| Age | Commit message (Expand) | Author |
|---|
| 2021-11-08 | Merge remote-tracking branch 'origin/master' into core-updates-frozen | Efraim Flashner |
| 2021-11-03 | gnu: bedtools-2.18: Fix build with newer toolchain....* 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.
| Ricardo Wurmus |
| 2021-10-31 | Merge remote-tracking branch 'origin/master' into core-updates-frozen | Efraim Flashner |
| 2021-10-24 | gnu: sailfish: Use TBB 2020....* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
| Ricardo Wurmus |
| 2021-10-24 | gnu: sailfish: Remove trailing #T....* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in
build phases...
[inputs]: ...and in the origin snippet of "rapmap".
| Ricardo Wurmus |
| 2021-10-24 | gnu: sailfish: Do not attempt to unpack a directory....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.
| Ricardo Wurmus |
| 2021-10-24 | gnu: jellyfish: Remove Ruby bindings....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.
| Ricardo Wurmus |
| 2021-10-24 | gnu: cutadapt: Regenerate Cython files....* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
| Ricardo Wurmus |
| 2021-10-24 | gnu: python-dnaio: Update to 0.6.0....* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
| Ricardo Wurmus |
| 2021-10-24 | gnu: macs: Fix build by setting HOME....* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
| Ricardo Wurmus |
| 2021-10-24 | gnu: methyldackel: Remove trailing #T....* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
| Ricardo Wurmus |
| 2021-10-24 | gnu: methyldackel: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
| Ricardo Wurmus |
| 2021-10-24 | gnu: flexbar: Use TBB 2020....* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
| Ricardo Wurmus |
| 2021-10-24 | gnu: flexbar: Remove trailing #T....* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
| Ricardo Wurmus |
| 2021-10-24 | gnu: bwa: Remove trailing #T....* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
| Ricardo Wurmus |
| 2021-10-24 | gnu: bwa: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
| Ricardo Wurmus |
| 2021-10-24 | gnu: bowtie1: Use TBB 2020....* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
| Ricardo Wurmus |
| 2021-10-24 | gnu: bowtie: Replace invalid characters....* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
| Ricardo Wurmus |
| 2021-10-24 | gnu: bowtie: Remove trailing #T....* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
| Ricardo Wurmus |
| 2021-10-24 | gnu: bowtie: Use TBB 2020....* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
| Ricardo Wurmus |
| 2021-10-24 | gnu: Add r-umi4cpackage....* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
| Ricardo Wurmus |
| 2021-10-24 | gnu: tbb-for-salmon: Rename....* gnu/packages/tbb.scm (tbb-for-salmon): Rename this variable...
(tbb-2020): ...to this.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Rename it.
| Ricardo Wurmus |
| 2021-10-22 | gnu: Add qtltools....* gnu/packages/bioinformatics.scm (qtltools): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add gdc-client....* gnu/packages/bioinformatics.scm (gdc-client): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add r-shaman....* gnu/packages/bioinformatics.scm (r-shaman): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add r-misha....* gnu/packages/bioinformatics.scm (r-misha): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add ciri-long....* gnu/packages/bioinformatics.scm (ciri-long): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: python-biopython: Update to 1.76....* 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.
| Ricardo Wurmus |
| 2021-10-21 | gnu: instrain: Update to 1.5.4....* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add python-bwapy....* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
| Ricardo Wurmus |
| 2021-10-21 | gnu: Add python-pyspoa....* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
| Ricardo Wurmus |
| 2021-10-19 | gnu: salmon: Use older version of TBB....* gnu/packages/bioinformatics.scm (salmon)[arguments]: Define
HAVE_NUMERIC_LIMITS128; compute TBB_VERSION.
[inputs]: Replace tbb with tbb-for-salmon.
| Ricardo Wurmus |
| 2021-10-12 | Merge remote-tracking branch 'origin/master' into core-updates-frozen. | Mathieu Othacehe |
| 2021-10-12 | gnu: clipper: Disable non-deterministic test....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>
| Felix Gruber |
| 2021-10-08 | gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-chipseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-bsseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: ngless: Fix build....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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: Update Haskell ecosystem....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>
| Lars-Dominik Braun |
| 2021-09-29 | gnu: pigx-chipseq: Update to 0.0.53....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
| Ricardo Wurmus |
| 2021-09-22 | gnu: Update some packages using old JavaScript minifier....* 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>
| Charles |
| 2021-09-20 | gnu: Add r-presto....* gnu/packages/bioinformatics.scm (r-presto): New variable.
| zimoun |
| 2021-09-13 | gnu: discrover: Update package name in texlive-union....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
| Ricardo Wurmus |
| 2021-09-07 | Merge branch 'master' into core-updates-frozen | Ludovic Courtès |
| 2021-09-06 | gnu: Use the non-deprecated TeX packages....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.
| Ludovic Courtès |
| 2021-09-06 | gnu: Add megadepth....* gnu/packages/bioinformatics.scm (megadepth): New variable.
| Ricardo Wurmus |
| 2021-09-06 | gnu: Replace PYTHONPATH with GUIX_PYTHONPATH....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>
| Felix Gruber |
| 2021-09-01 | gnu: Add r-catch....* gnu/packages/bioinformatics.scm (r-catch): New variable.
| Ricardo Wurmus |
