ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2025-01-19 01:11:55 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions
86244 commits 1 branch 0 tags 491 MiB
Commit graph

2962 commits

Author SHA1 Message Date
Efraim Flashner
bc5155b952
Merge remote-tracking branch 'origin/master' into core-updates-frozen 2021-10-31 14:49:47 +02:00
Ricardo Wurmus
41e5c12c4a
gnu: sailfish: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 21:38:25 +00:00
Ricardo Wurmus
1bf55a4850
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".
 2021-10-24 21:37:39 +00:00
Ricardo Wurmus
4392783232
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.
 2021-10-24 21:35:57 +00:00
Ricardo Wurmus
57c233b37b
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.
 2021-10-24 21:34:26 +00:00
Ricardo Wurmus
da526f33f2
gnu: cutadapt: Regenerate Cython files. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
 2021-10-24 21:23:20 +00:00
Ricardo Wurmus
4faca03bed
gnu: python-dnaio: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
 2021-10-24 19:47:20 +00:00
Ricardo Wurmus
238f47c76f
gnu: macs: Fix build by setting HOME. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
 2021-10-24 19:09:35 +00:00
Ricardo Wurmus
1d01043a4f
gnu: methyldackel: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
 2021-10-24 19:01:22 +00:00
Ricardo Wurmus
2820b03509
gnu: methyldackel: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
 2021-10-24 19:00:53 +00:00
Ricardo Wurmus
cc331ad7eb
gnu: flexbar: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:50:09 +00:00
Ricardo Wurmus
084bdf9d69
gnu: flexbar: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
 2021-10-24 18:49:43 +00:00
Ricardo Wurmus
d0a1d798ee
gnu: bwa: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
 2021-10-24 18:48:53 +00:00
Ricardo Wurmus
2da99b671e
gnu: bwa: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
 2021-10-24 18:48:20 +00:00
Ricardo Wurmus
724972bcca
gnu: bowtie1: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:47:45 +00:00
Ricardo Wurmus
f336cc4fe7
gnu: bowtie: Replace invalid characters. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
 2021-10-24 18:44:57 +00:00
Ricardo Wurmus
e5a26a1f02
gnu: bowtie: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
 2021-10-24 16:59:39 +00:00
Ricardo Wurmus
2ec601580b
gnu: bowtie: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
 2021-10-24 16:58:58 +00:00
Ricardo Wurmus
973b21aa6a
gnu: Add r-umi4cpackage. 
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
 2021-10-24 13:45:46 +00:00
Ricardo Wurmus
42873c2b06
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.
 2021-10-24 13:28:05 +00:00
Ricardo Wurmus
4a0cd6297a
gnu: Add qtltools. 
* gnu/packages/bioinformatics.scm (qtltools): New variable.
 2021-10-22 21:29:25 +00:00
Ricardo Wurmus
a8bac123f0
gnu: Add gdc-client. 
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
 2021-10-21 14:49:01 +00:00
Ricardo Wurmus
f65917f607
gnu: Add r-shaman. 
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
 2021-10-21 14:34:35 +00:00
Ricardo Wurmus
4885f40b80
gnu: Add r-misha. 
* gnu/packages/bioinformatics.scm (r-misha): New variable.
 2021-10-21 14:25:44 +00:00
Ricardo Wurmus
42c9b75b25
gnu: Add ciri-long. 
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
 2021-10-21 13:39:36 +00:00
Ricardo Wurmus
10664fcc8c
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.
 2021-10-21 13:33:51 +00:00
Ricardo Wurmus
36cf0253a9
gnu: instrain: Update to 1.5.4. 
* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
 2021-10-21 13:32:37 +00:00
Ricardo Wurmus
57841a91f5
gnu: Add python-bwapy. 
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
 2021-10-21 12:23:25 +00:00
Ricardo Wurmus
6526c35df5
gnu: Add python-pyspoa. 
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
 2021-10-21 12:23:22 +00:00
Ricardo Wurmus
174c29a8e0
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.
 2021-10-19 06:28:30 +00:00
Mathieu Othacehe
a1eca979fb
Merge remote-tracking branch 'origin/master' into core-updates-frozen. 2021-10-12 17:46:23 +00:00
Felix Gruber
9101c7bf8e
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>
 2021-10-12 18:13:29 +02:00
Lars-Dominik Braun
c8a7ba621b
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.
 2021-10-08 09:13:55 +02:00
Lars-Dominik Braun
26488f63b8
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.
 2021-10-08 09:13:55 +02:00
Lars-Dominik Braun
07f2e4993b
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.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun
e51a3f4a72
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.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun
fb1ffc53ba
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.
 2021-10-08 09:13:54 +02:00
Lars-Dominik Braun
7eb9fe4e53
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.
 2021-10-08 09:13:53 +02:00
Lars-Dominik Braun
b97f549b14
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>
 2021-10-08 09:13:52 +02:00
Ricardo Wurmus
53611ab5c5
gnu: pigx-chipseq: Update to 0.0.53. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
 2021-09-29 09:58:45 +02:00
Charles
f36b789f78
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>
 2021-09-22 16:03:19 +03:00
zimoun
f80824fe09
gnu: Add r-presto. 
* gnu/packages/bioinformatics.scm (r-presto): New variable.
 2021-09-20 17:23:16 +02:00
Ricardo Wurmus
0406f1c2e1
gnu: discrover: Update package name in texlive-union. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
 2021-09-13 22:49:56 +02:00
Ludovic Courtès
d9dfbf886d
Merge branch 'master' into core-updates-frozen 2021-09-07 14:19:08 +02:00
Ludovic Courtès
b949f34f31
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.
 2021-09-06 22:02:15 +02:00
Ricardo Wurmus
c82b723bf8
gnu: Add megadepth. 
* gnu/packages/bioinformatics.scm (megadepth): New variable.
 2021-09-06 14:48:24 +02:00
Felix Gruber
93bf42361c
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>
 2021-09-06 10:47:54 +02:00
Ricardo Wurmus
c75b30d58f
gnu: Add r-catch. 
* gnu/packages/bioinformatics.scm (r-catch): New variable.
 2021-09-01 14:53:36 +02:00
Ricardo Wurmus
4abf226833
gnu: Add scregseg. 
* gnu/packages/bioinformatics.scm (scregseg): New variable.
 2021-08-31 23:11:06 +02:00
Ricardo Wurmus
a1ee212184
gnu: python-strawc: Propagate pybind11. 
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00