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Author SHA1 Message Date
zimoun
90bbab5cff
gnu: r-topgo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
f78ff75b41
gnu: r-genomicfeatures: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
a88230a1bc
gnu: r-rtracklayer: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun
ca1a015777
gnu: r-genomicalignments: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
 2021-05-31 15:34:39 +02:00
Ricardo Wurmus
e3cde9aaf8
gnu: Add mosaicatcher. 
* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-29 07:26:15 +02:00
Christopher Baines
6417b97c7e
Revert "gnu: Add mosaicatcher." 
mosaicatcher-unbundle-htslib.patch is missing.

This reverts commit b1ae0f30d8.
 2021-05-29 01:21:14 +01:00
Ricardo Wurmus
b1ae0f30d8
gnu: Add mosaicatcher. 
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-28 23:00:47 +02:00
Roel Janssen
87c9f63fce
gnu: Add python-pyega3. 
* gnu/packages/bioinformatics.scm (python-pyega3): New variable.
 2021-05-27 23:01:35 +02:00
Roel Janssen
a30e616ccc
gnu: Add python-htsget. 
* gnu/packages/bioinformatics.scm (python-htsget): New variable.
 2021-05-27 22:50:46 +02:00
Efraim Flashner
c5f7203e3e
gnu: minimap2: Install more files. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules.
Adjust custom 'install phase to also install library, headers and a
pkg-config file.
 2021-05-26 15:22:10 +03:00
Efraim Flashner
36a90d0637
gnu: minimap2: Update to 2.18. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.18.
[source]: Remove patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-05-26 15:22:10 +03:00
Roel Janssen
af163badb4
gnu: Add r-phantompeakqualtools. 
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable.
 2021-05-26 09:34:37 +02:00
Roel Janssen
b1fee8a003
gnu: Add r-spp. 
* gnu/packages/bioinformatics.scm (r-spp): New variable.
 2021-05-26 09:29:01 +02:00
Marius Bakke
4ea6852c5f
Merge branch 'master' into core-updates 2021-05-22 17:21:57 +02:00
Ricardo Wurmus
7ff515aa51
gnu: r-rhdf5filters: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Update to 1.2.1.
 2021-05-20 14:43:34 +02:00
Ricardo Wurmus
48b8a5e701
gnu: pigx-chipseq: Update to 0.0.52. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.52.
 2021-05-17 18:45:55 +02:00
Ludovic Courtès
25487c3fe6
Merge branch 'master' into core-updates 2021-05-15 22:55:24 +02:00
Ricardo Wurmus
848126d008
gnu: prinseq: Fix references to perl executable. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Embed concrete
references to the "perl" executable.
 2021-05-14 17:11:52 +02:00
Marius Bakke
f034264204
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/bioinformatics.scm
	gnu/packages/django.scm
	gnu/packages/gtk.scm
	gnu/packages/llvm.scm
	gnu/packages/python-web.scm
	gnu/packages/python.scm
	gnu/packages/tex.scm
	guix/build-system/asdf.scm
	guix/build/emacs-build-system.scm
	guix/profiles.scm
 2021-05-09 21:29:46 +02:00
Ricardo Wurmus
9b99b6d947
gnu: Add ensembl-vep. 
* gnu/packages/bioinformatics.scm (ensembl-vep): New variable.
 2021-05-07 08:52:49 +02:00
Ricardo Wurmus
ce7b202f9b
gnu: Add perl-bio-db-hts. 
* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable.
 2021-05-06 18:56:24 +02:00
Ricardo Wurmus
da7f89c737
gnu: python-pybedtools: Update to 0.8.2. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2.
[arguments]: Remove outdated substitutions; simplify check phase.
 2021-05-05 16:18:13 +02:00
Ricardo Wurmus
7694acebd1
gnu: r-summarizedexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here...
* gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here.
 2021-05-04 10:11:34 +02:00
Ricardo Wurmus
d4051161e7
gnu: r-ensembldb: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus
7072dc8c53
gnu: r-gage: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus
3b002a49d4
gnu: r-annotationhub: Update to 2.22.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1.
 2021-05-04 09:47:36 +02:00
Roel Janssen
f09e4dd8ea
gnu: Add pbgzip. 
* gnu/packages/bioinformatics.scm (pbgzip): New variable.
 2021-04-30 18:44:46 +02:00
Roel Janssen
7540f6915c
gnu: Update bedtools to 2.30.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
  [inputs]: Use latest samtools.
 2021-04-29 12:14:06 +02:00
Roel Janssen
558d11c3a8
gnu: Update samtools to 1.12. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
 2021-04-29 12:14:02 +02:00
Roel Janssen
b904bb89a0
gnu: Update bcftools to 1.12. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
 2021-04-29 12:13:56 +02:00
Roel Janssen
241994230b
gnu: htslib: Update to 1.12. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
 2021-04-29 12:13:46 +02:00
Ricardo Wurmus
e7707d5262
gnu: pigx-bsseq: Update to 0.1.3. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3.
[inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
 2021-04-28 21:58:05 +02:00
Ricardo Wurmus
01e33a031e
gnu: Add lofreq. 
* gnu/packages/bioinformatics.scm (lofreq): New variable.
 2021-04-28 17:41:47 +02:00
Ricardo Wurmus
f01b3cd063
gnu: kraken2: Replace references to rsync. 
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
 2021-04-28 14:50:50 +02:00
Ricardo Wurmus
5ea5ea6066
gnu: Add python-pyliftover. 
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
 2021-04-28 10:52:12 +02:00
Vinicius Monego
76fb1a5cf2
gnu: Add python-louvain 0.15. 
* gnu/packages/graph.scm (python-louvain): Rename variable to
python-louvain-0.6.
(python-louvain): New variable.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Use
python-louvain-0.6.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2021-04-25 14:49:57 -04:00
Ricardo Wurmus
f1f17c7bba
gnu: Add shorah. 
* gnu/packages/bioinformatics.scm (shorah): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus
c9371b698d
gnu: Add r-shinycell. 
* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus
92032d8081
gnu: Add kraken2. 
* gnu/packages/bioinformatics.scm (kraken2): New variable.
 2021-04-22 08:31:17 +02:00
Roel Janssen
c3926120ba
gnu: Update blast+ to 2.11.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.11.0.
 2021-04-16 20:56:43 +02:00
Efraim Flashner
fcc39864db
Merge remote-tracking branch 'origin/master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/boost.scm
	gnu/packages/chez.scm
	gnu/packages/compression.scm
	gnu/packages/crates-io.scm
	gnu/packages/docbook.scm
	gnu/packages/engineering.scm
	gnu/packages/gcc.scm
	gnu/packages/gl.scm
	gnu/packages/gtk.scm
	gnu/packages/nettle.scm
	gnu/packages/python-check.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/rust.scm
	gnu/packages/sqlite.scm
	guix/build-system/node.scm
 2021-04-16 14:39:48 +03:00
Arun Isaac
563e4bd884
gnu: cwltool: Update to 3.0.20210319143721. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.0.20210319143721.
[arguments]: In the loosen-version-restrictions phase, relax pytest version
restriction. In the modify-tests phase, delete file tests/test_content_type.py
since it contains tests that require network access.
 2021-04-14 22:39:54 +05:30
Arun Isaac
12e210d907
gnu: python-schema-salad: Update to 7.1.20210316164414. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
7.1.20210316164414.
[arguments]: Add skip-failing-tests phase.
 2021-04-14 22:39:54 +05:30
Tobias Geerinckx-Rice
e5852655b8
gnu: sortmerna: Mark up description. 
* gnu/packages/bioinformatics.scm (sortmerna)[description]: Use @acronym{}.
 2021-04-10 14:11:26 +02:00
Ricardo Wurmus
5f0c3535aa
gnu: r-genomicfeatures: Update to 1.42.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3.
 2021-04-08 13:28:24 +02:00
zimoun
23686ba3eb
Revert "Revert some commits that caused guix pull to fail." 
This reverts commit 8ec0ca8faf.
 2021-03-31 21:23:45 +02:00
Efraim Flashner
04ba7a196a
gnu: plink-ng: Build prettify binary. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to also build prettify.
 2021-03-31 14:33:42 +03:00
Efraim Flashner
5f3f2a7cc8
gnu: plink-ng: Remove custom install phase. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags and remove custom 'install phase.
 2021-03-31 14:33:34 +03:00
Efraim Flashner
977ea2c0a3
gnu: plink-ng: Sort inputs alphabetically. 
* gnu/packages/bioinformatics.scm (plink-ng)[inputs]: Sort
alphabetically.
 2021-03-31 14:32:43 +03:00
Efraim Flashner
58e9e0e142
gnu: plink-ng: Update to 2.00a2.3. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a2.3.
[arguments]: Adjust make-flags.
 2021-03-31 14:32:43 +03:00