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Author SHA1 Message Date
Maxim Cournoyer
b736af1824
gnu: catch-framework2: Rename variable to catch2. 
Automated with:

    git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i
 2022-09-15 20:15:56 -04:00
Ricardo Wurmus
a7af25ad31
gnu: kraken2: Update to 2.1.2. 
* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2.
 2022-09-13 17:35:38 +02:00
Christopher Baines
ad1d3f98b1
gnu: Add comments to the bottom of a few package modules. 
This will hopefully discourage patches which add new packages to the bottom of
files, as this increases the likelihood of conflicts when applying patches.

If there are more specific ways that packages should be arranged in specific
modules, this message can be updated accordingly.

* gnu/packages/bioconductor.scm: Add comment discouraging adding packages to
the bottom of the file.
* gnu/packages/bioinformatics.scm: ditto.
* gnu/packages/cran.scm: ditto.
* gnu/packages/crates-io.scm: ditto.
* gnu/packages/emacs-xyz.scm: ditto.
* gnu/packages/golang.scm: ditto.
* gnu/packages/guile-xyz.scm: ditto.
* gnu/packages/haskell-xyz.scm: ditto.
* gnu/packages/java.scm: ditto.
* gnu/packages/julia-xyz.scm: ditto.
* gnu/packages/lisp-xyz.scm: ditto.
* gnu/packages/ocaml.scm: ditto.
* gnu/packages/perl.scm: ditto.
* gnu/packages/python-science.scm: ditto.
* gnu/packages/python-xyz.scm: ditto.
* gnu/packages/ruby.scm: ditto.
* gnu/packages/tex.scm: ditto.
 2022-09-10 10:45:27 +01:00
Marius Bakke
453e7dd8c4
gnu: tombo: Disable tests. 
* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field.
 2022-09-07 17:36:42 +02:00
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