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2021-05-31gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here... * gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
2021-05-31gnu: r-edaseq: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here... * gnu/packages/bioconductor.scm (r-edaseq): ...to here.
2021-05-31gnu: r-deseq: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-deseq): Move from here... * gnu/packages/bioconductor.scm (r-deseq): ...to here.
2021-05-31gnu: r-aroma-light: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here... * gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
2021-05-31gnu: r-mzid: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-mzid): Move from here... * gnu/packages/bioconductor.scm (r-mzid): ...to here.
2021-05-31gnu: r-pcamethods: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here... * gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
2021-05-31gnu: r-genomationdata: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here... * gnu/packages/bioconductor.scm (r-genomationdata): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31gnu: r-genomation: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genomation): Move from here... * gnu/packages/bioconductor.scm (r-genomation): ...to here.
2021-05-31gnu: r-go-db: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-go-db): Move from here... * gnu/packages/bioconductor.scm (r-go-db): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
2021-05-31gnu: r-seqpattern: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here... * gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
2021-05-31gnu: r-impute: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-impute): Move from here... * gnu/packages/bioconductor.scm (r-impute): ...to here.
2021-05-31gnu: r-msnbase: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here... * gnu/packages/bioconductor.scm (r-msnbase): ...to here.
2021-05-31gnu: r-msnid: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-msnid): Move from here... * gnu/packages/bioconductor.scm (r-msnid): ...to here.
2021-05-31gnu: r-bsgenome: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
2021-05-31gnu: r-topgo: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-topgo): Move from here... * gnu/packages/bioconductor.scm (r-topgo): ...to here.
2021-05-31gnu: r-genomicfeatures: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here... * gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
2021-05-31gnu: r-rtracklayer: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here... * gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
2021-05-31gnu: r-genomicalignments: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here... * gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
2021-05-29gnu: Add mosaicatcher.Ricardo Wurmus
* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
2021-05-29Revert "gnu: Add mosaicatcher."Christopher Baines
mosaicatcher-unbundle-htslib.patch is missing. This reverts commit b1ae0f30d856503fa311d380584a6d7c80559332.
2021-05-28gnu: Add mosaicatcher.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
2021-05-27gnu: Add python-pyega3.Roel Janssen
* gnu/packages/bioinformatics.scm (python-pyega3): New variable.
2021-05-27gnu: Add python-htsget.Roel Janssen
* gnu/packages/bioinformatics.scm (python-htsget): New variable.
2021-05-26gnu: minimap2: Install more files.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules. Adjust custom 'install phase to also install library, headers and a pkg-config file.
2021-05-26gnu: minimap2: Update to 2.18.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.18. [source]: Remove patch. * gnu/packages/patches/minimap2-aarch64-support.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2021-05-26gnu: Add r-phantompeakqualtools.Roel Janssen
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable.
2021-05-26gnu: Add r-spp.Roel Janssen
* gnu/packages/bioinformatics.scm (r-spp): New variable.
2021-05-20gnu: r-rhdf5filters: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Update to 1.2.1.
2021-05-17gnu: pigx-chipseq: Update to 0.0.52.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.52.
2021-05-14gnu: prinseq: Fix references to perl executable.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Embed concrete references to the "perl" executable.
2021-05-07gnu: Add ensembl-vep.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ensembl-vep): New variable.
2021-05-06gnu: Add perl-bio-db-hts.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable.
2021-05-05gnu: python-pybedtools: Update to 0.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2. [arguments]: Remove outdated substitutions; simplify check phase.
2021-05-04gnu: r-summarizedexperiment: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here... * gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here.
2021-05-04gnu: r-ensembldb: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1.
2021-05-04gnu: r-gage: Update to 2.40.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2.
2021-05-04gnu: r-annotationhub: Update to 2.22.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1.
2021-04-30gnu: Add pbgzip.Roel Janssen
* gnu/packages/bioinformatics.scm (pbgzip): New variable.
2021-04-29gnu: Update bedtools to 2.30.0.Roel Janssen
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0, [inputs]: Use latest samtools.
2021-04-29gnu: Update samtools to 1.12.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
2021-04-29gnu: Update bcftools to 1.12.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
2021-04-29gnu: htslib: Update to 1.12.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
2021-04-28gnu: pigx-bsseq: Update to 0.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3. [inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
2021-04-28gnu: Add lofreq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lofreq): New variable.
2021-04-28gnu: kraken2: Replace references to rsync.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync. [arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to avoid repeating "scripts".
2021-04-28gnu: Add python-pyliftover.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
2021-04-25gnu: Add python-louvain 0.15.Vinicius Monego
* gnu/packages/graph.scm (python-louvain): Rename variable to python-louvain-0.6. (python-louvain): New variable. * gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Use python-louvain-0.6. Co-authored-by: Leo Famulari <leo@famulari.name>
2021-04-23gnu: Add shorah.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (shorah): New variable.
2021-04-23gnu: Add r-shinycell.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
2021-04-22gnu: Add kraken2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kraken2): New variable.
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