} package: name: metaxa @@ -7,13 +6,13 @@ package: source: url: http://microbiology.se/sw/Metaxa2_{{ version }}.tar.gz - sha256: {{ sha256 }} + sha256: 2f423c075301ed93c0eb79aa57a56eadd6b07396d250d06f6869a489a0c30468 patches: - "perl-shebang.patch" build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/metfrag/meta.yaml b/recipes/metfrag/meta.yaml index 76db759f0ba2f..0031792421e0a 100644 --- a/recipes/metfrag/meta.yaml +++ b/recipes/metfrag/meta.yaml @@ -4,11 +4,11 @@ package: source: url: http://msbi.ipb-halle.de/~cruttkie/metfrag/MetFrag2.4.5-CL.jar - sha256: 7d05cb5d7e72872b6ed13495811f1eb9155943ff9f8903cb4240c6f379731174 + sha256: 5595524f75c0705528e703d1e3f8657db4d4cc649dfd800e0739919982c21c06 build: noarch: generic - number: 3 + number: 4 requirements: run: diff --git a/recipes/methylextract/meta.yaml b/recipes/methylextract/meta.yaml index b41e98d132066..9a654feac5820 100644 --- a/recipes/methylextract/meta.yaml +++ b/recipes/methylextract/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: generic - number: 0 + number: 1 source: url: http://bioinfo2.ugr.es/MethylExtract/downloads/MethylExtract.tar.gz diff --git a/recipes/mhcflurry/meta.yaml b/recipes/mhcflurry/meta.yaml index dda1f4d3366e6..2e56070c134e7 100644 --- a/recipes/mhcflurry/meta.yaml +++ b/recipes/mhcflurry/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 469bab44f6fff5dc78dcc5b032b67917b36d68c6e71f6baadf42847ee203ca96 build: - number: 0 + number: 1 noarch: python entry_points: - mhcflurry-downloads = mhcflurry.downloads_command:run diff --git a/recipes/micropita/build.sh b/recipes/micropita/build.sh index ae5cbd1d666ad..7afd22d269bb3 100644 --- a/recipes/micropita/build.sh +++ b/recipes/micropita/build.sh @@ -1,6 +1,7 @@ #!/bin/bash chmod +x *.py +mkdir -p ${PREFIX}/bin cp *.py ${PREFIX}/bin/ cp -a src ${PREFIX}/bin/ diff --git a/recipes/micropita/meta.yaml b/recipes/micropita/meta.yaml index 2603e3bf292dc..b07c377ff18b0 100644 --- a/recipes/micropita/meta.yaml +++ b/recipes/micropita/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: @@ -39,3 +39,5 @@ extra: identifiers: - biotools:micropita - doi:10.1038/ismej.2013.139 + container: + extended-base: true diff --git a/recipes/midas/1.2.2/meta.yaml b/recipes/midas/1.2.2/meta.yaml index bb8801ac91fbe..8381c1f34e267 100644 --- a/recipes/midas/1.2.2/meta.yaml +++ b/recipes/midas/1.2.2/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/midas/meta.yaml b/recipes/midas/meta.yaml index 2741505d44128..ccda8b3232f00 100644 --- a/recipes/midas/meta.yaml +++ b/recipes/midas/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/migmap/meta.yaml b/recipes/migmap/meta.yaml index 625e3e2d1a57a..0d98c413627ab 100644 --- a/recipes/migmap/meta.yaml +++ b/recipes/migmap/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/mimeo/meta.yaml b/recipes/mimeo/meta.yaml index 448f1ce8cd28b..12bc24ed38e28 100644 --- a/recipes/mimeo/meta.yaml +++ b/recipes/mimeo/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - mimeo-self=mimeo.run_self:main diff --git a/recipes/minimap/build.sh b/recipes/minimap/build.sh index c6f71996f2d48..e9f90e7e29ccd 100644 --- a/recipes/minimap/build.sh +++ b/recipes/minimap/build.sh @@ -4,8 +4,8 @@ mkdir -p $PREFIX/bin export C_INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib -make -make extra +make CC=$CC CFLAGS="$CFLAGS" LIBS="-L${PREFIX}/lib -lm -lz -lpthread" LDFLAGS="$LDFLAGS" +make extra CC=$CC CFLAGS="$CFLAGS" LIBS="-L${PREFIX}/lib -lm -lz -lpthread" LDFLAGS="$LDFLAGS" cp minimap $PREFIX/bin cp minimap-lite $PREFIX/bin diff --git a/recipes/minimap/meta.yaml b/recipes/minimap/meta.yaml index cfb9555149d30..ab403c3d8ebc4 100644 --- a/recipes/minimap/meta.yaml +++ b/recipes/minimap/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.2_r124" build: - number: 1 + number: 2 source: url: https://github.com/lh3/minimap/archive/1cd6ae3bc7c7a6f9e7c03c0b7a93a12647bba244.tar.gz diff --git a/recipes/mintmap/meta.yaml b/recipes/mintmap/meta.yaml index b6d67b332aad5..d0d565a4ce46a 100644 --- a/recipes/mintmap/meta.yaml +++ b/recipes/mintmap/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/minvar/meta.yaml b/recipes/minvar/meta.yaml index 540b3e592cef4..47df80804b92b 100644 --- a/recipes/minvar/meta.yaml +++ b/recipes/minvar/meta.yaml @@ -6,7 +6,7 @@ package: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/mir-prefer/meta.yaml b/recipes/mir-prefer/meta.yaml index 62ed5cdb2decb..e9ef48786fb9b 100644 --- a/recipes/mir-prefer/meta.yaml +++ b/recipes/mir-prefer/meta.yaml @@ -17,7 +17,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/mirge/meta.yaml b/recipes/mirge/meta.yaml index 70bdce43cb695..a63cbceba113c 100644 --- a/recipes/mirge/meta.yaml +++ b/recipes/mirge/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 2c80a5759d93406d5f861a17b4d36f428a4525b4f7f09ce37c7fe8b011f52950 build: - number: 5 + number: 6 noarch: python requirements: diff --git a/recipes/mlst/2.9/meta.yaml b/recipes/mlst/2.9/meta.yaml index fda448dcc2ad4..093c6f46c114a 100644 --- a/recipes/mlst/2.9/meta.yaml +++ b/recipes/mlst/2.9/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.9" build: - number: 1 + number: 2 source: url: https://github.com/tseemann/mlst/archive/2.9.tar.gz diff --git a/recipes/mlst/meta.yaml b/recipes/mlst/meta.yaml index bdac7b959a175..1d402a5668629 100644 --- a/recipes/mlst/meta.yaml +++ b/recipes/mlst/meta.yaml @@ -12,23 +12,14 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: generic requirements: - host: - - any2fasta - - blast >=2.9.0 - - perl >=5.26 - - perl-bioperl >=1.7.2 - - perl-moo - - perl-list-moreutils - - perl-json - - zlib run: - any2fasta - blast >=2.9.0 - - perl >=5.26 + - perl - perl-bioperl >=1.7.2 - perl-moo - perl-list-moreutils diff --git a/recipes/moca/meta.yaml b/recipes/moca/meta.yaml index edcddef71814b..8f401917df4f8 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 preserve_egg_dir: true script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: diff --git a/recipes/mockinbird/meta.yaml b/recipes/mockinbird/meta.yaml index 51b5c455805fc..a152e3babeaa8 100644 --- a/recipes/mockinbird/meta.yaml +++ b/recipes/mockinbird/meta.yaml @@ -11,7 +11,7 @@ source: build: script: python -m pip install --no-deps --ignore-installed . - number: 2 + number: 3 skip: True # [not py3k] requirements: diff --git a/recipes/moff/build.sh b/recipes/moff/build.sh index 37c7df18385e6..b1874709da9b6 100644 --- a/recipes/moff/build.sh +++ b/recipes/moff/build.sh @@ -2,6 +2,7 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir +mkdir -p ${PREFIX}/bin cp -r * $outdir ln -s $outdir/moff_all.py $PREFIX/bin/moff_all.py diff --git a/recipes/moff/meta.yaml b/recipes/moff/meta.yaml index f10c7a6ca22fb..8cc9dc11376c3 100644 --- a/recipes/moff/meta.yaml +++ b/recipes/moff/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/monovar/build.sh b/recipes/monovar/build.sh index d68a257ddd8e0..a1b2482ede5cb 100644 --- a/recipes/monovar/build.sh +++ b/recipes/monovar/build.sh @@ -1,4 +1,6 @@ #!/bin/sh +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/lib cp -r ${SRC_DIR}/src/ $PREFIX/lib/monovar ln -s $PREFIX/lib/monovar/monovar.py $PREFIX/bin/monovar diff --git a/recipes/monovar/meta.yaml b/recipes/monovar/meta.yaml index 233d6c578ed3a..60e8bd4e38539 100644 --- a/recipes/monovar/meta.yaml +++ b/recipes/monovar/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/motifraptor/meta.yaml b/recipes/motifraptor/meta.yaml index 5cdfa2a565c49..b9d5b3395cbd6 100644 --- a/recipes/motifraptor/meta.yaml +++ b/recipes/motifraptor/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 24bab93d80bb340202c027819feab24e7369ccb3f0565c36f0220977a833b6c9 build: - number: 0 + number: 1 skip: True # [py != 36] requirements: diff --git a/recipes/motifscan/meta.yaml b/recipes/motifscan/meta.yaml index 3e0463e64cc63..085075047d65b 100644 --- a/recipes/motifscan/meta.yaml +++ b/recipes/motifscan/meta.yaml @@ -7,16 +7,19 @@ source: sha256: 7ba31fed062fc1d228ac9178383dc12711bf4f65d98ade383eccf23a4abe0099 build: - noarch: python - number: 0 + skip: True # [py3k] + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - python <3 + - python - pip run: - - python <3 + - python - numpy - pandas >=0.17.0 - scipy diff --git a/recipes/mugsy/meta.yaml b/recipes/mugsy/meta.yaml index 143dc3ad52d59..338622aa2e1eb 100644 --- a/recipes/mugsy/meta.yaml +++ b/recipes/mugsy/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/mummer/build.sh b/recipes/mummer/build.sh index 2c33df2902727..1291a7cdd1596 100644 --- a/recipes/mummer/build.sh +++ b/recipes/mummer/build.sh @@ -12,7 +12,7 @@ cp -R $SRC_DIR/* $MUMMER_HOME cd $MUMMER_HOME -make +make CC=$CC CXX=$CXX binaries="\ combineMUMs \ diff --git a/recipes/mummer/meta.yaml b/recipes/mummer/meta.yaml index 95319dcb4bfbe..4921c0cef7996 100644 --- a/recipes/mummer/meta.yaml +++ b/recipes/mummer/meta.yaml @@ -13,10 +13,11 @@ source: - patches/gnuplot_mouse_clipboardformat.patch build: - number: 8 + number: 9 requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} host: - perl # [not osx] diff --git a/recipes/muscle/build.sh b/recipes/muscle/build.sh index 868381f7307e2..5c7f3c6a638c5 100644 --- a/recipes/muscle/build.sh +++ b/recipes/muscle/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -make +make GPP=$CXX binaries="\ muscle \ diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index 517af01c7b772..df978aa786262 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -12,7 +12,7 @@ source: - osx-makefile.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/musicc/meta.yaml b/recipes/musicc/meta.yaml index 1c134323a5216..443da4a3b4a09 100644 --- a/recipes/musicc/meta.yaml +++ b/recipes/musicc/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/mykrobe/meta.yaml b/recipes/mykrobe/meta.yaml index 128a861a95b82..5bfad974c6135 100644 --- a/recipes/mykrobe/meta.yaml +++ b/recipes/mykrobe/meta.yaml @@ -9,7 +9,7 @@ source: sha256: c1fba091bf72f95112211d53d5610297b4bcbca135592585ce2cde3e98156ef0 build: - number: 0 + number: 2 skip: True # [py2k] entry_points: - mykrobe = mykrobe.cli:main @@ -37,6 +37,7 @@ requirements: - mongoengine - pyvcf - biopython + - cython test: imports: diff --git a/recipes/mzml2isa/0.4.24/meta.yaml b/recipes/mzml2isa/0.4.24/meta.yaml deleted file mode 100644 index 35a30c92057c1..0000000000000 --- a/recipes/mzml2isa/0.4.24/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -package: - name: mzml2isa - version: "0.4.24" - -source: - url: https://pypi.python.org/packages/dd/03/bea5554f2cba1a52f26fc497a775e3c078d5efff0f489e5d948a5b6c24b6/mzml2isa-0.4.24.tar.bz2 - md5: 01c71fae82689807f0126c2b7bcf986f - -build: - noarch: python - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 2 - entry_points: - - mzml2isa = mzml2isa.parsing:run - -requirements: - host: - - python <3 - - pip - run: - - python <3 - - lxml - - six - - pronto - - chainmap - -test: - imports: - - mzml2isa - - commands: - - mzml2isa --help - -about: - home: http://www.biosciences.bham.ac.uk/labs/viant/ - license: GNU General Public License v3 (GPLv3) - summary: 'mzml2isa - mzML to ISA-tab parsing tool' diff --git a/recipes/mzml2isa/meta.yaml b/recipes/mzml2isa/meta.yaml index a4853f0b7d589..52023b3df0915 100644 --- a/recipes/mzml2isa/meta.yaml +++ b/recipes/mzml2isa/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv entry_points: - mzml2isa = mzml2isa.parsing:main diff --git a/recipes/nanolyse/meta.yaml b/recipes/nanolyse/meta.yaml index c5fe0f11de4a1..6282cfa3525ac 100644 --- a/recipes/nanolyse/meta.yaml +++ b/recipes/nanolyse/meta.yaml @@ -13,7 +13,7 @@ build: noarch: python entry_points: - NanoLyse=nanolyse.NanoLyse:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/nanomath/meta.yaml b/recipes/nanomath/meta.yaml index d21a118499c13..9e6bb5c104e89 100644 --- a/recipes/nanomath/meta.yaml +++ b/recipes/nanomath/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/nanoplotter/meta.yaml b/recipes/nanoplotter/meta.yaml index a444e98890cb3..07ed9afb25447 100644 --- a/recipes/nanoplotter/meta.yaml +++ b/recipes/nanoplotter/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 1e97bd043668cd3066300695747eb49594720583975252947da33214bc72caa2 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv " diff --git a/recipes/nanopore_simulation/meta.yaml b/recipes/nanopore_simulation/meta.yaml index 9dd63b04428e0..c228b816b357f 100644 --- a/recipes/nanopore_simulation/meta.yaml +++ b/recipes/nanopore_simulation/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/nanoraw/meta.yaml b/recipes/nanoraw/meta.yaml index 898b3f3fcd264..017e30853b064 100644 --- a/recipes/nanoraw/meta.yaml +++ b/recipes/nanoraw/meta.yaml @@ -14,7 +14,7 @@ build: noarch: python entry_points: - nanoraw = nanoraw.__main__:main - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/nanostat/meta.yaml b/recipes/nanostat/meta.yaml index 4ac84e4971cb9..f16a984e15770 100644 --- a/recipes/nanostat/meta.yaml +++ b/recipes/nanostat/meta.yaml @@ -12,7 +12,7 @@ build: noarch: python entry_points: - NanoStat=nanostat.NanoStat:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/nasp/meta.yaml b/recipes/nasp/meta.yaml index 8ab1ee2ba3960..27e20890631d9 100644 --- a/recipes/nasp/meta.yaml +++ b/recipes/nasp/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: true # [not linux] - number: 0 + number: 1 requirements: build: diff --git a/recipes/ndex-python/meta.yaml b/recipes/ndex-python/meta.yaml index 78b4a70dfd5d4..fc0b503704741 100644 --- a/recipes/ndex-python/meta.yaml +++ b/recipes/ndex-python/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/neptune/meta.yaml b/recipes/neptune/meta.yaml index 531ce0c6027bd..79a33a356bda2 100644 --- a/recipes/neptune/meta.yaml +++ b/recipes/neptune/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/ngs-disambiguate/meta.yaml b/recipes/ngs-disambiguate/meta.yaml index 7901b964ae694..eb0df00385bc9 100644 --- a/recipes/ngs-disambiguate/meta.yaml +++ b/recipes/ngs-disambiguate/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d5b05caec68db7596fc31564f44afdce27c4d5215785f9c97581d58e87d9cc94 build: - number: 3 + number: 4 skip: true # [osx] requirements: diff --git a/recipes/ngsutils/meta.yaml b/recipes/ngsutils/meta.yaml index 085530df6048a..7eaafe642d188 100644 --- a/recipes/ngsutils/meta.yaml +++ b/recipes/ngsutils/meta.yaml @@ -7,7 +7,7 @@ source: md5: 6212d6de740c42aa2c6b5f6785465860 build: - number: 1 + number: 2 skip: True # [py3k] requirements: diff --git a/recipes/nim-falcon/meta.yaml b/recipes/nim-falcon/meta.yaml index ecdb901b64242..d85f723c3fecc 100644 --- a/recipes/nim-falcon/meta.yaml +++ b/recipes/nim-falcon/meta.yaml @@ -17,7 +17,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 requirements: host: diff --git a/recipes/nucleoatac/meta.yaml b/recipes/nucleoatac/meta.yaml index 33ceeb2ddee20..6b4bfb1e98729 100644 --- a/recipes/nucleoatac/meta.yaml +++ b/recipes/nucleoatac/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{sha256}} build: - number: 2 + number: 3 script: python -m pip install --no-deps --ignore-installed . requirements: @@ -27,6 +27,7 @@ requirements: - matplotlib - pysam >=0.8.1 - zlib + - cython >=0.22 test: commands: diff --git a/recipes/nudup/build.sh b/recipes/nudup/build.sh deleted file mode 100644 index 0a3ad4ef14083..0000000000000 --- a/recipes/nudup/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -mkdir -p ${PREFIX}/bin -cp nudup.py ${PREFIX}/bin -chmod a+x ${PREFIX}/bin/nudup.py diff --git a/recipes/nudup/meta.yaml b/recipes/nudup/meta.yaml index b097d318f100a..d5627e5fbc189 100644 --- a/recipes/nudup/meta.yaml +++ b/recipes/nudup/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/nvc/meta.yaml b/recipes/nvc/meta.yaml index 77faf25305df1..e170248086235 100644 --- a/recipes/nvc/meta.yaml +++ b/recipes/nvc/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/oncotator/meta.yaml b/recipes/oncotator/meta.yaml index b927206a6521c..ccdb67f5f8e69 100644 --- a/recipes/oncotator/meta.yaml +++ b/recipes/oncotator/meta.yaml @@ -11,8 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 1 - skip: True # [py3k] + number: 2 + # the required natsort version was never built of OSX on python 2.7 + skip: True # [py3k or osx] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" requirements: diff --git a/recipes/ont-fast5-api/meta.yaml b/recipes/ont-fast5-api/meta.yaml index 34c1c45a619bb..6018fc9cb7a0a 100644 --- a/recipes/ont-fast5-api/meta.yaml +++ b/recipes/ont-fast5-api/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - multi_to_single_fast5=ont_fast5_api.conversion_tools.multi_to_single_fast5:main - single_to_multi_fast5=ont_fast5_api.conversion_tools.single_to_multi_fast5:main diff --git a/recipes/ont-tombo/meta.yaml b/recipes/ont-tombo/meta.yaml index 1e134c0eed99d..822c4247cccd5 100644 --- a/recipes/ont-tombo/meta.yaml +++ b/recipes/ont-tombo/meta.yaml @@ -13,12 +13,13 @@ source: build: entry_points: - tombo = tombo.__main__:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - pip diff --git a/recipes/optitype/1.2.1/meta.yaml b/recipes/optitype/1.2.1/meta.yaml index 7a2f140c2491f..8f92edf0b14dd 100644 --- a/recipes/optitype/1.2.1/meta.yaml +++ b/recipes/optitype/1.2.1/meta.yaml @@ -2,7 +2,7 @@ package: name: optitype version: '1.2.1' build: - number: 1 + number: 2 noarch: python source: url: https://github.com/FRED-2/OptiType/archive/v1.2.1.tar.gz diff --git a/recipes/optitype/build.sh b/recipes/optitype/build.sh deleted file mode 100644 index 2dbb7b956b90f..0000000000000 --- a/recipes/optitype/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -mkdir -p $PREFIX/bin -cp -r data $outdir -sed -i 's/__file__/os.path.realpath(__file__)/' OptiTypePipeline.py -sed -i '1i#!/opt/anaconda1anaconda2anaconda3/bin/python' OptiTypePipeline.py -sed -i '/^from __future__/a import os\nthis_dir = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(os.path.realpath(__file__))))\nimport sys\nsys.path.append(this_dir)' OptiTypePipeline.py -chmod a+x OptiTypePipeline.py -cp *.py $outdir -cp config* $outdir -ln -s $outdir/OptiTypePipeline.py $PREFIX/bin diff --git a/recipes/optitype/meta.yaml b/recipes/optitype/meta.yaml index a5ae104ba3f33..3754fbb5696b4 100644 --- a/recipes/optitype/meta.yaml +++ b/recipes/optitype/meta.yaml @@ -6,7 +6,7 @@ package: build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/orthofinder/meta.yaml b/recipes/orthofinder/meta.yaml index 41d1275ce9e35..06761d7df148b 100644 --- a/recipes/orthofinder/meta.yaml +++ b/recipes/orthofinder/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: True - number: 0 + number: 1 source: url: https://github.com/davidemms/OrthoFinder/releases/download/{{ version }}/OrthoFinder-{{ version }}_source.tar.gz diff --git a/recipes/orthomcl/meta.yaml b/recipes/orthomcl/meta.yaml index 7332c711dde43..d4b09814b6ad3 100644 --- a/recipes/orthomcl/meta.yaml +++ b/recipes/orthomcl/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 3 + number: 4 source: url: http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz diff --git a/recipes/pacbio_falcon/meta.yaml b/recipes/pacbio_falcon/meta.yaml index 4fd6da61f0d13..c4883c7b58b16 100644 --- a/recipes/pacbio_falcon/meta.yaml +++ b/recipes/pacbio_falcon/meta.yaml @@ -15,17 +15,19 @@ source: md5: be4a225262ee4bd9729b6b7e81a83615 build: - noarch: python - number: 1 + skip: True # [py3k] + number: 2 requirements: + build: + - {{ compiler('c') }} host: - - python <3 + - python - setuptools - pypeflow - networkx run: - - python <3 + - python - pypeflow - rdflib - rdfextras diff --git a/recipes/pal2nal/meta.yaml b/recipes/pal2nal/meta.yaml index 8659c85b5e903..a51db8ccd392e 100644 --- a/recipes/pal2nal/meta.yaml +++ b/recipes/pal2nal/meta.yaml @@ -1,38 +1,38 @@ -{% set name = "pal2nal" %} -{% set version = "14.1" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://github.com/liaochenlanruo/{{ name|upper }}/archive/v{{ version }}.tar.gz - sha256: 94c77f793d7b8d2b280eaf6245b50ce2cd38f35cb12a8e7cd3d0d9dd58284ce4 - -build: - number: 0 - noarch: generic - -requirements: - host: - - perl - run: - - perl - - perl-getopt-long - -test: - commands: - - pal2nal.pl -h - -about: - home: http://www.bork.embl.de/pal2nal/ - license: GPLv2.0 - license_family: GPL - license_file: LICENSE - summary: robust conversion of protein sequence alignments into the corresponding codon alignments - -extra: - identifiers: - - biotools:pal2nal - recipe-maintainers: - - liaochenlanruo +{% set name = "pal2nal" %} +{% set version = "14.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/liaochenlanruo/{{ name|upper }}/archive/v{{ version }}.tar.gz + sha256: 94c77f793d7b8d2b280eaf6245b50ce2cd38f35cb12a8e7cd3d0d9dd58284ce4 + +build: + number: 1 + noarch: generic + +requirements: + host: + - perl + run: + - perl + - perl-getopt-long + +test: + commands: + - pal2nal.pl -h + +about: + home: http://www.bork.embl.de/pal2nal/ + license: GPLv2.0 + license_family: GPL + license_file: LICENSE + summary: robust conversion of protein sequence alignments into the corresponding codon alignments + +extra: + identifiers: + - biotools:pal2nal + recipe-maintainers: + - liaochenlanruo diff --git a/recipes/pal_finder/meta.yaml b/recipes/pal_finder/meta.yaml index b9b22062cff0c..ba54d3ce426c1 100644 --- a/recipes/pal_finder/meta.yaml +++ b/recipes/pal_finder/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/paml/build.sh b/recipes/paml/build.sh index ac5da30439d2a..a13e2d46bb363 100644 --- a/recipes/paml/build.sh +++ b/recipes/paml/build.sh @@ -5,7 +5,7 @@ set -eu -o pipefail mkdir -p ${PREFIX}/bin cd src -make -j 4 +make -j 4 CC=$CC cp baseml ${PREFIX}/bin/ cp basemlg ${PREFIX}/bin/ diff --git a/recipes/paml/meta.yaml b/recipes/paml/meta.yaml index 6c1ea6961349c..403ac8f036cc3 100644 --- a/recipes/paml/meta.yaml +++ b/recipes/paml/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/pancake/meta.yaml b/recipes/pancake/meta.yaml index 57a2c9f0ca063..c4a84c8dc743d 100644 --- a/recipes/pancake/meta.yaml +++ b/recipes/pancake/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/panphlan/1.2/meta.yaml b/recipes/panphlan/1.2/meta.yaml index 4fe9e2d1226c4..e51affb39e2d4 100644 --- a/recipes/panphlan/1.2/meta.yaml +++ b/recipes/panphlan/1.2/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 4 + number: 5 requirements: run: diff --git a/recipes/pantools/meta.yaml b/recipes/pantools/meta.yaml index ee59313e5201c..fb707a95b0a9e 100644 --- a/recipes/pantools/meta.yaml +++ b/recipes/pantools/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: run: diff --git a/recipes/parasail-python/meta.yaml b/recipes/parasail-python/meta.yaml index 82ba628cf9329..63650d861a37d 100644 --- a/recipes/parasail-python/meta.yaml +++ b/recipes/parasail-python/meta.yaml @@ -13,7 +13,7 @@ source: - darwin-libtool-name.patch build: - number: 0 + number: 1 requirements: host: diff --git a/recipes/pathoscope/meta.yaml b/recipes/pathoscope/meta.yaml index aea9e724589d2..d2542895a820b 100644 --- a/recipes/pathoscope/meta.yaml +++ b/recipes/pathoscope/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/pauda/meta.yaml b/recipes/pauda/meta.yaml index a4193578fada3..ae7411463d38a 100644 --- a/recipes/pauda/meta.yaml +++ b/recipes/pauda/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/pb-assembly/meta.yaml b/recipes/pb-assembly/meta.yaml index db74c7e15ede1..80a8e9add770d 100644 --- a/recipes/pb-assembly/meta.yaml +++ b/recipes/pb-assembly/meta.yaml @@ -2,7 +2,7 @@ package: name: pb-assembly version: "0.0.6" build: - number: 5 + number: 6 noarch: generic requirements: run: diff --git a/recipes/pb-falcon/meta.yaml b/recipes/pb-falcon/meta.yaml index aa44ba371d93d..920dc9d242b80 100644 --- a/recipes/pb-falcon/meta.yaml +++ b/recipes/pb-falcon/meta.yaml @@ -24,7 +24,7 @@ source: folder: pb-falcon-phase build: - number: 0 + number: 1 skip: True # [py27 or py36 or osx] requirements: diff --git a/recipes/pbalign/meta.yaml b/recipes/pbalign/meta.yaml index 1926e6715bcb1..ebbc9f71ce6a8 100644 --- a/recipes/pbalign/meta.yaml +++ b/recipes/pbalign/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/pbbam/meta.yaml b/recipes/pbbam/meta.yaml index 40d9e32507e67..20daf199d998f 100644 --- a/recipes/pbbam/meta.yaml +++ b/recipes/pbbam/meta.yaml @@ -22,7 +22,7 @@ extra: - pezmaster31 build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/pbcommand/meta.yaml b/recipes/pbcommand/meta.yaml index 4465900da9189..b93e230e9a461 100644 --- a/recipes/pbcommand/meta.yaml +++ b/recipes/pbcommand/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 2 + number: 3 entry_points: - pbservice = pbcommand.services.cli:main diff --git a/recipes/pbgzip/meta.yaml b/recipes/pbgzip/meta.yaml index 035d8a9da2a2a..a493658284e75 100644 --- a/recipes/pbgzip/meta.yaml +++ b/recipes/pbgzip/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 544820be0da38f6af7be18792d00d6d3dd2fe3f7f3b08a67c3aa35fb1bbeaeb1 build: - number: 0 + number: 1 skip: False requirements: diff --git a/recipes/pbh5tools/meta.yaml b/recipes/pbh5tools/meta.yaml index cf8d65ad1c9a3..6a7900801a207 100644 --- a/recipes/pbh5tools/meta.yaml +++ b/recipes/pbh5tools/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [not py27] - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/pbhoover/meta.yaml b/recipes/pbhoover/meta.yaml index f720c8c7b792d..66e9165611ba5 100644 --- a/recipes/pbhoover/meta.yaml +++ b/recipes/pbhoover/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: diff --git a/recipes/pbmm2/meta.yaml b/recipes/pbmm2/meta.yaml index 96621fc18421f..e23ce6e64a870 100644 --- a/recipes/pbmm2/meta.yaml +++ b/recipes/pbmm2/meta.yaml @@ -22,7 +22,7 @@ extra: - mhsieh build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/pbwt/meta.yaml b/recipes/pbwt/meta.yaml index fe459011ab0df..2db6c70b21517 100644 --- a/recipes/pbwt/meta.yaml +++ b/recipes/pbwt/meta.yaml @@ -8,7 +8,7 @@ source: sha256: 57b02f4ec56d236a3f4e6e9789dbefbc505a3157840edcbee2201a831806003e build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/ped_parser/1.6.5/meta.yaml b/recipes/ped_parser/1.6.5/meta.yaml deleted file mode 100644 index 34bf258456f96..0000000000000 --- a/recipes/ped_parser/1.6.5/meta.yaml +++ /dev/null @@ -1,32 +0,0 @@ -package: - name: ped_parser - version: "1.6.5" - -build: - noarch: python - number: 1 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - -source: - url: https://pypi.python.org/packages/source/p/ped_parser/ped_parser-1.6.5.tar.gz - md5: 1f404e131c3d210d32e6253ac500b200 - -requirements: - host: - - python - - pip - run: - - python - - click - -test: - imports: - - ped_parser - commands: - # click requires a unicode locale - - LANG=C.UTF-8 ped_parser --help - -about: - home: https://github.com/moonso/ped_parser - license: BSD License - summary: 'A ped file parser.' diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index c59c6aa3aa006..f73931e306b86 100644 --- a/recipes/ped_parser/meta.yaml +++ b/recipes/ped_parser/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/pepr/meta.yaml b/recipes/pepr/meta.yaml index 9815bd31450f7..6f4d0188a2fcc 100644 --- a/recipes/pepr/meta.yaml +++ b/recipes/pepr/meta.yaml @@ -15,7 +15,7 @@ build: - PePr=PePr.PePr:argless_main - PePr-preprocess=PePr.PePr:pre_processing_module - PePr-postprocess=PePr.post_processing.post_process_PePr:post_processing_module - number: 1 + number: 2 requirements: host: diff --git a/recipes/perl-bio-asn1-entrezgene/meta.yaml b/recipes/perl-bio-asn1-entrezgene/meta.yaml index 34b3638bcf13b..ed932f6107a41 100644 --- a/recipes/perl-bio-asn1-entrezgene/meta.yaml +++ b/recipes/perl-bio-asn1-entrezgene/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/perl-bio-automatedannotation/1.182770/meta.yaml b/recipes/perl-bio-automatedannotation/1.182770/meta.yaml index 8d3dfadd83b41..8e4408c6041f7 100644 --- a/recipes/perl-bio-automatedannotation/1.182770/meta.yaml +++ b/recipes/perl-bio-automatedannotation/1.182770/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/perl-bio-cigar/meta.yaml b/recipes/perl-bio-cigar/meta.yaml index 45e100cebcf50..2c9e59426bbbe 100644 --- a/recipes/perl-bio-cigar/meta.yaml +++ b/recipes/perl-bio-cigar/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 4 + number: 5 requirements: host: diff --git a/recipes/perl-bio-coordinate/meta.yaml b/recipes/perl-bio-coordinate/meta.yaml index 92152e8be5f11..5e63166721d30 100644 --- a/recipes/perl-bio-coordinate/meta.yaml +++ b/recipes/perl-bio-coordinate/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/perl-bio-featureio/meta.yaml b/recipes/perl-bio-featureio/meta.yaml index 9e9f6ce6fb118..0ed9582d59d94 100644 --- a/recipes/perl-bio-featureio/meta.yaml +++ b/recipes/perl-bio-featureio/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/perl-bio-gff3/meta.yaml b/recipes/perl-bio-gff3/meta.yaml index 319f5c3dd5342..7397658f0f839 100644 --- a/recipes/perl-bio-gff3/meta.yaml +++ b/recipes/perl-bio-gff3/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: host: diff --git a/recipes/perl-bio-mlst-check/meta.yaml b/recipes/perl-bio-mlst-check/meta.yaml index 7e4f347abee88..4ad7f4ac04e21 100644 --- a/recipes/perl-bio-mlst-check/meta.yaml +++ b/recipes/perl-bio-mlst-check/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/perl-bio-phylo/meta.yaml b/recipes/perl-bio-phylo/meta.yaml index dd9d345f04ee8..7517c9339ea59 100644 --- a/recipes/perl-bio-phylo/meta.yaml +++ b/recipes/perl-bio-phylo/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: # NOTE: We cannot use components that rely XML::XML2JSON package as that's diff --git a/recipes/perl-bio-rna-rnaalisplit/meta.yaml b/recipes/perl-bio-rna-rnaalisplit/meta.yaml index e2e8f8dc31243..fed4013852ac4 100644 --- a/recipes/perl-bio-rna-rnaalisplit/meta.yaml +++ b/recipes/perl-bio-rna-rnaalisplit/meta.yaml @@ -12,12 +12,10 @@ source: build: noarch: generic - number: 0 + number: 1 skip: True # [osx] requirements: - build: - host: - perl - perl-lib diff --git a/recipes/perl-bio-samtools/meta.yaml b/recipes/perl-bio-samtools/meta.yaml index 2ca7cef0f0cdb..b411b1d0b044c 100644 --- a/recipes/perl-bio-samtools/meta.yaml +++ b/recipes/perl-bio-samtools/meta.yaml @@ -9,10 +9,11 @@ source: - build-pl.patch build: - noarch: generic - number: 1 + number: 2 requirements: + build: + - {{ compiler('c') }} host: - perl - perl-bioperl-core diff --git a/recipes/perl-bio-tools-phylo-paml/meta.yaml b/recipes/perl-bio-tools-phylo-paml/meta.yaml index 6ca4245df5bcf..720e832bfaf8e 100644 --- a/recipes/perl-bio-tools-phylo-paml/meta.yaml +++ b/recipes/perl-bio-tools-phylo-paml/meta.yaml @@ -12,10 +12,10 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: - build: + host: - perl - perl-getopt-long - perl-io-string @@ -24,7 +24,6 @@ requirements: - perl-extutils-makemaker - perl-bioperl-run - paml - run: - perl - perl-io-string diff --git a/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml b/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml index b20f463336c8f..0871e87c19c4f 100644 --- a/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml +++ b/recipes/perl-bio-tools-run-alignment-clustalw/meta.yaml @@ -12,10 +12,10 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: - build: + host: - perl - perl-devel-checkbin - perl-file-temp diff --git a/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml b/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml index 92e9d65bcb675..7db5bec80e7a9 100644 --- a/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml +++ b/recipes/perl-bio-tools-run-alignment-tcoffee/meta.yaml @@ -13,17 +13,16 @@ source: build: noarch: generic skip: True # [osx] - number: 1 + number: 2 requirements: - build: + host: - perl - perl-extutils-makemaker - perl-test-exception - perl-devel-checkbin - perl-bioperl-run - t_coffee - run: - perl - perl-bioperl-run diff --git a/recipes/perl-bioperl-core/meta.yaml b/recipes/perl-bioperl-core/meta.yaml index 72ab44082c2bb..5617b7b30bf81 100644 --- a/recipes/perl-bioperl-core/meta.yaml +++ b/recipes/perl-bioperl-core/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/perl-bioperl-run/meta.yaml b/recipes/perl-bioperl-run/meta.yaml index 82e64d0d264f1..c1ad0b0e271f1 100644 --- a/recipes/perl-bioperl-run/meta.yaml +++ b/recipes/perl-bioperl-run/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: host: @@ -18,7 +18,6 @@ requirements: - perl-file-sort - perl-module-build - perl-test-most - run: - perl - perl-bioperl-core diff --git a/recipes/perl-bioperl/meta.yaml b/recipes/perl-bioperl/meta.yaml index 804506ec5ae25..ed0bf21a1c989 100644 --- a/recipes/perl-bioperl/meta.yaml +++ b/recipes/perl-bioperl/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 10 + number: 11 requirements: host: diff --git a/recipes/perl-biosails/0.02/meta.yaml b/recipes/perl-biosails/0.02/meta.yaml index c32a92fc61aee..2f1b49ee598ea 100644 --- a/recipes/perl-biosails/0.02/meta.yaml +++ b/recipes/perl-biosails/0.02/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/perl-biox-seq/0.006007/meta.yaml b/recipes/perl-biox-seq/0.006007/meta.yaml index 67a7091bee015..b170f19e10dcd 100644 --- a/recipes/perl-biox-seq/0.006007/meta.yaml +++ b/recipes/perl-biox-seq/0.006007/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/perl-biox-workflow-command/meta.yaml b/recipes/perl-biox-workflow-command/meta.yaml index 69ac23a52b335..d61e3a5d32dcd 100644 --- a/recipes/perl-biox-workflow-command/meta.yaml +++ b/recipes/perl-biox-workflow-command/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 #skip: True # [osx] requirements: diff --git a/recipes/perl-sanger-cgp-allelecount/meta.yaml b/recipes/perl-sanger-cgp-allelecount/meta.yaml index 43670f253a71c..4377e6301d024 100644 --- a/recipes/perl-sanger-cgp-allelecount/meta.yaml +++ b/recipes/perl-sanger-cgp-allelecount/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 3841dee52b79ec520d5a2faa83dff048badb46dafddb0053b7553eb20aa7fea1 build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/perl-sanger-cgp-vagrent/meta.yaml b/recipes/perl-sanger-cgp-vagrent/meta.yaml index 534b2a0251528..4002af0bd2900 100644 --- a/recipes/perl-sanger-cgp-vagrent/meta.yaml +++ b/recipes/perl-sanger-cgp-vagrent/meta.yaml @@ -7,7 +7,7 @@ source: sha256: aa4ac20f240da7b250a6c8b0bfa2b442d8b96e2c738ae936ff2474195ca28dd2 build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/pfam_scan/meta.yaml b/recipes/pfam_scan/meta.yaml index 3f3a27fd397f0..0e785c6f93baf 100644 --- a/recipes/pfam_scan/meta.yaml +++ b/recipes/pfam_scan/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/pgsa/build.sh b/recipes/pgsa/build.sh index 3f60763a145f9..bdf77ff8b0b6a 100644 --- a/recipes/pgsa/build.sh +++ b/recipes/pgsa/build.sh @@ -1,4 +1,7 @@ #!/bin/bash +for f in nbproject/*.mk ; do + sed -i.bak "s#gcc#$CC#g;s#g++#$CXX#g" $f +done mkdir -p ${PREFIX}/bin mkdir -p ${PREFIX}/lib diff --git a/recipes/pgsa/meta.yaml b/recipes/pgsa/meta.yaml index 2c4689c4b55d5..90b14c7512843 100644 --- a/recipes/pgsa/meta.yaml +++ b/recipes/pgsa/meta.yaml @@ -7,7 +7,7 @@ source: md5: e69596048ed3831a6c92580814d48f19 build: - number: 1 + number: 2 skip: True # [osx] patches: - patch diff --git a/recipes/phame/build.sh b/recipes/phame/build.sh index 8856ab1493399..349bf0d3566d3 100644 --- a/recipes/phame/build.sh +++ b/recipes/phame/build.sh @@ -1,7 +1,8 @@ #!/bin/bash mkdir -p $PREFIX/lib +mkdir -p $PREFIX/bin cp -R src/* $PREFIX/bin cp -R lib/PhaME.pm $PREFIX/lib cp -R lib/misc_funcs.pm $PREFIX/lib -cp -R lib/fastq_utility.pm $PREFIX/lib \ No newline at end of file +cp -R lib/fastq_utility.pm $PREFIX/lib diff --git a/recipes/phame/meta.yaml b/recipes/phame/meta.yaml index 7051d4bf73bb3..1ec865d377b3c 100644 --- a/recipes/phame/meta.yaml +++ b/recipes/phame/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/phyloflash/build.sh b/recipes/phyloflash/build.sh index 8ab3ec0471e03..bf141674d17d2 100644 --- a/recipes/phyloflash/build.sh +++ b/recipes/phyloflash/build.sh @@ -2,6 +2,7 @@ INSTALL_DIR=$PREFIX/lib/phyloFlash +mkdir -p ${PREFIX}/bin mkdir -p $INSTALL_DIR cp -av * $INSTALL_DIR for n in *.{R,pl}; do diff --git a/recipes/phyloflash/meta.yaml b/recipes/phyloflash/meta.yaml index 3af9a7fbdfc0e..6f87567d2a2db 100644 --- a/recipes/phyloflash/meta.yaml +++ b/recipes/phyloflash/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/phylowgs/build.sh b/recipes/phylowgs/build.sh index e86048fb4fc31..3591b145c3b04 100644 --- a/recipes/phylowgs/build.sh +++ b/recipes/phylowgs/build.sh @@ -1,12 +1,13 @@ #!/bin/bash OUTDIR=$PREFIX/share/phylowgs mkdir -p $OUTDIR -g++ -o mh.o mh.cpp util.cpp `gsl-config --cflags --libs` +$CXX -o mh.o mh.cpp util.cpp `gsl-config --cflags --libs` cp -r * $OUTDIR chmod a+x $OUTDIR/evolve.py chmod a+x $OUTDIR/parser/create_phylowgs_inputs.py chmod a+x $OUTDIR/multievolve.py chmod a+x $OUTDIR/write_results.py +mkdir -p ${PREFIX}/bin ln -s $OUTDIR/evolve.py $PREFIX/bin/evolve.py ln -s $OUTDIR/parser/create_phylowgs_inputs.py $PREFIX/bin/create_phylowgs_inputs.py echo "#!/usr/bin/env python2" > $PREFIX/bin/multievolve.py diff --git a/recipes/phylowgs/meta.yaml b/recipes/phylowgs/meta.yaml index c6c8269148600..29ceb17a9c5a3 100644 --- a/recipes/phylowgs/meta.yaml +++ b/recipes/phylowgs/meta.yaml @@ -10,12 +10,13 @@ source: sha256: 762a76f53638be956d5178cce56ba59518d3ddaa6e3e386fbe9c4dafe5cafadf build: - number: 0 + number: 2 skip: true # [not py27] requirements: build: - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - setuptools diff --git a/recipes/pilon/meta.yaml b/recipes/pilon/meta.yaml index 802e41d4dbcb4..a14c1b2d5bd24 100644 --- a/recipes/pilon/meta.yaml +++ b/recipes/pilon/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/pipmir/meta.yaml b/recipes/pipmir/meta.yaml index 95caa54c8676e..4ccf9d475ced8 100644 --- a/recipes/pipmir/meta.yaml +++ b/recipes/pipmir/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: run: diff --git a/recipes/pirate/meta.yaml b/recipes/pirate/meta.yaml index ee1424c7c4a8c..4f37bae26d57e 100644 --- a/recipes/pirate/meta.yaml +++ b/recipes/pirate/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: generic requirements: diff --git a/recipes/piret/meta.yaml b/recipes/piret/meta.yaml index 8f50ba702d074..0def3908b763e 100644 --- a/recipes/piret/meta.yaml +++ b/recipes/piret/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 94e77fcc89163..c3fa7fff8f67a 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5933afb0bb2d0e4baccb1e8660d288c6c494cc2a63442a798fe58ece245c742e build: - number: 1 + number: 2 noarch: python entry_points: - planemo=planemo.cli:planemo diff --git a/recipes/plant_tribes_gene_family_classifier/meta.yaml b/recipes/plant_tribes_gene_family_classifier/meta.yaml index a133b2b7c4d1c..9dfd1284a58d7 100644 --- a/recipes/plant_tribes_gene_family_classifier/meta.yaml +++ b/recipes/plant_tribes_gene_family_classifier/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: run: diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.0/build.sh b/recipes/plant_tribes_gene_family_integrator/1.0.0/build.sh deleted file mode 100644 index 920f7334f82f6..0000000000000 --- a/recipes/plant_tribes_gene_family_integrator/1.0.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/GeneFamilyIntegrator $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyIntegrator -ln -s $PREFIX/bin/GeneFamilyIntegrator $PREFIX/pipelines/GeneFamilyIntegrator -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml b/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml deleted file mode 100644 index 82fc93edffb4d..0000000000000 --- a/recipes/plant_tribes_gene_family_integrator/1.0.0/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -package: - name: plant_tribes_gene_family_integrator - version: "1.0.0" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.0.tar.gz - md5: ef556a78118a03045391464102f8ae18 - -build: - noarch: generic - number: 1 - -requirements: - run: - - perl - -test: - commands: - - GeneFamilyIntegrator 2>&1 | grep INTEGRATE - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family integrator pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.2/build.sh b/recipes/plant_tribes_gene_family_integrator/1.0.2/build.sh deleted file mode 100644 index fc4f5c05e0ecd..0000000000000 --- a/recipes/plant_tribes_gene_family_integrator/1.0.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data - -cp ./pipelines/GeneFamilyIntegrator $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyIntegrator -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml b/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml deleted file mode 100644 index 3e9a14a2edca0..0000000000000 --- a/recipes/plant_tribes_gene_family_integrator/1.0.2/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -package: - name: plant_tribes_gene_family_integrator - version: "1.0.2" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.2.tar.gz - md5: c0a4217048fe8a18e0c13d67667da638 - -build: - noarch: generic - number: 1 - -requirements: - run: - - perl - -test: - commands: - - GeneFamilyIntegrator 2>&1 | grep INTEGRATE - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family integrator pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.3/build.sh b/recipes/plant_tribes_gene_family_integrator/build.sh similarity index 100% rename from recipes/plant_tribes_gene_family_integrator/1.0.3/build.sh rename to recipes/plant_tribes_gene_family_integrator/build.sh diff --git a/recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml b/recipes/plant_tribes_gene_family_integrator/meta.yaml similarity index 97% rename from recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml rename to recipes/plant_tribes_gene_family_integrator/meta.yaml index 42b83dcf3e5db..910dc4711c8ff 100644 --- a/recipes/plant_tribes_gene_family_integrator/1.0.3/meta.yaml +++ b/recipes/plant_tribes_gene_family_integrator/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/build.sh b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/build.sh deleted file mode 100644 index a6dbade619cff..0000000000000 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data -mkdir -p $PREFIX/pipelines -mkdir -p $PREFIX/scripts - -cp ./pipelines/GeneFamilyPhylogenyBuilder $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyPhylogenyBuilder -ln -s $PREFIX/bin/GeneFamilyPhylogenyBuilder $PREFIX/pipelines/GeneFamilyPhylogenyBuilder -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data -cp ./scripts/* $PREFIX/scripts diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml deleted file mode 100644 index 2bae1e111cc9a..0000000000000 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.0/meta.yaml +++ /dev/null @@ -1,26 +0,0 @@ -package: - name: plant_tribes_gene_family_phylogeny_builder - version: "1.0.0" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.0.tar.gz - md5: ef556a78118a03045391464102f8ae18 - -build: - noarch: generic - number: 1 - -requirements: - run: - - fasttree >=2,<3 - - perl - - raxml >=8,<9 - -test: - commands: - - GeneFamilyPhylogenyBuilder 2>&1 | grep PHYLOGENETIC - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family phylogeny builder pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/build.sh b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/build.sh deleted file mode 100644 index e408a4935d6b7..0000000000000 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/sh - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/config -mkdir -p $PREFIX/data - -cp ./pipelines/GeneFamilyPhylogenyBuilder $PREFIX/bin -chmod +x $PREFIX/bin/GeneFamilyPhylogenyBuilder -cp ./config/* $PREFIX/config -cp ./data/* $PREFIX/data diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml b/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml deleted file mode 100644 index 281f81f98afe7..0000000000000 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.2/meta.yaml +++ /dev/null @@ -1,26 +0,0 @@ -package: - name: plant_tribes_gene_family_phylogeny_builder - version: "1.0.2" - -source: - url: https://github.com/dePamphilis/PlantTribes/archive/v1.0.2.tar.gz - md5: c0a4217048fe8a18e0c13d67667da638 - -build: - noarch: generic - number: 1 - -requirements: - run: - - fasttree >=2,<3 - - perl - - raxml >=8,<9 - -test: - commands: - - GeneFamilyPhylogenyBuilder 2>&1 | grep PHYLOGENETIC - -about: - home: 'https://github.com/dePamphilis/PlantTribes' - summary: 'Gene family phylogeny builder pipeline' - license: GNU General Public License v3 (GPLv3) diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/build.sh b/recipes/plant_tribes_gene_family_phylogeny_builder/build.sh similarity index 100% rename from recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/build.sh rename to recipes/plant_tribes_gene_family_phylogeny_builder/build.sh diff --git a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml b/recipes/plant_tribes_gene_family_phylogeny_builder/meta.yaml similarity index 97% rename from recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml rename to recipes/plant_tribes_gene_family_phylogeny_builder/meta.yaml index 26bcd29283f4d..664a1a2f98bbe 100644 --- a/recipes/plant_tribes_gene_family_phylogeny_builder/1.0.3/meta.yaml +++ b/recipes/plant_tribes_gene_family_phylogeny_builder/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/plascope/build.sh b/recipes/plascope/build.sh index 141349acb1bd7..da8bd453fa218 100644 --- a/recipes/plascope/build.sh +++ b/recipes/plascope/build.sh @@ -1,5 +1,6 @@ #!/bin/bash +mkdir -p ${PREFIX}/bin install -m 755 plaScope.sh $PREFIX/bin SHARE_DIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM DOC_DIR=$SHARE_DIR/doc diff --git a/recipes/plascope/meta.yaml b/recipes/plascope/meta.yaml index 8c2d74fb2b172..54fdc1c6f7c25 100644 --- a/recipes/plascope/meta.yaml +++ b/recipes/plascope/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/plasmidtron/meta.yaml b/recipes/plasmidtron/meta.yaml index 03eeba1b25f3e..505c3dac467ef 100644 --- a/recipes/plasmidtron/meta.yaml +++ b/recipes/plasmidtron/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/platypus-conquistador/meta.yaml b/recipes/platypus-conquistador/meta.yaml index edf6634c94410..4012b59cb410e 100644 --- a/recipes/platypus-conquistador/meta.yaml +++ b/recipes/platypus-conquistador/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 2 + number: 3 noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/plink/meta.yaml b/recipes/plink/meta.yaml index 431f9e0ff16af..053c55d957a53 100644 --- a/recipes/plink/meta.yaml +++ b/recipes/plink/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.90b5" build: - number: 0 + number: 1 source: url: https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz diff --git a/recipes/pneumocat/meta.yaml b/recipes/pneumocat/meta.yaml index 42189f35533ef..6839a29ec4fcd 100644 --- a/recipes/pneumocat/meta.yaml +++ b/recipes/pneumocat/meta.yaml @@ -12,7 +12,7 @@ source: sha256: '{{sha256}}' build: noarch: generic - number: 2 + number: 3 requirements: host: diff --git a/recipes/poa/build.sh b/recipes/poa/build.sh index 1f1102c7fcca3..0b89e785b8c44 100644 --- a/recipes/poa/build.sh +++ b/recipes/poa/build.sh @@ -1,14 +1,9 @@ #!/bin/bash -#strictly use anaconda build environment -CC=${PREFIX}/bin/gcc -CXX=${PREFIX}/bin/g++ - - mkdir -p $PREFIX/bin mkdir -p $PREFIX/lib -make poa +make poa CC=$CC CXX=$CXX cp poa $PREFIX/bin cp make_pscores.pl $PREFIX/bin diff --git a/recipes/poa/meta.yaml b/recipes/poa/meta.yaml index d25543e079053..e248e44bcfe3f 100644 --- a/recipes/poa/meta.yaml +++ b/recipes/poa/meta.yaml @@ -3,14 +3,12 @@ package: version: "2.0" build: - number: 1 + number: 2 skip: True # [osx] source: md5: 9e2eb270d4867114406f53dab1311b2b url: https://downloads.sourceforge.net/project/poamsa/poamsa/2.0/poaV2.tar.gz - - patches: - pscores.patch diff --git a/recipes/porechop/meta.yaml b/recipes/porechop/meta.yaml index 483ac63952ba6..d6b82b6530286 100644 --- a/recipes/porechop/meta.yaml +++ b/recipes/porechop/meta.yaml @@ -15,7 +15,7 @@ source: sha256: 817371dceed77e583e387e9ca7c10214c0faff7c0a89320d60a66efdc6c0d35a build: - number: 3 + number: 4 skip: True # [py27] entry_points: - porechop = porechop.porechop:main diff --git a/recipes/poretools/meta.yaml b/recipes/poretools/meta.yaml index 35b442fc10844..db37cb8fcb31b 100644 --- a/recipes/poretools/meta.yaml +++ b/recipes/poretools/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: python - number: 6 + number: 7 requirements: host: diff --git a/recipes/pp/meta.yaml b/recipes/pp/meta.yaml index d52407b85298c..23951774ed616 100644 --- a/recipes/pp/meta.yaml +++ b/recipes/pp/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: @@ -16,7 +16,7 @@ requirements: - python <3 - pip run: - - python + - python <3 test: imports: diff --git a/recipes/presto/meta.yaml b/recipes/presto/meta.yaml index 8f0df956587d0..7d1a68d695f16 100644 --- a/recipes/presto/meta.yaml +++ b/recipes/presto/meta.yaml @@ -7,7 +7,7 @@ source: sha256: c3cdc4d501d39e5c20593286f2d3ff1c9e341cf4fc751d1bf42858285055b2f4 build: - number: 0 + number: 1 noarch: python requirements: diff --git a/recipes/primer3/build.sh b/recipes/primer3/build.sh index 5ad93014582e2..dd888f060ecd4 100644 --- a/recipes/primer3/build.sh +++ b/recipes/primer3/build.sh @@ -7,5 +7,5 @@ export CPATH=${PREFIX}/include mkdir -p $PREFIX/bin mkdir -p $PREFIX/share cd src -make -make PREFIX=${PREFIX} install +make CC=$CC CXX=$CXX +make PREFIX=${PREFIX} CC=$CC CXX=$CXX install diff --git a/recipes/primer3/meta.yaml b/recipes/primer3/meta.yaml index 9be8e9d08884b..72948b91fcf3d 100644 --- a/recipes/primer3/meta.yaml +++ b/recipes/primer3/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: url: https://github.com/primer3-org/primer3/archive/{{ commit }}.tar.gz diff --git a/recipes/prodigal/build.sh b/recipes/prodigal/build.sh index 2162a6b5377b8..15bf945056cfe 100644 --- a/recipes/prodigal/build.sh +++ b/recipes/prodigal/build.sh @@ -3,6 +3,6 @@ # the executable is not installed in $PREFIX though # make install prefix=$PREFIX -make +make CC=$CC mkdir -p $PREFIX/bin cp $PKG_NAME $PREFIX/bin diff --git a/recipes/prodigal/meta.yaml b/recipes/prodigal/meta.yaml index ef6ff4bece66a..2fef53af44f38 100644 --- a/recipes/prodigal/meta.yaml +++ b/recipes/prodigal/meta.yaml @@ -1,18 +1,24 @@ package: name: prodigal version: "2.6.3" + source: url: https://github.com/hyattpd/Prodigal/archive/v2.6.3.zip sha256: 4f73f64ea09be8421e08afabdc641db7775632210f5ef896f5fab4604c9dfcd9 + build: - noarch: generic - number: 1 + number: 2 + requirements: build: + - {{ compiler('c') }} + - unzip run: + test: commands: - prodigal -h + about: home: http://prodigal.ornl.gov/ license: GPL v3 diff --git a/recipes/prokka/1.12/build.sh b/recipes/prokka/1.12/build.sh deleted file mode 100644 index 4a6b6e5581a29..0000000000000 --- a/recipes/prokka/1.12/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/sh -set -e - -rm -rf ./binaries ./perl5 - -./bin/prokka --setupdb - -mkdir -p "${PREFIX}/bin" "${PREFIX}/db" "${PREFIX}/share/doc/prokka" -mv bin/* "${PREFIX}/bin/" -mv db/* "${PREFIX}/db/" -mv doc/* "${PREFIX}/share/doc/prokka/" - -prokka --listdb -prokka --version diff --git a/recipes/prokka/1.12/meta.yaml b/recipes/prokka/1.12/meta.yaml deleted file mode 100644 index 6485050e0c3eb..0000000000000 --- a/recipes/prokka/1.12/meta.yaml +++ /dev/null @@ -1,55 +0,0 @@ -{% set version = "1.12" %} -{% set sha256 = "845e46c9db167fb1fc9d16c934b7cfd89ddfeb6cd44bd8f42204ae7b4e87adba" %} - -package: - name: prokka - version: '{{ version }}' - -source: - url: https://github.com/tseemann/prokka/archive/v{{ version }}.tar.gz - sha256: '{{ sha256 }}' - -build: - noarch: generic - number: 0 - -requirements: - host: - - perl - - perl-bioperl >=1.7.2 - - blast >=2.7.1 - - infernal >=1.1.2 - - hmmer >=3.1b2 - run: - - perl - - aragorn >=1.2 - - barrnap >=0.7 - - blast >=2.7.1 - - hmmer >=3.1b2 - - infernal >=1.1.2 - - minced >=0.3 - - parallel >=20180522 - - perl-bioperl >=1.7.2 - - perl-xml-simple - - prodigal >=2.6 - - tbl2asn >=25.6 - -test: - commands: - - prokka --listdb - - prokka --version - - blastp -help - - barrnap --help 2>&1 | grep Options - - prodigal -h - - tbl2asn --help - -about: - home: http://www.vicbioinformatics.com/software.prokka.shtml - license: GPLv2 - license_family: GPL - summary: A tool for the rapid annotation of prokaryotic genomes - dev_url: https://github.com/tseemann/prokka - -extra: - identifiers: - - biotools:prokka diff --git a/recipes/prokka/meta.yaml b/recipes/prokka/meta.yaml index cf8dd5c11a9ae..86d75e18b11de 100644 --- a/recipes/prokka/meta.yaml +++ b/recipes/prokka/meta.yaml @@ -11,11 +11,12 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: generic requirements: - build: + host: + - perl - perl-bioperl >=1.7.2 - blast >=2.7.1 - infernal >=1.1.2 diff --git a/recipes/pronto/0.3.3/build.sh b/recipes/pronto/0.3.3/build.sh deleted file mode 100644 index 4899c226c8dd0..0000000000000 --- a/recipes/pronto/0.3.3/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/pronto/0.3.3/meta.yaml b/recipes/pronto/0.3.3/meta.yaml deleted file mode 100644 index 6704e9250ece8..0000000000000 --- a/recipes/pronto/0.3.3/meta.yaml +++ /dev/null @@ -1,32 +0,0 @@ -package: - name: pronto - version: "0.3.3" - -source: - url: https://pypi.python.org/packages/43/0b/abfdb921e0c869d4ee2f31b9e68cbc55ea07c57a45eb7054ad3b27b05965/pronto-0.3.3.tar.gz - md5: 512eee78637add914a1b62195007aa2c - -build: - noarch: python - number: 2 - -requirements: - host: - - python <3 - - setuptools - - lxml - - six - run: - - python <3 - - lxml - - six - -test: - imports: - - pronto - - pronto.parser - -about: - home: http://github.com/althonos/pronto - license: GNU General Public License v3 (GPLv3) - summary: 'Python frontend to ontologies - a library to parse, create, browse and export ontologies.' diff --git a/recipes/prophyle/0.1.0/meta.yaml b/recipes/prophyle/0.1.0/meta.yaml deleted file mode 100644 index 282237d1d681e..0000000000000 --- a/recipes/prophyle/0.1.0/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set version = "0.1.0.38" %} -{% set sha256 = "eee1d2d88fba130acd48b39810f97bc1d95b14a1a3bb206938508897468a802e" %} - -package: - name: prophyle - version: {{ version }} - -source: - url: https://pypi.io/packages/source/p/prophyle/prophyle-{{ version }}.tar.gz - sha256: {{ sha256 }} - -build: - noarch: python - number: 2 - script: python -m pip install --no-deps --ignore-installed . - -requirements: - host: - - python >=3 - - pip - run: - - python >=3 - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - -test: - commands: - - prophyle -h - -about: - home: https://github.com/karel-brinda/prophyle - license: MIT - summary: 'ProPhyle is a metagenomic classifier based on BWT-index and phylogenetic trees. Its indexing strategy uses bottom-up propagation of k-mers in the tree, assembling contigs at each node and matching using a standard full-text search.' diff --git a/recipes/prophyle/0.2.0/meta.yaml b/recipes/prophyle/0.2.0/meta.yaml deleted file mode 100644 index d7e18b2f7cf8e..0000000000000 --- a/recipes/prophyle/0.2.0/meta.yaml +++ /dev/null @@ -1,51 +0,0 @@ -{% set version = "0.2.0.3" %} -{% set sha256 = "0646ae5dcaa82b7c39595de590f8ab912917da1f3264f92006e3d77d05bc989d" %} - -package: - name: prophyle - version: {{ version }} - -source: - url: https://pypi.io/packages/source/p/prophyle/prophyle-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 2 - skip: True # [py27] - script: python -m pip install --no-deps --ignore-installed . - -requirements: - build: - - {{ compiler('c') }} - host: - - python - - pip - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - - pysam - - zlib - run: - - python - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - - pysam - - zlib - -test: - commands: - - prophyle -h - -about: - home: https://github.com/karel-brinda/prophyle - license: MIT - summary: 'ProPhyle is a metagenomic classifier based on BWT-index and phylogenetic trees. Its indexing strategy uses bottom-up propagation of k-mers in the tree, assembling contigs at each node and matching using a standard full-text search.' diff --git a/recipes/prophyle/0.2.1/build.sh b/recipes/prophyle/0.2.1/build.sh deleted file mode 100755 index d62e6f7fd1d83..0000000000000 --- a/recipes/prophyle/0.2.1/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#! /usr/bin/env bash - -set -e -set -o pipefail - -#ls -#find . - -make -C prophyle -PROPHYLE_PACKBIN=1 $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/prophyle/0.2.1/meta.yaml b/recipes/prophyle/0.2.1/meta.yaml deleted file mode 100644 index d7afbdd48e973..0000000000000 --- a/recipes/prophyle/0.2.1/meta.yaml +++ /dev/null @@ -1,83 +0,0 @@ -{% set version = "0.2.1.3" %} -{% set sha256 = "caea476aeb9d235d4776ca8a5d91acbac1d72982e3f48dad558b43b2b7cd2f98" %} - -package: - name: prophyle - version: {{ version }} - -source: - url: https://pypi.io/packages/source/p/prophyle/prophyle-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 2 - skip: True # [py27] - script: - entry_points: - - prophyle = prophyle.prophyle:main - - prophyle_analyze.py = prophyle.prophyle_analyze:main - - prophyle_assignment.py = prophyle.prophyle_assignment:main - - prophyle_ncbi_tree.py = prophyle.prophyle_ncbi_tree:main - - prophyle_otu_table.py = prophyle.prophyle_otu_table:main - - prophyle_paired_end.py = prophyle.prophyle_paired_end:main - - prophyle_plot_tree.py = prophyle.prophyle_plot_tree:main - - prophyle_propagation_makefile.py = prophyle.prophyle_propagation_makefile:main - - prophyle_propagation_postprocessing.py = prophyle.prophyle_propagation_postprocessing:main - - prophyle_propagation_preprocessing.py = prophyle.prophyle_propagation_preprocessing:main - - prophyle_split_allseq.py = prophyle.prophyle_split_allseq:main - -requirements: - build: - - {{ compiler('c') }} - host: - - python - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - - pysam - - zlib - run: - - python - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - - pysam - - zlib - -test: - imports: - - prophyle - commands: - - prophyle --help - - prophyle download --help - - prophyle index --help - - prophyle classify --help - - prophyle analyze --help - - prophyle compress --help - - prophyle decompress --help - - prophyle compile --help - - - prophyle_analyze.py --help - - prophyle_assignment.py --help - - prophyle_ncbi_tree.py --help - - prophyle_otu_table.py --help - - prophyle_paired_end.py --help - - prophyle_plot_tree.py --help - - prophyle_propagation_makefile.py --help - - prophyle_propagation_postprocessing.py --help || true # todo: once fixed, remove '|| true' - - prophyle_propagation_preprocessing.py --help - - prophyle_split_allseq.py --help - -about: - home: https://github.com/karel-brinda/prophyle - license: MIT - summary: ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier. - diff --git a/recipes/prophyle/0.3.0/build.sh b/recipes/prophyle/0.3.0/build.sh deleted file mode 100755 index 3ca4e9308ebd6..0000000000000 --- a/recipes/prophyle/0.3.0/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#! /usr/bin/env bash - -set -e -set -o pipefail - -export C_INCLUDE_PATH=${PREFIX}/include -export CPLUS_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib -make -C prophyle -PROPHYLE_PACKBIN=1 $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/prophyle/0.3.0/meta.yaml b/recipes/prophyle/0.3.0/meta.yaml deleted file mode 100644 index 55c89a196c1b6..0000000000000 --- a/recipes/prophyle/0.3.0/meta.yaml +++ /dev/null @@ -1,84 +0,0 @@ -{% set version = "0.3.0.3" %} -{% set sha256 = "8a615c890d2765ba9d59a32c174e1c60416a2d1918c85ea0b245c06c28ec5873" %} - -package: - name: prophyle - version: {{ version }} - -source: - url: https://pypi.io/packages/source/p/prophyle/prophyle-{{version }}.tar.gz - sha256: {{ sha256 }} - -build: - number: 3 - skip: True # [py27] - script: - entry_points: - - prophyle = prophyle.prophyle:main - - prophyle_analyze.py = prophyle.prophyle_analyze:main - - prophyle_assignment.py = prophyle.prophyle_assignment:main - - prophyle_ncbi_tree.py = prophyle.prophyle_ncbi_tree:main - - prophyle_otu_table.py = prophyle.prophyle_otu_table:main - - prophyle_paired_end.py = prophyle.prophyle_paired_end:main - - prophyle_plot_tree.py = prophyle.prophyle_plot_tree:main - - prophyle_propagation_makefile.py = prophyle.prophyle_propagation_makefile:main - - prophyle_propagation_postprocessing.py = prophyle.prophyle_propagation_postprocessing:main - - prophyle_propagation_preprocessing.py = prophyle.prophyle_propagation_preprocessing:main - - prophyle_split_allseq.py = prophyle.prophyle_split_allseq:main - -requirements: - build: - - {{ compiler('cxx') }} - - {{ compiler('c') }} - host: - - python - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - - pysam - - zlib - run: - - python - - samtools - - ete3 - - bitarray - - scipy - - wheel - - zlib - - psutil - - pysam - - zlib - -test: - imports: - - prophyle - commands: - - prophyle --help - - prophyle download --help - - prophyle index --help - - prophyle classify --help - - prophyle analyze --help - - prophyle compress --help - - prophyle decompress --help - - prophyle compile --help - - - prophyle_analyze.py --help - - prophyle_assignment.py --help - - prophyle_ncbi_tree.py --help - - prophyle_otu_table.py --help - - prophyle_paired_end.py --help - - prophyle_plot_tree.py --help - - prophyle_propagation_makefile.py --help - - prophyle_propagation_postprocessing.py --help || true # todo: once fixed, remove '|| true' - - prophyle_propagation_preprocessing.py --help - - prophyle_split_allseq.py --help - -about: - home: https://github.com/karel-brinda/prophyle - license: MIT - summary: ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier. - diff --git a/recipes/protrac/meta.yaml b/recipes/protrac/meta.yaml index 2fb2ec3070c10..c462c79f778c0 100644 --- a/recipes/protrac/meta.yaml +++ b/recipes/protrac/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/pvacseq/meta.yaml b/recipes/pvacseq/meta.yaml index 224cf07ac7787..9cbccec6ea7ae 100644 --- a/recipes/pvacseq/meta.yaml +++ b/recipes/pvacseq/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 3 script: python -m pip install --no-deps --ignore-installed . entry_points: - pvacseq = pvacseq.pvacseq:main diff --git a/recipes/pybamparser/meta.yaml b/recipes/pybamparser/meta.yaml index 2e8bc0259da27..ecd377073ae7e 100644 --- a/recipes/pybamparser/meta.yaml +++ b/recipes/pybamparser/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/pybamtools/meta.yaml b/recipes/pybamtools/meta.yaml index 4b885c99de6c5..eaca9be0d7651 100644 --- a/recipes/pybamtools/meta.yaml +++ b/recipes/pybamtools/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: diff --git a/recipes/pydemult/meta.yaml b/recipes/pydemult/meta.yaml index 34e6f2529c092..5ef56bbe64be3 100644 --- a/recipes/pydemult/meta.yaml +++ b/recipes/pydemult/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - pydemult = pydemult.pydemult:demultiplex script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 2a06f710881f9..033a3f5acd19f 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 script: python -m pip install --no-deps --ignore-installed . entry_points: - pyensembl = pyensembl.shell:run diff --git a/recipes/pyexcelerator/meta.yaml b/recipes/pyexcelerator/meta.yaml index 4f079e437c18a..321a523239a1e 100644 --- a/recipes/pyexcelerator/meta.yaml +++ b/recipes/pyexcelerator/meta.yaml @@ -16,7 +16,7 @@ requirements: - python <3 - pip run: - - python + - python <3 test: imports: diff --git a/recipes/pygenometracks/meta.yaml b/recipes/pygenometracks/meta.yaml index 1a1d90a1a11a3..72ab45cd7a7d5 100644 --- a/recipes/pygenometracks/meta.yaml +++ b/recipes/pygenometracks/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3f76919c046fff2724d3ff734053339476cf3d67eff79a36b7397126866302f6 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv" noarch: python diff --git a/recipes/pyimzml/meta.yaml b/recipes/pyimzml/meta.yaml index b0dbe3e63653e..772aa82b9ed6f 100644 --- a/recipes/pyimzml/meta.yaml +++ b/recipes/pyimzml/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: $PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . requirements: diff --git a/recipes/pyloh/meta.yaml b/recipes/pyloh/meta.yaml index be9792e4c1f9a..895ea73665c53 100644 --- a/recipes/pyloh/meta.yaml +++ b/recipes/pyloh/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/pymot/meta.yaml b/recipes/pymot/meta.yaml index 1c4d4be9bb6ef..e7cd56bd2c007 100644 --- a/recipes/pymot/meta.yaml +++ b/recipes/pymot/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/pymummer/0.10.1/meta.yaml b/recipes/pymummer/0.10.1/meta.yaml index 760a6d24606ef..b50d580190c4b 100644 --- a/recipes/pymummer/0.10.1/meta.yaml +++ b/recipes/pymummer/0.10.1/meta.yaml @@ -8,13 +8,15 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: - python >=3 - pip + - pyfastaq >=3.10.0 + - mummer run: - python >=3 - pyfastaq >=3.10.0 diff --git a/recipes/pynast/1.2.2/meta.yaml b/recipes/pynast/1.2.2/meta.yaml index 90b4e392d9874..dcf453c601c83 100644 --- a/recipes/pynast/1.2.2/meta.yaml +++ b/recipes/pynast/1.2.2/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/pypore/meta.yaml b/recipes/pypore/meta.yaml index 6ce654c66b402..b65e2d9cb10f8 100644 --- a/recipes/pypore/meta.yaml +++ b/recipes/pypore/meta.yaml @@ -7,16 +7,19 @@ source: sha256: 47827b073317cee8a22d38cde5fba11f722bde3cc594ecd632c157469dc8ab00 build: - noarch: python - number: 0 + skip: True # [py3k] + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: + build: + - {{ compiler('c') }} host: - - python <3 + - python - pip + - numpy run: - - python <3 + - python - numpy test: diff --git a/recipes/pyrad/meta.yaml b/recipes/pyrad/meta.yaml index fc3b7ffc490c8..07504f578d7b6 100644 --- a/recipes/pyrad/meta.yaml +++ b/recipes/pyrad/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 2 + number: 3 entry_points: - pyrad = pyrad.pyRAD:main diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index 0f7e9c5e6adf7..ab5fd56a6b143 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f553d48d0345404b6b103d0b82bad09c8d78420e1cc6bef33040553fc579e284 build: - number: 1 + number: 3 binary_relocation: False # [linux] requirements: diff --git a/recipes/pyscaf/meta.yaml b/recipes/pyscaf/meta.yaml index 323e74218985e..ebd7ce7b9caa0 100644 --- a/recipes/pyscaf/meta.yaml +++ b/recipes/pyscaf/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 entry_points: - pyScaf = pyScaf:main script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/pysnptools/meta.yaml b/recipes/pysnptools/meta.yaml index 3a35b1e00f575..12d0acd71bf9a 100644 --- a/recipes/pysnptools/meta.yaml +++ b/recipes/pysnptools/meta.yaml @@ -11,15 +11,19 @@ source: md5: {{ hash }} build: - noarch: python - number: 2 + number: 3 + skip: True # [py3k] requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - python <3 + - python - pip + - numpy >=1.9.2 run: - - python <3 + - python - scipy >=0.15.1 - numpy >=1.9.2 - pandas >=0.16.2 diff --git a/recipes/pythomics/meta.yaml b/recipes/pythomics/meta.yaml index d7df6376a8ea1..e315b427b2478 100644 --- a/recipes/pythomics/meta.yaml +++ b/recipes/pythomics/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 73dee720352448f7f5bddf36ac54b29a99284ea934b230ab08e8044b61dd1204 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/python-cluster/meta.yaml b/recipes/python-cluster/meta.yaml index e47ceeec4ee47..7c77227eff8ed 100644 --- a/recipes/python-cluster/meta.yaml +++ b/recipes/python-cluster/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 script: $PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir . requirements: diff --git a/recipes/python-fakemp/meta.yaml b/recipes/python-fakemp/meta.yaml index 92bd86917e49d..0cfcd551e7c4e 100644 --- a/recipes/python-fakemp/meta.yaml +++ b/recipes/python-fakemp/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/python-hppy/meta.yaml b/recipes/python-hppy/meta.yaml index d8fcb8cc07680..b5317f1ba7a16 100644 --- a/recipes/python-hppy/meta.yaml +++ b/recipes/python-hppy/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.9.8 build: - number: 0 + number: 1 source: url: https://github.com/veg/hppy/archive/0.9.8.tar.gz diff --git a/recipes/python-mailund-newick/meta.yaml b/recipes/python-mailund-newick/meta.yaml index 22884892a6b9e..9cf11054b072a 100644 --- a/recipes/python-mailund-newick/meta.yaml +++ b/recipes/python-mailund-newick/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/python-msgpack/meta.yaml b/recipes/python-msgpack/meta.yaml index 3f7ac25e529b4..18ab17cb6334d 100644 --- a/recipes/python-msgpack/meta.yaml +++ b/recipes/python-msgpack/meta.yaml @@ -7,7 +7,7 @@ source: url: https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-{{ version }}.tar.gz sha256: 4008c72f5ef2b7936447dcb83db41d97e9791c83221be13d5e19db0796df1972 build: - number: 0 + number: 1 requirements: build: - {{ compiler('cxx') }} diff --git a/recipes/python-omero/meta.yaml b/recipes/python-omero/meta.yaml index 4dfec57581fc8..fd2a7e09dbf2e 100644 --- a/recipes/python-omero/meta.yaml +++ b/recipes/python-omero/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/qcli/meta.yaml b/recipes/qcli/meta.yaml index f0131852c5680..b2c3d0b1a8d33 100644 --- a/recipes/qcli/meta.yaml +++ b/recipes/qcli/meta.yaml @@ -10,14 +10,14 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: - - python + - python <3 - pip run: - - python + - python <3 test: # Python imports diff --git a/recipes/qiimetomaaslin/meta.yaml b/recipes/qiimetomaaslin/meta.yaml index 1428aeb29322c..575477a5f2e6c 100644 --- a/recipes/qiimetomaaslin/meta.yaml +++ b/recipes/qiimetomaaslin/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/quicksect/meta.yaml b/recipes/quicksect/meta.yaml index 358a8b025039b..15d7e238eff3c 100644 --- a/recipes/quicksect/meta.yaml +++ b/recipes/quicksect/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "d3e65b55b7f48e6105b11b1e1d6f37ccbf8caecfc7d7db7aba73dfaf6d732a9c" build: - number: 0 + number: 1 script: rm -f src/*.c ; {{ PYTHON }} -m pip install --no-deps --ignore-installed . requirements: diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index 9b7ce440ddbba..5b2f1065c5b34 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index f6444a05ce971..4838a16fa35c5 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 62951191cc8e4..2ddadd4bcf3ec 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 34b157c1908478b972ddf6c900ed0990b2ab34732355b4075ec6526231279222 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-bisquerna/meta.yaml b/recipes/r-bisquerna/meta.yaml index 58d6a956e2d9b..66175919a263d 100644 --- a/recipes/r-bisquerna/meta.yaml +++ b/recipes/r-bisquerna/meta.yaml @@ -10,7 +10,7 @@ source: - {{ cran_mirror }}/src/contrib/Archive/BisqueRNA/BisqueRNA_{{ version }}.tar.gz sha256: 6b276c39c0211a3fbce71e96714674c466862dcb0d8c0448795259e6e40b49cf build: - number: 0 + number: 1 noarch: generic # This is required to make R link correctly on Linux. diff --git a/recipes/r-cellassign/meta.yaml b/recipes/r-cellassign/meta.yaml index 0525a4c685593..ef041897cb9e7 100644 --- a/recipes/r-cellassign/meta.yaml +++ b/recipes/r-cellassign/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-chbutils/meta.yaml b/recipes/r-chbutils/meta.yaml index c3b935d07966e..707ecf9663a4d 100644 --- a/recipes/r-chbutils/meta.yaml +++ b/recipes/r-chbutils/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-classdiscovery/meta.yaml b/recipes/r-classdiscovery/meta.yaml index 3703281700c9c..3738a49432120 100644 --- a/recipes/r-classdiscovery/meta.yaml +++ b/recipes/r-classdiscovery/meta.yaml @@ -1,8 +1,5 @@ {% set version = '3.3.12' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-classdiscovery version: {{ version|replace("-", "_") }} @@ -15,20 +12,13 @@ source: build: noarch: generic - merge_build_host: True # [win] - # If this is a new build for the same version, increment the build number. - number: 0 - - # This is required to make R link correctly on Linux. + number: 1 rpaths: - lib/R/lib/ - lib/ # Suggests: xtable requirements: - build: - - {{posix}}zip # [win] - host: - r-base - bioconductor-biobase @@ -36,7 +26,6 @@ requirements: - r-mclust - r-oompabase >=3.0.1 - r-oompadata - run: - r-base - bioconductor-biobase @@ -51,19 +40,12 @@ test: - $R -e "library('ClassDiscovery')" # [not win] - "\"%R%\" -e \"library('ClassDiscovery')\"" # [win] - # You can also put a file called run_test.py, run_test.sh, or run_test.bat - # in the recipe that will be run at test time. - - # requires: - # Put any additional test requirements here. - about: home: http://oompa.r-forge.r-project.org/ license: Apache (== 2.0) summary: 'Defines the classes used for "class discovery" problems in the OOMPA project (). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. ' - license_family: APACHE # The original CRAN metadata for this package was: diff --git a/recipes/r-coloc/meta.yaml b/recipes/r-coloc/meta.yaml index f3a37f0c624d9..f7168f6fdf0d4 100644 --- a/recipes/r-coloc/meta.yaml +++ b/recipes/r-coloc/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-deconstructsigs/meta.yaml b/recipes/r-deconstructsigs/meta.yaml index 0eb43b38e828d..90dd46c774728 100644 --- a/recipes/r-deconstructsigs/meta.yaml +++ b/recipes/r-deconstructsigs/meta.yaml @@ -17,7 +17,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml index 05532dd3b5e77..23b9b8e786d9e 100644 --- a/recipes/r-diffcorr/meta.yaml +++ b/recipes/r-diffcorr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 15125ae871949ef2be89916384e46c665079e6826ecbba6b3608701e574bb7cf build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-empiricalfdr.deseq2/meta.yaml b/recipes/r-empiricalfdr.deseq2/meta.yaml index 5327c925bb63e..76cebfb9c1c85 100644 --- a/recipes/r-empiricalfdr.deseq2/meta.yaml +++ b/recipes/r-empiricalfdr.deseq2/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.0.3' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-empiricalfdr.deseq2 version: {{ version|replace("-", "_") }} @@ -15,31 +12,24 @@ source: build: noarch: generic - merge_build_host: True # [win] - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{posix}}zip # [win] - host: - r-base - bioconductor-deseq2 - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - + - bioconductor-genomicranges run: - r-base - bioconductor-deseq2 - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - bioconductor-genomicranges test: commands: - - - $R -e "library('empiricalFDR.DESeq2')" # [not win] - - "\"%R%\" -e \"library('empiricalFDR.DESeq2')\"" # [win] + - $R -e "library('empiricalFDR.DESeq2')" about: home: https://CRAN.R-project.org/package=empiricalFDR.DESeq2 @@ -49,12 +39,3 @@ about: and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate. license_family: GPL3 -extra: - recipe-maintainers: - - MathiasHaudgaard - - FrodePedersen - - ArneKr - - johanneskoester - - bgruening - - daler - - jdblischak diff --git a/recipes/r-fgwas/meta.yaml b/recipes/r-fgwas/meta.yaml index 00c0099470260..4322887b1a458 100644 --- a/recipes/r-fgwas/meta.yaml +++ b/recipes/r-fgwas/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml index 6d343ca657040..2bb290e1e85e6 100644 --- a/recipes/r-grain/meta.yaml +++ b/recipes/r-grain/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 5e1acec4fec41079242fb4e08619c8bd74ea5620ff7c8b54e06822e8af216775 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-gwpcr/meta.yaml b/recipes/r-gwpcr/meta.yaml index 95c7c143e906e..330ee2d7679a8 100644 --- a/recipes/r-gwpcr/meta.yaml +++ b/recipes/r-gwpcr/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 6673467f8302535cbd266b9c772cbc6217d10b4db61595eb24fa60cf20caee37 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-imputelcmd/meta.yaml b/recipes/r-imputelcmd/meta.yaml index 8f70cfe966737..eba67d309be5a 100644 --- a/recipes/r-imputelcmd/meta.yaml +++ b/recipes/r-imputelcmd/meta.yaml @@ -14,7 +14,7 @@ source: build: merge_build_host: True # [win] - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-minionqc/meta.yaml b/recipes/r-minionqc/meta.yaml index f2209963f867a..5ac080c900092 100644 --- a/recipes/r-minionqc/meta.yaml +++ b/recipes/r-minionqc/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/r-mixkernel/meta.yaml b/recipes/r-mixkernel/meta.yaml index 59f39725faa6f..df9a0949bef85 100644 --- a/recipes/r-mixkernel/meta.yaml +++ b/recipes/r-mixkernel/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ diff --git a/recipes/r-msqrob/meta.yaml b/recipes/r-msqrob/meta.yaml index efb580c15ebfa..9b9d4b6b4b489 100644 --- a/recipes/r-msqrob/meta.yaml +++ b/recipes/r-msqrob/meta.yaml @@ -6,7 +6,7 @@ source: sha256: 334a7d2b323058b61b8cdf651a6daf6e28e0310bc8c61e83075561da8cad93e9 build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-mutoss/meta.yaml b/recipes/r-mutoss/meta.yaml index e8abff45e3081..b2625c9df2e59 100644 --- a/recipes/r-mutoss/meta.yaml +++ b/recipes/r-mutoss/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-nabor/meta.yaml b/recipes/r-nabor/meta.yaml index cfa113b7f12c0..8ff5874bfe13d 100644 --- a/recipes/r-nabor/meta.yaml +++ b/recipes/r-nabor/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-nanostringnorm/meta.yaml b/recipes/r-nanostringnorm/meta.yaml index 9903b4acdc8a6..d2009f049544a 100644 --- a/recipes/r-nanostringnorm/meta.yaml +++ b/recipes/r-nanostringnorm/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-phyext2/meta.yaml b/recipes/r-phyext2/meta.yaml index 5ef82f923d438..2c5422398ced0 100644 --- a/recipes/r-phyext2/meta.yaml +++ b/recipes/r-phyext2/meta.yaml @@ -17,7 +17,7 @@ build: noarch: generic merge_build_host: True # [win] - number: 3 + number: 4 rpaths: - lib/R/lib/ diff --git a/recipes/r-phylobase/meta.yaml b/recipes/r-phylobase/meta.yaml index a29f2ea545556..aa1a7814aa767 100644 --- a/recipes/r-phylobase/meta.yaml +++ b/recipes/r-phylobase/meta.yaml @@ -11,7 +11,7 @@ source: sha256: e7117b210ef406115e5523b794d8c2c5779640cee8c06e73751dc14c69322fd9 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-popgenreport/meta.yaml b/recipes/r-popgenreport/meta.yaml index 79e08119a1318..d8ddbd5681f07 100644 --- a/recipes/r-popgenreport/meta.yaml +++ b/recipes/r-popgenreport/meta.yaml @@ -15,8 +15,7 @@ source: build: noarch: generic - number: 0 - + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index 650015349163b..7acd71d1ad7ed 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.65.0' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-pscbs version: {{ version|replace("-", "_") }} @@ -15,14 +12,12 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ requirements: - build: - host: - r-base - bioconductor-dnacopy diff --git a/recipes/r-rapidr/meta.yaml b/recipes/r-rapidr/meta.yaml index 7d7d8a958b2bb..5c2cde667679c 100644 --- a/recipes/r-rapidr/meta.yaml +++ b/recipes/r-rapidr/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: generic merge_build_host: True # [win] - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-riborex/meta.yaml b/recipes/r-riborex/meta.yaml index a67037583abe6..3d00024347951 100644 --- a/recipes/r-riborex/meta.yaml +++ b/recipes/r-riborex/meta.yaml @@ -12,8 +12,7 @@ source: build: noarch: generic - number: 0 - + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-rnexml/meta.yaml b/recipes/r-rnexml/meta.yaml index 3b4c31691e629..3605db4c1a1ce 100644 --- a/recipes/r-rnexml/meta.yaml +++ b/recipes/r-rnexml/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-rtfbs/meta.yaml b/recipes/r-rtfbs/meta.yaml index ed5b25e388a8c..c122e6a21cd07 100644 --- a/recipes/r-rtfbs/meta.yaml +++ b/recipes/r-rtfbs/meta.yaml @@ -13,7 +13,7 @@ source: sha256: df6dcf42064e7ee6180bcd9c0ffaeb09c45bf282b5fdb2bc20f7397b9891390a build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sbpiper/meta.yaml b/recipes/r-sbpiper/meta.yaml index b5c04e452c905..92b59e46e42d8 100644 --- a/recipes/r-sbpiper/meta.yaml +++ b/recipes/r-sbpiper/meta.yaml @@ -17,7 +17,7 @@ build: noarch: generic merge_build_host: True # [win] - number: 2 + number: 3 rpaths: - lib/R/lib/ diff --git a/recipes/r-shaman/meta.yaml b/recipes/r-shaman/meta.yaml index c55df2773e8d1..84a79c30b2c90 100644 --- a/recipes/r-shaman/meta.yaml +++ b/recipes/r-shaman/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-shazam/meta.yaml b/recipes/r-shazam/meta.yaml index 3d0ac4eaf335a..41b207db8bcb0 100644 --- a/recipes/r-shazam/meta.yaml +++ b/recipes/r-shazam/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sigqc/meta.yaml b/recipes/r-sigqc/meta.yaml index 96d5014428135..71024a506cf4e 100644 --- a/recipes/r-sigqc/meta.yaml +++ b/recipes/r-sigqc/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sigtree/meta.yaml b/recipes/r-sigtree/meta.yaml index ff9c9f42a8149..a56752e90b0c5 100644 --- a/recipes/r-sigtree/meta.yaml +++ b/recipes/r-sigtree/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 3ce57e37d1c328720bb3ffc8c1f349c62b22e4d4de132f988ce9a42cbf3af0a1 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-stampp/meta.yaml b/recipes/r-stampp/meta.yaml index 3b28f0fef070c..245c133a28915 100644 --- a/recipes/r-stampp/meta.yaml +++ b/recipes/r-stampp/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: generic merge_build_host: True # [win] - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-stitch/meta.yaml b/recipes/r-stitch/meta.yaml index 244a4191d05b3..dd6aea69a52a4 100644 --- a/recipes/r-stitch/meta.yaml +++ b/recipes/r-stitch/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 script: '$R CMD INSTALL --build --install-tests .' requirements: diff --git a/recipes/r-structssi/meta.yaml b/recipes/r-structssi/meta.yaml index c5fdd52e1a321..503befa2fd499 100644 --- a/recipes/r-structssi/meta.yaml +++ b/recipes/r-structssi/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.1.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-structssi version: {{ version|replace("-", "_") }} @@ -15,15 +12,12 @@ source: build: noarch: generic - merge_build_host: True # [win] - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{posix}}zip # [win] host: - r-base - r-ggplot2 @@ -50,12 +44,3 @@ about: summary: Performs multiple testing corrections that take specific structure of hypotheses into account. license_family: GPL2 -extra: - recipe-maintainers: - - MathiasHaudgaard - - FrodePedersen - - ArneKr - - johanneskoester - - bgruening - - daler - - jdblischak diff --git a/recipes/r-swamp/meta.yaml b/recipes/r-swamp/meta.yaml index d618524a27283..1259b7ce31cde 100644 --- a/recipes/r-swamp/meta.yaml +++ b/recipes/r-swamp/meta.yaml @@ -1,8 +1,5 @@ {% set version = '1.4.1' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-swamp version: {{ version|replace("-", "_") }} @@ -15,35 +12,28 @@ source: build: noarch: generic - merge_build_host: True # [win] - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ requirements: - build: - - {{posix}}zip # [win] - host: - r-base - r-mass - r-amap - r-gplots - - 'bioconductor-impute >=1.54.0,<1.56.0' - + - bioconductor-impute run: - r-base - r-mass - r-amap - r-gplots - - 'bioconductor-impute >=1.54.0,<1.56.0' + - bioconductor-impute test: commands: - - - $R -e "library('swamp')" # [not win] - - "\"%R%\" -e \"library('swamp')\"" # [win] + - $R -e "library('swamp')" about: home: https://CRAN.R-project.org/package=swamp @@ -56,12 +46,3 @@ about: and removal of principal components.' license_family: GPL3 -extra: - recipe-maintainers: - - MathiasHaudgaard - - FrodePedersen - - ArneKr - - johanneskoester - - bgruening - - daler - - jdblischak diff --git a/recipes/r-tcga2stat/meta.yaml b/recipes/r-tcga2stat/meta.yaml index fcb756acef3a4..7e48967daec6f 100644 --- a/recipes/r-tcga2stat/meta.yaml +++ b/recipes/r-tcga2stat/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: generic merge_build_host: True # [win] - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-tigger/meta.yaml b/recipes/r-tigger/meta.yaml index 3642d15cad287..a2af35cdaf457 100644 --- a/recipes/r-tigger/meta.yaml +++ b/recipes/r-tigger/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 666908fbda5916581bd5cc01c2c1fae4679b7be7c3efe4a17ab42b4536d444db build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-umi4c/meta.yaml b/recipes/r-umi4c/meta.yaml index 302277e272f89..3ae921544f29e 100644 --- a/recipes/r-umi4c/meta.yaml +++ b/recipes/r-umi4c/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-vcfr/meta.yaml b/recipes/r-vcfr/meta.yaml index b637b54451efe..32027c84ae191 100644 --- a/recipes/r-vcfr/meta.yaml +++ b/recipes/r-vcfr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 5ffcf9980c1936b9be41b92d5887c56a7ec6e3cf197e5ef7c78aefa8aba20499 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-xcell/meta.yaml b/recipes/r-xcell/meta.yaml index c135e8e4f7ba8..c06d172303a0e 100755 --- a/recipes/r-xcell/meta.yaml +++ b/recipes/r-xcell/meta.yaml @@ -13,7 +13,7 @@ source: build: script: $R CMD INSTALL --build . - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/rabix-bunny/meta.yaml b/recipes/rabix-bunny/meta.yaml index 66d1390fb0d38..5d0ffcfcdacad 100644 --- a/recipes/rabix-bunny/meta.yaml +++ b/recipes/rabix-bunny/meta.yaml @@ -10,7 +10,7 @@ source: md5: 6533e187795e0cc69b1dd3119a724a48 build: - number: 7 + number: 8 noarch: generic requirements: diff --git a/recipes/rad_haplotyper/meta.yaml b/recipes/rad_haplotyper/meta.yaml index 179d4115b8828..48f16e1bd288d 100644 --- a/recipes/rad_haplotyper/meta.yaml +++ b/recipes/rad_haplotyper/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 1a9ca21ec215e6dae7233918daa2f48b9bb2262a630e0acbdde49ab1f2b8984e build: - number: 1 + number: 2 skip: True # [osx] # needs ddocent, only available on linux diff --git a/recipes/razers3/meta.yaml b/recipes/razers3/meta.yaml index 9ee745307b67e..2029d7692fa10 100644 --- a/recipes/razers3/meta.yaml +++ b/recipes/razers3/meta.yaml @@ -7,7 +7,7 @@ source: sha256: df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/rdp_classifier/meta.yaml b/recipes/rdp_classifier/meta.yaml index 11222c0eeec0d..2a9a638e5f15e 100644 --- a/recipes/rdp_classifier/meta.yaml +++ b/recipes/rdp_classifier/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/recycler/meta.yaml b/recipes/recycler/meta.yaml index b0732dee24f69..0177a7333fc04 100644 --- a/recipes/recycler/meta.yaml +++ b/recipes/recycler/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: python - number: 2 + number: 3 source: url: https://github.com/Shamir-Lab/Recycler/archive/v{{version}}.tar.gz diff --git a/recipes/refseq_masher/meta.yaml b/recipes/refseq_masher/meta.yaml index d9572d4d5e3cc..7ee354c65d612 100644 --- a/recipes/refseq_masher/meta.yaml +++ b/recipes/refseq_masher/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 script: python -m pip install --no-deps --ignore-installed . entry_points: - refseq_masher = refseq_masher.cli:cli diff --git a/recipes/repeatscout/build.sh b/recipes/repeatscout/build.sh index e2918015006f7..d4edcbd28acb1 100644 --- a/recipes/repeatscout/build.sh +++ b/recipes/repeatscout/build.sh @@ -1,5 +1,6 @@ #!/bin/sh set -x -e +mkdir -p ${PREFIX}/bin make cp RepeatScout build_lmer_table ${PREFIX}/bin diff --git a/recipes/repeatscout/meta.yaml b/recipes/repeatscout/meta.yaml index b854f1919ae96..0b9fda9b7bf2c 100644 --- a/recipes/repeatscout/meta.yaml +++ b/recipes/repeatscout/meta.yaml @@ -7,7 +7,7 @@ source: sha256: bda6f782382f2b7dcb6a004b7da586d5046b3c12429b158e24787be62de6199c build: - number: 1 + number: 2 skip: True # [not linux] requirements: diff --git a/recipes/repenrich/build.sh b/recipes/repenrich/build.sh index ff88ccaf879be..2b1fd798788c9 100644 --- a/recipes/repenrich/build.sh +++ b/recipes/repenrich/build.sh @@ -1,4 +1,4 @@ #!/bin/bash - +mkdir -p ${PREFIX}/bin cp RepEnrich.py $PREFIX/bin cp RepEnrich_setup.py $PREFIX/bin diff --git a/recipes/repenrich/meta.yaml b/recipes/repenrich/meta.yaml index aaf72a0d475a8..c45a0d1aefcfd 100644 --- a/recipes/repenrich/meta.yaml +++ b/recipes/repenrich/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/reveal/meta.yaml b/recipes/reveal/meta.yaml index e6e3ced187d4a..a37b3e96e282b 100644 --- a/recipes/reveal/meta.yaml +++ b/recipes/reveal/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 skip: True # [not py27] source: @@ -16,20 +16,20 @@ source: requirements: build: - - {{ compiler('c') }} + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - python - - setuptools - - intervaltree - - networkx 2.0* - - libdivsufsort - + - python + - setuptools + - intervaltree + - networkx 2.0* + - libdivsufsort run: - - python - - intervaltree - - networkx 2.0* - - libdivsufsort - - matplotlib + - python + - intervaltree + - networkx 2.0* + - libdivsufsort + - matplotlib test: commands: diff --git a/recipes/revtrans/meta.yaml b/recipes/revtrans/meta.yaml index 7cc10428adc0c..73dde27d2227a 100644 --- a/recipes/revtrans/meta.yaml +++ b/recipes/revtrans/meta.yaml @@ -19,7 +19,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/ribodiff/meta.yaml b/recipes/ribodiff/meta.yaml index 4fdf107cf26a6..0e8d8266b9006 100644 --- a/recipes/ribodiff/meta.yaml +++ b/recipes/ribodiff/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/riboplot/meta.yaml b/recipes/riboplot/meta.yaml index a3f12b2716e42..d52825e9de65d 100644 --- a/recipes/riboplot/meta.yaml +++ b/recipes/riboplot/meta.yaml @@ -8,7 +8,8 @@ source: build: noarch: python - number: 2 + number: 3 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - riboplot = riboplot.riboplot:run - ribocount = riboplot.ribocount:run @@ -17,9 +18,15 @@ requirements: host: - python <3 - pip + - matplotlib <=1.4.3 + - numpy + - pysam <=0.8.3 + - mock ==1.0.1 + - bedtools <=2.24.0 run: - python <3 - matplotlib <=1.4.3 + - numpy - pysam <=0.8.3 - mock ==1.0.1 - bedtools <=2.24.0 diff --git a/recipes/riboraptor/meta.yaml b/recipes/riboraptor/meta.yaml index 3c9257e71ebfb..85b0e349100a3 100644 --- a/recipes/riboraptor/meta.yaml +++ b/recipes/riboraptor/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - riboraptor=riboraptor.cli:cli script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/rmats2sashimiplot/meta.yaml b/recipes/rmats2sashimiplot/meta.yaml index cf3472e661803..c94cdc8066d98 100644 --- a/recipes/rmats2sashimiplot/meta.yaml +++ b/recipes/rmats2sashimiplot/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv preserve_egg_dir: true diff --git a/recipes/rnashapes/2.1.6/meta.yaml b/recipes/rnashapes/2.1.6/meta.yaml index 5258d53827889..403144a40cc8a 100644 --- a/recipes/rnashapes/2.1.6/meta.yaml +++ b/recipes/rnashapes/2.1.6/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/bgruening/download_store/raw/master/RNAshapes/RNAshapes-2.1.6.tar.gz build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/rnasketch/meta.yaml b/recipes/rnasketch/meta.yaml index 581c05d9061a7..61e36ef597098 100644 --- a/recipes/rnasketch/meta.yaml +++ b/recipes/rnasketch/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 1 + number: 2 requirements: host: diff --git a/recipes/rnaz/meta.yaml b/recipes/rnaz/meta.yaml index b1870f2a42c1e..4c145f042e073 100644 --- a/recipes/rnaz/meta.yaml +++ b/recipes/rnaz/meta.yaml @@ -9,7 +9,7 @@ source: - "rnaz.patch" build: - number: 0 + number: 1 skip: True # [osx] diff --git a/recipes/roary/meta.yaml b/recipes/roary/meta.yaml index 6e41697beae3b..e400b6d180432 100644 --- a/recipes/roary/meta.yaml +++ b/recipes/roary/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: url: http://search.cpan.org/CPAN/authors/id/A/AJ/AJPAGE/Bio-Roary-{{ version }}.tar.gz diff --git a/recipes/rpkmforgenes/build.sh b/recipes/rpkmforgenes/build.sh index 50c69548e36f0..afef0220b2b50 100644 --- a/recipes/rpkmforgenes/build.sh +++ b/recipes/rpkmforgenes/build.sh @@ -2,4 +2,5 @@ set -x set -e fn=rpkmforgenes.py +mkdir -p ${PREFIX}/bin chmod +x ${fn} && mv ${fn} ${PREFIX}/bin diff --git a/recipes/rpkmforgenes/meta.yaml b/recipes/rpkmforgenes/meta.yaml index 283756ba7b374..8e77186ff4655 100644 --- a/recipes/rpkmforgenes/meta.yaml +++ b/recipes/rpkmforgenes/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/danielramskold/S3_species-specific_sequencing/archive/1.0.1.tar.gz diff --git a/recipes/rscape/0.8.3/meta.yaml b/recipes/rscape/0.8.3/meta.yaml index 23e0419a6b3fb..db146f3e71c39 100644 --- a/recipes/rscape/0.8.3/meta.yaml +++ b/recipes/rscape/0.8.3/meta.yaml @@ -11,7 +11,7 @@ source: - R2R_Makefile.in.patch build: - number: 2 + number: 3 skip: True # [osx] diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml index 179375c392abc..5a90984a0ca0a 100644 --- a/recipes/rseqc/meta.yaml +++ b/recipes/rseqc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d5f4cb2c24a7348929f5c4947d84c5869e8cd2cba5ba5248d991ebb37c4c6b3d build: - number: 0 + number: 1 skip: True # [py2k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " @@ -21,6 +21,7 @@ requirements: - pip - python - cython >=0.12 + - nose run: - bx-python - numpy diff --git a/recipes/ruby-dna-tools/meta.yaml b/recipes/ruby-dna-tools/meta.yaml index cff4356e9e39a..7e46042dd40d7 100644 --- a/recipes/ruby-dna-tools/meta.yaml +++ b/recipes/ruby-dna-tools/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/Carldeboer/Ruby-DNA-Tools/archive/{{ version }}.tar.gz diff --git a/recipes/ruffus/2.4.1/meta.yaml b/recipes/ruffus/2.4.1/meta.yaml index 8dd6fc40045fa..4ba1dcc8da97f 100644 --- a/recipes/ruffus/2.4.1/meta.yaml +++ b/recipes/ruffus/2.4.1/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/rust-bio-tools/build.sh b/recipes/rust-bio-tools/build.sh index ff59ae121d0e9..8d3054248e442 100644 --- a/recipes/rust-bio-tools/build.sh +++ b/recipes/rust-bio-tools/build.sh @@ -5,6 +5,7 @@ if [ "$(uname)" == "Darwin" ]; then # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory export HOME="/Users/distiller" + echo "HOME is $HOME" # according to https://github.com/rust-lang/cargo/issues/2422#issuecomment-198458960 removing circle ci default configuration solves cargo trouble downloading crates git config --global --unset url.ssh://git@github.com.insteadOf diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index d9d7cf2cd6913..d0984bacfb077 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{version}} build: - number: 0 + number: 1 source: url: https://github.com/rust-bio/rust-bio-tools/archive/v{{ version }}.tar.gz diff --git a/recipes/rust-overlaps/meta.yaml b/recipes/rust-overlaps/meta.yaml index 46ff35e76bdac..d1ed2e95d5fb6 100644 --- a/recipes/rust-overlaps/meta.yaml +++ b/recipes/rust-overlaps/meta.yaml @@ -5,7 +5,7 @@ package: version: {{version}} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/rvtests/meta.yaml b/recipes/rvtests/meta.yaml index e0c081d5a8170..89b45bd20dbcd 100644 --- a/recipes/rvtests/meta.yaml +++ b/recipes/rvtests/meta.yaml @@ -3,16 +3,12 @@ package: version: "2.0.7" build: - number: 2 + number: 3 source: url: https://github.com/zhanxw/rvtests/releases/download/v2.1.0/rvtests_linux64.tar.gz sha256: 516637f08edeadf0bd7c0277ad2b5badc4e80e416b7c8b5cf4bc1a243405455e -channels: - - defaults - - conda-forge - requirements: build: - {{ compiler('cxx') }} @@ -24,12 +20,10 @@ requirements: host: - zlib - clangdev # [osx] - - libcxx 4.0.* # [osx] - - openmp 4.0.* # [osx] + - llvm-openmp # [osx] run: - zlib - - libcxx >=4.0 # [osx] - - openmp >=4.0 # [osx] + - llvm-openmp # [osx] test: commands: diff --git a/recipes/samclip/meta.yaml b/recipes/samclip/meta.yaml index e7e868cf079ac..5db264267cf57 100644 --- a/recipes/samclip/meta.yaml +++ b/recipes/samclip/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/samsift/meta.yaml b/recipes/samsift/meta.yaml index e06546ca434a6..2a12576480703 100644 --- a/recipes/samsift/meta.yaml +++ b/recipes/samsift/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 3 entry_points: - samsift = samsift.samsift:main - samsift-norm-sam = samsift.samsift_norm_sam:main diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 00a23491e2c09..40e25f68c730c 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 3 + number: 4 entry_points: - compile_stats=samsifter.stats.compile_stats:main - count_taxon_reads=samsifter.tools.count_taxon_reads:main diff --git a/recipes/samtools/1.6/meta.yaml b/recipes/samtools/1.6/meta.yaml index e40a56f0c8496..189f88699de35 100644 --- a/recipes/samtools/1.6/meta.yaml +++ b/recipes/samtools/1.6/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 diff --git a/recipes/sbg-cwl-runner/meta.yaml b/recipes/sbg-cwl-runner/meta.yaml index 727a049e2e63d..1cf7e3866ff56 100644 --- a/recipes/sbg-cwl-runner/meta.yaml +++ b/recipes/sbg-cwl-runner/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: $PYTHON -m pip install --no-deps --ignore-installed --no-cache-dir . requirements: diff --git a/recipes/scaffold_builder/meta.yaml b/recipes/scaffold_builder/meta.yaml index bffcbf2686650..6040b5d11eafc 100644 --- a/recipes/scaffold_builder/meta.yaml +++ b/recipes/scaffold_builder/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/scg/meta.yaml b/recipes/scg/meta.yaml index 84abfc8db9d87..10a5e1a6c7cef 100644 --- a/recipes/scg/meta.yaml +++ b/recipes/scg/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python script: python -m pip install --no-deps --ignore-installed . - number: 1 + number: 2 requirements: host: diff --git a/recipes/scrublet/meta.yaml b/recipes/scrublet/meta.yaml index ee1192f2db094..ea7e7ad0b02c6 100644 --- a/recipes/scrublet/meta.yaml +++ b/recipes/scrublet/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 592b443292fdc69d4228ffdf63493d81a537d6ae987c3c631c5ca0d7654c99f6 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " requirements: diff --git a/recipes/secapr/meta.yaml b/recipes/secapr/meta.yaml index 8c7a8da9e9da3..d95f433d611c1 100644 --- a/recipes/secapr/meta.yaml +++ b/recipes/secapr/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 1 + number: 2 script: python -m pip install --no-deps --ignore-installed . entry_points: - secapr = secapr.__main__:main diff --git a/recipes/seedme/1.2.0/license.patch b/recipes/seedme/1.2.0/license.patch deleted file mode 100644 index 5398cc7340634..0000000000000 --- a/recipes/seedme/1.2.0/license.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- LICENSE.txt 2016-02-16 20:29:05.126504288 +0000 -+++ ../seedme-seedme-python-client-7cc673aa8bfd/LICENSE.txt 2015-12-16 05:44:57.000000000 +0000 -@@ -0,0 +1,10 @@ -+Copyright (c) The Regents of the University of California, 2015 -+All Rights Reserved -+ -+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -+ -+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -+ -+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -+ -+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/recipes/seedme/1.2.0/meta.yaml b/recipes/seedme/1.2.0/meta.yaml deleted file mode 100644 index 3a161e83a8393..0000000000000 --- a/recipes/seedme/1.2.0/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -package: - name: seedme - version: "1.2.0" - -source: - url: https://pypi.python.org/packages/source/s/seedme/seedme-1.2.0.tar.gz - md5: d8c342c6c5f345fd5a8afabdaf14a307 - patches: - - license.patch - -build: - noarch: python - number: 1 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - -requirements: - host: - - python <3 - - pip - run: - - python <3 - - requests ==2.7.0 - - curl - -test: - commands: - - seedme.py --help > /dev/null - -about: - home: https://www.seedme.org/downloads - license: GPL - license_file: LICENSE.txt - summary: 'Python REST like client for SeedMe.org' diff --git a/recipes/seedme/meta.yaml b/recipes/seedme/meta.yaml index 523619ef0faf1..4dcfc5603752d 100644 --- a/recipes/seedme/meta.yaml +++ b/recipes/seedme/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - number: 1 + number: 2 requirements: host: diff --git a/recipes/segemehl/meta.yaml b/recipes/segemehl/meta.yaml index 841078bf6c490..7a27c02660ecf 100644 --- a/recipes/segemehl/meta.yaml +++ b/recipes/segemehl/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] source: diff --git a/recipes/segway/meta.yaml b/recipes/segway/meta.yaml index 5f26c6f00b334..b704cb84ad895 100644 --- a/recipes/segway/meta.yaml +++ b/recipes/segway/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/seq-seq-pan/meta.yaml b/recipes/seq-seq-pan/meta.yaml index c669b40c09299..31bdd8ab656d0 100644 --- a/recipes/seq-seq-pan/meta.yaml +++ b/recipes/seq-seq-pan/meta.yaml @@ -9,7 +9,7 @@ source: md5: 3d2b2c835d9a7f8412551e9462202c60 build: - number: 3 + number: 4 noarch: python requirements: diff --git a/recipes/seq2hla/meta.yaml b/recipes/seq2hla/meta.yaml index 362afdfeba483..8145cff900139 100644 --- a/recipes/seq2hla/meta.yaml +++ b/recipes/seq2hla/meta.yaml @@ -3,7 +3,7 @@ package: version: '2.2' build: noarch: generic - number: 1 + number: 2 source: url: https://bitbucket.org/sebastian_boegel/seq2hla/get/95e554b1d191.zip sha256: 2dbafd409ecb2a1d0dac9a6d6c33cd0044503263b00a8e2cd662f82437112555 diff --git a/recipes/seqan/2.1.1/meta.yaml b/recipes/seqan/2.1.1/meta.yaml index e76b19a5754da..057dd3cdc6d88 100644 --- a/recipes/seqan/2.1.1/meta.yaml +++ b/recipes/seqan/2.1.1/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 test: commands: diff --git a/recipes/seqan/meta.yaml b/recipes/seqan/meta.yaml index 3237a15dda3c2..3ee3b88d622c3 100644 --- a/recipes/seqan/meta.yaml +++ b/recipes/seqan/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 test: commands: diff --git a/recipes/seqmagick/meta.yaml b/recipes/seqmagick/meta.yaml index 64aa1bb95d93d..1ce8ddfba4e86 100644 --- a/recipes/seqmagick/meta.yaml +++ b/recipes/seqmagick/meta.yaml @@ -10,13 +10,15 @@ build: noarch: python entry_points: - seqmagick = seqmagick.scripts.cli:main - number: 2 + number: 3 script: python -m pip install --no-deps --ignore-installed . requirements: host: - python >3 - pip + - nose + - biopython >=1.70 run: - python >3 - biopython >=1.70 diff --git a/recipes/seqprep/1.1/build.sh b/recipes/seqprep/1.1/build.sh deleted file mode 100644 index 47700485ccc3f..0000000000000 --- a/recipes/seqprep/1.1/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -mkdir -p ${PREFIX}/bin -make CC=$CC CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS -lz -lm" -cp SeqPrep ${PREFIX}/bin diff --git a/recipes/seqprep/1.1/cflags.patch b/recipes/seqprep/1.1/cflags.patch deleted file mode 100644 index 37b0529e4a6c6..0000000000000 --- a/recipes/seqprep/1.1/cflags.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- Makefile 2013-05-31 17:44:45.000000000 +0000 -+++ Makefile.new 2015-11-12 19:07:34.066685982 +0000 -@@ -1,8 +1,8 @@ - CC=gcc --CFLAGS=-c -Wall -Werror -O0 -g -+CFLAGS=-c -Wall -O0 -g -I${PREFIX}/include - #recommended options: -ffast-math -ftree-vectorize -march=core2 -mssse3 -O3 --COPTS= --LDFLAGS=-lz -lm -+COPTS= -ffast-math -ftree-vectorize -mtune=core2 -mssse3 -O3 -+LDFLAGS=-L${PREFIX}/lib -lz -lm - SOURCES=SeqPrep.c utils.c stdaln.c - OBJECTS=$(SOURCES:.c=.o) - EXECUTABLE=SeqPrep diff --git a/recipes/seqprep/1.1/meta.yaml b/recipes/seqprep/1.1/meta.yaml deleted file mode 100644 index 8147c800653a4..0000000000000 --- a/recipes/seqprep/1.1/meta.yaml +++ /dev/null @@ -1,34 +0,0 @@ -build: - number: 2 - -package: - name: seqprep - version: 1.1 - -source: - url: https://github.com/jstjohn/SeqPrep/archive/v1.1.tar.gz - md5: 42bd8e62e8bf99befb37ed29ce047115 - patches: - - cflags.patch - -requirements: - build: - - {{ compiler('c') }} - host: - - zlib - run: - - zlib - -test: - commands: - - 'SeqPrep -h 2>&1 | grep SeqPrep' - -about: - home: https://github.com/jstjohn/SeqPrep - summary: 'Tool for stripping adaptors and/or merging paired reads with overlap into single reads.' - license: MIT - -extra: - identifiers: - - biotools:seqprep - - doi:10.1134/S1021443716020175 diff --git a/recipes/sequana/meta.yaml b/recipes/sequana/meta.yaml index 25c94d1b51dde..07a3040593b40 100644 --- a/recipes/sequana/meta.yaml +++ b/recipes/sequana/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: python preserve_egg_dir: True - number: 1 + number: 2 entry_points: - sequana_gui=sequana.gui.sequana_gui:main - sequanix=sequana.gui.sequana_gui:main diff --git a/recipes/sequencetools/meta.yaml b/recipes/sequencetools/meta.yaml index df71be668a62f..5904bed6cae89 100644 --- a/recipes/sequencetools/meta.yaml +++ b/recipes/sequencetools/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/sga/meta.yaml b/recipes/sga/meta.yaml index 2d4bb1797503e..6a00741747c80 100644 --- a/recipes/sga/meta.yaml +++ b/recipes/sga/meta.yaml @@ -14,7 +14,7 @@ source: - configure.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/shorah/1.0.0/meta.yaml b/recipes/shorah/1.0.0/meta.yaml index 9cf0759e916bf..02a046fb995d5 100644 --- a/recipes/shorah/1.0.0/meta.yaml +++ b/recipes/shorah/1.0.0/meta.yaml @@ -4,7 +4,7 @@ package: build: skip: True # [py3k] - number: 2 + number: 3 source: url: https://github.com/cbg-ethz/shorah/releases/download/v1.0.0/shorah-1.0.0.tar.bz2 diff --git a/recipes/shorah/1.1.3/meta.yaml b/recipes/shorah/1.1.3/meta.yaml index c34bf36e02597..514870fca5981 100644 --- a/recipes/shorah/1.1.3/meta.yaml +++ b/recipes/shorah/1.1.3/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml index eb2cafbd6d174..cfc4ecbca1f86 100644 --- a/recipes/shortstack/meta.yaml +++ b/recipes/shortstack/meta.yaml @@ -12,11 +12,11 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: - - perl 5.* + - perl - samtools 1.* - bowtie - viennarna 2.* diff --git a/recipes/sibelia/meta.yaml b/recipes/sibelia/meta.yaml index 50483dd07d56c..ebd5d0ba04a68 100644 --- a/recipes/sibelia/meta.yaml +++ b/recipes/sibelia/meta.yaml @@ -9,10 +9,11 @@ source: sha256: bfc530190967cadd2d1e9779eeb1700f494c115049da878116c4540c5586e813 build: - number: 1 + number: 2 requirements: build: + - {{ compiler('c') }} - {{ compiler('cxx') }} - cmake run: diff --git a/recipes/sicer/meta.yaml b/recipes/sicer/meta.yaml index 6c696afb41bcb..611f2b35b2d67 100644 --- a/recipes/sicer/meta.yaml +++ b/recipes/sicer/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: run: diff --git a/recipes/sickle-trim/build.sh b/recipes/sickle-trim/build.sh index aa77c7f72f432..46403c59d26b2 100644 --- a/recipes/sickle-trim/build.sh +++ b/recipes/sickle-trim/build.sh @@ -3,6 +3,6 @@ LDFLAGS="$LDFLAGS -L$PREFIX/lib" CFLAGS="$CFLAGS -Wall -pedantic -I$PREFIX/include -DVERSION=$PKG_VERSION" -make CC=cc CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" -j$CPU_COUNT +make CC=$CC CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" -j$CPU_COUNT mkdir -p $PREFIX/bin cp sickle $PREFIX/bin diff --git a/recipes/sickle-trim/meta.yaml b/recipes/sickle-trim/meta.yaml index 9a12a8789651f..85c264999de34 100644 --- a/recipes/sickle-trim/meta.yaml +++ b/recipes/sickle-trim/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/sickle/meta.yaml b/recipes/sickle/meta.yaml index 2c405e2a85226..8987f02aa32b0 100644 --- a/recipes/sickle/meta.yaml +++ b/recipes/sickle/meta.yaml @@ -11,8 +11,8 @@ source: build: noarch: python - number: 0 - script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt + number: 1 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: host: diff --git a/recipes/sierrapy/meta.yaml b/recipes/sierrapy/meta.yaml index 5c058f94f1f0b..64b2335bdaad2 100644 --- a/recipes/sierrapy/meta.yaml +++ b/recipes/sierrapy/meta.yaml @@ -14,7 +14,7 @@ build: script: python -m pip install --no-deps --ignore-installed . entry_points: - sierrapy = sierrapy.cmds:main - number: 1 + number: 2 requirements: host: diff --git a/recipes/simlord/build.sh b/recipes/simlord/build.sh deleted file mode 100644 index 0456c5ca37e6b..0000000000000 --- a/recipes/simlord/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - diff --git a/recipes/simlord/meta.yaml b/recipes/simlord/meta.yaml index 8e257e25af9a8..e38b16c21f886 100644 --- a/recipes/simlord/meta.yaml +++ b/recipes/simlord/meta.yaml @@ -7,8 +7,9 @@ source: sha256: 40abec8e31c88f69b485a262abae200b27ebe4e937fe58a3d7508dfa22739dac build: - number: 2 + number: 3 skip: True # [py2k] + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - simlord = simlord.simlord:main @@ -17,12 +18,8 @@ requirements: - {{ compiler('c') }} host: - python - - setuptools - - numpy - - scipy - - pysam >=0.8.4 + - pip - cython - - dinopy run: - python - numpy diff --git a/recipes/singlecell-barcodes/meta.yaml b/recipes/singlecell-barcodes/meta.yaml index 265bbbad20574..9306cc86fcd07 100644 --- a/recipes/singlecell-barcodes/meta.yaml +++ b/recipes/singlecell-barcodes/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/roryk/singlecell-barcodes/archive/6a669fb.tar.gz diff --git a/recipes/sis/meta.yaml b/recipes/sis/meta.yaml index 5a67f2b35cd1f..13828c3951e85 100644 --- a/recipes/sis/meta.yaml +++ b/recipes/sis/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 2 + number: 3 requirements: host: - python >=3 diff --git a/recipes/sistr_cmd/meta.yaml b/recipes/sistr_cmd/meta.yaml index c5e59adbb476d..f2654d24181ec 100644 --- a/recipes/sistr_cmd/meta.yaml +++ b/recipes/sistr_cmd/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/smallgenomeutilities/0.1/meta.yaml b/recipes/smallgenomeutilities/0.1/meta.yaml deleted file mode 100644 index b8b1696de529b..0000000000000 --- a/recipes/smallgenomeutilities/0.1/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -package: - name: smallgenomeutilities - version: "0.1" - -source: - url: https://pypi.io/packages/source/s/smallgenomeutilities/smallgenomeutilities-0.1.tar.gz - md5: 339439b1f97ecb1fc91378f78a06bebe - -build: - noarch: python - number: 1 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - -requirements: - host: - - python >=3 - - pip - run: - - python >=3 - - biopython - - numpy - - progress - - pysam - -test: - imports: - - smallgenomeutilities - commands: - - convert_qr -h - - convert_reference -h - -about: - home: https://github.com/cbg-ethz/smallgenomeutilities - license: GNU General Public License v2 or later (GPLv2+) - summary: 'A collection of scripts that are useful for dealing with viral RNA NGS data' diff --git a/recipes/smallgenomeutilities/0.2.1/meta.yaml b/recipes/smallgenomeutilities/0.2.1/meta.yaml index 57daa69a49d6f..827d6409a280c 100644 --- a/recipes/smallgenomeutilities/0.2.1/meta.yaml +++ b/recipes/smallgenomeutilities/0.2.1/meta.yaml @@ -1,6 +1,5 @@ {% set name = "smallgenomeutilities" %} {% set version = "0.2.1" %} -{% set md5 = "ad135513329f90d116a71177b7c567b6" %} {% set sha256 = "81bf3c83169b1fe3304f32a73773ddf559bbde7adda59c1a5a3d816cb746b138" %} package: @@ -9,12 +8,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0]|lower }}/{{ name|lower }}/{{ name|lower }}-{{ version }}.tar.gz - md5: {{ md5 }} sha256: {{ sha256 }} build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/smcounter2/meta.yaml b/recipes/smcounter2/meta.yaml index 13389082339e3..8b7eb82563e2c 100644 --- a/recipes/smcounter2/meta.yaml +++ b/recipes/smcounter2/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/qiaseq/qiaseq-smcounter-v2/archive/{{ revision }}.tar.gz diff --git a/recipes/smeg/meta.yaml b/recipes/smeg/meta.yaml index 7a712bb4d13e6..519a4034d4617 100644 --- a/recipes/smeg/meta.yaml +++ b/recipes/smeg/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 0 + number: 1 source: url: https://github.com/ohlab/SMEG/archive/1.1.tar.gz diff --git a/recipes/snakeparse/meta.yaml b/recipes/snakeparse/meta.yaml index 4521518043d33..a772bac44b944 100644 --- a/recipes/snakeparse/meta.yaml +++ b/recipes/snakeparse/meta.yaml @@ -6,7 +6,7 @@ package: build: noarch: python - number: 1 + number: 2 script: python -m pip install --no-deps --ignore-installed . entry_points: - snakeparse=snakeparse.__main__:main diff --git a/recipes/snns/meta.yaml b/recipes/snns/meta.yaml index 434827614b4e9..4f2e43c0e76b6 100644 --- a/recipes/snns/meta.yaml +++ b/recipes/snns/meta.yaml @@ -4,7 +4,7 @@ package: build: skip: True # [not linux] - number: 1 + number: 2 source: # Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz diff --git a/recipes/snpeff/4.1l/meta.yaml b/recipes/snpeff/4.1l/meta.yaml index 050e245a3586d..26dca7ef69372 100644 --- a/recipes/snpeff/4.1l/meta.yaml +++ b/recipes/snpeff/4.1l/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 6 + number: 7 source: md5: 43dd4b41f3223bbb4cc094ec5c5e2aac diff --git a/recipes/snpiphy/meta.yaml b/recipes/snpiphy/meta.yaml index bfed51f3e0e4a..a8256c349a205 100644 --- a/recipes/snpiphy/meta.yaml +++ b/recipes/snpiphy/meta.yaml @@ -9,15 +9,15 @@ source: md5: efa7722d020283a4308f11bb59692025 build: - number: 0 + number: 1 noarch: python requirements: host: - - python <3 + - python >=3 - pip run: - - python <3 + - python >=3 - biopython - numpy - pandas diff --git a/recipes/snpsift/4.2/meta.yaml b/recipes/snpsift/4.2/meta.yaml index 0cd351d6a4243..7b0e72ea016f0 100644 --- a/recipes/snpsift/4.2/meta.yaml +++ b/recipes/snpsift/4.2/meta.yaml @@ -9,7 +9,7 @@ package: build: noarch: generic - number: 3 + number: 4 source: url: https://downloads.sourceforge.net/project/snpeff/snpEff_{{ snpeff_ver }}_core.zip diff --git a/recipes/snpsplit/0.3.3/build.sh b/recipes/snpsplit/0.3.3/build.sh deleted file mode 100644 index f79dc1366a439..0000000000000 --- a/recipes/snpsplit/0.3.3/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -grep -l -r "/usr/bin/perl" . | xargs sed -i.bak -e 's/usr\/bin\/perl/usr\/bin\/env perl/g' - -mkdir -p $PREFIX/bin -cp SNPsplit $PREFIX/bin -cp SNPsplit_genome_preparation $PREFIX/bin -cp tag2sort $PREFIX/bin - -chmod a+x $PREFIX/bin/SNPsplit -chmod a+x $PREFIX/bin/SNPsplit_genome_preparation -chmod a+x $PREFIX/bin/tag2sort diff --git a/recipes/snpsplit/0.3.3/meta.yaml b/recipes/snpsplit/0.3.3/meta.yaml deleted file mode 100644 index ebf0b79a03e3d..0000000000000 --- a/recipes/snpsplit/0.3.3/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "0.3.3" %} - -package: - name: snpsplit - version: {{ version }} - -source: - url: https://github.com/FelixKrueger/SNPsplit/archive/{{ version }}.tar.gz - sha256: 7912581e0aa08155f140edf55ef0a19a9dd3b4d568fe13c2d1e38192b3cc6981 - -build: - noarch: generic - number: 1 - -requirements: - run: - - perl - - samtools >=1.7 - -test: - commands: - - SNPsplit_genome_preparation --version - - SNPsplit --version - -about: - home: https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/ - summary: SNPsplit is an allele-specific alignment sorter which is designed to - read in alignment files in SAM/BAM format and determine the allelic - origin of reads that cover known SNP positions. - license: GNU General Public License v3 (GPLv3) - license_family: GPL3 - -extra: - identifiers: - - doi:10.12688/f1000research.9037.2 diff --git a/recipes/snpsplit/meta.yaml b/recipes/snpsplit/meta.yaml index fd3e4723c6280..7263b1e97394e 100644 --- a/recipes/snpsplit/meta.yaml +++ b/recipes/snpsplit/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/snvphyl-tools/meta.yaml b/recipes/snvphyl-tools/meta.yaml index 064100a1fe9c7..3a7a770f80a86 100644 --- a/recipes/snvphyl-tools/meta.yaml +++ b/recipes/snvphyl-tools/meta.yaml @@ -7,7 +7,7 @@ source: sha256: cf9ea45b221a69a10adc2bc09db6f0891cfeb990cc1d5be2be86d730e985b16c build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/sonicparanoid/meta.yaml b/recipes/sonicparanoid/meta.yaml index 37ee348bf5683..06d1ede826d72 100644 --- a/recipes/sonicparanoid/meta.yaml +++ b/recipes/sonicparanoid/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 7ec5737d5cbebbf58e4f970dae5de1075da7a549a66f9b2cf22192acb95b9353 build: - number: 0 + number: 1 skip: True # [py2k] requirements: @@ -28,6 +28,7 @@ requirements: - mmseqs2 ==6.f5a1c - make - python + - cython - biopython >=1.67 - pandas >=0.22.0 - numpy >=1.13.0 diff --git a/recipes/sonlib/meta.yaml b/recipes/sonlib/meta.yaml index 520d847ddea0d..73ab7fdf6ae2d 100644 --- a/recipes/sonlib/meta.yaml +++ b/recipes/sonlib/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/spades/3.11.1/meta.yaml b/recipes/spades/3.11.1/meta.yaml index 713dfcf125d4e..6c4cb60df1a9a 100644 --- a/recipes/spades/3.11.1/meta.yaml +++ b/recipes/spades/3.11.1/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474 # [linux] build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/spades/3.9.0/meta.yaml b/recipes/spades/3.9.0/meta.yaml index e06fe88459095..412f1e0caa759 100644 --- a/recipes/spades/3.9.0/meta.yaml +++ b/recipes/spades/3.9.0/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 3 + number: 4 requirements: run: diff --git a/recipes/spectacle/meta.yaml b/recipes/spectacle/meta.yaml index d98fea2f2ace3..15ef7040e2ba8 100644 --- a/recipes/spectacle/meta.yaml +++ b/recipes/spectacle/meta.yaml @@ -12,13 +12,14 @@ source: build: noarch: generic detect_binary_files_with_prefix: true - number: 1 + number: 2 requirements: host: - unzip run: - openjdk + - python - scipy - numpy diff --git a/recipes/spectrassembler/meta.yaml b/recipes/spectrassembler/meta.yaml index 63db891dd7910..6fe4641c0666d 100644 --- a/recipes/spectrassembler/meta.yaml +++ b/recipes/spectrassembler/meta.yaml @@ -7,7 +7,7 @@ package: build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/spectrum_utils/meta.yaml b/recipes/spectrum_utils/meta.yaml index 5fa200eabecf1..96fe0b00f68fc 100644 --- a/recipes/spectrum_utils/meta.yaml +++ b/recipes/spectrum_utils/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c874687c110995e0f8a0706a09683ac308fa892fe4613cad83622d56e8d82c82 build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python diff --git a/recipes/spotyping/build.sh b/recipes/spotyping/build.sh index 660d6285dc87f..f1798e75f6e85 100644 --- a/recipes/spotyping/build.sh +++ b/recipes/spotyping/build.sh @@ -1,9 +1,10 @@ #!/bin/sh SPOTYPING_DIR=${PREFIX}/share/SpoTyping -mkdir $SPOTYPING_DIR +mkdir -p $SPOTYPING_DIR cp -r SpoTyping-v${PKG_VERSION}-commandLine/* $SPOTYPING_DIR +mkdir -p ${PREFIX}/bin PLOT_CMD=${PREFIX}/bin/SpoTyping_plot.r echo '#!/usr/bin/env Rscript' > $PLOT_CMD cat SpoTyping-v${PKG_VERSION}-commandLine/SpoTyping_plot.r >> $PLOT_CMD diff --git a/recipes/spotyping/meta.yaml b/recipes/spotyping/meta.yaml index b8270f98c1664..3019a7c5599f3 100644 --- a/recipes/spotyping/meta.yaml +++ b/recipes/spotyping/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: run: diff --git a/recipes/srnapipe/meta.yaml b/recipes/srnapipe/meta.yaml index 690d5615bc863..88685de7f6867 100644 --- a/recipes/srnapipe/meta.yaml +++ b/recipes/srnapipe/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/srprism/meta.yaml b/recipes/srprism/meta.yaml index a7ce2c7c48335..18e28ad8b9bfb 100644 --- a/recipes/srprism/meta.yaml +++ b/recipes/srprism/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 3 + number: 4 skip: true # [osx] requirements: diff --git a/recipes/srst2/meta.yaml b/recipes/srst2/meta.yaml index 298b00f22b8f7..a689706a4d262 100644 --- a/recipes/srst2/meta.yaml +++ b/recipes/srst2/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/ssake/build.sh b/recipes/ssake/build.sh index 6f050edfc9118..33fb8d63c1231 100644 --- a/recipes/ssake/build.sh +++ b/recipes/ssake/build.sh @@ -4,6 +4,7 @@ chmod +x ssake/SSAKE chmod +x ssake/tools/*.pl chmod +x ssake/tools/*.py +mkdir -p ${PREFIX}/bin cp ssake/SSAKE ${PREFIX}/bin cp ssake/tools/*.pl ${PREFIX}/bin cp ssake/tools/*.py ${PREFIX}/bin diff --git a/recipes/ssake/meta.yaml b/recipes/ssake/meta.yaml index 1f6a1992b2f3f..ab5b1a6829f2f 100644 --- a/recipes/ssake/meta.yaml +++ b/recipes/ssake/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 2 + number: 4 requirements: run: diff --git a/recipes/stacks/1.37/meta.yaml b/recipes/stacks/1.37/meta.yaml index f45e50db01060..dfab75dbcd3d8 100644 --- a/recipes/stacks/1.37/meta.yaml +++ b/recipes/stacks/1.37/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.37" build: - number: 2 + number: 3 skip: True # [osx] source: diff --git a/recipes/stacks/2.3d/meta.yaml b/recipes/stacks/2.3d/meta.yaml deleted file mode 100644 index aa1c2f7eeb163..0000000000000 --- a/recipes/stacks/2.3d/meta.yaml +++ /dev/null @@ -1,66 +0,0 @@ -{% set version="2.3d" %} -{% set hash="970e2aef0c1e92ee5a17dfef69d4c8cf864657c0a4bf0b6b67b15ccc13a24a59" %} - -package: - name: stacks - version: {{ version }} - -build: - number: 0 - -source: - sha256: {{ hash }} - url: http://catchenlab.life.illinois.edu/stacks/source/stacks-{{ version }}.tar.gz - patches: - - at.patch - -requirements: - build: - - {{ compiler('cxx') }} - host: - - zlib - - openmp # [linux] - run: - - perl - - perl-bioperl-core - - perl-file-spec - - perl-file-temp - - perl-posix - - python >=3 - - velvet - - samtools - - zlib - - openmp # [linux] - -test: - commands: - - command -v cstacks - - command -v gstacks - - command -v sstacks - - command -v ustacks - - command -v phasedstacks - - command -v populations - - command -v process_radtags - - command -v process_shortreads - - command -v clone_filter - - command -v kmer_filter - - command -v stacks-dist-extract - - command -v stacks-integrate-alignments - - command -v tsv2bam - - command -v convert_stacks.pl - - command -v count_fixed_catalog_snps.py - - command -v denovo_map.pl - - command -v extract_interpop_chars.pl - - command -v integrate_alignments.py - - command -v ref_map.pl - -about: - home: http://catchenlab.life.illinois.edu/stacks/ - license: GPL - license_file: LICENSE - summary: Stacks is a software pipeline for building loci from RAD-seq - -extra: - identifiers: - - biotools:Stacks - - doi:10.1111/mec.12354 diff --git a/recipes/stacks/2.4/at.patch b/recipes/stacks/2.4/at.patch deleted file mode 100644 index 3a518c68cc610..0000000000000 --- a/recipes/stacks/2.4/at.patch +++ /dev/null @@ -1,71 +0,0 @@ -# the stacks perl scripts don't work if there is an '@' in the exe_path -# (where stacks searches for the binaries) this patch sets and ensures that the -# exe_path is the empty string, i.e. PATH is used (ie conda takes care). -diff -ruN stacks-2.3c/scripts/denovo_map.pl stacks-2.3c/scripts/denovo_map.pl ---- stacks-2.3c/scripts/denovo_map.pl 2018-04-19 18:17:23.000000000 +0200 -+++ stacks-2.3c/scripts/denovo_map.pl 2019-01-03 08:28:27.174444559 +0100 -@@ -28,7 +28,7 @@ - use constant false => 0; - - my $dry_run = false; --my $exe_path = "_BINDIR_"; -+my $exe_path = ""; - my $out_path = ""; - my $popmap_path = ""; - my $sample_path = ""; -@@ -50,13 +50,6 @@ - - parse_command_line(); - --# --# Check for the existence of the necessary pipeline programs --# --foreach my $prog ("ustacks", "cstacks", "sstacks", "tsv2bam", "gstacks", "populations") { -- die "Unable to find '" . $exe_path . $prog . "'.\n" if (!-e $exe_path . $prog); --} -- - my ($log, $log_fh, $sample); - - my (@sample_list, %pop_ids, %pops, %grp_ids, %grps, %sample_ids); -@@ -558,7 +551,6 @@ - } - } - -- $exe_path = $exe_path . "/" if (substr($exe_path, -1) ne "/"); - $out_path = substr($out_path, 0, -1) if (substr($out_path, -1) eq "/"); - - if (scalar(@parents) > 0 && scalar(@samples) > 0) { -diff -ruN stacks-2.3c/scripts/ref_map.pl stacks-2.3c/scripts/ref_map.pl ---- stacks-2.3c/scripts/ref_map.pl 2018-03-21 15:51:20.000000000 +0100 -+++ stacks-2.3c/scripts/ref_map.pl 2019-01-03 08:29:17.974257301 +0100 -@@ -28,7 +28,7 @@ - use constant false => 0; - - my $dry_run = false; --my $exe_path = "_BINDIR_"; -+my $exe_path = ""; - my $out_path = ""; - my $popmap_path = ""; - my $sample_path = ""; -@@ -47,13 +47,6 @@ - - parse_command_line(); - --# --# Check for the existence of the necessary pipeline programs --# --foreach my $prog ("gstacks", "populations") { -- die "Unable to find '" . $exe_path . $prog . "'.\n" if (!-e $exe_path . $prog); --} -- - my ($log, $log_fh, $sample); - - my (@sample_list, %pop_ids, %pops, %grp_ids, %grps, %sample_ids); -@@ -385,7 +378,6 @@ - } - } - -- $exe_path = $exe_path . "/" if (substr($exe_path, -1) ne "/"); - $out_path = substr($out_path, 0, -1) if (substr($out_path, -1) eq "/"); - - if (length($popmap_path) == 0) { diff --git a/recipes/stacks/2.4/build.sh b/recipes/stacks/2.4/build.sh deleted file mode 100644 index dc90dfd11d9ee..0000000000000 --- a/recipes/stacks/2.4/build.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash - -if [[ "$(uname)" == Darwin ]]; then - # Fix for install_name_tool error: - # error: install_name_tool: changing install names or rpaths can't be - # redone for: $PREFIX/bin/abyss-overlap (for architecture x86_64) because - # larger updated load commands do not fit (the program must be relinked, - # and you may need to use -headerpad or -headerpad_max_install_names) - export LDFLAGS="$LDFLAGS -headerpad_max_install_names" -fi - -export CXXFLAGS="${CXXFLAGS} -std=c++11" - -./configure --prefix="$PREFIX" --enable-bam -make -make install -# copy missing scripts -cp -p scripts/{convert_stacks.pl,extract_interpop_chars.pl} "$PREFIX/bin/" - diff --git a/recipes/stacks/2.3d/at.patch b/recipes/stacks/at.patch similarity index 100% rename from recipes/stacks/2.3d/at.patch rename to recipes/stacks/at.patch diff --git a/recipes/stacks/2.3d/build.sh b/recipes/stacks/build.sh similarity index 100% rename from recipes/stacks/2.3d/build.sh rename to recipes/stacks/build.sh diff --git a/recipes/stacks/2.4/meta.yaml b/recipes/stacks/meta.yaml similarity index 97% rename from recipes/stacks/2.4/meta.yaml rename to recipes/stacks/meta.yaml index 052de5f9b84a3..5f5c9e1d535c5 100644 --- a/recipes/stacks/2.4/meta.yaml +++ b/recipes/stacks/meta.yaml @@ -6,7 +6,8 @@ package: version: {{ version }} build: - number: 0 + number: 1 + skip: True # [osx] source: sha256: {{ hash }} diff --git a/recipes/staden_io_lib/meta.yaml b/recipes/staden_io_lib/meta.yaml index f84a2dd8400e3..ec7137f230e74 100644 --- a/recipes/staden_io_lib/meta.yaml +++ b/recipes/staden_io_lib/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/star-fusion/0.7.0/build.sh b/recipes/star-fusion/0.7.0/build.sh deleted file mode 100644 index b7ef3dfbc71ff..0000000000000 --- a/recipes/star-fusion/0.7.0/build.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/lib/STAR-Fusion - -cp -r * $PREFIX/lib/STAR-Fusion - -echo "#!/bin/bash" > $PREFIX/bin/STAR-Fusion -echo "$PREFIX/lib/STAR-Fusion/STAR-Fusion \$@" >> $PREFIX/bin/STAR-Fusion -chmod +x $PREFIX/bin/STAR-Fusion - -echo "#!/bin/bash" > $PREFIX/bin/blast_and_promiscuity_filter.pl -echo "$PREFIX/lib/STAR-Fusion/FusionFilter/blast_and_promiscuity_filter.pl \$@" >> $PREFIX/bin/blast_and_promiscuity_filter.pl -chmod +x $PREFIX/bin/blast_and_promiscuity_filter.pl - -echo "#!/bin/bash" > $PREFIX/bin/prep_genome_lib.pl -echo "$PREFIX/lib/STAR-Fusion/FusionFilter/prep_genome_lib.pl \$@" >> $PREFIX/bin/prep_genome_lib.pl -chmod +x $PREFIX/bin/prep_genome_lib.pl diff --git a/recipes/star-fusion/0.7.0/meta.yaml b/recipes/star-fusion/0.7.0/meta.yaml deleted file mode 100644 index fe0fbcc0fdd10..0000000000000 --- a/recipes/star-fusion/0.7.0/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set version = "0.7.0" %} -{% set sha256 = "cf40d9f45fae89d43c214d3c7e95a1c83be9076cbc2902f1117e17f95b27af0a" %} - -package: - name: star-fusion - version: {{ version }} - -source: - url: https://github.com/STAR-Fusion/STAR-Fusion/releases/download/v{{ version }}/STAR-Fusion_v{{ version }}_FULL.tar.gz - sha256: {{ sha256 }} - -build: - noarch: generic - number: 1 - -requirements: - run: - - blast - - perl - - perl-set-intervaltree - - perl-db-file - - perl-uri - - star - - gmap - - bowtie - -test: - commands: - - STAR-Fusion --help 2>&1 | grep Optional > /dev/null - - prep_genome_lib.pl -h 2>&1 | grep "STAR-Fusion" > /dev/null - - blast_and_promiscuity_filter.pl -h 2>&1 | grep Optional > /dev/null - -about: - home: https://github.com/STAR-Fusion/STAR-Fusion - license: BSD-3-Clause - summary: A fusion gene caller for STAR. The FusionFilter tools to create needed index data structures are not included. diff --git a/recipes/stellar/meta.yaml b/recipes/stellar/meta.yaml index cdaf89b22f34b..2740392c7eae9 100644 --- a/recipes/stellar/meta.yaml +++ b/recipes/stellar/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: - url: http://packages.seqan.de/stellar/stellar-1.4.9-Mac-x86_64.zip # [osx] diff --git a/recipes/stream/meta.yaml b/recipes/stream/meta.yaml index e3ad746dad6c6..98876346cdd34 100644 --- a/recipes/stream/meta.yaml +++ b/recipes/stream/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 62ba2c303ac5da8e24105e7adfd3097447ec84a6d1b077ef77d128a324853858 build: - number: 0 + number: 1 skip: True # [py27] requirements: diff --git a/recipes/stream_atac/meta.yaml b/recipes/stream_atac/meta.yaml index 10b09537e4da6..f9a43e9b72e90 100644 --- a/recipes/stream_atac/meta.yaml +++ b/recipes/stream_atac/meta.yaml @@ -1,13 +1,15 @@ +{% set version = "0.3.4" %} + package: name: stream_atac - version: 0.3.4 + version: {{ version }} source: - url: https://github.com/pinellolab/STREAM_atac/archive/v0.3.4.zip - sha256: a809204318c10b20022c0d164cf8139d0f317631d874ff728305b1db9cca8193 + url: https://github.com/pinellolab/STREAM_atac/archive/v{{ version }}.tar.gz + sha256: 1836462881b12d2c0d0c5956b8ff8e2edf2182a6b833da820745286bfd992871 build: - number: 0 + number: 1 skip: True # [py27] requirements: diff --git a/recipes/stringmlst/meta.yaml b/recipes/stringmlst/meta.yaml index 994ff185559c7..22a43d4824d1a 100644 --- a/recipes/stringmlst/meta.yaml +++ b/recipes/stringmlst/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: diff --git a/recipes/structureharvester/meta.yaml b/recipes/structureharvester/meta.yaml index 85a33c8d41381..5ed401e73daac 100644 --- a/recipes/structureharvester/meta.yaml +++ b/recipes/structureharvester/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/suppa/meta.yaml b/recipes/suppa/meta.yaml index 06388a5c4fe3f..aa0f9d2e2b4d1 100644 --- a/recipes/suppa/meta.yaml +++ b/recipes/suppa/meta.yaml @@ -9,7 +9,7 @@ source: build: noarch: python - number: 1 + number: 2 requirements: host: diff --git a/recipes/surpyvor/meta.yaml b/recipes/surpyvor/meta.yaml index 3077e68919f05..fe280940cb500 100644 --- a/recipes/surpyvor/meta.yaml +++ b/recipes/surpyvor/meta.yaml @@ -12,7 +12,7 @@ build: entry_points: - surpyvor=surpyvor.surpyvor:main noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv" requirements: diff --git a/recipes/sv2/meta.yaml b/recipes/sv2/meta.yaml index 950839b34c9a8..71d906b2a1d97 100644 --- a/recipes/sv2/meta.yaml +++ b/recipes/sv2/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.4.3.4" build: - number: 2 + number: 3 skip: true # [py3k or osx] script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/svdb/meta.yaml b/recipes/svdb/meta.yaml index a0cb4bea1126c..eeefc36ecdfc1 100644 --- a/recipes/svdb/meta.yaml +++ b/recipes/svdb/meta.yaml @@ -13,7 +13,8 @@ build: entry_points: - svdb = svdb.__main__:main script: python -m pip install --no-deps --ignore-installed . - number: 0 + skip: True # [not py2k] + number: 1 requirements: build: diff --git a/recipes/svviz/meta.yaml b/recipes/svviz/meta.yaml index 2c1deaca9c114..91effa9ece927 100644 --- a/recipes/svviz/meta.yaml +++ b/recipes/svviz/meta.yaml @@ -7,17 +7,19 @@ source: sha256: 16a419b9be5f25a0d2393ed13eeccadcdbaf8047c244be108f891c897c5349ed build: - noarch: python + skip: True # [py3k] entry_points: - svviz = svviz.app:main - number: 0 + number: 2 requirements: + build: + - {{ compiler('c') }} host: - - python <3 + - python - pip run: - - python <3 + - python - requests - numpy - pyfaidx diff --git a/recipes/swalign/meta.yaml b/recipes/swalign/meta.yaml index 1d0f149a2f4fa..85cd077c9496f 100644 --- a/recipes/swalign/meta.yaml +++ b/recipes/swalign/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/t-coffee/meta.yaml b/recipes/t-coffee/meta.yaml index 22740633fc3a2..691e802abb219 100644 --- a/recipes/t-coffee/meta.yaml +++ b/recipes/t-coffee/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: url: http://tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_{{ version }}.tar.gz diff --git a/recipes/taeper/meta.yaml b/recipes/taeper/meta.yaml index b1b761fb37bdc..f89e066e2c55d 100644 --- a/recipes/taeper/meta.yaml +++ b/recipes/taeper/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - taeper=taeper.cli:main script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/targetfinder/meta.yaml b/recipes/targetfinder/meta.yaml index b97801c83d435..f84f91e65646e 100644 --- a/recipes/targetfinder/meta.yaml +++ b/recipes/targetfinder/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 2 + number: 3 source: url: https://github.com/carringtonlab/TargetFinder/archive/v1.7.tar.gz diff --git a/recipes/tassel/3.0.174/build.sh b/recipes/tassel/3.0.174/build.sh deleted file mode 100644 index 09f69f449c4f4..0000000000000 --- a/recipes/tassel/3.0.174/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -BINARY_HOME=$PREFIX/bin -TASSEL_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM - -# Copy source to the conda environment -mkdir -p $TASSEL_HOME -cp -R $SRC_DIR/* $TASSEL_HOME/ - -# Convert CRLF in wrappers to LF -sed -i 's/\r//' $TASSEL_HOME/*.pl - -# Create symbolic links for TASSEL's wrappers -ln -s $TASSEL_HOME/run_anything.pl $BINARY_HOME/ -ln -s $TASSEL_HOME/run_pipeline.pl $BINARY_HOME/ -ln -s $TASSEL_HOME/start_tassel.pl $BINARY_HOME/ \ No newline at end of file diff --git a/recipes/tassel/3.0.174/meta.yaml b/recipes/tassel/3.0.174/meta.yaml deleted file mode 100644 index e771ae564354c..0000000000000 --- a/recipes/tassel/3.0.174/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "TASSEL" %} -{% set version = "3.0.174" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - git_url: https://git.code.sf.net/p/tassel/tassel3-standalone - git_rev: 612a92c0f677d6ec040c17e146671974a3cdc2da - patches: - - patches/run_anything.patch - - patches/run_pipeline.patch - - patches/start_tassel.patch - -build: - noarch: generic - number: 1 - -requirements: - run: - - openjdk >=6.0 - - perl - -test: - commands: - - run_pipeline.pl - -about: - home: 'https://tassel.bitbucket.io/TasselArchived.html' - license: LGPL V2.1 - summary: "TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium." - -extra: - skip-lints: - # SourceForge Git snapshots do not persist - - uses_vcs_url - - missing_hash diff --git a/recipes/tassel/3.0.174/patches/run_anything.patch b/recipes/tassel/3.0.174/patches/run_anything.patch deleted file mode 100644 index bb2d13be52c9a..0000000000000 --- a/recipes/tassel/3.0.174/patches/run_anything.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/run_anything.pl b/run_anything.pl -index 7dcddab..ab77ed0 100755 ---- a/run_anything.pl -+++ b/run_anything.pl -@@ -1,9 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - use strict; - use File::Basename; -+use Cwd 'abs_path'; - --my $dirname = dirname(__FILE__); -+my $filepath = abs_path(__FILE__); -+my $dirname = dirname($filepath); - my $top = defined($dirname) ? $dirname : '.'; - - my $libdir = "$top/lib"; diff --git a/recipes/tassel/3.0.174/patches/run_pipeline.patch b/recipes/tassel/3.0.174/patches/run_pipeline.patch deleted file mode 100644 index a4942a2fc8c53..0000000000000 --- a/recipes/tassel/3.0.174/patches/run_pipeline.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/run_pipeline.pl b/run_pipeline.pl -index ce7c212..6d144f9 100755 ---- a/run_pipeline.pl -+++ b/run_pipeline.pl -@@ -1,9 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - use strict; - use File::Basename; -+use Cwd 'abs_path'; - --my $dirname = dirname(__FILE__); -+my $filepath = abs_path(__FILE__); -+my $dirname = dirname($filepath); - my $top = defined($dirname) ? $dirname : '.'; - - my $libdir = "$top/lib"; diff --git a/recipes/tassel/3.0.174/patches/start_tassel.patch b/recipes/tassel/3.0.174/patches/start_tassel.patch deleted file mode 100644 index d3a7eac047bf1..0000000000000 --- a/recipes/tassel/3.0.174/patches/start_tassel.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/start_tassel.pl b/start_tassel.pl -index 18b9fd2..d53370a 100755 ---- a/start_tassel.pl -+++ b/start_tassel.pl -@@ -1,9 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - use strict; - use File::Basename; -+use Cwd 'abs_path'; - --my $dirname = dirname(__FILE__); -+my $filepath = abs_path(__FILE__); -+my $dirname = dirname($filepath); - my $top = defined($dirname) ? $dirname : '.'; - - my $libdir = "$top/lib"; diff --git a/recipes/tassel/4.3.15/build.sh b/recipes/tassel/4.3.15/build.sh deleted file mode 100644 index 09f69f449c4f4..0000000000000 --- a/recipes/tassel/4.3.15/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -BINARY_HOME=$PREFIX/bin -TASSEL_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM - -# Copy source to the conda environment -mkdir -p $TASSEL_HOME -cp -R $SRC_DIR/* $TASSEL_HOME/ - -# Convert CRLF in wrappers to LF -sed -i 's/\r//' $TASSEL_HOME/*.pl - -# Create symbolic links for TASSEL's wrappers -ln -s $TASSEL_HOME/run_anything.pl $BINARY_HOME/ -ln -s $TASSEL_HOME/run_pipeline.pl $BINARY_HOME/ -ln -s $TASSEL_HOME/start_tassel.pl $BINARY_HOME/ \ No newline at end of file diff --git a/recipes/tassel/4.3.15/meta.yaml b/recipes/tassel/4.3.15/meta.yaml deleted file mode 100644 index fa739105a1965..0000000000000 --- a/recipes/tassel/4.3.15/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "TASSEL" %} -{% set version = "4.3.15" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - git_url: https://git.code.sf.net/p/tassel/tassel4-standalone - git_rev: 17dced772e1bab7d36f195f41c4c1b8b5e9ad55d - patches: - - patches/run_anything.patch - - patches/run_pipeline.patch - - patches/start_tassel.patch - -build: - noarch: generic - number: 1 - -requirements: - run: - - openjdk >=7.0 - - perl - -test: - commands: - - run_pipeline.pl - -about: - home: 'https://tassel.bitbucket.io/TasselArchived.html' - license: LGPL V2.1 - summary: "TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium." - -extra: - skip-lints: - # SourceForge Git snapshots do not persist - - uses_vcs_url - - missing_hash diff --git a/recipes/tassel/4.3.15/patches/run_anything.patch b/recipes/tassel/4.3.15/patches/run_anything.patch deleted file mode 100644 index bb2d13be52c9a..0000000000000 --- a/recipes/tassel/4.3.15/patches/run_anything.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/run_anything.pl b/run_anything.pl -index 7dcddab..ab77ed0 100755 ---- a/run_anything.pl -+++ b/run_anything.pl -@@ -1,9 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - use strict; - use File::Basename; -+use Cwd 'abs_path'; - --my $dirname = dirname(__FILE__); -+my $filepath = abs_path(__FILE__); -+my $dirname = dirname($filepath); - my $top = defined($dirname) ? $dirname : '.'; - - my $libdir = "$top/lib"; diff --git a/recipes/tassel/4.3.15/patches/run_pipeline.patch b/recipes/tassel/4.3.15/patches/run_pipeline.patch deleted file mode 100644 index a4942a2fc8c53..0000000000000 --- a/recipes/tassel/4.3.15/patches/run_pipeline.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/run_pipeline.pl b/run_pipeline.pl -index ce7c212..6d144f9 100755 ---- a/run_pipeline.pl -+++ b/run_pipeline.pl -@@ -1,9 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - use strict; - use File::Basename; -+use Cwd 'abs_path'; - --my $dirname = dirname(__FILE__); -+my $filepath = abs_path(__FILE__); -+my $dirname = dirname($filepath); - my $top = defined($dirname) ? $dirname : '.'; - - my $libdir = "$top/lib"; diff --git a/recipes/tassel/4.3.15/patches/start_tassel.patch b/recipes/tassel/4.3.15/patches/start_tassel.patch deleted file mode 100644 index d3a7eac047bf1..0000000000000 --- a/recipes/tassel/4.3.15/patches/start_tassel.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/start_tassel.pl b/start_tassel.pl -index 18b9fd2..d53370a 100755 ---- a/start_tassel.pl -+++ b/start_tassel.pl -@@ -1,9 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - use strict; - use File::Basename; -+use Cwd 'abs_path'; - --my $dirname = dirname(__FILE__); -+my $filepath = abs_path(__FILE__); -+my $dirname = dirname($filepath); - my $top = defined($dirname) ? $dirname : '.'; - - my $libdir = "$top/lib"; diff --git a/recipes/tassel/build.sh b/recipes/tassel/build.sh index 64292a1798037..79dc2025dc1b0 100644 --- a/recipes/tassel/build.sh +++ b/recipes/tassel/build.sh @@ -9,6 +9,7 @@ cp -R $SRC_DIR/* $TASSEL_HOME/ sed -i 's/\r//' $TASSEL_HOME/*.pl # Create symbolic links for TASSEL's wrappers +mkdir -p $BINARY_HOME ln -s $TASSEL_HOME/run_anything.pl $BINARY_HOME/ ln -s $TASSEL_HOME/run_pipeline.pl $BINARY_HOME/ ln -s $TASSEL_HOME/start_tassel.pl $BINARY_HOME/ diff --git a/recipes/tassel/meta.yaml b/recipes/tassel/meta.yaml index 522ff7e0ad45b..ad7ab27faf0d0 100644 --- a/recipes/tassel/meta.yaml +++ b/recipes/tassel/meta.yaml @@ -15,7 +15,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/taxator-tk/meta.yaml b/recipes/taxator-tk/meta.yaml index 50483335a2efb..749b29c31dea3 100644 --- a/recipes/taxator-tk/meta.yaml +++ b/recipes/taxator-tk/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: build: diff --git a/recipes/taxmapper/meta.yaml b/recipes/taxmapper/meta.yaml index 3515b61aa6d87..f6a5921e72884 100644 --- a/recipes/taxmapper/meta.yaml +++ b/recipes/taxmapper/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 2 + number: 3 entry_points: - taxmapper=taxmapper:main diff --git a/recipes/tb_variant_filter/meta.yaml b/recipes/tb_variant_filter/meta.yaml index 268c591cb0906..f2a78c5c18d15 100644 --- a/recipes/tb_variant_filter/meta.yaml +++ b/recipes/tb_variant_filter/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv && {{ PYTHON }} -mpytest" requirements: diff --git a/recipes/tdrmapper/meta.yaml b/recipes/tdrmapper/meta.yaml index 50c1a67bd1370..d4a0081174a5d 100644 --- a/recipes/tdrmapper/meta.yaml +++ b/recipes/tdrmapper/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 3 + number: 4 requirements: run: diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml index 1e33c6c2a2123..90ad81721cf80 100644 --- a/recipes/teloclip/meta.yaml +++ b/recipes/teloclip/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - teloclip=teloclip.run_self:main - teloclip-extract=teloclip.run_extract:main diff --git a/recipes/tepid/meta.yaml b/recipes/tepid/meta.yaml index a020694f9cd45..f161eeb5fcfb0 100644 --- a/recipes/tepid/meta.yaml +++ b/recipes/tepid/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 2f9ff777705f74abe54f916bd33783085696a4687c47efe61146dd9827c4e241 build: - number: 2 + number: 3 script: sed -i.bak "25,30d" setup.py && {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv noarch: python diff --git a/recipes/tetoolkit/meta.yaml b/recipes/tetoolkit/meta.yaml index 99f6aac4ccee5..977a436f8afbe 100644 --- a/recipes/tetoolkit/meta.yaml +++ b/recipes/tetoolkit/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/theta2/meta.yaml b/recipes/theta2/meta.yaml index ef266b7c5edcb..f800fd4c51bd8 100644 --- a/recipes/theta2/meta.yaml +++ b/recipes/theta2/meta.yaml @@ -2,14 +2,14 @@ package: name: theta2 version: '0.7' build: - number: 1 + number: 2 noarch: python source: url: https://github.com/raphael-group/THetA/archive/v0.7.tar.gz sha256: 474452fa87a1ca0228137693bfede3200b91e4e166b2216c4bd24f8b270c1dea requirements: - build: + host: - python <3 - numpy - scipy diff --git a/recipes/tinscan/meta.yaml b/recipes/tinscan/meta.yaml index 5792b14c34592..09101a5711553 100644 --- a/recipes/tinscan/meta.yaml +++ b/recipes/tinscan/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - tinscan-prep=tinscan.run_prep:main - tinscan-align=tinscan.run_align:main diff --git a/recipes/tinysink/meta.yaml b/recipes/tinysink/meta.yaml index 70be6f7135ced..9188807181434 100644 --- a/recipes/tinysink/meta.yaml +++ b/recipes/tinysink/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: build: diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml index ea44d5f7f664c..1c17ffd143921 100644 --- a/recipes/tirmite/meta.yaml +++ b/recipes/tirmite/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - tirmite=tirmite.cmd_tirmite:main - tsplit-LTR=tirmite.cmd_LTR:main @@ -43,11 +43,9 @@ about: home: https://github.com/Adamtaranto/TIRmite license: MIT License license_family: MIT - license_file: '' summary: Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons. description: "Build profile Hidden Markov Models for Terminal Inverted repeat families (TIR-pHMMs) and map to genomic sequences for annotation of MITES and complete DNA-Transposons with variable internal sequence composition." - doc_url: '' - dev_url: '' extra: - recipe-maintainers: 'Adam Taranto' + recipe-maintainers: + - 'Adam Taranto' diff --git a/recipes/tmalign/build.sh b/recipes/tmalign/build.sh index 6d71626a49422..ef9f79fd69086 100644 --- a/recipes/tmalign/build.sh +++ b/recipes/tmalign/build.sh @@ -5,5 +5,6 @@ FFLAGS="-O3 -ffast-math -lm" # backup to "gfortran" in conda GFORTRAN is not set GFORTRAN=${GFORTRAN:-gfortran} +mkdir -p ${PREFIX}/bin $GFORTRAN $FFLAGS -o "$PREFIX/bin/TMalign" TMalign.f $GFORTRAN $FFLAGS -o "$PREFIX/bin/TMscore" TMscore.f diff --git a/recipes/tmalign/meta.yaml b/recipes/tmalign/meta.yaml index 554bc7d6d609c..bcd131bb18be8 100644 --- a/recipes/tmalign/meta.yaml +++ b/recipes/tmalign/meta.yaml @@ -1,4 +1,3 @@ -# inspired by https://anaconda.org/speleo3/tmalign {% set version = "20170708" %} package: @@ -9,13 +8,13 @@ source: url: http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools{{ version }}.tar.gz sha256: bb67e0924f34dc6f427de5f14734e3daa13be9f0394504efc8d5938da575f58d +build: + number: 1 + requirements: build: - {{ compiler('fortran') }} -build: - number: 0 - test: commands: - TMalign | grep "Brief instruction for running TM-align program" > /dev/null diff --git a/recipes/toolshed/meta.yaml b/recipes/toolshed/meta.yaml index eb72223082a3d..5ecb9843f4e8a 100644 --- a/recipes/toolshed/meta.yaml +++ b/recipes/toolshed/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/tophat-recondition/meta.yaml b/recipes/tophat-recondition/meta.yaml index c3950deaabf51..c682a9a4c7105 100644 --- a/recipes/tophat-recondition/meta.yaml +++ b/recipes/tophat-recondition/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 1 + number: 2 source: url: https://github.com/cbrueffer/tophat-recondition/archive/v1.4.tar.gz diff --git a/recipes/transabyss/meta.yaml b/recipes/transabyss/meta.yaml index 9ac3e44ed273c..d54bc35bba6e6 100644 --- a/recipes/transabyss/meta.yaml +++ b/recipes/transabyss/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 4 + number: 5 requirements: host: diff --git a/recipes/transdecoder/2.1.0/build.sh b/recipes/transdecoder/2.1.0/build.sh deleted file mode 100644 index baacb3402508c..0000000000000 --- a/recipes/transdecoder/2.1.0/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -# install in opt/ -mkdir -p $PREFIX/opt/ -cp -r $SRC_DIR $PREFIX/opt/$PKG_NAME - -# symlink to binaries -mkdir -p $PREFIX/bin/ -ln -s $PREFIX/opt/$PKG_NAME/TransDecoder.Predict $PREFIX/bin/ -ln -s $PREFIX/opt/$PKG_NAME/TransDecoder.LongOrfs $PREFIX/bin/ -ln -s $PREFIX/opt/$PKG_NAME/util/*.pl $PREFIX/bin/ diff --git a/recipes/transdecoder/2.1.0/meta.yaml b/recipes/transdecoder/2.1.0/meta.yaml deleted file mode 100644 index a163fdf3dde09..0000000000000 --- a/recipes/transdecoder/2.1.0/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{% set name = "transdecoder" %} -{% set version = "2.1.0" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -build: - noarch: generic - number: 4 - -source: - url: https://github.com/TransDecoder/TransDecoder/archive/v{{ version }}.tar.gz - md5: f86c688e13ced3cc51fed3d508a2ea05 - -requirements: - build: - - run: - - perl - - perl-db-file - - perl-uri - - cd-hit - -test: - commands: - - 'TransDecoder.Predict -h 2>&1 | grep USAGE' - - 'TransDecoder.LongOrfs -h 2>&1 | grep USAGE' - - 'perl -e "use DB_File"' - -about: - home: https://transdecoder.github.io/ - license: Broad Institute - summary: TransDecoder identifies candidate coding regions within transcript - sequences, such as those generated by de novo RNA-Seq transcript - assembly using Trinity, or constructed based on RNA-Seq alignments - to the genome using Tophat and Cufflinks. diff --git a/recipes/transdecoder/3.0.1/build.sh b/recipes/transdecoder/3.0.1/build.sh deleted file mode 100644 index baacb3402508c..0000000000000 --- a/recipes/transdecoder/3.0.1/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -# install in opt/ -mkdir -p $PREFIX/opt/ -cp -r $SRC_DIR $PREFIX/opt/$PKG_NAME - -# symlink to binaries -mkdir -p $PREFIX/bin/ -ln -s $PREFIX/opt/$PKG_NAME/TransDecoder.Predict $PREFIX/bin/ -ln -s $PREFIX/opt/$PKG_NAME/TransDecoder.LongOrfs $PREFIX/bin/ -ln -s $PREFIX/opt/$PKG_NAME/util/*.pl $PREFIX/bin/ diff --git a/recipes/transdecoder/3.0.1/meta.yaml b/recipes/transdecoder/3.0.1/meta.yaml deleted file mode 100644 index 2158c40c2780a..0000000000000 --- a/recipes/transdecoder/3.0.1/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{% set name = "transdecoder" %} -{% set version = "3.0.1" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -build: - noarch: generic - number: 2 - -source: - url: https://github.com/TransDecoder/TransDecoder/archive/v{{ version }}.tar.gz - md5: f62b86a15fcb78b1dada9f80cc25f300 - -requirements: - build: - - run: - - perl - - perl-db-file - - perl-uri - - cd-hit - -test: - commands: - - 'TransDecoder.Predict -h 2>&1 | grep USAGE' - - 'TransDecoder.LongOrfs -h 2>&1 | grep USAGE' - - 'perl -e "use DB_File"' - -about: - home: https://transdecoder.github.io/ - license: Broad Institute - summary: TransDecoder identifies candidate coding regions within transcript - sequences, such as those generated by de novo RNA-Seq transcript - assembly using Trinity, or constructed based on RNA-Seq alignments - to the genome using Tophat and Cufflinks. diff --git a/recipes/transdecoder/meta.yaml b/recipes/transdecoder/meta.yaml index ab767f90619b1..7d09c706967d4 100644 --- a/recipes/transdecoder/meta.yaml +++ b/recipes/transdecoder/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: host: diff --git a/recipes/translatorx/build.sh b/recipes/translatorx/build.sh index 45f194d331531..22c437dcfb25d 100644 --- a/recipes/translatorx/build.sh +++ b/recipes/translatorx/build.sh @@ -1,4 +1,5 @@ #!/bin/bash +mkdir -p ${PREFIX}/bin cp translatorx_vLocal.pl $PREFIX/bin chmod +x $PREFIX/bin/translatorx_vLocal.pl diff --git a/recipes/translatorx/meta.yaml b/recipes/translatorx/meta.yaml index d8bc1df91b7b4..2c7dabe298713 100644 --- a/recipes/translatorx/meta.yaml +++ b/recipes/translatorx/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: run: diff --git a/recipes/trawler/build.sh b/recipes/trawler/build.sh index 8c0020bbc94de..66262ec94f161 100644 --- a/recipes/trawler/build.sh +++ b/recipes/trawler/build.sh @@ -12,6 +12,7 @@ mkdir -p $outdir cp -r * $outdir # Short wrapper script +mkdir $PREFIX/bin cat > $PREFIX/bin/trawler <=3.6 - - setuptools + - python + - pip - cython - numpy - cyvcf2 - click - tqdm run: - - python >=3.6 + - python - numpy - cyvcf2 - click @@ -41,13 +41,19 @@ test: imports: - vtools commands: - - vtools-filter --help - - vtools-stats --help - - vtools-gcoverage --help - - vtools-evaluate --help + - LC_ALL="en_US.UTF-8" vtools-filter --help + - LC_ALL="en_US.UTF-8" vtools-stats --help + - LC_ALL="en_US.UTF-8" vtools-gcoverage --help + - LC_ALL="en_US.UTF-8" vtools-evaluate --help about: home: https://github.com/LUMC/vtools license: MIT license_family: MIT summary: Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed + +extra: + container: + # click requires a unicode locale when used with Python 3 + # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly + extended-base: true diff --git a/recipes/weblogo/2.8.2/build.sh b/recipes/weblogo/2.8.2/build.sh deleted file mode 100644 index 38f98f33fb8c6..0000000000000 --- a/recipes/weblogo/2.8.2/build.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash -set -eu -o pipefail - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' seqlogo -mv $SRC_DIR/* $outdir -BINDIR=$PREFIX/bin -mkdir -p $BINDIR -seqlogo=$BINDIR/seqlogo -echo "#! /bin/bash" > $seqlogo; -echo 'DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )' >> $seqlogo; -echo '$DIR/../share/'$(basename $outdir)/seqlogo '$@' >> $seqlogo; -chmod +x $seqlogo diff --git a/recipes/weblogo/2.8.2/meta.yaml b/recipes/weblogo/2.8.2/meta.yaml deleted file mode 100644 index 9c96adb4ec193..0000000000000 --- a/recipes/weblogo/2.8.2/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: weblogo - version: 2.8.2 - -build: - noarch: generic - number: 7 - -source: - url: http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz - md5: 12886e0f41757e32ac2823d0f990ce0c - -requirements: - run: - - perl - -test: - commands: - - seqlogo 2>&1 | grep usage > /dev/null - - seqlogo -f foo.bar 2>&1 | grep "input filename" > /dev/null - -about: - home: http://weblogo.berkeley.edu/ - license: MIT - summary: Web based application designed to generate sequence logos - -extra: - identifiers: - - biotools:weblogo - - doi:10.1101/gr.849004 diff --git a/recipes/weblogo/meta.yaml b/recipes/weblogo/meta.yaml index 5eec1db59b229..8f334cf78d537 100644 --- a/recipes/weblogo/meta.yaml +++ b/recipes/weblogo/meta.yaml @@ -6,7 +6,7 @@ package: build: noarch: python - number: 0 + number: 1 source: url: https://github.com/WebLogo/weblogo/archive/{{ version }}.tar.gz diff --git a/recipes/wgfast/meta.yaml b/recipes/wgfast/meta.yaml index bea55771c5db9..954dc0c894f76 100644 --- a/recipes/wgfast/meta.yaml +++ b/recipes/wgfast/meta.yaml @@ -9,7 +9,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . -v" entry_points: diff --git a/recipes/wgs2ncbi/meta.yaml b/recipes/wgs2ncbi/meta.yaml index 2df4c632f14d0..84e02b5ab082d 100644 --- a/recipes/wgs2ncbi/meta.yaml +++ b/recipes/wgs2ncbi/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 requirements: host: diff --git a/recipes/wisecondorx/meta.yaml b/recipes/wisecondorx/meta.yaml index 1c9616998f83f..5830b4ebcf5ed 100644 --- a/recipes/wisecondorx/meta.yaml +++ b/recipes/wisecondorx/meta.yaml @@ -8,7 +8,7 @@ source: sha256: c4bab8ec9c2f374f98a7425458d1a342ae69665b8542ba60ade2ae675ddb2c5f build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps -vv" diff --git a/recipes/xtail/meta.yaml b/recipes/xtail/meta.yaml index c90dead36346e..fbcd961705e00 100644 --- a/recipes/xtail/meta.yaml +++ b/recipes/xtail/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/yanagiba/meta.yaml b/recipes/yanagiba/meta.yaml index 1d8710dbb9133..78b8e83c28157 100644 --- a/recipes/yanagiba/meta.yaml +++ b/recipes/yanagiba/meta.yaml @@ -12,7 +12,7 @@ build: noarch: python entry_points: - yanagiba=yanagiba.cmd_line:main - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: