| Age | Commit message (Expand) | Author |
|---|
| 2022-08-23 | gnu: Add flair.•••* gnu/packages/bioinformatics.scm (flair): New variable.
| Ricardo Wurmus |
| 2022-08-23 | gnu: python-mappy: Update to 2.24.•••* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
| Ricardo Wurmus |
| 2022-08-18 | gnu: Add r-kbet.•••* gnu/packages/bioinformatics.scm (r-kbet): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-biogo.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-fai.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-csi.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-cram.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-bgzf.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-tabix.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-sam.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-hts-bam.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-store-step.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-store-llrb.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-store-kdtree.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-store-interval.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add go-github-com-biogo-graph.•••* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add stpipeline.•••* gnu/packages/bioinformatics.scm (stpipeline): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: Add python-taggd.•••* gnu/packages/bioinformatics.scm (python-taggd): New variable.
| Ricardo Wurmus |
| 2022-08-16 | gnu: htseq: Update to 2.0.2.•••* 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.
| Ricardo Wurmus |
| 2022-08-15 | gnu: plink-ng: Build sources from 2.0 directory•••* 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.
| Ricardo Wurmus |
| 2022-08-10 | gnu: Add r-liana.•••* gnu/packages/bioinformatics.scm (r-liana): New variable.
| Ricardo Wurmus |
| 2022-08-10 | gnu: Add r-omnipathr/devel.•••* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
| Ricardo Wurmus |
| 2022-08-10 | gnu: cereal: Update to 1.3.2.•••* 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.
| Marius Bakke |
| 2022-08-08 | gnu: Add phyml.•••* gnu/packages/bioinformatics.scm (phyml): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2022-08-02 | gnu: Add python-scanorama.•••* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
| Ricardo Wurmus |
| 2022-08-02 | gnu: python-intervaltree: Update to 3.1.0.•••* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
| Ricardo Wurmus |
| 2022-08-01 | gnu: python-bbknn: Update to 1.5.1.•••* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1.
[propagated-inputs]: Add python-pandas.
| Ricardo Wurmus |
| 2022-08-01 | gnu: Add r-millefy.•••* gnu/packages/bioinformatics.scm (r-millefy): New variable.
| Mădălin Ionel Patrașcu |
| 2022-08-01 | gnu: python-bbknn: Set NUMBA_CACHE_DIR.•••* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'set-numba-cache-dir.
| Ricardo Wurmus |
| 2022-07-31 | gnu: qtsvg: Rename variable to qtsvg-5.•••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
| Maxim Cournoyer |
| 2022-07-28 | gnu: plink-ng: Fix building on other architectures.•••* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to add simde includes to CFLAGS.
[native-inputs]: Add simde.
| Efraim Flashner |
| 2022-07-28 | gnu: plink-ng: Update to 2.00a3.3.•••* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
| Efraim Flashner |
| 2022-07-09 | gnu: Add python-cellbender.•••* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
| Ricardo Wurmus |
| 2022-07-06 | gnu: Add hh-suite.•••* gnu/packages/bioinformatics.scm (hh-suite): New variable.
| Ricardo Wurmus |
| 2022-07-04 | gnu: Add r-sccustomize.•••* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
| Ricardo Wurmus |
| 2022-07-02 | gnu: libsbml: Use regular check.•••* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14
with check.
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
| Thiago Jung Bauermann |
| 2022-07-01 | gnu: Add python-ikarus.•••* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
| Ricardo Wurmus |
| 2022-06-16 | gnu: Add pyscenic.•••* gnu/packages/bioinformatics.scm (pyscenic): New variable.
| Ricardo Wurmus |
| 2022-06-16 | gnu: Add python-arboreto.•••* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
| Ricardo Wurmus |
| 2022-06-16 | gnu: Add python-ctxcore.•••* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
| Ricardo Wurmus |
| 2022-06-09 | gnu: python-pybedtools: Update to 0.9.0.•••* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0.
[description]: Update to satisfy guix lint.
[license]: Update to expat and lgpl2.1+.
| Vagrant Cascadian |
| 2022-06-06 | gnu: discrover: Use reproducible timestamps.•••* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add
'set-force-source-date phase.
| Vagrant Cascadian |
| 2022-06-01 | gnu: pigx-scrnaseq: Update to 1.1.9.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
| Ricardo Wurmus |
| 2022-06-01 | gnu: pigx-bsseq: Update to 0.1.7.•••* 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.
| Ricardo Wurmus |
| 2022-06-01 | gnu: pigx-chipseq: Update to 0.1.0.•••* 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.
| Ricardo Wurmus |
| 2022-06-01 | gnu: pigx-rnaseq: Update to 0.1.0.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
| Ricardo Wurmus |
| 2022-06-01 | gnu: pigx-rnaseq: Update to 0.0.21.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
| Ricardo Wurmus |
| 2022-06-01 | gnu: pigx-rnaseq: Fix build.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
| Ricardo Wurmus |
| 2022-06-01 | gnu: Add sylamer.•••* gnu/packages/bioinformatics.scm (sylamer): New variable.
| Ricardo Wurmus |
| 2022-05-31 | gnu: Remove python2-biopython.•••* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
| Maxim Cournoyer |
