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* gnu: bioperl-minimal: Avoid top-level cross-module references.Ludovic Courtès2021-07-01
| | | | | | | | This could lead to circular reference breakage. * gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level references to perl-* variables and their transitive inputs to 'arguments' and 'inputs'.
* gnu: Do not import (gnu packages commencement).Ludovic Courtès2021-07-01
| | | | | | | Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64. * gnu/packages/bioinformatics.scm: Remove unused (gnu packages commencement) import.
* gnu: ensembl-vep: Use a source file-name.Efraim Flashner2021-06-22
| | | | | * gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name field.
* gnu: Add perl-cworld-dekker.Ricardo Wurmus2021-06-22
| | | | * gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
* gnu: Add python-iced.Ricardo Wurmus2021-06-21
| | | | * gnu/packages/bioinformatics.scm (python-iced): New variable.
* gnu: Add python-cgatcore.Ricardo Wurmus2021-06-14
| | | | * gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
* gnu: Rename qtbase to qtbase-5.Maxim Cournoyer2021-06-14
| | | | | | | | | | | | This change was automated via the following command: $ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g' $ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g' $ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g' $ git checkout etc # to clear some spurious changes This is done so the qtbase package can be upgraded to version 6 in the following commit.
* gnu: pigx-sars-cov2-ww: Update to 0.0.2.Ricardo Wurmus2021-06-08
| | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2. [inputs]: Add wget.
* gnu: pigx-bsseq: Update to 0.1.5.Ricardo Wurmus2021-06-08
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
* gnu: python-hicmatrix: Update to 15.Mădălin Ionel Patrașcu2021-06-08
| | | | | | | | * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15. [arguments]: Enabled tests. Remove 'relax-requirements phase. [native-inputs]: Add python-pytest. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python-mappy: Move to (gnu packages bioinformatics).Efraim Flashner2021-06-08
| | | | | * gnu/packages/python-xyz.scm (python-mappy): Move to ... * gnu/packages/bioinformatics.scm: ... here.
* gnu: pigx-rnaseq: Update to 0.0.17.Ricardo Wurmus2021-06-08
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17. [arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase. [inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and python-deeptools. [native-inputs]: Add tzdata.
* gnu: pigx-rnaseq: Adjust to upgrade of salmon.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase "use-latest-salmon".
* gnu: salmon: Update to 1.4.0.Ricardo Wurmus2021-06-07
| | | | | | | | | * gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0. [arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags; remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add "fix-error-message-in-tests" phase, simplify "use-system-libraries" phase. [inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap sources.
* gnu: macs: Update to 2.2.7.1.Ricardo Wurmus2021-06-07
| | | | * gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
* gnu: libgff: Update to 2.0.0.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0. [home-page]: Update to new home.
* gnu: jellyfish: Update to 2.3.0.Ricardo Wurmus2021-06-07
| | | | | | | * gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0. [arguments]: Disable SSE to avoid tuning to the build node's CPU. [native-inputs]: Replace python-2 with python-wrapper. [license]: Update.
* gnu: multiqc: Update to 1.10.1.Ricardo Wurmus2021-06-07
| | | | | | | | * 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.
* gnu: python-hic2cool: Update to 0.8.3.Mădălin Ionel Patrașcu2021-06-07
| | | | | | | | | | * 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>
* gnu: freebayes: Update to 1.3.5.Efraim Flashner2021-06-06
| | | | | | | | | * 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.
* gnu: python-cooler: Update to 0.8.11.Mădălin Ionel Patrașcu2021-06-06
| | | | | | | | * 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.
* gnu: pigx-rnaseq: Update to 0.0.13.Ricardo Wurmus2021-06-05
| | | | | | * 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.
* gnu: python-scanpy: Update to 1.7.2.Roel Janssen2021-06-04
| | | | * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
* gnu: Add pigx-sars-cov2-ww.Ricardo Wurmus2021-06-04
| | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
* gnu: Add fit-sne.Ricardo Wurmus2021-06-03
| | | | * gnu/packages/bioinformatics.scm (fit-sne): New variable.
* gnu: Add biobambam2.Ricardo Wurmus2021-06-02
| | | | * gnu/packages/bioinformatics.scm (biobambam2): New variable.
* gnu: Add libmaus2.Ricardo Wurmus2021-06-02
| | | | * gnu/packages/bioinformatics.scm (libmaus2): New variable.
* gnu: Add bamutils.Roel Janssen2021-06-01
| | | | * gnu/packages/bioinformatics.scm (bamutils): New variable.
* gnu: bits: Use git-version and git-file-name.Ricardo Wurmus2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (bits)[version]: Use git-version. [source]: Use git-file-name.
* gnu: piranha: Use git-version.Ricardo Wurmus2021-05-31
| | | | * gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
* gnu: r-chipkernels: Use git-version and git-file-name.Ricardo Wurmus2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version. [source]: Use git-file-name.
* gnu: f-seq: Use git-version and git-file-name.Ricardo Wurmus2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version. [source]: Use git-file-name.
* gnu: bismark: Use git-file-name.Ricardo Wurmus2021-05-31
| | | | * gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
* gnu: filevercmp: Use git-version.Ricardo Wurmus2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind "revision" in outer let.
* gnu: r-spp: Move to (gnu packages bioconductor).Ricardo Wurmus2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-spp): Move from here... * gnu/packages/bioconductor.scm (r-spp): ...to here.
* gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.Ricardo Wurmus2021-05-31
| | | | | | | * gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit outside of the package value. [version]: Use git-version. [source]: Use git-file-name.
* gnu: r-methylkit: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here.
* gnu: r-copywriter: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here.
* gnu: r-copyhelper: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | | * 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.
* gnu: r-chipseq: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here.
* gnu: r-rhdf5: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-rhdf5): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
* gnu: r-annotationfilter: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here... * gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
* gnu: r-rhdf5filters: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
* gnu: r-tximport: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-tximport): Move from here... * gnu/packages/bioconductor.scm (r-tximport): ...to here.
* gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
* gnu: r-rcas: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here.
* gnu: r-bamsignals: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
* gnu: r-rhtslib: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
* gnu: r-zlibbioc: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here... * gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
* gnu: r-seqlogo: Move to (gnu packages bioconductor).zimoun2021-05-31
| | | | | * gnu/packages/bioinformatics.scm (r-seqlogo): Move from here... * gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
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