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2023-01-04gnu: bamtools: Build shared libraries.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared libraries instead of static libs.
2023-01-04gnu: Add scallop.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scallop): New variable.
2023-01-03gnu: Add python-bcbio-gff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
2022-12-30gnu: Add r-domultibarheatmap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
2022-12-28gnu: r-giotto: Update to 1.1.2-1.3c8067c.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c.
2022-12-22gnu: Add r-bedtorch.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
2022-12-22gnu: Add r-rhtslib12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable.
2022-12-22gnu: Add wiggletools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (wiggletools): New variable.
2022-12-22gnu: Add python-episcanpy.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-episcanpy): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-22gnu: Add python-bamnostic.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-bamnostic): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-21gnu: Add vembrane.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vembrane): New variable.
2022-12-21gnu: python-plastid: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.0. [source]: Fetch from git repository. [build-system]: Use pyproject-build-system. [arguments]: Enable tests; add build phases 'unpack-test-data and 'build-extensions. [inputs]: Add openssl. [native-inputs]: Add test data.
2022-12-21gnu: python-pysam: Update to 0.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.20.0. [build-system]: Use pyproject-build-system.
2022-12-21gnu: htslib: Update to 1.16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): Update to 1.16.
2022-12-21gnu: pbbam: Use htslib 1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam)[propagated-inputs]: Replace htslib with htslib-1.14.
2022-12-21gnu: Add htslib-1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-1.14): New variable.
2022-12-18gnu: python-scanpy: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases; move pytest arguments to #:test-flags; add 'pretend-version phase; replace custom 'check phase with 'delete-bad-tests phase.
2022-12-18gnu: python-multivelo: Simplify with pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases.
2022-12-14gnu: bedtools-2.18: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp. [native-inputs]: Drop package label.
2022-12-13gnu: bedops: Update to 2.4.41.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41. [arguments]: Remove trailing #T from build phases; do not set BINDIR in make-flags; set CC; replace 'install phase. [native-inputs]: Add diffutils, perl, and which.
2022-12-13gnu: tophat: Remove trailing #T from build phases and snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from snippet. [arguments]: Remove trailing #T from build phases.
2022-12-13gnu: python-bx-python: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0. [build-system]: Use pyproject-build-system. [arguments]: Add phase 'build-extensions and 'disable-cython-doctests. [native-inputs]: Replace python-nose with python-pytest.
2022-12-13gnu: bioawk: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify 'install phase.
2022-12-13gnu: blasr-libcpp: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove trailing #T from build phases.
2022-12-13gnu: pbbam: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
2022-12-13gnu: pbbam: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
2022-12-13gnu: pbcopper: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
2022-12-13gnu: bedtools: Remove unnecessary quasiquotation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote. [native-inputs]: Drop input label.
2022-12-13gnu: bamutils: Update to 1.0.15.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15. [arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags. [native-inputs]: Update libstatgen.
2022-12-13gnu: bamtools: Update to 2.5.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2. [arguments]: Enable tests; remove extra phases. [inputs]: Add jsoncpp. [native-inputs]: Add pkg-config.
2022-12-13gnu: aragorn: Update to 1.2.41.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41. [source]: Fetch C source file from new location. [arguments]: Drop trailing #T in build phases; use gexp. [native-inputs]: Add origin for man page. [home-page]: Update to new home page. [license]: Update to GPLv3+.
2022-12-13gnu: cnvkit: Update to 0.9.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9. [build-system]: Use pyproject-build-system. [arguments]: Relax restriction on python-joblib. [propagated-inputs]: Add python-pomegranate and python-scikit-learn.
2022-12-13gnu: seqmagick: Update to 0.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4. [build-system]: Use pyproject-build-system. [inputs]: Add python-pygtrie. [native-inputs]: Replace python-nose with python-pytest.
2022-12-13gnu: python-cgatcore: Update to 0.6.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14. [build-system]: Use pyproject-build-system. [arguments]: Disable broken tests with #:test-flags; do not replace 'check phase; add phase 'sqlite-compatibility. [native-inputs]: Drop input labels.
2022-12-13gnu: python-dna-features-viewer: Update to 3.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): Update to 3.1.1. [build-system]: Use pyproject-build-system. [arguments]: Add build phase to fix a compatibility problem with biopython. [propagated-inputs]: Add python-packaging.
2022-12-13gnu: python-hicexplorer: Update to 3.7.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2. [build-system]: Use pyproject-build-system. [arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a dependency on an unlicensed package; add phase "fix-references"; add phase "run-only-low-mem-tests". [propagated-inputs]: Remove python-configparser and python-six; add python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz, python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn, python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks, python-scikit-learn, and python-tqdm. [native-inputs]: Add graphviz.
2022-12-13gnu: python-pygenometracks: Update to 3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5. [build-system]: Use pyproject-build-system. [arguments]: Quote phases instead of full list of arguments; remove trailing #T from build phase.
2022-12-13gnu: python-hicmatrix: Update to 16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16. [build-system]: Use pyproject-build-system. [arguments]: Shuffle the quote.
2022-12-13gnu: python-biopython: Update to 1.80.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase.
2022-12-12gnu: bioperl-minimal: Remove trailing #T from build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioperl-minimal)[arguments]: Remove trailing #T from build phase.
2022-12-02gnu: python-biom-format: Update to 2.1.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12. [arguments]: Remove "relax" phase; update "disable-broken-tests" phase. [propagated-inputs]: Add python-scikit-bio.
2022-12-02gnu: Add python-scikit-bio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
2022-12-02gnu: python-pairtools: Update to 1.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2. [source]: Update Github URL. [arguments]: Update patch in "fix-references" phase. [native-inputs]: Remove python-nose. [inputs]: Remove. [propagated-inputs]: Add python-bioframe, python-pandas, python-pysam, python-pyyaml, and python-scipy. [home-page]: Update.
2022-12-02gnu: python-pairtools: Run tests conditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests conditionally.
2022-12-02gnu: python-pybedtools: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use pyproject-build-system. [arguments]: Import (guix build pyproject-build-system).
2022-12-02gnu: python-htsget: Update to 0.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6. [build-system]: Use pyproject-build-system.
2022-12-02gnu: python-cellbender: Update to 0.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2. [build-system]: Use pyproject-build-system.
2022-12-02gnu: Add python-fanc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fanc): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02gnu: Add python-genomic-regions.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-11-25gnu: Add r-btools.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-btools): New variable.
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