| Commit message (Collapse) | Author | Age |
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Conflicts:
gnu/local.mk
gnu/packages/algebra.scm
gnu/packages/bioinformatics.scm
gnu/packages/curl.scm
gnu/packages/docbook.scm
gnu/packages/emacs-xyz.scm
gnu/packages/maths.scm
gnu/packages/plotutils.scm
gnu/packages/python-web.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/readline.scm
gnu/packages/tls.scm
gnu/packages/xml.scm
gnu/packages/xorg.scm
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
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* gnu/packages/bioinformatics.scm (fit-sne): New variable.
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* gnu/packages/bioinformatics.scm (biobambam2): New variable.
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* gnu/packages/bioinformatics.scm (libmaus2): New variable.
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* gnu/packages/bioinformatics.scm (bamutils): New variable.
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* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
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* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
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* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
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* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
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* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
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* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
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* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
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* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
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* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
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* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
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* 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.
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* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
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* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
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* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
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* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
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* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
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* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
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* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
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* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
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* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
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* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
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* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
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* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
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* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
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* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
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* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
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* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
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* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
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* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
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* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
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* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
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* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
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* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
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* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
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* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
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* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
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* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
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