| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-05-31 | gnu: Remove pplacer-scripts.•••* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove pplacer.•••* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-checkm-genome.•••* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove fraggenescan.•••* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pysam.•••* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove find-circ.•••* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove gess.•••* gnu/packages/bioinformatics.scm (gess): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove pyicoteo.•••* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pbcore.•••* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pyfaidx.•••* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-screed.•••* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove miso.•••* gnu/packages/bioinformatics.scm (miso): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-warpedlmm.•••* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove poretools.•••* gnu/packages/bioinformatics.scm (poretools): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-dendropy.•••* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove bamm.•••* gnu/packages/bioinformatics.scm (bamm): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pybedtools.•••* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-htseq.•••* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove pepr.•••* gnu/packages/bioinformatics.scm (pepr): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: tetoolkit: Update to 2.2.1b.•••* 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.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pybigwig.•••* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove ribodiff.•••* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove grit.•••* gnu/packages/bioinformatics.scm (grit): Delete variable.
| Maxim Cournoyer |
