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2022-09-30gnu: salmon: Update to 1.9.0.Ricardo Wurmus
* 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.
2022-09-30gnu: Add centrifuge.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (centrifuge): New variable.
2022-09-29gnu: blast+: Build reproducibly.Ricardo Wurmus
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.
2022-09-27Merge branch 'staging' into core-updatesMaxim Cournoyer
Conflicts resolved in: gnu/local.mk gnu/packages/cran.scm gnu/packages/gnome.scm gnu/packages/gtk.scm gnu/packages/icu4c.scm gnu/packages/java.scm gnu/packages/machine-learning.scm gnu/packages/tex.scm
2022-09-26gnu: Add r-compgenomrdata.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable.
2022-09-23gnu: Add mudskipper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mudskipper): New variable.
2022-09-21gnu: python-cooler: Skip broken test.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add another patch for tests/test_util.py.
2022-09-21gnu: python-cooler: Do not use flake8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add build phase 'do-not-use-flake8.
2022-09-21gnu: Add r-chromunity.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chromunity): New variable.
2022-09-21gnu: Add r-skitools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-skitools): New variable.
2022-09-21gnu: Add r-gchain.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gchain): New variable.
2022-09-21gnu: Add r-gtrack.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gtrack): New variable.
2022-09-21gnu: Add r-bamutils.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils): New variable.
2022-09-21gnu: Add r-gutils.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gutils): New variable.
2022-09-20gnu: python-pyvcf: Update to 0.6.8-0.476169c.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
2022-09-20gnu: python-pyvcf: Use older setuptools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Replace python-setuptools with python-setuptools-for-tensorflow.
2022-09-18gnu: Python: Update to 3.10.7.Marius Bakke
* gnu/packages/python.scm (python-3.9): Rename to ... (python-3.10): ... this. Update to 3.10.7. [source](patches): Remove 'python-3-no-static-libs.patch' in favor of ... [arguments]: Add #:configure-flags. (python-3): Refer to PYTHON-3.10. * gnu/packages/patches/python-3-fix-tests.patch: Refresh. * gnu/packages/patches/python-3-no-static-lib.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/version-control.scm (mercurial)[native-search-paths]: Adjust Python version. * gnu/packages/admin.scm (ansible)[native-search-paths]: Likewise. * gnu/packages/bioinformatics.scm (scvelo)[arguments]: Replace hard-coded python3.9 paths with python3.10. * gnu/packages/cran.scm (r-torch)[arguments]: Likewise. * gnu/packages/machine-learning.scm (liblantern)[arguments]: Likewise.
2022-09-16Merge branch 'staging' into core-updatesMarius Bakke
2022-09-15gnu: catch-framework2: Rename variable to catch2.Maxim Cournoyer
Automated with: git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i
2022-09-15Merge branch 'staging' into core-updatesMaxim Cournoyer
Conflicts resolved in: gnu/local.mk gnu/packages/cmake.scm gnu/packages/glib.scm gnu/packages/gnome.scm gnu/packages/gtk.scm gnu/packages/sdl.scm pango-next, vala-next and librsvg-bootstrap were removed in the process.
2022-09-13gnu: kraken2: Update to 2.1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2.
2022-09-10Merge branch 'staging' into core-updatesMarius Bakke
2022-09-10gnu: Add comments to the bottom of a few package modules.Christopher Baines
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.
2022-09-08Merge branch 'staging' into core-updatesMarius Bakke
2022-09-07gnu: tombo: Disable tests.Marius Bakke
* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
2022-09-01Merge branch 'staging' into core-updatesMarius Bakke
2022-08-31gnu: pigx-bsseq: Update to 0.1.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.8.
2022-08-30gnu: r-dyngen: Update to 1.0.4.Mădălin Ionel Patrașcu
* 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>
2022-08-27Merge branch 'staging' into core-updatesMarius Bakke
2022-08-23gnu: Add flair.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flair): New variable.
2022-08-23gnu: python-mappy: Update to 2.24.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
2022-08-18gnu: Add r-kbet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-kbet): New variable.
2022-08-16gnu: Add go-github-com-biogo-biogo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-fai.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-csi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-cram.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-bgzf.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-tabix.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-sam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-bam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-step.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-llrb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-kdtree.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-interval.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
2022-08-16gnu: Add go-github-com-biogo-graph.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
2022-08-16gnu: Add stpipeline.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (stpipeline): New variable.
2022-08-16gnu: Add python-taggd.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-taggd): New variable.
2022-08-16gnu: htseq: Update to 2.0.2.Ricardo Wurmus
* 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.
2022-08-15gnu: plink-ng: Build sources from 2.0 directoryRicardo Wurmus
* 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.
2022-08-11Merge branch 'staging' into core-updatesMarius Bakke
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