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Author SHA1 Message Date
Ricardo Wurmus
36445e4d96
gnu: pigx-bsseq: Update to 0.1.8. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.8.
 2022-08-31 09:12:03 +02:00
Mădălin Ionel Patrașcu
8c5246677c
gnu: r-dyngen: Update to 1.0.4. 
* 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>
 2022-08-30 23:01:58 +02:00
Ricardo Wurmus
d26b29d263
gnu: Add flair. 
* gnu/packages/bioinformatics.scm (flair): New variable.
 2022-08-23 13:30:52 +02:00
Ricardo Wurmus
8d42898572
gnu: python-mappy: Update to 2.24. 
* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24.
 2022-08-23 13:29:17 +02:00
Ricardo Wurmus
f3a7d43281
gnu: Add r-kbet. 
* gnu/packages/bioinformatics.scm (r-kbet): New variable.
 2022-08-18 12:21:07 +02:00
Ricardo Wurmus
8aab1f7c73
gnu: Add go-github-com-biogo-biogo. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable.
 2022-08-16 16:52:15 +02:00
Ricardo Wurmus
2407416d0f
gnu: Add go-github-com-biogo-hts-fai. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable.
 2022-08-16 16:50:16 +02:00
Ricardo Wurmus
31e0ac6dcf
gnu: Add go-github-com-biogo-hts-csi. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable.
 2022-08-16 16:50:01 +02:00
Ricardo Wurmus
b4f389e1b9
gnu: Add go-github-com-biogo-hts-cram. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable.
 2022-08-16 16:44:58 +02:00
Ricardo Wurmus
e9bec5bd40
gnu: Add go-github-com-biogo-hts-bgzf. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable.
 2022-08-16 16:28:33 +02:00
Ricardo Wurmus
bb162a5103
gnu: Add go-github-com-biogo-hts-tabix. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable.
 2022-08-16 16:28:23 +02:00
Ricardo Wurmus
4645a5d3f6
gnu: Add go-github-com-biogo-hts-sam. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
 2022-08-16 16:28:11 +02:00
Ricardo Wurmus
b986325b13
gnu: Add go-github-com-biogo-hts-bam. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
 2022-08-16 16:23:04 +02:00
Ricardo Wurmus
2345cd49de
gnu: Add go-github-com-biogo-store-step. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
 2022-08-16 16:18:57 +02:00
Ricardo Wurmus
c42745ba39
gnu: Add go-github-com-biogo-store-llrb. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
 2022-08-16 16:18:48 +02:00
Ricardo Wurmus
5fae9e158d
gnu: Add go-github-com-biogo-store-kdtree. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
 2022-08-16 16:18:40 +02:00
Ricardo Wurmus
a33ee9bd51
gnu: Add go-github-com-biogo-store-interval. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
 2022-08-16 16:18:31 +02:00
Ricardo Wurmus
2b4dcc477b
gnu: Add go-github-com-biogo-graph. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
 2022-08-16 16:09:54 +02:00
Ricardo Wurmus
872e17ddc1
gnu: Add stpipeline. 
* gnu/packages/bioinformatics.scm (stpipeline): New variable.
 2022-08-16 15:22:07 +02:00
Ricardo Wurmus
9c2400c282
gnu: Add python-taggd. 
* gnu/packages/bioinformatics.scm (python-taggd): New variable.
 2022-08-16 15:22:07 +02:00
Ricardo Wurmus
752be79bf3
gnu: htseq: Update to 2.0.2. 
* 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.
 2022-08-16 15:22:06 +02:00
Ricardo Wurmus
c3c2dfdb5e
gnu: plink-ng: Build sources from 2.0 directory 
* 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.
 2022-08-15 18:08:20 +02:00
Ricardo Wurmus
26bdefd172
gnu: Add r-liana. 
* gnu/packages/bioinformatics.scm (r-liana): New variable.
 2022-08-10 15:44:28 +02:00
Ricardo Wurmus
fd4b8e9873
gnu: Add r-omnipathr/devel. 
* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
 2022-08-10 15:44:28 +02:00
Marius Bakke
0b55b036c1
gnu: cereal: Update to 1.3.2. 
* 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.
 2022-08-10 00:28:59 +02:00
Mădălin Ionel Patrașcu
ec6499aad2
gnu: Add phyml. 
* gnu/packages/bioinformatics.scm (phyml): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2022-08-08 12:38:41 +02:00
Ricardo Wurmus
03858a7908
gnu: Add python-scanorama. 
* gnu/packages/bioinformatics.scm (python-scanorama): New variable.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus
c69c2c1c4d
gnu: python-intervaltree: Update to 3.1.0. 
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.1.0.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus
f1b9ae8c20
gnu: python-bbknn: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.5.1.
[propagated-inputs]: Add python-pandas.
 2022-08-01 17:46:21 +02:00
Mădălin Ionel Patrașcu
8d7a721400
gnu: Add r-millefy. 
* gnu/packages/bioinformatics.scm (r-millefy): New variable.
 2022-08-01 15:14:47 +02:00
Ricardo Wurmus
dc3ad40c6b
gnu: python-bbknn: Set NUMBA_CACHE_DIR. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'set-numba-cache-dir.
 2022-08-01 12:46:19 +02:00
Maxim Cournoyer
1ef04fb228
gnu: qtsvg: Rename variable to qtsvg-5. 
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
 2022-07-31 21:55:43 -04:00
Efraim Flashner
e6bdd94c38
gnu: plink-ng: Fix building on other architectures. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to add simde includes to CFLAGS.
[native-inputs]: Add simde.
 2022-07-28 23:47:40 +03:00
Efraim Flashner
99d1122f8b
gnu: plink-ng: Update to 2.00a3.3. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
 2022-07-28 22:55:07 +03:00
Ricardo Wurmus
d84bedd830
gnu: Add python-cellbender. 
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
 2022-07-09 10:37:22 +02:00
Ricardo Wurmus
6211ecfec8
gnu: Add hh-suite. 
* gnu/packages/bioinformatics.scm (hh-suite): New variable.
 2022-07-06 14:00:21 +02:00
Ricardo Wurmus
a0125732ef
gnu: Add r-sccustomize. 
* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
 2022-07-04 13:48:58 +02:00
Thiago Jung Bauermann
4d77072c56
gnu: libsbml: Use regular check. 
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14
with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-07-02 11:28:28 +02:00
Ricardo Wurmus
81cf674a5d
gnu: Add python-ikarus. 
* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
 2022-07-01 14:54:26 +02:00
Ricardo Wurmus
f700223c3b
gnu: Add pyscenic. 
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
 2022-06-16 15:20:59 +02:00
Ricardo Wurmus
3535d8dc5a
gnu: Add python-arboreto. 
* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
 2022-06-16 15:20:59 +02:00
Ricardo Wurmus
fbe5707b73
gnu: Add python-ctxcore. 
* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
 2022-06-16 15:20:59 +02:00
Vagrant Cascadian
b483ef1a88
gnu: python-pybedtools: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0.
  [description]: Update to satisfy guix lint.
  [license]: Update to expat and lgpl2.1+.
 2022-06-09 23:10:15 -07:00
Vagrant Cascadian
964cdd57fa
gnu: discrover: Use reproducible timestamps. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add
  'set-force-source-date phase.
 2022-06-06 15:08:18 -07:00
Ricardo Wurmus
b540e5e6bb
gnu: pigx-scrnaseq: Update to 1.1.9. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
 2022-06-01 12:57:22 +02:00
Ricardo Wurmus
93c97bfffb
gnu: pigx-bsseq: Update to 0.1.7. 
* 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.
 2022-06-01 12:41:59 +02:00
Ricardo Wurmus
6e54ce9ca9
gnu: pigx-chipseq: Update to 0.1.0. 
* 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.
 2022-06-01 12:19:48 +02:00
Ricardo Wurmus
cd95d7ddd1
gnu: pigx-rnaseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
 2022-06-01 11:07:27 +02:00
Ricardo Wurmus
0aae2f7f01
gnu: pigx-rnaseq: Update to 0.0.21. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
 2022-06-01 10:46:00 +02:00
Ricardo Wurmus
0c26c8da9d
gnu: pigx-rnaseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
 2022-06-01 10:46:00 +02:00