| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
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* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
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* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
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* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.471.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI.
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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>
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* 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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* 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>
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* 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>
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* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ...
* gnu/packages/cran.scm: ... here.
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This reverts commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea.
This package is not free software.
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* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
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* gnu/packages/bioinformatics.scm (r-loomr): New variable.
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* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
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* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3.
[inputs]: Order alphabetically.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom
'install phase to add vcflib.pc.
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* 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.
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* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom
'install phase to add fastahack.pc.
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* 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.
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* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust
custom 'install phase to add smithwaterman.pc file.
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* 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.
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* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'install phase to add tabixpp.pc file.
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* 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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* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
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* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
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* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
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Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2.
[inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
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