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2021-06-07gnu: multiqc: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1. [arguments]: Remove build phase "relax-requirements"; replace "check" phase. [propagated-inputs]: Add python-coloredlogs, python-future, python-networkx, and python-rich; remove python-nose. [native-inputs]: Add python-pytest and the test suite.
2021-06-07gnu: python-hic2cool: Update to 0.8.3.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. [source]: Download using git-fetch. [arguments]: Enable tests. Add phase to make test data writable. [propagated-inputs]: Add python-h5py, python-numpy, python-pandas, python-scipy. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-06-06gnu: freebayes: Update to 1.3.5.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5. [source]: Remove patch. [arguments]: Adjust custom 'patch-source phase for changes in source. [inputs]: Remove zlib. * gnu/packages/patches/freebayes-devendor-deps.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2021-06-06gnu: python-cooler: Update to 0.8.11.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11. [arguments]: Add build phase "patch-tests"; replace "check" phase. [native-inputs]: Add python-codecov, python-pytest-cov, and python-pytest-flake8. [propagated-inputs]: Add python-six and python-sparse.
2021-06-05gnu: pigx-rnaseq: Update to 0.0.13.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13. [arguments]: Remove obsolete substitutions. [inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
2021-06-04gnu: python-scanpy: Update to 1.7.2.Roel Janssen
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04gnu: Add pigx-sars-cov2-ww.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
2021-06-03gnu: Add fit-sne.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
2021-06-02gnu: Add biobambam2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
2021-06-02gnu: Add libmaus2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
2021-06-01gnu: Add bamutils.Roel Janssen
* gnu/packages/bioinformatics.scm (bamutils): New variable.
2021-05-31gnu: bits: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: piranha: Use git-version.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
2021-05-31gnu: r-chipkernels: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: f-seq: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: bismark: Use git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
2021-05-31gnu: filevercmp: Use git-version.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind "revision" in outer let.
2021-05-31gnu: r-spp: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spp): Move from here... * gnu/packages/bioconductor.scm (r-spp): ...to here.
2021-05-31gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit outside of the package value. [version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: r-methylkit: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here.
2021-05-31gnu: r-copywriter: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here.
2021-05-31gnu: r-copyhelper: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here... * gnu/packages/bioconductor.scm (r-copyhelper): ...to here. [source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31gnu: r-chipseq: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here.
2021-05-31gnu: r-rhdf5: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
2021-05-31gnu: r-annotationfilter: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here... * gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
2021-05-31gnu: r-rhdf5filters: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
2021-05-31gnu: r-tximport: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-tximport): Move from here... * gnu/packages/bioconductor.scm (r-tximport): ...to here.
2021-05-31gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
2021-05-31gnu: r-rcas: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here.
2021-05-31gnu: r-bamsignals: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
2021-05-31gnu: r-rhtslib: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
2021-05-31gnu: r-zlibbioc: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here... * gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
2021-05-31gnu: r-seqlogo: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here... * gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
2021-05-31gnu: r-motifrg: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here... * gnu/packages/bioconductor.scm (r-motifrg): ...to here.
2021-05-31gnu: r-sva: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-sva): Move from here... * gnu/packages/bioconductor.scm (r-sva): ...to here.
2021-05-31gnu: r-protgenerics: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here... * gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
2021-05-31gnu: r-mzr: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-mzr): Move from here... * gnu/packages/bioconductor.scm (r-mzr): ...to here.
2021-05-31gnu: r-ensembldb: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here... * gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
2021-05-31gnu: r-biovizbase: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here... * gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
2021-05-31gnu: r-vsn: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-vsn): Move from here... * gnu/packages/bioconductor.scm (r-vsn): ...to here.
2021-05-31gnu: r-affyio: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-affyio): Move from here... * gnu/packages/bioconductor.scm (r-affyio): ...to here.
2021-05-31gnu: r-organismdbi: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here... * gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
2021-05-31gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here... * gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
2021-05-31gnu: r-genomicfiles: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here... * gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
2021-05-31gnu: r-complexheatmap: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here... * gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
2021-05-31gnu: r-gage: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gage): Move from here... * gnu/packages/bioconductor.scm (r-gage): ...to here.
2021-05-31gnu: r-keggrest: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here... * gnu/packages/bioconductor.scm (r-keggrest): ...to here.
2021-05-31gnu: r-affy: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-affy): Move from here... * gnu/packages/bioconductor.scm (r-affy): ...to here.
2021-05-31gnu: r-fastseg: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here... * gnu/packages/bioconductor.scm (r-fastseg): ...to here.
2021-05-31gnu: r-annotationhub: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here... * gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
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