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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.
2020-11-09gnu: 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.
2020-10-29gnu: 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.
2020-10-07gnu: 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.
2020-09-25gnu: 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>
2020-09-22gnu: 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>
2020-09-11gnu: r-qtl2: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-qtl2): Move from here... * gnu/packages/cran.scm (r-qtl2): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-qtl: Move to (gnu packages cran).zimoun
* gnu/packages/bioinformatics.scm (r-qtl): Move from here... * gnu/packages/cran.scm (r-qtl): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-10gnu: Move r-bisquerna.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ... * gnu/packages/cran.scm: ... here.
2020-09-09Revert "gnu: Add r-loomr."Ricardo Wurmus
This reverts commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea. This package is not free software.
2020-09-09gnu: Add r-bisquerna.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
2020-09-09gnu: Add r-loomr.Roel Janssen
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
2020-09-05gnu: seqmagick: Update to 0.8.0.Andreas Enge
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
2020-08-30gnu: delly: Update to 0.8.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3. [inputs]: Order alphabetically.
2020-08-27gnu: vcflib: Install pkgconfig file.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom 'install phase to add vcflib.pc.
2020-08-27gnu: vcflib: Use shared libraries.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add snippet to adjust files for new locations. [inputs]: Add fastahack, smithwaterman, tabixpp, xz. [native-inputs]: Add pkg-config. Remove the package-source of fastahack, fsom, smithwaterman, tabixpp. [arguments]: Remove make-flags. Add custom phase to add the output lib directory to the rpath. Adjust custom 'unpack-submodule-sources for the change in native-inputs. Adjust custom 'install phase to also install libraries and headers. * gnu/packages/patches/vcflib-use-shared-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2020-08-27gnu: fastahack: Install pkgconfig file.Efraim Flashner
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom 'install phase to add fastahack.pc.
2020-08-27gnu: fastahack: Build and install shared library and headers.Efraim Flashner
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to build PIE objects. Add custom phase to build dynamic library. Adjust custom 'install phase to install shared library and headers.
2020-08-27gnu: smithwaterman: Install pkgconfig file.Efraim Flashner
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust custom 'install phase to add smithwaterman.pc file.
2020-08-27gnu: smithwaterman: Build and install shared library and headers.Efraim Flashner
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom phase to build PIE objects. Add custom 'build-dynamic phase to build dynamic library. Adjust custom 'install phase to install shared library and headers.
2020-08-27gnu: tabixpp: Install pkgconfig file.Efraim Flashner
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom 'install phase to add tabixpp.pc file.
2020-08-27gnu: tabixpp: Build and install shared library and headers.Efraim Flashner
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom 'build phase to build shared library. Adjust custom 'install phase to install libraries and header.
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