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1100 Commits

Author SHA1 Message Date
Ricardo Wurmus ff9d1a2f0c
Merge branch 'master' into core-updates 2018-02-18 00:39:25 +01:00
Ben Woodcroft 369eee8763
gnu: vsearch: Update to 2.7.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.1.
 2018-02-17 12:44:29 +10:00
Mark H Weaver 150062f190
Merge branch 'master' into core-updates 2018-02-16 13:14:26 -05:00
Ben Woodcroft 5ebc8e7f41
gnu: diamond: Update to 0.9.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
 2018-02-16 08:13:24 +10:00
Ricardo Wurmus 152d30c346
gnu: Add python-loompy. 
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
 2018-02-15 17:19:00 +01:00
Ricardo Wurmus 3082de04c2
gnu: Add r-dropbead. 
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
 2018-02-15 17:18:54 +01:00
Ricardo Wurmus 05f7296012
gnu: Add r-delayedmatrixstats. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
 2018-02-15 17:18:52 +01:00
Mark H Weaver 932c98326d
Merge branch 'master' into core-updates 2018-02-14 03:40:08 -05:00
Ben Woodcroft 119c09c219
gnu: vsearch: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
 2018-02-14 07:43:19 +10:00
Mark H Weaver 288b8fd5e9
Merge branch 'master' into core-updates 2018-02-13 13:17:15 -05:00
Ricardo Wurmus 97bf74076c
gnu: r-gprofiler: Update to 0.6.3. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 169942368f
gnu: r-ensembldb: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 34d077b8bc
gnu: r-gage: Update to 2.28.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus f5f9442703
gnu: r-keggrest: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 26e3e28cc9
gnu: r-seurat: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0.
[propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 53f0dea9d7
gnu: r-msnbase: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus b1f2753627
gnu: r-methylkit: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 5ef76bc28c
gnu: r-gkmsvm: Update to 0.79.0. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b24dc95b5
gnu: r-wgcna: Update to 1.62. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus e1129446ec
gnu: r-genomation: Update to 1.11.3. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b18856532
gnu: r-genomicfeatures: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 99b3236e65
gnu: r-rtracklayer: Update to 1.38.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus c37b361e44
gnu: r-summarizedexperiment: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 373430672d
gnu: r-biomart: Update to 2.34.2. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 024f19c68b
gnu: r-genomicranges: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0674657908
gnu: r-limma: Update to 3.34.8. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 5fb1fee67b
gnu: r-variantannotation: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus d22abe1e5d
gnu: r-edger: Update to 3.20.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 66ae706c24
gnu: r-bookdown: Update to 0.6. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6.
[propagated-inputs]: Add r-xfun and ghc-pandoc.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 2e9da3390c
gnu: r-vegan: Update to 2.4-6. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 7f1d9bef50
gnu: Add r-scran. 
* gnu/packages/bioinformatics.scm (r-scran): New variable.
 2018-02-12 15:29:44 +01:00
Ricardo Wurmus 658ab21d2e
gnu: Add r-scater. 
* gnu/packages/bioinformatics.scm (r-scater): New variable.

Co-authored-by: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus 6fb1dc17a3
gnu: Add r-singlecellexperiment. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus 9ec0898824
gnu: Add r-beachmat. 
* gnu/packages/bioinformatics.scm (r-beachmat): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus 748e9f163a
gnu: Add r-rhdf5lib. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus aba3e482b9
gnu: Add r-hdf5array. 
* gnu/packages/bioinformatics.scm (r-hdf5array): New variable.
 2018-02-11 11:42:09 +01:00
Marius Bakke 9e94d063ab
gnu: multiqc: Update to 1.4. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.4.
[propagated-inputs]: Remove PYTHON-ENUM34.
 2018-02-07 15:34:08 +01:00
Mark H Weaver e7ca634912
Merge branch 'master' into core-updates 2018-02-03 22:46:07 -05:00
Ben Woodcroft 7502badb81
gnu: diamond: Update to 0.9.17. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.17.
 2018-02-02 23:04:46 +10:00
Marius Bakke bee7bb315c
Merge branch 'master' into core-updates 2018-02-01 13:18:47 +01:00
Ben Woodcroft ae8522d265
gnu: diamond: Update to 0.9.16. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.16.
 2018-01-27 10:21:06 +10:00
Mark H Weaver b89d8a4271
Merge branch 'master' into core-updates 2018-01-26 00:15:26 -05:00
Ben Woodcroft a81f7eb858
gnu: diamond: Update to 0.9.15. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.15.
 2018-01-26 12:47:02 +10:00
Tobias Geerinckx-Rice cd70f9bdb0
gnu: deeptools: Update URI. 
* gnu/packages/bioinformatics.scm (deeptools)[source, home-page]: Update
URI.
 2018-01-26 00:09:19 +01:00
Mark H Weaver a102d359a6
Merge branch 'master' into core-updates 2018-01-23 17:01:07 -05:00
Ricardo Wurmus 625cdc3fde
gnu: star: Make reproducible. 
* gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase
"make-reproducible".
 2018-01-22 22:49:10 +01:00
Efraim Flashner 3df57b3a97
gnu: khmer: Add aarch64-linux to supported systems. 
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: Add
aarch64-linux to the supported systems.
 2018-01-22 09:39:59 +02:00
Ricardo Wurmus 7762646d95
gnu: Add salmon. 
* gnu/packages/bioinformatics.scm (libstadenio-for-salmon,
spdlog-for-salmon, bwa-for-salmon, salmon): New variables.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus 8d77a085a7
gnu: Add sailfish. 
* gnu/packages/bioinformatics.scm (sailfish): New variable.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus 1fe0bde34d
gnu: Add libdivsufsort. 
* gnu/packages/bioinformatics.scm (libdivsufsort): New variable.
 2018-01-21 14:18:09 +01:00