| Commit message (Collapse) | Author | Age |
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (cwltool): New variable.
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* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9,
samtools-1.9, and bcftools-1.9.
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* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
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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.
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* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
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* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
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* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove
cython generated code.
[native-inputs]: Add python-cython.
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* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check
phase before using custom 'check phase.
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* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update
URIs to new location.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
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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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