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* gnu: Add flair.Ricardo Wurmus2022-08-23
| | | | * gnu/packages/bioinformatics.scm (flair): New variable.
* gnu: python-mappy: Update to 2.24.Ricardo Wurmus2022-08-23
| | | | * gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
* gnu: Add r-kbet.Ricardo Wurmus2022-08-18
| | | | * gnu/packages/bioinformatics.scm (r-kbet): New variable.
* gnu: Add go-github-com-biogo-biogo.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable.
* gnu: Add go-github-com-biogo-hts-fai.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable.
* gnu: Add go-github-com-biogo-hts-csi.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable.
* gnu: Add go-github-com-biogo-hts-cram.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable.
* gnu: Add go-github-com-biogo-hts-bgzf.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable.
* gnu: Add go-github-com-biogo-hts-tabix.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable.
* gnu: Add go-github-com-biogo-hts-sam.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
* gnu: Add go-github-com-biogo-hts-bam.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
* gnu: Add go-github-com-biogo-store-step.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
* gnu: Add go-github-com-biogo-store-llrb.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
* gnu: Add go-github-com-biogo-store-kdtree.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
* gnu: Add go-github-com-biogo-store-interval.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
* gnu: Add go-github-com-biogo-graph.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
* gnu: Add stpipeline.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (stpipeline): New variable.
* gnu: Add python-taggd.Ricardo Wurmus2022-08-16
| | | | * gnu/packages/bioinformatics.scm (python-taggd): New variable.
* gnu: htseq: Update to 2.0.2.Ricardo Wurmus2022-08-16
| | | | | | | | | | | * gnu/packages/bioinformatics.scm (htseq): Update to 2.0.2. [source]: Fetch from git repository. [arguments]: Delete 'build phase; run tests with pytest in 'check phase. [propagated-inputs]: Add python-matplotlib and python-pysam. [inputs]: Remove python-matplotlib and python-pysam. [native-inputs]: Add python-pandas, python-pytest, python-scipy, and swig. [synopsis]: Update. [description]: Update.
* gnu: plink-ng: Build sources from 2.0 directoryRicardo Wurmus2022-08-15
| | | | | | * gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Disable tests; adjust make flags; enter 2.0 directory in 'chdir phase; replace 'install phase. [inputs]: Add zstd:lib.
* gnu: Add r-liana.Ricardo Wurmus2022-08-10
| | | | * gnu/packages/bioinformatics.scm (r-liana): New variable.
* gnu: Add r-omnipathr/devel.Ricardo Wurmus2022-08-10
| | | | * gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
* gnu: cereal: Update to 1.3.2.Marius Bakke2022-08-10
| | | | | | | | | * gnu/packages/serialization.scm (cereal): Update to 1.3.2. [arguments]: Use G-expression. (cereal-1.3.0): New variable. * gnu/packages/bioinformatics.scm (salmon)[inputs]: Change from CEREAL to CEREAL-1.3.0. * gnu/packages/engineering.scm (prusa-slicer)[inputs]: Likewise.
* gnu: Add phyml.Mădălin Ionel Patrașcu2022-08-08
| | | | | | * gnu/packages/bioinformatics.scm (phyml): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add python-scanorama.Ricardo Wurmus2022-08-02
| | | | * gnu/packages/bioinformatics.scm (python-scanorama): New variable.
* gnu: python-intervaltree: Update to 3.1.0.Ricardo Wurmus2022-08-02
| | | | * gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
* gnu: python-bbknn: Update to 1.5.1.Ricardo Wurmus2022-08-01
| | | | | * gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1. [propagated-inputs]: Add python-pandas.
* gnu: Add r-millefy.Mădălin Ionel Patrașcu2022-08-01
| | | | * gnu/packages/bioinformatics.scm (r-millefy): New variable.
* gnu: python-bbknn: Set NUMBA_CACHE_DIR.Ricardo Wurmus2022-08-01
| | | | | * gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'set-numba-cache-dir.
* gnu: qtsvg: Rename variable to qtsvg-5.Maxim Cournoyer2022-07-31
| | | | | | | | This is in preparation of the qtsvg update to version 6. This change was automated via the following command: git grep -l '\bqtsvg\b' | xargs sed 's/qtsvg/qtsvg-5/g' -i
* gnu: plink-ng: Fix building on other architectures.Efraim Flashner2022-07-28
| | | | | | * gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust make-flags to add simde includes to CFLAGS. [native-inputs]: Add simde.
* gnu: plink-ng: Update to 2.00a3.3.Efraim Flashner2022-07-28
| | | | * gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
* gnu: Add python-cellbender.Ricardo Wurmus2022-07-09
| | | | * gnu/packages/bioinformatics.scm (python-cellbender): New variable.
* gnu: Add hh-suite.Ricardo Wurmus2022-07-06
| | | | * gnu/packages/bioinformatics.scm (hh-suite): New variable.
* gnu: Add r-sccustomize.Ricardo Wurmus2022-07-04
| | | | * gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
* gnu: libsbml: Use regular check.Thiago Jung Bauermann2022-07-02
| | | | | | | * gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14 with check. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
* gnu: Add python-ikarus.Ricardo Wurmus2022-07-01
| | | | * gnu/packages/bioinformatics.scm (python-ikarus): New variable.
* gnu: Add pyscenic.Ricardo Wurmus2022-06-16
| | | | * gnu/packages/bioinformatics.scm (pyscenic): New variable.
* gnu: Add python-arboreto.Ricardo Wurmus2022-06-16
| | | | * gnu/packages/bioinformatics.scm (python-arboreto): New variable.
* gnu: Add python-ctxcore.Ricardo Wurmus2022-06-16
| | | | * gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
* gnu: python-pybedtools: Update to 0.9.0.Vagrant Cascadian2022-06-09
| | | | | | * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0. [description]: Update to satisfy guix lint. [license]: Update to expat and lgpl2.1+.
* gnu: discrover: Use reproducible timestamps.Vagrant Cascadian2022-06-06
| | | | | * gnu/packages/bioinformatics.scm (discrover)[arguments]: Add 'set-force-source-date phase.
* gnu: pigx-scrnaseq: Update to 1.1.9.Ricardo Wurmus2022-06-01
| | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake.
* gnu: pigx-bsseq: Update to 0.1.7.Ricardo Wurmus2022-06-01
| | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove automake and autoconf. * gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu: pigx-chipseq: Update to 0.1.0.Ricardo Wurmus2022-06-01
| | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake. * gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu: pigx-rnaseq: Update to 0.1.0.Ricardo Wurmus2022-06-01
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0. [arguments]: Remove phase 'patch-knitr.
* gnu: pigx-rnaseq: Update to 0.0.21.Ricardo Wurmus2022-06-01
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
* gnu: pigx-rnaseq: Fix build.Ricardo Wurmus2022-06-01
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
* gnu: Add sylamer.Ricardo Wurmus2022-06-01
| | | | * gnu/packages/bioinformatics.scm (sylamer): New variable.
* gnu: Remove python2-biopython.Maxim Cournoyer2022-05-31
| | | | * gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
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