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Update panacus recipe to include third-party licenses #53676
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mencian
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Feb 5, 2025
stuber
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Feb 7, 2025
* Bump panacus version * Add cargo bundle licenses * Reset build number * Update panacus to include serde derive feature * Add THIRDPARTY.yml to licence_file * s/-/./ in version * Bump panacus version * Update build.sh --------- Co-authored-by: Peter Heringer <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]>
bgruening
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Feb 9, 2025
* Update varfish-cli to 0.7.0 (#53454) * update package version and dependencies for ViroConstrictor 1.5.0 (#53456) * Disable mac builds for pyopenms again (#53396) * Update meta.yaml * Update ICU dependency version range * Update meta.yaml * Update recipes/pyopenms/meta.yaml Co-authored-by: Martin Grigorov <[email protected]> * Bump build number to 4 * Skip build on OSX and increment version --------- Co-authored-by: Martin Grigorov <[email protected]> * Add missing dependencies for CAT_pack reads (#53459) * Update bakta to 1.10.4 (#53461) * Update piscem to 0.12.0 (#53439) * Update piscem to 0.12.0 * Update conda_build_config.yaml * Update meta.yaml --------- Co-authored-by: Rob Patro <[email protected]> * gdc-client: remove pyopenssl pin (#53463) * Update mgnify-pipelines-toolkit to 0.2.0 (#53464) * Update rbpbench to 1.0.2 (#53466) * Update strangepg to 0.8.18 (#53462) * Update solvebio to 2.30.0 (#53467) * Update autobigs-engine to 0.8.0 (#53469) * Update notramp to 1.1.8 (#53465) * seismic-rna: add aarch64/arm64 builds (#53423) Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update paraphase to 3.1.2 (#53471) * Add nbitk to bioconda (#53460) * Update grepq to 1.4.2 (#53472) * Add autobigs-cli (#53470) * Update diamond to 2.1.11 (#53473) * Update flexynesis to 0.2.14 (#53478) * Update paraphase to 3.2.0 (#53479) * Update pybarrnap to 0.5.1 (#53476) * Update pybarrnap to 0.5.1 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update simpleaf to 0.19.0 (#53475) * Update simpleaf to 0.19.0 * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh --------- Co-authored-by: Rob Patro <[email protected]> * Add osx-arm64 build to py2bit (#53398) * Build for osx-arm64 * Update meta.yaml * Update build.sh * Delete recipes/py2bit/build.sh * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update mummer4 to 4.0.0 (#53477) * Update mummer4 to 4.0.0 * clean up patches * add m4 * Update build.sh --------- Co-authored-by: mencian <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> * Update genomad to 1.9.0 (#53480) * Fix geNomad 1.9.0 dependencies (#53482) * Update r-locuszoomr to 0.3.6 (#53483) * Update doc metadata for eastr (#53481) * Update grepq to 1.4.3 (#53494) * Update notramp to 1.1.9 (#53491) * [biobb_morph] update 5.0.1 (#53492) * Update r-tidyheatmap to 1.11.4 (#53487) * Update r-tidyheatmap to 1.11.4 * add run_exports --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update perl-io-interactive to 1.026 (#41845) * Update perl-io-interactive to 1.025 * Update perl-io-interactive to 1.026 * Add run_exports --------- Co-authored-by: Martin Grigorov <[email protected]> * Update runjob to 2.10.9 (#49329) * Update runjob to 2.10.8 * Update meta.yaml * Update runjob to 2.10.9 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * miniasm: add arm64 build (#53495) * unicycler: add aarch64 build (#53496) * Add recipe for FragGeneScanRs (#53490) * Add recipe for FragGeneScanRs * Fix the download url. Add linux-aarch64 and osx-arm64 * Do not run `cargo test` in the test phase. --------- Co-authored-by: Felix Van der Jeugt <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> * Update to v2.7.5 (#53499) * Manta boost fix: add boost-cpp dependency at runtime. (#53424) * Add boost-cpp to run dependencies - #53419. * Bump the build * Add better error checking for #53419 * Typo. * Update meta.yaml: make a test that will fail on error * Update meta.yaml: switch out boost-cpp to libboost in runtime reqs * Update meta.yaml: remove ':' from test. * [curves_biobb] update 3.0.3 (#53498) * [curves_biobb] update 3.0.3 * [curves_biobb] update 3.0.3 * [curves_biobb] update 3.0.3 * [curves_biobb] update 3.0.3 * tgsgapcloser: add aarch64/arm64 builds (#53497) * tgsgapcloser: add aarch64/arm64 builds * Update build.sh * Update build.sh * Update build.sh * add patch * Update build.sh * add patch * Update build.sh * clean up recipe * clean up recipe * Update nanomotif to 0.5.5 (#53503) * Rebuild tgsgapcloser (#53506) * Rebuild tgsgapcloser * Update build.sh * Update Earl Grey meta.yaml (#53507) * Update meta.yaml * Update meta.yaml * Update of ngs-bits to version 2025_01 (#53500) * Updated ngs-bits to version 2018_10 * bla * ngs-bits update * update build * add haplogrep3 (#53504) * add haplograph3 * Update nf-core to 3.2.0 (#53509) * Update earlgrey to 5.1.1 (#53508) * Update dnachisel to 3.2.13 (#53511) * Update regenie to 4.1 (#53516) * Update pangolin-data to 1.32 (#53514) * Updated eggnog-mapper: Added upper bound on python (#53518) * Update ms2pip recipe (#53502) * Update to AMRFinderPlus 4.0.15 (#53515) * Update pybigwig to 0.3.24 (#53512) * Update pybwa to 1.4.4 (#53519) * Update t1k to 1.0.7 (#53521) * Update gempipe to 1.37.6 (#53523) * Update snk-cli to 0.7.2 (#53530) * Update kegg-pathways-completeness to 1.3.0 (#53532) * Add recipe for GET_PANGENES (#53489) * 1st draft * version 15012025 * remove blank * 1st draft * added notes * removed src_file test and added description * added HPC instructions * fails tests * works with default minimap2, not yet with gsalign * documented other minimap2 version * bioconda-utils build --docker --mulled-test --packages get_pangenes ok * works now with GSAlign * uses ISO date format for versions and import get_homologues * Update recipes/get_pangenes/meta.yaml remove previous minimap2 version Co-authored-by: Björn Grüning <[email protected]> * Update recipes/get_pangenes/meta.yaml removed unused test requirements wget, tar, coreutils (sort) Co-authored-by: Björn Grüning <[email protected]> * removed commented out tests --------- Co-authored-by: eead-csic-compbio <[email protected]> Co-authored-by: Björn Grüning <[email protected]> * Update libcifpp to 7.0.9 (#53539) * [curves_biobb] update 3.0.3b1 (#53524) * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * [curves_biobb] update 3.0.3b1 * Update dependencies (#53531) * Update excludonfinder to 0.1.3 (#53538) * Update ucsc-cell-browser to 1.2.10 (#53543) * Update picrust2 to 2.6.0 (#53510) * Update picrust2 to 2.6.0 * Update picrust2 to 2.6.0 * Update meta.yaml * add ete3 --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update dendropy to 5.0.2 (#53545) * Update mgnify-pipelines-toolkit to 0.2.1 (#53541) * Update mgnify-pipelines-toolkit to 0.2.1 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update egglib to 3.3.5 (#53547) * Update egglib to 3.3.5 * try osx builds * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update pairix to 0.3.9 (#53548) * Update metabolabpy to 0.9.67 (#53549) * Update bactopia-py to 1.4.0 (#53551) * Update bactopia-py to 1.4.0 * add depends * Update tests --------- Co-authored-by: Robert A. Petit III <[email protected]> * Update captus to 1.1.1 (#53546) * Bump up abnumber to 0.4.3 (#53544) * Update grepq to 1.4.4 (#53550) * perl-html-parser: add linux-aarch64, bump build (#53542) * Update goldrush to 1.2.2 (#53553) * bioconductor-copynumber restore to enable aarch64 supporting package (#53513) * Update perl-html-parser to 3.83 (#53554) * Update vg to v.1.63.1 (#53555) * Update vvv2_display to 0.2.3.4 (#53557) * Update pybiolib to 1.2.298 (#53558) * Update flashlfq to 2.0.0 (#52720) * Update flashlfq to 2.0.0 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * maxbin2: start enabling linux-aarch64 (#52771) * Replace blacklisted perl-lwp-simple with perl-libwww-perl * spacing for version constraint on perl (don't know if the constraint is necessary) * maxbin2: Remove perl=5.26 limit - not documented if it is needed and not built on linux-aarch64 * Bump the build number --------- Co-authored-by: Martin Grigorov <[email protected]> * Add recipe for pb-CpG-tools (#53520) * Add recipe for pb-CpG-tools * Update recipes/pb-cpg-tools/meta.yaml Co-authored-by: Martin Grigorov <[email protected]> --------- Co-authored-by: Martin Grigorov <[email protected]> * Update bioconda-utils to 3.7.1 (#53562) * Update pacu_snp to 0.0.7 (#53563) * Update rnanorm to 2.2.0 (#53561) * hops: update openjdk dependency to enable aarch64 support (#53564) * perl-lwp-simple: bump the version number of perl-libwww-perl to match (#53560) * Update rmlst_api to 0.1.6 (#53570) * Update rmlst_api to 0.1.6 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update harpy to 1.16.2 (#53568) Co-authored-by: Joshua Zhuang <[email protected]> * Update superintervals to 0.2.9 (#53559) * Update superintervals to 0.2.8 * Update superintervals to 0.2.9 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Tidy up `vartrix` recipe (#53565) * no deps; license; bump build; stricter pin vendoring static binaries * bundle license from https://github.com/10XGenomics/vartrix/blob/3dd49885e9c2cdce72b1c0e58e125a5285a184bc/LICENSE * skip noarch linting * Update perl-libwww-perl to 6.77 (#53569) * Update perl-libwww-perl to 6.77 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update r-ukbrapr to 0.3.0 (#53573) * Update shasta to 0.14.0 (#53576) * Update resistify to 1.1.5 (#53575) * Update snakebids to 0.14.0 (#53578) * Update jbrowse2 to 3.0.0 (#53577) * Updated sequenceTools (#53566) * updated meta.yaml for sequenceTools * updated build number * Update hybracter to 0.11.2 (#53580) * Update scirpy to 0.20.1 (#53581) * Update scirpy to 0.20.1 * Fix logomaker dependency --------- Co-authored-by: Gregor Sturm <[email protected]> * Update jbrowse2 to 3.0.1 (#53582) * Update matchtigs to 2.1.9 (#53585) * Update matchtigs to 2.1.9 Also add a reference to the Eulertigs paper. * Reset build number to zero. * Update ms2rescore (#53367) * Update ms2rescore to 3.1.0 * clean up recipe * add im2deep * Update ms2rescore to 3.1.1 * Update ms2rescore to 3.1.2 * Update ms2rescore to 3.1.3 * Update ms2rescore to 3.1.3.post1 * update dependencies * Update meta.yaml * Update meta.yaml * Update ms2rescore to 3.1.4 * Update recipe * Linter doesn't like tildes * Relax DeepLC requirement, skip linux-aarch64 build (no tf etc) * Remove optional pyopenms dependency * Retry with new pyopenms and ms2pip builds * Add flit-core dependency --------- Co-authored-by: BiocondaBot <[email protected]> Co-authored-by: mencian <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> * Add ESME bundle (Earth System Modelling Environment) - Work in progress (#53556) * Add ESME bundle * Enhancements and fixes for ESME bundle: - Add ParallelIO - Correct usage of pin_subpackage - Build for all MPIs - Add OMB - Adjust run requirements - Fix build string - Skip-lint version_constraints_missing_whitespace - Add ESMF_CPP * Build for MPIch only * Add CPP flags * Add compilers in run requirements and skip final test for ESME * Update wipertools to 1.1.5 (#53593) * Update sylph-tax to 1.1.1 (#53591) * Update excludonfinder to 0.1.4 (#53590) * Update harpy to 1.16.3 (#53589) * Update meta.yaml (#53586) * Update r-ukbrapr - remove deprecated dependencies (#53592) * Update snakebids (#53579) * Update meta.yaml `raumel_yaml` version >= 0.17.2 doesn't exist on conda-forge * Bump build number * change ruamel_yaml to ruamel.yaml * remove channel pin from ruamel.yaml * Update dxpy to 0.388.0 (#53598) * Update augur to 28.0.0 (#53594) * Update ont-modkit to 0.4.3 (#53597) * Update nanocaller to 3.6.1 (#53601) * update dxpy requirements of current recipe to reflect dependencies used for pypi (#53602) update dxpy requirements to reflect those used for pypi; see: https://github.com/dnanexus/dx-toolkit/blob/v0.388.0/src/python/requirements.txt https://github.com/dnanexus/dx-toolkit/blob/master/src/python/setup.py * Update dxpy: comment out optional extra dependencies (#53603) * Update dxpy: comment out optional extra dependencies Update the `dxpy` recipe to comment out optional extra dependencies: pandas, numpy, and xattr since they're somewhat large in size and not required apart from using the `dx extract_dataset` command. A metapackage with these extra dependencies could be added in the future if needed. * increment build number * krakenuniq, kmer-jellyfish 1.1.12: enable aarch64, reenable x86 (#53606) * krakenuniq: add linux-aarch64, bump the build * kmer-jellyfish 1.1.12: add linux-aarch64 - needed by krakenuniq * kmer-jellyfish-1.1.12: add linux-aarch64, fix configure error, make -fsigned-char due to (very valid) warnings * Workaround a broken autoconf setup with jellyfish. autoconf produces a syntax error in the AS_IF which I have otherwise been unable to resolve. * krakenuniq: add build_config * Update build.sh: add std=c++14 - reqd for os/x compilation * Update piranha-polio to 1.4.2 (#53604) * Update piranha-polio to 1.4 * Update piranha-polio to 1.4.1 * Update piranha-polio to 1.4.2 * Update pybwa to 1.4.5 (#53605) * Update gtotree to 1.8.9 (#53613) * Update ucsc-cell-browser to 1.2.11 (#53616) * Update grenedalf to 0.6.3 (#53615) * Update mutmap to 2.3.9 (#53612) * Update qtlseq to 2.2.9 (#53610) * Update nanomotif to 0.5.6 (#53607) * Update pymzml to 2.5.11 (#53609) * Update pymzml to 2.5.11 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update genomic_address_service to 0.1.4 (#53618) * Update `nafcodec` to `v0.3.1` (#53611) * Update pybwa to 1.4.6 (#53620) * Enable `linux-aarch64` for `nafcodec` (#53621) * Update piscem to 0.12.1 (#53622) * Update grepq to 1.4.5 (#53623) * Update piscem to 0.12.2 (#53627) * Update needletail to 0.6.2 (#53628) * Update needletail to 0.6.2 * Remove `needletail` patch * Bump minimum `maturin` version --------- Co-authored-by: Antônio Camargo <[email protected]> * Update comparem2 to 2.13.1 (#53624) * Update simpleaf to 0.19.1 (#53631) * Update simpleaf to 0.19.1 * Update meta.yaml --------- Co-authored-by: Rob Patro <[email protected]> * Update msstitch to 3.17 (#53625) * Update grepq to 1.4.7 (#53632) * Update twopaco to 1.1.0 (#53630) * Update twopaco to 1.1.0 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update NanoPlot to v1.44.1 (#53635) * Update NanoPlot to v1.44.1 for some reason, need capitalized NanoPlot again in the URL. Not sure * woopsie * reset build number * Add `osx-arm64` build to `pydustmasker` (#53629) * Add `osx-arm64` build to `pydustmasker` * Skip `version_constraints_missing_whitespace` lint * Update truvari to 5.1.0 (#53636) * Update dfast to 1.3.5 (#53637) * Add EGAP recipe (#53614) * Add EGAP recipe * Update EGAP meta.yaml and build.sh for stable tarball and sha256 * Fix lint errors: matplotlib-base, run_exports, compilers in build * Fix lint build errors to Update EGAP recipe * Update meta.yaml reduced python version limit to <3.9 * Update meta.yaml removed script: bash build.sh * Update meta.yaml set compiler from 'cxx' -> 'c' * Update meta.yaml updated compiler to have BOTH 'c' and 'cxx' * Update build.sh added make CC="$CC" * Update meta.yaml added zlib to host and run * Update meta.yaml updated to have zlib >=1.2.13,<1.30 * Update meta.yaml updated quast to 5.3.0 and zlib set to 1.3 * Update meta.yaml updated zlib and python build allowances * Update build.sh added exports for CPPFLAGS and LDFLAGS We export CPPFLAGS and LDFLAGS to ensure we can find zlib.h and libz.so. In the make command for purge_dups, we explicitly pass CC="$CC" and LDFLAGS="$LDFLAGS" to avoid “cannot find -lz.” If purge_dups’s Makefile tries to do something like gcc calcuts.o -lz, it will see -L$PREFIX/lib from $LDFLAGS and properly locate libz. * Delete recipes/egap/build.sh Ratatosk and purge_dups can be installed via conda * Update meta.yaml removed build.sh requirements moved into conda installs ratatosk =0.9.0 purge_dups =1.2.6 Removed depencies found in the build.sh (and the file itself) now that that they can be called via python. * Update meta.yaml to guarantee that there should be linux specific Made exclusive linux distribution * Update meta.yaml attempting to set as noarch * Update meta.yaml attempted to update to noarch * Update meta.yaml corrected adding EGAP.py to bin * Update meta.yaml with shebang * Update meta.yaml updated with shebang fixes * Update meta.yaml added run_exports and corrected dependencies * Update meta.yaml to resolve reviewer comments Adjusted the tarbal url to use "version" instead of hardcoded number. Moved python and co to host. Use >= instead of = to loosen version restrictions. * Update meta.yaml updated flye version, removed zlib and java requirements * Update meta.yaml updated to v2.5.3 Updated to new tarball * Add a3partitioner v0.1.0 (#53633) * Add a3partitioner v0.1.0 * Add run_exports to a3partitioner recipe * . * Update meta.yaml following working example * Update a3partitioner recipe with working build configuration * Apply suggestions from code review --------- Co-authored-by: Martin Grigorov <[email protected]> * Update pathogen-profiler to 4.7.0 (#53643) * Update perl-perl-version to 1.018 (#45060) * Update perl-perl-version to 1.015 * Update perl-perl-version to 1.016 * Update perl-perl-version to 1.017 * Update perl-perl-version to 1.018 * Add run_exports --------- Co-authored-by: Martin Grigorov <[email protected]> * SPP-DCJ (#53626) * Update gfaffix to 0.1.2.2 * Update gfaffix to 0.2.0 * Use compiler(rust) * add macos-arm64/linux-aarch64 support; improve build.sh * initial commit * Update meta.yaml matplotlib -> matpliblib-base * Update meta.yaml Remove unnecessary lines in test --------- Co-authored-by: BiocondaBot <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: Dany Doerr <[email protected]> * Update pybiolib to 1.2.347 (#53641) * Update parascopy to 1.17.4 (#53645) * Update deeplc to 3.1.5 (#53653) * Update vsearch to 2.29.3 (#53654) * Update deeplcretrainer to 1.0.2 (#53660) * twopaco: add aarch64/arm64 builds (#53638) * twopaco: add aarch64/arm64 builds Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Fix the path to the built binaries Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * perl-gd & perl-gdtextutil: add aarch64/arm64 builds (#53608) * fastx_toolkit: add aarch64/arm64 builds Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * perl-gd: add aarch64/arm64 builds Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add `expat` as a host dependency for perl-gd ``` the PKG_CONFIG_PATH environment variable␛[0m 12:56:51 ␛[32mBIOCONDA INFO␛[0m (OUT) Package 'expat', required by 'fontconfig', not found␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * perl-gdtextutil: add aarch64/arm64 builds Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update perl-gd to 2.83 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add perl-file-which as a host requirement for perl-gd Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add perl-test-nowarnings as a host dependency to perl-gd Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Do not import modules which $VERSION is not 2.83 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Disable aarch64/arm64 for now Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Do not build for osx-arm64. perl-extutils-constant is not available Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Run `make test` only for Linux OSX-64 fails with: ``` 21:56:54 BIOCONDA INFO (OUT) t/GD.t .................... 21:56:54 BIOCONDA INFO (OUT) Dubious, test returned 255 (wstat 65280, 0xff00) 21:56:54 BIOCONDA INFO (OUT) Failed 13/15 subtests `` Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Revert fastx_toolkit changes Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update gtotree to 1.8.10 (#53666) * Update ntm-profiler to 0.6.0 (#53646) * Update ntm-profiler to 0.6.0 * update recipe deps --------- Co-authored-by: Jody Phelan <[email protected]> * Update deeplc to 3.1.7 (#53661) Co-authored-by: Joshua Zhuang <[email protected]> * Update eukcc to 2.1.3 (#53659) * Update eukcc to 2.1.3 * add run_exports * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update HATCHet to v2.1.1 (#53664) * Egap recipe update (#53662) * Update meta.yaml (#53668) * Update meta.yaml (#53663) * Update sylph-tax recipe (fix python versioning) (#53658) * Update GW to v1.1.3 (#53670) * Update taxopy to 0.14.0 (#53672) * Update taxopy to 0.14.0 * Update `run_exports` * Update install script --------- Co-authored-by: Antônio Camargo <[email protected]> * Update rdeval to 0.0.5 (#53619) * Update rdeval to 0.0.5 * edit patches --------- Co-authored-by: mencian <[email protected]> * Rebuild hatchet (#53673) * Add recipe for ctyper v1.0 (#53674) * Add recipe for ctyper v1.0 * Update build.sh * Update build.sh * Fix the license file name --------- Co-authored-by: Martin Grigorov <[email protected]> * Update dfast_qc to 1.0.6 (#53677) * UPDATE troubleshoot transannot build (#53488) * troubleshoot * troubleshoot * troubleshoot * troubleshoot * Update meta.yaml * Update meta.yaml after the review * Update excludonfinder to 0.1.4 (#53596) * Update excludonfinder to 0.1.4 * Update excludonfinder: increment build number and add run_exports --------- Co-authored-by: Alvarosmb <[email protected]> * fastx_toolkit: add linux-aarch64 build (#53667) * fastx_toolkit: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Use newer config.sub/.guess for aarch64 support Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update fastx.patch * add patch * Update meta.yaml * add macos patch * Update build.sh * Update build.sh --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: mencian <[email protected]> * Update ESME for CESM compatibility, relax version constraints, and fix licensing: (#53642) - Relax version requirements for compilers and MPI. - Added copyrights for NetCDF - Changed license type for PnetCDF and ESMF * Update vvv2_display to 0.2.3.5 (#53678) * Update seismic-rna to 0.23.0 (#53675) * Update seismic-rna to 0.23.0 * Update meta.yaml * Update build.sh * Delete recipes/seismic-rna/build.sh * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * Add magneto (#53583) * add magneto recipe * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * update transannot after the 2nd revision (#53452) * update transannot after the 2nd revision * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build_failure.osx-arm64.yaml * Delete recipes/transannot/build_failure.osx-arm64.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update cramino to 0.16.0 (#53679) * Update cramino to 0.16.0 * change build to 0 --------- Co-authored-by: Alexandra Pancikova <[email protected]> * Update seqnado to 0.6.0 (#53682) * Update mummer4 to 4.0.1 (#53683) * Mash patch fixes: resolve build failures on Linux (#53680) * mash: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try with `libzlib` instead of `zlib` Trying to solve: ``` Encountered problems while solving: 12:56:27 BIOCONDA INFO (OUT) - package capnproto-1.0.2-h8ea4ab2_2 requires libzlib >=1.3.1,<2.0a0, but none of the providers can be installed 12:56:27 BIOCONDA INFO (OUT) 12:56:27 BIOCONDA INFO (OUT) Could not solve for environment specs 12:56:27 BIOCONDA INFO (OUT) The following packages are incompatible 12:56:27 BIOCONDA INFO (OUT) ├─ capnproto 1.0.2.* is installable and it requires 12:56:27 BIOCONDA INFO (OUT) │ └─ libzlib >=1.3.1,<2.0a0 with the potential options 12:56:27 BIOCONDA INFO (OUT) │ ├─ libzlib 1.3.1 would require 12:56:27 BIOCONDA INFO (OUT) │ │ └─ zlib 1.3.1 *_0, which can be installed; 12:56:27 BIOCONDA INFO (OUT) │ ├─ libzlib 1.3.1 would require 12:56:27 BIOCONDA INFO (OUT) │ │ └─ zlib 1.3.1 *_1, which can be installed; 12:56:27 BIOCONDA INFO (OUT) │ └─ libzlib 1.3.1 would require 12:56:27 BIOCONDA INFO (OUT) │ └─ zlib 1.3.1 *_2, which can be installed; 12:56:27 BIOCONDA INFO (OUT) └─ zlib 1.2.* is not installable because it conflicts with any installable versions previously reported ``` * Re-add zlib as dependency * Try with zlib 1.3.* * Update meta.yaml * Update build.sh * bump build number * Update build.sh * add limits patch to relax compiler version * Fix C++ compiler version to handle uint32_t without include * mash: don't wrap memcpy: only needed for distributing to support older Linux versions. bioconda shouldn't need this. marbl/Mash#103 * add patch * Update meta.yaml: remove osx-arm64 Is already a skip for OS/X x86. Should resolve separately to this. * Update meta.yaml: restore osx-arm64 * Add std=c++14 to compile with capnproto on os/x * Update conda_build_config.yaml: use later os/x compiler * don't link non-existent librt on Darwin --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Andreas Sjödin <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> * Update manta - Add back missing scripts (#53640) * update yaml (#53681) * krbalancing: add arm64 build (#53688) * update biobox_add_tagid (#53685) * Update gseapy to 1.1.5 (#53696) * Update oakvar to 2.12.9 (#53693) * Updating bioconductor-limma for osx-arm64 (#53690) * Updating bioconductor-pcamethods for osx-arm64 (#53694) * Updating bioconductor-biocparallel for osx-arm64 (#53697) * Update meta.yaml for NanoCaller (#53698) * Update panacus recipe to include third-party licenses (#53676) * Bump panacus version * Add cargo bundle licenses * Reset build number * Update panacus to include serde derive feature * Add THIRDPARTY.yml to licence_file * s/-/./ in version * Bump panacus version * Update build.sh --------- Co-authored-by: Peter Heringer <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> * Update tmalign to 20190818 (#53699) * Update tmalign to 20190818 * Update meta.yaml * Update r-jackstraw to 1.3.17 (#53119) * Update r-jackstraw to 1.3.17 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <[email protected]> * Update perl-data-uuid to 1.227 (#53117) * Update perl-data-uuid to 1.227 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <[email protected]> * dialign-tx: add arm64 build (#53700) * Update perl-datetime to 1.65 (#53132) * Update perl-datetime to 1.65 * add run_exports --------- Co-authored-by: Joshua Zhuang <[email protected]> * perl-data-uuid: add aarch64/arm64 builds (#53701) * perl-data-uuid: add aarch64/arm64 builds Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Do not build osx-arm64. It depends on missing dependencies --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update perl-cgi to 4.67 (#53120) * Update perl-cgi to 4.66 * Update perl-cgi to 4.67 * Update meta.yaml * Update meta.yaml * Disable the test for CGI::Cookie. It's version is 4.59 instead of 4.67 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add builds for aarch64 and arm64 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Do not build aarch64 and arm64. perl-sub-uplevel is not yet available for them --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> * Update perl-template-toolkit to 3.102 (#53112) * Update perl-template-toolkit to 3.102 * add run_exports * Add run_exports Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update the expected version in the tests Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try to build for aarch64 and arm64 --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> * clustalw: add arm64 build (#53702) * Add muset recipe (#53080) * Add kmtricks dependency to decom recipe * increment build number and remove noarch specification * Increment build number * Add noarch: python and setuptools * Resolve conflicts in decom recipe * Add muset recipe version 0.5.1 * Add muset recipe version 0.5.1 - Add run_exports to build section - Follows Bioconda linting guidelines * Add muset recipe v0.5.1 - Added run_exports for dependency pinning - Specified build script location - Added pkg-config and libstdcxx-ng to dependencies * Remove build.sh script * Minimal muset recipe * Add run_exports to build section * Simplify build.sh script * Improve muset recipe build configuration - Add make and pkg-config to build requirements - Update build script to explicitly set compiler paths * Add recursive flag to git clone * Add git recursive to build.sh * add git dependency to meta.yaml! * Simplify muset recipe build process * Update muset recipe to explicitly set CONDA_BUILD=ON for proper conda packaging * Add patch for fmt external project in muset * add external projects patch * Try original conda recipe * run exports + reset build number + summary * Add verbose build.sh * Try external projects patch * Modify ExternalProject configurations to prevent library downloads and improve Bioconda build compatibility for bundled external libraries. * Fix xxHash library patch for Bioconda build * go back to simpler external_proj_projects.patch * go back to simpler patch * add one path per external project * fix indentation error in meta.yaml * Edit white spaces and indentation in patches * Ensure newline at the end of every patchç * Try verbose build to debug patches * Going back to standard build + no patches * correct build.sh that points to non existing patch * Try only fmt patch * remove trash file * added verbose build + modified fmt patch * Add an even more verbose build.sh * Attempt to fmt patch * Avoid unnecessary download in fmt patch * adapt build.sh * Correct fmt patch * No patches * Explicitly set some variables in build.sh * add cmake path to build.sh * add alternative fmt patch * Try adding dependencies from conda directly * remove duplicated compiler * Remove compiler from host section in meta.yaml * Navigate muset as subdirectory in build.sh * Remove external ref to build.sh in meta.yaml * Change build.sh to verify folder structure is correct * list external directories * specify git version and recursive git cloning * try git commands inside build.sh * git checkout from the version which is passed as an env variable * git init before git fetch * Fix version for checkout using version tag * remove any existing directories to prevent issues * Undo the rm -rf .git action and simply git submodule init and update recursively * Verbose build.sh to find executables * fix build.sh to avoid copying non-existing binaries * add check for dynamic dependencias in bin folder and add test commands in meta.yaml * Change print binary informaiton after copying files, remove use of command file * Remove test section * actually tests can't be removed :) * Remove git init and remote add origin commands from build.sh * Try different url * add additional echo test after muset --help * Explicitly exit with success statusç * More verbose build.sh to see if binary copying suceeds * Add verbose version of build.sh * add more verbose build.sh * Added a run_test.sh file * Uset git_url in meta.yaml and remove git init in build.sh * Add sha256 * Remove checksum * Extra note to skip lint as no checksum will be provided * Add skip-lints missing hash * Keep old run_test.sh file * Minor cleanup of build.sh * Remove default values to simplify the config * Update meta.yaml * cmake --verbose * Do not build for linux-aarch64. It uses x86_64 intrinsics and needs patching for ARM NEON * fix run_test.sh to remove || echo and || true fallbacks * Try simpler run_test.sh script * Edit run_test.sh since exit was in the middle of the file * remove ldd command * Try simpler run_test.sh script * More verbose run_test.sh * Check muset --help output * Add test commands on meta.yaml only * It looks like `--version` returns non-0 status code. Pipe it to grep to recover * '--help' returns non-0 status code. Pipe it to `grep` to recover --------- Co-authored-by: Martin Grigorov <[email protected]> * Update perl-file-copy-link to 0.200 (#53109) * Update perl-file-copy-link to 0.200 * Update meta.yaml * Update version.patch * No need to patch the version * Delete recipes/perl-file-copy-link/version.patch * Try to build for aarch64 and arm64 * Do not build osx-arm64. perl-data-dumper is not yet available --------- Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> * Update trackplot to 0.5.2 (#53704) * perl-params-validate: add linux-aarch64 (#53705) * Add linux-aarch64 * declare name * add Vpt segmentation packing (#53649) * add vpt-segmentation-packing * update meta * Update recipes/vpt-segmentation-packing/meta.yaml Co-authored-by: Björn Grüning <[email protected]> * pin python version --------- Co-authored-by: Björn Grüning <[email protected]> * Update pysam to 0.23.0 (#53706) * create corona_lineage_dynamics (#53522) * create corona_lineage_dynamics * Update recipes/corona_lineage_dynamics/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/corona_lineage_dynamics/meta.yaml Co-authored-by: Martin Grigorov <[email protected]> * fixing errors by bio-conda * fixing errors * Fixed issues as per review comments * Fixed issues as per review comments * library link changed * Fixed issues as per review comments * Fixed issues as per review comments * Fixed issues as per review comments * Fixed issues as per review comments * Fixed issues as per review comments * Cleanup meta.yaml * Update meta.yaml * Remove the version range for r-base For some reason conda-build does not like it: ``` conda.exceptions.InvalidVersionSpec: Invalid version '>=4': invalid character(s) ``` * Do not build aarch64 and arm64. r-binom is not yet available for them --------- Co-authored-by: Martin Grigorov <[email protected]> * Update recipe for corona_lineage_dynamics: r-xml is added as a requir… (#53710) * Update recipe for corona_lineage_dynamics: r-xml is added as a required package. * Update recipe for corona_lineage_dynamics: r-xml is added as a required package. * Update truvari to 5.1.1 (#53711) * Update tower-cli to 0.11.0 (#53712) * Update biobox_add_taxid to 1.1 (#53713) * Update dendropy to 5.0.3 (#53714) * Update dendropy to 5.0.4 (#53717) * Update taseq to 1.1.1 (#53720) * Update dendropy to 5.0.5 (#53721) * Updating bioconductor-globalancova for osx-arm64 (#53718) * Updating bioconductor-globalancova for osx-arm64 * Updating bioconductor-graph for osx-arm64 * Updating bioconductor packages for osx-arm64 (#53715) * Update biox to 1.2.0 (#53716) * Update biox to 1.2.0: fix taxonomy dependency * Update biox to 1.2.0 * Update biox to 1.2.0 * Update biox to 1.2.0 * Update biox to 1.2.0 * Update dendropy to 5.0.6 (#53722) Co-authored-by: Martin Grigorov <[email protected]> * Update pybiolib to 1.2.366 (#53724) * Update learnmsa to 2.0.10 (#53725) * Updating bioconductor packages for osx-arm64 (#53719) * Update amplify to 2.0.1 (#53728) * Update seqnado to 0.6.1 (#53729) * Update ncbi-stxtyper to 1.0.40 (#53734) * Updating bioconductor-rbgl for osx-arm64 (#53736) * Updating bioconductor-multtest for osx-arm64 (#53735) * Updating bioconductor-msnbase for osx-arm64 (#53733) * Add linux-aarch64 to bioconductor-globalancova (#53723) Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Update biobox_add_taxid to 1.2 (#53741) * Update freyja to 1.5.3 (#53740) * Update for AMRFinderPlus 4.0.19 (#53738) * Updating bioconductor-camera for osx-arm64 (#53739) * Updating bioconductor-fgsea version, osx-arm64 (#53737) * Add adas v0.1.2 (#53742) * Add adas v0.1.2 * Add adas v0.1.2 * Collect third party licenses with cargo-bundle-licenses. Add linux-aarch64 * collect third party licences * Drop linux-aarch64. A dependency does not compile on this platform --------- Co-authored-by: Jianshu Zhao <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> * Update seqnado dependencies (#53731) * Update seqnado dependencies: replace click, cookiecutter, and drmaa with pandera and pyranges; update pulp version and refine snakemake constraints. * Refine formatting of dependency constraints in seqnado meta.yaml * Bump build number to 1 in seqnado meta.yaml * Update perl-mime-types to 2.27 (#45653) * Update perl-mime-types to 2.26 * Update perl-mime-types to 2.27 * Add run_exports --------- Co-authored-by: Martin Grigorov <[email protected]> * Relax run requirements (#53743) * Relax run requirements for compilers & MPI * Bump build number * Change syntax * Start with MPI for run requirements * Fix indentation * Use a single line for {% if mpi_name == ... * Update meta.yaml (#53745) * Update gw to 1.1.4 (#53746) * genoflu version 1.06 --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Bioconda Bot <[email protected]> Co-authored-by: Florian Zwagemaker <[email protected]> Co-authored-by: Timo Sachsenberg <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Rob Patro <[email protected]> Co-authored-by: Filipe G. Vieira <[email protected]> Co-authored-by: Konstantinn Bonnet <[email protected]> Co-authored-by: Harrison Deng <[email protected]> Co-authored-by: Rutger Vos <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: Wolfgang Maier <[email protected]> Co-authored-by: mencian <[email protected]> Co-authored-by: Antônio Camargo <[email protected]> Co-authored-by: coperni <[email protected]> Co-authored-by: Pau Andrio <[email protected]> Co-authored-by: Felix Van der Jeugt <[email protected]> Co-authored-by: Felix Van der Jeugt <[email protected]> Co-authored-by: nickjcroucher <[email protected]> Co-authored-by: dslarm <[email protected]> Co-authored-by: Genís Bayarri <[email protected]> Co-authored-by: Tobias Baril <[email protected]> Co-authored-by: Marc Sturm <[email protected]> Co-authored-by: Ramprasad Neethiraj <[email protected]> Co-authored-by: Usman Rashid <[email protected]> Co-authored-by: Ralf Gabriels <[email protected]> Co-authored-by: Arjun Prasad <[email protected]> Co-authored-by: Michael S. Cuoco <[email protected]> Co-authored-by: brunocontrerasmoreira <[email protected]> Co-authored-by: eead-csic-compbio <[email protected]> Co-authored-by: Björn Grüning <[email protected]> Co-authored-by: Robert A. Petit III <[email protected]> Co-authored-by: David Příhoda <[email protected]> Co-authored-by: Felix Mölder <[email protected]> Co-authored-by: Chris Saunders <[email protected]> Co-authored-by: Mervin Fansler <[email protected]> Co-authored-by: Stephan Schiffels <[email protected]> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: Sebastian Schmidt <[email protected]> Co-authored-by: Jean Iaquinta <[email protected]> Co-authored-by: nsandau <[email protected]> Co-authored-by: Dhananjhay Bansal (Djay) <[email protected]> Co-authored-by: Chris Tomkins-Tinch <[email protected]> Co-authored-by: Martin Larralde <[email protected]> Co-authored-by: Wouter De Coster <[email protected]> Co-authored-by: Ian M. B. <[email protected]> Co-authored-by: DaanJansen94 <[email protected]> Co-authored-by: Daniel Doerr <[email protected]> Co-authored-by: Dany Doerr <[email protected]> Co-authored-by: Jody Phelan <[email protected]> Co-authored-by: RunpengLuo <[email protected]> Co-authored-by: Steven Sutcliffe <[email protected]> Co-authored-by: Jim Shaw <[email protected]> Co-authored-by: Kez Cleal <[email protected]> Co-authored-by: Mariia Zelenskaia <[email protected]> Co-authored-by: Alvarosmb <[email protected]> Co-authored-by: Alvarosmb <[email protected]> Co-authored-by: Hugo Lefeuvre <[email protected]> Co-authored-by: Alexandra P <[email protected]> Co-authored-by: Alexandra Pancikova <[email protected]> Co-authored-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Andreas Sjödin <[email protected]> Co-authored-by: Pontus Höjer <[email protected]> Co-authored-by: SantaMcCloud <[email protected]> Co-authored-by: Tyler Funnell <[email protected]> Co-authored-by: Sebastian Bassi <[email protected]> Co-authored-by: Peter Heringer <[email protected]> Co-authored-by: Peter Heringer <[email protected]> Co-authored-by: Camila Duitama <[email protected]> Co-authored-by: Amirhossein <[email protected]> Co-authored-by: Hadi <[email protected]> Co-authored-by: TianMayCry9 <[email protected]> Co-authored-by: Felix Becker <[email protected]> Co-authored-by: Jianshu_Zhao <[email protected]> Co-authored-by: Jianshu Zhao <[email protected]> Co-authored-by: Alastair Smith <[email protected]>
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Updates the panacus recipe so it includes the licenses of dependencies
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