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2022-08-08gnu: Add phyml.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (phyml): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-02gnu: Add python-scanorama.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
2022-08-02gnu: python-intervaltree: Update to 3.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
2022-08-01gnu: python-bbknn: Update to 1.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1. [propagated-inputs]: Add python-pandas.
2022-08-01gnu: Add r-millefy.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
2022-08-01gnu: python-bbknn: Set NUMBA_CACHE_DIR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'set-numba-cache-dir.
2022-07-31gnu: qtsvg: Rename variable to qtsvg-5.Maxim Cournoyer
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
2022-07-28gnu: plink-ng: Fix building on other architectures.Efraim Flashner
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust make-flags to add simde includes to CFLAGS. [native-inputs]: Add simde.
2022-07-28gnu: plink-ng: Update to 2.00a3.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
2022-07-09gnu: Add python-cellbender.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
2022-07-06gnu: Add hh-suite.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hh-suite): New variable.
2022-07-04gnu: Add r-sccustomize.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
2022-07-02gnu: libsbml: Use regular check.Thiago Jung Bauermann
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14 with check. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-07-01gnu: Add python-ikarus.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
2022-06-16gnu: Add pyscenic.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
2022-06-16gnu: Add python-arboreto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
2022-06-16gnu: Add python-ctxcore.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
2022-06-09gnu: python-pybedtools: Update to 0.9.0.Vagrant Cascadian
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0. [description]: Update to satisfy guix lint. [license]: Update to expat and lgpl2.1+.
2022-06-06gnu: discrover: Use reproducible timestamps.Vagrant Cascadian
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add 'set-force-source-date phase.
2022-06-01gnu: pigx-scrnaseq: Update to 1.1.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake.
2022-06-01gnu: pigx-bsseq: Update to 0.1.7.Ricardo Wurmus
* 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.
2022-06-01gnu: pigx-chipseq: Update to 0.1.0.Ricardo Wurmus
* 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.
2022-06-01gnu: pigx-rnaseq: Update to 0.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0. [arguments]: Remove phase 'patch-knitr.
2022-06-01gnu: pigx-rnaseq: Update to 0.0.21.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
2022-06-01gnu: pigx-rnaseq: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
2022-06-01gnu: Add sylamer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sylamer): New variable.
2022-05-31gnu: Remove python2-biopython.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
2022-05-31gnu: Remove pplacer-scripts.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
2022-05-31gnu: Remove pplacer.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
2022-05-31gnu: Remove python2-checkm-genome.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
2022-05-31gnu: Remove fraggenescan.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
2022-05-31gnu: Remove python2-pysam.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
2022-05-31gnu: Remove find-circ.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
2022-05-31gnu: Remove gess.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (gess): Delete variable.
2022-05-31gnu: Remove pyicoteo.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
2022-05-31gnu: Remove python2-pbcore.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31gnu: Remove python2-pyfaidx.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31gnu: Remove python2-screed.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31gnu: Remove miso.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31gnu: Remove python2-warpedlmm.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31gnu: Remove poretools.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31gnu: Remove python2-dendropy.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31gnu: Remove bamm.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31gnu: Remove python2-pybedtools.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31gnu: Remove python2-htseq.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31gnu: Remove pepr.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31gnu: tetoolkit: Update to 2.2.1b.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b. [python]: Delete argument. [phases]: Delete trailing #t. {make-writable}: Delete phase. {adjust-requirements}: New phase. {patch-invocations}: Use search-input-file. {wrap-program}: Use search-input-file. [inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam. [home-page]: Update URL.
2022-05-31gnu: Remove python2-pybigwig.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31gnu: Remove ribodiff.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31gnu: Remove grit.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (grit): Delete variable.
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