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2903 Commits

Author SHA1 Message Date
Ricardo Wurmus
d54a4285ea
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.
 2021-11-03 21:07:29 +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
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
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
Ricardo Wurmus
c82b723bf8
gnu: Add megadepth. 
* gnu/packages/bioinformatics.scm (megadepth): New variable.
 2021-09-06 14:48:24 +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
Ricardo Wurmus
55cb5a62a1
gnu: python-scanpy: Propagate sinfo. 
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
 2021-08-31 23:11:05 +02:00
Ricardo Wurmus
7712154ccb
gnu: Add python-coolbox. 
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus
b105655670
gnu: python-scanpy: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
 2021-08-30 18:29:57 +02:00
Ricardo Wurmus
d84ead8174
gnu: Add python-dna-features-viewer. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus
e85b35070c
gnu: Add python-pybbi. 
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
 2021-08-30 18:29:56 +02:00
Ricardo Wurmus
db13eb962f
gnu: Add python-strawc. 
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus
17c765e2e1
gnu: Add r-cytonorm. 
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
 2021-08-27 13:37:29 +02:00
Ricardo Wurmus
f66759e0b2
gnu: Add ivar. 
* gnu/packages/bioinformatics.scm (ivar): New variable.
 2021-08-25 11:22:02 +02:00
Ricardo Wurmus
27952318a5
gnu: fastp: Update to 0.20.1. 
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
 2021-08-20 10:49:48 +02:00
Ricardo Wurmus
a79ad5fce5
gnu: pigx-rnaseq: Update to 0.0.19. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
 2021-08-13 15:23:39 +02:00
Ricardo Wurmus
907f835e19
gnu: pigx-rnaseq: Update to 0.0.18. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
 2021-08-11 19:33:38 +02:00
Ricardo Wurmus
f1b64c435a
gnu: pigx-sars-cov2-ww: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
 2021-08-05 16:46:34 +02:00
Ricardo Wurmus
2ab5d08fbe
gnu: Add r-spectre. 
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
 2021-08-03 10:43:08 +02:00
Ricardo Wurmus
3e5eff8c30
gnu: Add seqan 3. 
* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
 2021-07-26 11:54:21 +02:00
Ricardo Wurmus
99ca1ae4f8
gnu: Add segemehl. 
* gnu/packages/bioinformatics.scm (segemehl): New variable.
 2021-07-26 11:08:13 +02:00
Efraim Flashner
fd8aea010f
gnu: python-pysam: Make the check phase honor the tests? argument. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
 2021-07-22 10:58:22 +03:00
Efraim Flashner
877792a6a7
gnu: python-pysam: Update to 0.16.0.1. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
 2021-07-22 10:57:41 +03:00
Efraim Flashner
cc4906d13b
gnu: Add htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
 2021-07-22 10:50:58 +03:00
Efraim Flashner
309b38bed6
gnu: python-biopython: Update to 1.73. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
 2021-07-22 09:14:12 +03:00
Lars-Dominik Braun
73830b5da3
gnu: Add r-battenberg. 
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
ed636babfa
gnu: Add r-ascat. 
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
690df95d1a
gnu: Add nanosv. 
* gnu/packages/bioinformatics.scm (nanosv): New variable.
 2021-07-21 13:36:08 +02:00
Lars-Dominik Braun
2b665b8a49
gnu: Add python-pyvcf. 
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
 2021-07-21 13:36:08 +02:00