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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.
2022-09-07gnu: tombo: Disable tests.Marius Bakke
* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
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>
2022-08-23gnu: 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.
2022-08-10gnu: Add r-liana.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-liana): New variable.
2022-08-10gnu: Add r-omnipathr/devel.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
2022-08-10gnu: cereal: Update to 1.3.2.Marius Bakke
* 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.
2022-08-08gnu: Add phyml.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (phyml): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2022-08-02gnu: Add python-scanorama.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
2022-08-02gnu: python-intervaltree: Update to 3.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
2022-08-01gnu: python-bbknn: Update to 1.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1. [propagated-inputs]: Add python-pandas.
2022-08-01gnu: Add r-millefy.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
2022-08-01gnu: python-bbknn: Set NUMBA_CACHE_DIR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'set-numba-cache-dir.
2022-07-31gnu: qtsvg: Rename variable to qtsvg-5.Maxim Cournoyer
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
2022-07-28gnu: plink-ng: Fix building on other architectures.Efraim Flashner
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust make-flags to add simde includes to CFLAGS. [native-inputs]: Add simde.
2022-07-28gnu: plink-ng: Update to 2.00a3.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
2022-07-09gnu: Add python-cellbender.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
2022-07-06gnu: Add hh-suite.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hh-suite): New variable.
2022-07-04gnu: Add r-sccustomize.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
2022-07-02gnu: libsbml: Use regular check.Thiago Jung Bauermann
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14 with check. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-07-01gnu: Add python-ikarus.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
2022-06-16gnu: Add pyscenic.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
2022-06-16gnu: Add python-arboreto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
2022-06-16gnu: Add python-ctxcore.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
2022-06-09gnu: python-pybedtools: Update to 0.9.0.Vagrant Cascadian
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0. [description]: Update to satisfy guix lint. [license]: Update to expat and lgpl2.1+.
2022-06-06gnu: discrover: Use reproducible timestamps.Vagrant Cascadian
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add 'set-force-source-date phase.
2022-06-01gnu: pigx-scrnaseq: Update to 1.1.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake.
2022-06-01gnu: pigx-bsseq: Update to 0.1.7.Ricardo Wurmus
* 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.
2022-06-01gnu: pigx-chipseq: Update to 0.1.0.Ricardo Wurmus
* 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.
2022-06-01gnu: pigx-rnaseq: Update to 0.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0. [arguments]: Remove phase 'patch-knitr.
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