| Age | Commit message (Expand) | Author |
|---|
| 2022-10-08 | gnu: pigx-sars-cov-2: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.8.
[arguments]: Add build phase 'unpack-databases; enable tests.
[native-inputs]: Add origins for databases; remove automake and autoconf.
[inputs]: Add r-data-table, r-deconvr, r-htmltools, r-jsonlite, r-knitr, and
r-mass.
| Ricardo Wurmus |
| 2022-10-06 | gnu: plink: Change origin URL....pngu.mgh.harvard.edu seems to time out.
* gnu/packages/bioinformatics.scm (plink)[origin]. Change URL.
| Christopher Baines |
| 2022-10-05 | gnu: Add megahit....* gnu/packages/bioinformatics.scm (megahit): New variable.
| Ricardo Wurmus |
| 2022-10-05 | gnu: Add cd-hit-auxtools....* gnu/packages/bioinformatics.scm (cd-hit-auxtools): New variable.
| Ricardo Wurmus |
| 2022-10-05 | gnu: cd-hit: Update to 4.8.1....* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.8.1.
[arguments]: Do not use quasiquote; remove trailing #T from build phases.
[inputs]: Add zlib.
| Ricardo Wurmus |
| 2022-10-04 | gnu: kaiju: Update to 1.9.0....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0.
[arguments]: Use gexps; wrap scripts in install phase.
[inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip,
python-wrapper, tar, and wget.
| Ricardo Wurmus |
| 2022-09-30 | gnu: salmon: Update to 1.9.0....* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0.
[arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish
itlib headers.
[inputs]: Use new label-less list; move pufferfish origin from here...
[native-inputs]: ...to here.
| Ricardo Wurmus |
| 2022-09-30 | gnu: Add centrifuge....* gnu/packages/bioinformatics.scm (centrifuge): New variable.
| Ricardo Wurmus |
| 2022-09-29 | gnu: blast+: Build reproducibly....Fixes <https://issues.guix.gnu.org/42141>.
* gnu/packages/bioinformatics.scm (blast+)[source]: Do not record kernel
version and use fix set of random numbers.
| Ricardo Wurmus |
| 2022-09-26 | gnu: Add r-compgenomrdata....* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
| Ricardo Wurmus |
| 2022-09-23 | gnu: Add mudskipper....* gnu/packages/bioinformatics.scm (mudskipper): New variable.
| Ricardo Wurmus |
| 2022-09-21 | gnu: python-cooler: Skip broken test....* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add another
patch for tests/test_util.py.
| Ricardo Wurmus |
| 2022-09-21 | gnu: python-cooler: Do not use flake8....* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add build phase
'do-not-use-flake8.
| Ricardo Wurmus |
| 2022-09-21 | gnu: Add r-chromunity....* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
| Ricardo Wurmus |
| 2022-09-21 | gnu: Add r-skitools....* gnu/packages/bioinformatics.scm (r-skitools): New variable.
| Ricardo Wurmus |
| 2022-09-21 | gnu: Add r-gchain....* gnu/packages/bioinformatics.scm (r-gchain): New variable.
| Ricardo Wurmus |
| 2022-09-21 | gnu: Add r-gtrack....* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
| Ricardo Wurmus |
| 2022-09-21 | gnu: Add r-bamutils....* gnu/packages/bioinformatics.scm (r-bamutils): New variable.
| Ricardo Wurmus |
| 2022-09-21 | gnu: Add r-gutils....* gnu/packages/bioinformatics.scm (r-gutils): New variable.
| Ricardo Wurmus |
| 2022-09-20 | gnu: python-pyvcf: Update to 0.6.8-0.476169c....* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
| Ricardo Wurmus |
| 2022-09-20 | gnu: python-pyvcf: Use older setuptools....* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Replace
python-setuptools with python-setuptools-for-tensorflow.
| Ricardo Wurmus |
| 2022-09-15 | gnu: catch-framework2: Rename variable to catch2....Automated with:
git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i
| Maxim Cournoyer |
| 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 |
