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3280 Commits

Author SHA1 Message Date
Marius Bakke
77eb3008e3
Merge branch 'staging' into core-updates 2022-08-11 23:36:10 +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
Marius Bakke
9044b086dd
Merge branch 'staging' into core-updates 2022-07-22 01:09:14 +02:00
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
Ludovic Courtès
8655a71445
Merge branch master into core-updates 2022-06-22 18:48:00 +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
Ludovic Courtès
8c3e9da13a
Merge branch 'master' into core-updates 2022-06-08 14:46:24 +02:00
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
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
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
Ricardo Wurmus
b279e778ab
gnu: Add sylamer. 
* gnu/packages/bioinformatics.scm (sylamer): New variable.
 2022-06-01 00:17:05 +02:00
Maxim Cournoyer
c35e508b4a
gnu: Remove python2-biopython. 
* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer
ad030a0b7d
gnu: Remove pplacer-scripts. 
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer
d397cb6207
gnu: Remove pplacer. 
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer
026fca8b5b
gnu: Remove python2-checkm-genome. 
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
 2022-05-31 14:54:15 -04:00
Maxim Cournoyer
4d7bb37981
gnu: Remove fraggenescan. 
* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
 2022-05-31 14:54:02 -04:00
Maxim Cournoyer
6792b0b6cd
gnu: Remove python2-pysam. 
* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
 2022-05-31 14:53:35 -04:00
Maxim Cournoyer
955e7d628d
gnu: Remove find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
 2022-05-31 14:53:34 -04:00
Maxim Cournoyer
a5e29cd838
gnu: Remove gess. 
* gnu/packages/bioinformatics.scm (gess): Delete variable.
 2022-05-31 14:53:34 -04:00
Maxim Cournoyer
c30ab2c0b4
gnu: Remove pyicoteo. 
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer
ba09192168
gnu: Remove python2-pbcore. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer
8287979669
gnu: Remove python2-pyfaidx. 
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
850bd0c329
gnu: Remove python2-screed. 
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
a94bc7798a
gnu: Remove miso. 
* gnu/packages/bioinformatics.scm (miso): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
23e133a907
gnu: Remove python2-warpedlmm. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bb35b50adc
gnu: Remove poretools. 
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bcdd45be6f
gnu: Remove python2-dendropy. 
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
d2c971e67b
gnu: Remove bamm. 
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
 2022-05-31 14:52:17 -04:00