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2020-12-01gnu: java-picard-1.113: Use ant/java8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use ant/java8. [inputs]: Replace ant with ant/java8.
2020-11-30gnu: pigx-chipseq: Update to 0.0.51.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.51. [inputs]: Add r-corrplot, r-deseq2, r-dt, r-ggrepel, r-gprofiler2, r-pheatmap, and r-rsubread.
2020-11-30gnu: pigx-scrnaseq: Update to 1.1.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.7.
2020-11-26Merge branch 'master' into stagingMarius Bakke
2020-11-24gnu: tadbit: Update to 1.0.1.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1. [arguments]: Remove #:tests? and #:python arguments. [phases]{fix-problems-with-setup.py}: Remove no longer needed steps. {check}: Override phase. [native-inputs]: Add glib and pkg-config. [inputs]: Add python-future and python-h5py.
2020-11-24gnu: imp: Migrate to Python 3.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (imp) [arguments]: Enable tests by removing the #:tests? argument. Specify the arguments to pass to the ctest test running via the #:configure-flags argument. [inputs]: Add cgal and opencv. Remove python-2. Move swig to... [native-inputs]: ...here. Add python-wrapper. [propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas, python2-scikit-learn and python2-networkx by python-numpy, python-scipy, python-pandas, python-scikit-learn and python-networkx, respectively.
2020-11-23Merge branch 'master' into stagingMarius Bakke
2020-11-23gnu: Add cwltool.Efraim Flashner
* gnu/packages/bioinformatics.scm (cwltool): New variable.
2020-11-23gnu: Add python-schema-salad.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
2020-11-15Merge branch 'master' into stagingMarius Bakke
2020-11-15gnu: methyldackel: Update to 0.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1. [arguments]: Link with libbigwig. [inputs]: Add curl and libbigwig; replace htslib with htslib-1.9.
2020-11-13gnu: Fix build for python-pysam.Roel Janssen
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9, samtools-1.9, and bcftools-1.9.
2020-11-13gnu: Add bcftools-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
2020-11-13gnu: bedtools: Use samtools-1.9.Roel Janssen
The build for bedtools with samtools 1.11 triggers a testsuite failure which is reported here: https://github.com/arq5x/bedtools2/issues/814 * gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
2020-11-13gnu: Add samtools-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
2020-11-13gnu: Add htslib-1.9.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
2020-11-11Merge branch 'master' into stagingMarius Bakke
2020-11-09gnu: macs: Remove generated code.Efraim Flashner
* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove cython generated code. [native-inputs]: Add python-cython.
2020-11-09gnu: macs: Update check phase.Efraim Flashner
* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check phase before using custom 'check phase.
2020-11-09gnu: macs: Update source, home-page URIs.Efraim Flashner
* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update URIs to new location.
2020-11-07Merge branch 'master' into stagingMarius Bakke
Conflicts: gnu/local.mk gnu/packages/gdb.scm gnu/packages/lisp-xyz.scm gnu/packages/web-browsers.scm
2020-10-29gnu: Update samtools to 1.11.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
2020-10-29gnu: Update bcftools to 1.11.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
2020-10-29gnu: Update htslib to 1.11.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
2020-10-23gnu: imp: Update to 2.13.0.Ludovic Courtès
* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
2020-10-13gnu: Remove redundant MariaDB inputs.Marius Bakke
For well-behaved build systems, including the "dev" output suffices. * gnu/packages/bioinformatics.scm (kentutils)[inputs]: Remove MARIADB:LIB. * gnu/packages/cran.scm (r-rmysql)[inputs]: Likewise. * gnu/packages/databases.scm (python-mysqlclient, soci)[inputs]: Likewise. * gnu/packages/qt.scm (qt-4, qtbase): Likewise. * gnu/packages/ruby.scm (ruby-mysql2)[inputs]: Likewise.
2020-10-13Merge branch 'master' into stagingMarius Bakke
2020-10-07gnu: htslib: Enable support for custom URI schemes.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
2020-10-06gnu: r-gqtlbase: Update to 1.20.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.
2020-10-06gnu: r-rhdf5: Update to 2.32.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
2020-10-06gnu: r-biocstyle: Update to 2.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.
2020-10-05Merge branch 'master' into stagingGuillaume Le Vaillant
2020-09-25gnu: mafft: Update to 7.471.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (mafft): Update to 7.471. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2020-09-23Merge branch 'staging' into wip-lispGuillaume Le Vaillant
2020-09-22gnu: mafft: Use HTTPS home page URI.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI.
2020-09-14gnu: r-fithic: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-fithic): Move from here... * gnu/packages/bioconductor.scm (r-fithic): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-hitc: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-hitc): Move from here... * gnu/packages/bioconductor.scm (r-hitc): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-hdf5array: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here... * gnu/packages/bioconductor.scm (r-hdf5array): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-rhdf5lib: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-beachmat: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-beachmat): Move from here... * gnu/packages/bioconductor.scm (r-beachmat): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-singlecellexperiment: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here... * gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-scater: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-scater): Move from here... * gnu/packages/bioconductor.scm (r-scater): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-scran: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-scran): Move from here... * gnu/packages/bioconductor.scm (r-scran): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here... * gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-absfiltergsea: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here... * gnu/packages/cran.scm (r-absfiltergsea): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-diversitree: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-diversitree): Move from here... * gnu/packages/cran.scm (r-diversitree): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-phangorn: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-phangorn): Move from here... * gnu/packages/cran.scm (r-phangorn): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-seurat: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-seurat): Move from here... * gnu/packages/cran.scm (r-seurat): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-maldiquant: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here... * gnu/packages/cran.scm (r-maldiquant): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-seqminer: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-seqminer): Move from here... * gnu/packages/cran.scm (r-seqminer): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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