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
8d7a721400
gnu: Add r-millefy.
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* gnu/packages/bioinformatics.scm (r-millefy): New variable.
2022-08-01 15:14:47 +02:00
dc3ad40c6b
gnu: python-bbknn: Set NUMBA_CACHE_DIR.
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* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'set-numba-cache-dir.
2022-08-01 12:46:19 +02:00
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
e6bdd94c38
gnu: plink-ng: Fix building on other architectures.
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* 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
99d1122f8b
gnu: plink-ng: Update to 2.00a3.3.
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* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3.3.
2022-07-28 22:55:07 +03:00
d84bedd830
gnu: Add python-cellbender.
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* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
2022-07-09 10:37:22 +02:00
6211ecfec8
gnu: Add hh-suite.
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* gnu/packages/bioinformatics.scm (hh-suite): New variable.
2022-07-06 14:00:21 +02:00
a0125732ef
gnu: Add r-sccustomize.
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* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
2022-07-04 13:48:58 +02:00
4d77072c56
gnu: libsbml: Use regular check.
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* 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
81cf674a5d
gnu: Add python-ikarus.
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* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
2022-07-01 14:54:26 +02:00
f700223c3b
gnu: Add pyscenic.
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* gnu/packages/bioinformatics.scm (pyscenic): New variable.
2022-06-16 15:20:59 +02:00
3535d8dc5a
gnu: Add python-arboreto.
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* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
2022-06-16 15:20:59 +02:00
fbe5707b73
gnu: Add python-ctxcore.
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* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
2022-06-16 15:20:59 +02:00
b483ef1a88
gnu: python-pybedtools: Update to 0.9.0.
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* 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
964cdd57fa
gnu: discrover: Use reproducible timestamps.
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* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add
'set-force-source-date phase.
2022-06-06 15:08:18 -07:00
b540e5e6bb
gnu: pigx-scrnaseq: Update to 1.1.9.
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* 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
93c97bfffb
gnu: pigx-bsseq: Update to 0.1.7.
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* 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
6e54ce9ca9
gnu: pigx-chipseq: Update to 0.1.0.
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* 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
cd95d7ddd1
gnu: pigx-rnaseq: Update to 0.1.0.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
2022-06-01 11:07:27 +02:00
0aae2f7f01
gnu: pigx-rnaseq: Update to 0.0.21.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
2022-06-01 10:46:00 +02:00
0c26c8da9d
gnu: pigx-rnaseq: Fix build.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
2022-06-01 10:46:00 +02:00
b279e778ab
gnu: Add sylamer.
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* gnu/packages/bioinformatics.scm (sylamer): New variable.
2022-06-01 00:17:05 +02:00
c35e508b4a
gnu: Remove python2-biopython.
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* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
2022-05-31 14:54:17 -04:00
ad030a0b7d
gnu: Remove pplacer-scripts.
...
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
2022-05-31 14:54:17 -04:00
d397cb6207
gnu: Remove pplacer.
...
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
2022-05-31 14:54:16 -04:00
026fca8b5b
gnu: Remove python2-checkm-genome.
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* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
2022-05-31 14:54:15 -04:00
4d7bb37981
gnu: Remove fraggenescan.
...
* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
2022-05-31 14:54:02 -04:00
6792b0b6cd
gnu: Remove python2-pysam.
...
* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
2022-05-31 14:53:35 -04:00
955e7d628d
gnu: Remove find-circ.
...
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
2022-05-31 14:53:34 -04:00
a5e29cd838
gnu: Remove gess.
...
* gnu/packages/bioinformatics.scm (gess): Delete variable.
2022-05-31 14:53:34 -04:00
c30ab2c0b4
gnu: Remove pyicoteo.
...
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
2022-05-31 14:52:19 -04:00
ba09192168
gnu: Remove python2-pbcore.
...
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31 14:52:19 -04:00
8287979669
gnu: Remove python2-pyfaidx.
...
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31 14:52:18 -04:00
850bd0c329
gnu: Remove python2-screed.
...
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31 14:52:18 -04:00
a94bc7798a
gnu: Remove miso.
...
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31 14:52:18 -04:00
23e133a907
gnu: Remove python2-warpedlmm.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31 14:52:18 -04:00
bb35b50adc
gnu: Remove poretools.
...
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31 14:52:18 -04:00
bcdd45be6f
gnu: Remove python2-dendropy.
...
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31 14:52:17 -04:00
d2c971e67b
gnu: Remove bamm.
...
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31 14:52:17 -04:00
1010c05800
gnu: Remove python2-pybedtools.
...
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31 14:52:17 -04:00
725b562962
gnu: Remove python2-htseq.
...
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31 14:52:17 -04:00
8bcb07d089
gnu: Remove pepr.
...
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31 14:52:17 -04:00
3d63c5f1ba
gnu: tetoolkit: Update to 2.2.1b.
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* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam.
[home-page]: Update URL.
2022-05-31 14:52:16 -04:00
d29d50a556
gnu: Remove python2-pybigwig.
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* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31 14:52:16 -04:00
98c4f97d18
gnu: Remove ribodiff.
...
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31 14:52:16 -04:00
9f4c958d62
gnu: Remove grit.
...
* gnu/packages/bioinformatics.scm (grit): Delete variable.
2022-05-31 14:52:16 -04:00
7963e12568
gnu: Remove python2-fastalite.
...
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
2022-05-31 14:52:16 -04:00
0bcd28e58c
gnu: python-scanpy: Update to 1.9.1.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
2022-05-30 23:09:46 +02:00
cb115ba722
gnu: pigx-sars-cov-2: Fix build.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
2022-05-29 00:39:19 +02:00
Ricardo Wurmus
Mădălin Ionel Patrașcu
Maxim Cournoyer
Efraim Flashner
Thiago Jung Bauermann
Vagrant Cascadian
Vagrant Cascadian