| Age | Commit message (Expand) | Author |
|---|
| 2022-09-13 | gnu: kraken2: Update to 2.1.2....* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2.
| Ricardo Wurmus |
| 2022-09-10 | gnu: Add comments to the bottom of a few package modules....This will hopefully discourage patches which add new packages to the bottom of
files, as this increases the likelihood of conflicts when applying patches.
If there are more specific ways that packages should be arranged in specific
modules, this message can be updated accordingly.
* gnu/packages/bioconductor.scm: Add comment discouraging adding packages to
the bottom of the file.
* gnu/packages/bioinformatics.scm: ditto.
* gnu/packages/cran.scm: ditto.
* gnu/packages/crates-io.scm: ditto.
* gnu/packages/emacs-xyz.scm: ditto.
* gnu/packages/golang.scm: ditto.
* gnu/packages/guile-xyz.scm: ditto.
* gnu/packages/haskell-xyz.scm: ditto.
* gnu/packages/java.scm: ditto.
* gnu/packages/julia-xyz.scm: ditto.
* gnu/packages/lisp-xyz.scm: ditto.
* gnu/packages/ocaml.scm: ditto.
* gnu/packages/perl.scm: ditto.
* gnu/packages/python-science.scm: ditto.
* gnu/packages/python-xyz.scm: ditto.
* gnu/packages/ruby.scm: ditto.
* gnu/packages/tex.scm: ditto.
| Christopher Baines |
| 2022-09-07 | gnu: tombo: Disable tests....* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
| Marius Bakke |
| 2022-08-31 | gnu: pigx-bsseq: Update to 0.1.8....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.8.
| Ricardo Wurmus |
| 2022-08-30 | gnu: r-dyngen: Update to 1.0.4....* gnu/packages/bioinformatics.scm (r-dyngnen): Update to 1.0.4.
[source]: Change to cran-uri source.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 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 |
