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2021-11-08Merge remote-tracking branch 'origin/master' into core-updates-frozenEfraim Flashner
2021-11-03gnu: bedtools-2.18: Fix build with newer toolchain.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase 'compatibility, fixing syntax quirks that are problematic with newer toolchains. [native-inputs]: Do not inherit. [inherit]: Do not inherit.
2021-10-31Merge remote-tracking branch 'origin/master' into core-updates-frozenEfraim Flashner
2021-10-24gnu: sailfish: Use TBB 2020.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with tbb-2020.
2021-10-24gnu: sailfish: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in build phases... [inputs]: ...and in the origin snippet of "rapmap".
2021-10-24gnu: sailfish: Do not attempt to unpack a directory.Ricardo Wurmus
patch-and-repack no longer outputs a compressed archive when the input was a directory. * gnu/packages/bioinformatics.scm (sailfish)[arguments]: Adjust build phase 'prepare-rapmap.
2021-10-24gnu: jellyfish: Remove Ruby bindings.Ricardo Wurmus
These bindings no longer build and we have no package that would need them. * gnu/packages/bioinformatics.scm (jellyfish)[outputs]: Remove "ruby" output. [arguments]: Remove option for building Ruby bindings. [native-inputs]: Remove ruby.
2021-10-24gnu: cutadapt: Regenerate Cython files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase 'always-cythonize.
2021-10-24gnu: python-dnaio: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
2021-10-24gnu: macs: Fix build by setting HOME.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set HOME variable.
2021-10-24gnu: methyldackel: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T from build phase.
2021-10-24gnu: methyldackel: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to CFLAGS.
2021-10-24gnu: flexbar: Use TBB 2020.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with tbb-2020.
2021-10-24gnu: flexbar: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T from all build phases.
2021-10-24gnu: bwa: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in build phase.
2021-10-24gnu: bwa: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to CFLAGS.
2021-10-24gnu: bowtie1: Use TBB 2020.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with tbb-2020.
2021-10-24gnu: bowtie: Replace invalid characters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes with straight quotes in the 'configure phase.
2021-10-24gnu: bowtie: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet.
2021-10-24gnu: bowtie: Use TBB 2020.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
2021-10-24gnu: Add r-umi4cpackage.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
2021-10-24gnu: tbb-for-salmon: Rename.Ricardo Wurmus
* gnu/packages/tbb.scm (tbb-for-salmon): Rename this variable... (tbb-2020): ...to this. * gnu/packages/bioinformatics.scm (salmon)[inputs]: Rename it.
2021-10-22gnu: Add qtltools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (qtltools): New variable.
2021-10-21gnu: Add gdc-client.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
2021-10-21gnu: Add r-shaman.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
2021-10-21gnu: Add r-misha.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-misha): New variable.
2021-10-21gnu: Add ciri-long.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
2021-10-21gnu: python-biopython: Update to 1.76.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.76. (python-biopython-1.73): New variable. (instrain)[inputs]: Replace python-biopython with python-biopython-1.73.
2021-10-21gnu: instrain: Update to 1.5.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
2021-10-21gnu: Add python-bwapy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
2021-10-21gnu: Add python-pyspoa.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
2021-10-19gnu: salmon: Use older version of TBB.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Define HAVE_NUMERIC_LIMITS128; compute TBB_VERSION. [inputs]: Replace tbb with tbb-for-salmon.
2021-10-12Merge remote-tracking branch 'origin/master' into core-updates-frozen.Mathieu Othacehe
2021-10-12gnu: clipper: Disable non-deterministic test.Felix Gruber
This test fails/succeeds non-deterministically. * gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable non-deterministic test test_get_FDR_cutoff_mean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-10-08gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: ngless: Fix build.Lars-Dominik Braun
Apply upstream patch to restore compatibility with current Stackage. * gnu/packages/patches/ngless-unliftio.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/bioinformatics.scm (ngless): Use it.
2021-10-08gnu: Update Haskell ecosystem.Lars-Dominik Braun
Bump packages’ versions to the lastest Stackage or Hackage release. Since packages are interdependent, do so in a single commit. 525 packages have been updated. These packages have been removed, because they fail to build, have no newer version available and no dependencies: corrode ghc-easytest ghc-edisonapi ghc-edisoncore ghc-pandoc-types ghc-regex-tdfa-text These have been removed, because they are no longer required: ghc-happy-1.19.9 ghc-prettyprinter-1.6 ghc-protolude-0.3 ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc does not use them any more. Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
2021-09-29gnu: pigx-chipseq: Update to 0.0.53.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53. [inputs]: Add r-hexbin.
2021-09-22gnu: Update some packages using old JavaScript minifier.Charles
* gnu/packages/minetest.scm (minetest-basic-trains): New variable. * gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input. * gnu/packages/ci.scm (laminar): Update uglifyjs input. * gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input. * gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-09-20gnu: Add r-presto.zimoun
* gnu/packages/bioinformatics.scm (r-presto): New variable.
2021-09-13gnu: discrover: Update package name in texlive-union.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace texlive-fonts-cm with texlive-cm.
2021-09-07Merge branch 'master' into core-updates-frozenLudovic Courtès
2021-09-06gnu: Use the non-deprecated TeX packages.Ludovic Courtès
This commit leaves 'dblatex' and 'texlive-hyperref' as users of deprecated packages, but these have many dependents. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use non-deprecated TeX Live packages. (velvet)[native-inputs]: Likewise. * gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise. (chez-web)[native-inputs]: Likewise. * gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise. * gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise. * gnu/packages/maths.scm (hypre)[native-inputs]: Likewise. * gnu/packages/music.scm (lilypond)[native-inputs]: Likewise. * gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise. * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Likewise. (python-matplotlib-documentation)[native-inputs]: Likewise. (python-ipython-documentation)[native-inputs]: Likewise. (python-nbconvert)[native-inputs]: Likewise. (python-pypandoc)[native-inputs]: Likewise. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise. * gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise. (teximpatient)[native-inputs]: Likewise. (texlive-latex-pgf)[propagated-inputs]: Likewise. (texlive-beamer)[propagated-inputs]: Likewise.
2021-09-06gnu: Add megadepth.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (megadepth): New variable.
2021-09-06gnu: Replace PYTHONPATH with GUIX_PYTHONPATH.Felix Gruber
In packages that do not use python-build-system, PYTHONPATH is generally not defined. Instead we can use GUIX_PYTHONPATH which should contain all Python dependencies. * gnu/packages/bioinformatics.scm (shorah)[arguments]: Replace PYTHONPATH with GUIX_PYTHONPATH. * gnu/packages/debug.scm (c-vise)[arguments]: Idem. * gnu/packages/gnome.scm (drawing, apostrophe, ocrfeeder)[arguments]: Idem. * gnu/packages/music.scm (a2jmidid)[arguments]: Idem. * gnu/packages/syndication.scm (gfeeds)[arguments]: Idem. * gnu/packages/xdisorg.scm (gammastep)[arguments]: Idem. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-09-01gnu: Add r-catch.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-catch): New variable.
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