8322c860f9
gnu: r-methylkit: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.10.0.
[propagated-inputs]: Add r-mgcv.
2019-05-06 00:14:43 +02:00
b173dbe617
gnu: r-annotationhub: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.0.
[propagated-inputs]: Add r-biocfilecache, r-dplyr, and r-rappdirs.
2019-05-06 00:14:43 +02:00
a8abc8dd3a
gnu: r-fastseg: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.30.0.
2019-05-06 00:14:43 +02:00
e699e8e599
gnu: r-keggrest: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.0.
2019-05-06 00:14:43 +02:00
c798455d87
gnu: r-gage: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.34.0.
2019-05-06 00:14:43 +02:00
d4ef1d59cc
gnu: r-genomicfiles: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.20.0.
2019-05-06 00:14:43 +02:00
70a3e4499d
gnu: r-complexheatmap: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.0.0.
[propagated-inputs]: Add r-clue and r-png.
2019-05-06 00:14:43 +02:00
e2cb23404c
gnu: r-dirichletmultinomial: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.26.0.
2019-05-06 00:14:42 +02:00
0af6efa3c5
gnu: r-ensembldb: Update to 2.8.0.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.0.
2019-05-06 00:14:42 +02:00
96f98c5b72
gnu: r-organismdbi: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.26.0.
2019-05-06 00:14:42 +02:00
a98c3b4ae4
gnu: r-biovizbase: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.32.0.
2019-05-06 00:14:42 +02:00
d38fbacad1
gnu: r-ggbio: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.32.0.
2019-05-06 00:14:42 +02:00
623be1a443
gnu: r-gqtlbase: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.16.0.
2019-05-06 00:14:42 +02:00
ed7de45655
gnu: r-snpstats: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.34.0.
2019-05-06 00:14:42 +02:00
3c5f5b4154
gnu: r-erma: Update to 1.0.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.0.0.
2019-05-06 00:14:41 +02:00
89ba9a7226
gnu: r-ldblock: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.0.
2019-05-06 00:14:41 +02:00
a349d57a46
gnu: r-gqtlstats: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.16.0.
2019-05-06 00:14:41 +02:00
105d9e2cb4
gnu: r-gviz: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.0.
2019-05-06 00:14:41 +02:00
1b454f9f69
gnu: r-gwascat: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.0.
[propagated-inputs]: Remove r-annotationhub, r-ggbio, r-ggplot2, r-gqtlstats,
r-graph, r-gviz, r-snpstats, r-summarizedexperiment, and r-variantannotation.
2019-05-06 00:14:41 +02:00
256609eb46
gnu: r-sushi: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.22.0.
2019-05-06 00:14:41 +02:00
7705165882
gnu: r-fithic: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.10.0.
2019-05-06 00:14:40 +02:00
e998a26e1d
gnu: r-hitc: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.28.0.
2019-05-06 00:14:40 +02:00
65925573be
gnu: r-hdf5array: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
2019-05-06 00:14:40 +02:00
d5625b3a9e
gnu: r-rhdf5lib: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.0.
2019-05-06 00:14:40 +02:00
583b4fd6e3
gnu: r-beachmat: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.0.0.
[inputs]: Remove hdf5 and zlib.
[propagated-inputs]: Rmeove r-hdf5array, r-rcpp, r-rhdf5, and r-rhdf5lib.
2019-05-06 00:14:40 +02:00
029cefdd90
gnu: r-singlecellexperiment: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.6.0.
2019-05-06 00:14:40 +02:00
70d04dc183
gnu: r-scater: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.0.
[propagated-inputs]: Add r-biocneighbors and r-biocsingular; remove r-plyr,
r-reshape2, and r-rhdf5lib.
2019-05-06 00:14:40 +02:00
4540727a21
gnu: r-scran: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.0.
[propagated-inputs]: Add r-bh, r-biocsingular, and r-dqrng; remove r-rhdf5lib.
2019-05-06 00:14:39 +02:00
f2a63d1588
gnu: r-delayedmatrixstats: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.6.0.
2019-05-06 00:14:39 +02:00
fab5f7c8d9
gnu: r-interactivedisplaybase: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.22.0.
2019-05-06 00:14:39 +02:00
975b72fa10
gnu: r-edaseq: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.18.0.
2019-05-06 00:14:39 +02:00
b765fc4a4c
gnu: r-deseq: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.36.0.
2019-05-06 00:14:39 +02:00
95f3a46630
gnu: r-aroma-light: Update to 3.14.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.14.0.
2019-05-06 00:14:39 +02:00
dd03589939
gnu: r-msnid: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.0.
2019-05-06 00:14:38 +02:00
b65c264907
gnu: r-msnbase: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.0.
2019-05-06 00:14:38 +02:00
ee386fcb1a
gnu: r-pcamethods: Update to 1.76.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.76.0.
2019-05-06 00:14:38 +02:00
f955afdabf
gnu: r-mzid: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.22.0.
2019-05-06 00:14:38 +02:00
9421e6b610
gnu: r-vsn: Update to 3.52.0.
...
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.52.0.
2019-05-06 00:14:38 +02:00
15f240e317
gnu: r-affy: Update to 1.62.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.62.0.
2019-05-06 00:14:38 +02:00
fdbaa5c1e5
gnu: r-affyio: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.54.0.
2019-05-06 00:14:38 +02:00
5498cc46b3
gnu: r-mzr: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.18.0.
2019-05-06 00:14:37 +02:00
24aabd8fd9
gnu: r-protgenerics: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.16.0.
2019-05-06 00:14:37 +02:00
10cb9919fc
gnu: r-sva: Update to 3.32.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.0.
2019-05-06 00:14:37 +02:00
59bef6eaee
gnu: r-copywriter: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.16.0.
2019-05-06 00:14:37 +02:00
70c44443c3
gnu: r-chipseq: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.34.0.
2019-05-06 00:14:37 +02:00
dbb4aa4a34
gnu: r-annotationfilter: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.8.0.
2019-05-06 00:14:37 +02:00
f6ecdafa11
gnu: r-rhdf5: Update to 2.28.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.28.0.
2019-05-06 00:14:37 +02:00
c030eb50c5
gnu: r-tximport: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.0.
2019-05-06 00:14:36 +02:00
5b65a85949
gnu: r-mutationalpatterns: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.10.0.
2019-05-06 00:14:36 +02:00
45aeb4eb1d
gnu: r-bamsignals: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.16.0.
2019-05-06 00:14:36 +02:00
23ce7f3b0b
gnu: r-rhtslib: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.16.1.
2019-05-06 00:14:36 +02:00
c648e672b7
gnu: r-zlibbioc: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.30.0.
2019-05-06 00:14:36 +02:00
3be113b706
gnu: r-motifrg: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.28.0.
2019-05-06 00:14:35 +02:00
a7143246f8
gnu: r-seqlogo: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.50.0.
2019-05-06 00:14:35 +02:00
6ef47ac82e
gnu: r-genomation: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.16.0.
2019-05-06 00:14:35 +02:00
d726689a70
gnu: r-seqpattern: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.16.0.
2019-05-06 00:14:35 +02:00
651b62c697
gnu: r-bsgenome: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.52.0.
2019-05-06 00:14:35 +02:00
971df3a784
gnu: r-topgo: Update to 2.36.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.36.0.
2019-05-06 00:14:34 +02:00
d31f8d1bd8
gnu: r-genomicfeatures: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.0.
2019-05-06 00:14:34 +02:00
40d97367f0
gnu: r-rtracklayer: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.0.
2019-05-06 00:14:34 +02:00
6ff6973502
gnu: r-genomicalignments: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.0.
2019-05-06 00:14:34 +02:00
8671d1e9d6
gnu: r-summarizedexperiment: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.0.
2019-05-06 00:14:34 +02:00
14561bb9e7
gnu: r-delayedarray: Update to 0.10.0.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.10.0.
[propagated-inputs]: Add r-matrix.
2019-05-06 00:14:34 +02:00
d2e165496b
gnu: r-biostrings: Update to 2.52.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.52.0.
2019-05-06 00:14:33 +02:00
e10b67c797
gnu: r-biocparallel: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.0.
2019-05-06 00:14:33 +02:00
933571ddcd
gnu: r-biomart: Update to 2.40.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.0.
2019-05-06 00:14:33 +02:00
a1b9378a8e
gnu: r-annotationdbi: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.0.
2019-05-06 00:14:33 +02:00
4aadfcd296
gnu: r-biobase: Update to 2.44.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.44.0.
2019-05-06 00:14:33 +02:00
b35bc56a8a
gnu: r-genomicranges: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.0.
2019-05-06 00:14:33 +02:00
bc0e5bc12e
gnu: r-xvector: Update to 0.24.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.24.0.
2019-05-06 00:14:32 +02:00
5fadf39280
gnu: r-limma: Update to 3.40.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.0.
2019-05-06 00:14:32 +02:00
0d094ad9ab
gnu: r-variantannotation: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.0.
[propagated-inputs]: Add r-rhtslib.
2019-05-06 00:14:32 +02:00
1e3f53a489
gnu: r-edger: Update to 3.26.0.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.0.
2019-05-06 00:14:32 +02:00
6dc05d0a86
gnu: r-genomeinfodb: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.20.0.
2019-05-06 00:14:32 +02:00
38142114b7
gnu: r-iranges: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.0.
2019-05-06 00:14:32 +02:00
192ddab3e5
gnu: r-s4vectors: Update to 0.22.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.0.
2019-05-06 00:14:31 +02:00
8bdf7d55be
gnu: r-bioccheck: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.20.0.
2019-05-06 00:14:31 +02:00
e01b72d225
gnu: r-biocstyle: Update to 2.12.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.12.0.
2019-05-06 00:14:31 +02:00
440af6482a
gnu: r-biocviews: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.0.
2019-05-06 00:14:31 +02:00
ce52cab000
gnu: r-grohmm: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.18.0.
2019-05-06 00:14:31 +02:00
49f30903f0
gnu: r-shortread: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.42.0.
2019-05-06 00:14:31 +02:00
fe40f55094
gnu: r-gostats: Update to 2.50.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.50.0.
2019-05-06 00:14:30 +02:00
4d88dbe6eb
gnu: r-category: Update to 2.50.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.50.0.
2019-05-06 00:14:30 +02:00
08d2a26d47
gnu: r-gseabase: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.46.0.
2019-05-06 00:14:30 +02:00
aa51a241c5
gnu: r-rbgl: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.60.0.
[propagated-inputs]: Add r-bh.
2019-05-06 00:14:30 +02:00
7f737246d8
gnu: r-annotationforge: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.26.0.
2019-05-06 00:14:30 +02:00
0a58282de7
gnu: r-dexseq: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.30.0.
2019-05-06 00:14:30 +02:00
9a39193d45
gnu: r-deseq2: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.24.0.
2019-05-06 00:14:30 +02:00
0183163d1e
gnu: r-genefilter: Update to 1.66.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.66.0.
2019-05-06 00:14:29 +02:00
3153ca9d5f
gnu: r-rhtslib: Fix build.
...
* gnu/packages/bioinformatics.scm (r-rhtslib)[arguments]: Add
"--no-staged-install" to configure flags.
2019-04-27 22:45:02 +02:00
fc3ebc3023
gnu: r-ggbio: Fix build.
...
* gnu/packages/bioinformatics.scm (r-ggbio)[arguments]: Add build phase to
patch out typo.
2019-04-27 20:45:21 +02:00
7f55904558
gnu: Add umi-tools.
...
* gnu/packages/bioinformatics.scm (umi-tools): New variable.
2019-04-26 21:00:37 +02:00
296da6e624
gnu: r-seurat: Update to 3.0.0.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.0.
[propagated-inputs]: Remove r-dosnow, r-dplyr, r-dtw, r-foreach, r-fpc,
r-gplots, r-hdf5r, r-hmisc, r-httr, r-lars, r-mixtools, r-reshape2, and
r-tidyr; add r-future, r-future-apply, r-ggrepel, r-kernsmooth, r-rlang,
r-rsvd, r-scales, and r-sctransform.
2019-04-19 15:38:47 +02:00
c4a50a8a47
gnu: r-genomicfeatures: Update to 1.34.8.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.8.
2019-04-11 23:37:19 +02:00
c2f6f4e500
gnu: Add python2-checkm-genome.
...
* gnu/packages/bioinformatics.scm (python2-checkm-genome): New variable.
2019-04-11 17:54:57 +02:00
36f4f1e297
gnu: Add pplacer.
...
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
2019-04-11 17:18:08 +02:00
f613f9ae26
gnu: r-ldblock: Update to 1.12.1.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.1.
2019-04-06 23:13:26 +02:00
8f30d38238
gnu: r-ensembldb: Update to 2.6.8.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.8.
2019-04-06 23:13:26 +02:00
83546785b2
gnu: r-rcas: Add upstream name.
...
* gnu/packages/bioinformatics.scm (r-rcas)[properties]: Add upstream name.
2019-04-03 17:42:18 +02:00
cbe40b8b24
gnu: pigx-scrnaseq: Use older loompy.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
python-loompy with python-loompy-for-pigx-scrnaseq.
2019-04-02 16:11:23 +02:00
dc112a0fe2
gnu: Add python-loompy-for-pigx-scrnaseq.
...
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): New variable.
2019-04-02 16:11:12 +02:00
82cc117450
gnu: pigx-chipseq: Update to 0.0.40.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.40.
2019-04-02 15:53:23 +02:00
b4a33870f6
gnu: python-scanpy: Add python-louvain to inputs.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Sort
inputs and add python-louvain.
[arguments]: Do not delete test that depends on louvain.
2019-04-02 15:11:45 +02:00
36a4366d79
gnu: Fix descriptions to not use quotes.
...
* gnu/packages/admin.scm (wpa-supplicant-minimal, mingetty, di),
* gnu/packages/audio.scm (fil-plugins),
* gnu/packages/base.scm (make-ld-wrapper, make-glibc-locales),
* gnu/packages/bioinformatics.scm (r-samtools),
* gnu/packages/chez.scm (chez-mit),
* gnu/packages/commencement.scm (make-gcc-toolchain),
* gnu/packages/compression.scm (fastjar),
* gnu/packages/cran.scm (r-maps, r-rcpp),
* gnu/packages/databases.scm (sparql-query),
* gnu/packages/dunst.scm (dunst),
* gnu/packages/ftp.scm (ncftp),
* gnu/packages/gl.scm (freeglut),
* gnu/packages/haskell-check.scm (ghc-tasty-golden),
* gnu/packages/haskell.scm (ghc-case-insensitive, ghc-text,
ghc-haskell-src, ghc-syb, ghc-deepseq-generics, ghc-network-uri,
ghc-rerebase, ghc-zlib),
* gnu/packages/image.scm (jbig2dec),
* gnu/packages/kde-frameworks.scm (kinit, karchive),
* gnu/packages/linux.scm (wireless-tools, perf, module-init-tools, kbd),
* gnu/packages/lirc.scm (lirc),
* gnu/packages/lisp.scm (uglify-js),
* gnu/packages/mate.scm (mate-netbook),
* gnu/packages/microcom.scm (microcom),
* gnu/packages/music.scm (bristol),
* gnu/packages/networking.scm (perl-geo-ip),
* gnu/packages/patchutils.scm (patches),
* gnu/packages/perl-check.scm (perl-test-more-utf8),
* gnu/packages/perl.scm (perl-log-report-optional, perl-file-which,
perl-io-tty, perl-log-any, perl-digest-sha1, perl-class-load,
perl-regexp-common, perl-module-pluggable, perl-class-modifier),
* gnu/packages/python-xyz.scm (python-backports-abc, python-natsort),
* gnu/packages/samba.scm (iniparser),
* gnu/packages/search.scm (mlocate),
* gnu/packages/spice.scm (spice),
* gnu/packages/statistics.scm (r-dt, r-lubridate, r-estimability,
r-commonmark, r-digest, r-viridislite, r-stringr),
* gnu/packages/tex.scm (texlive-latex-changebar),
* gnu/packages/version-control.scm (subversion),
* gnu/packages/w3m.scm (w3m),
* gnu/packages/web.scm (perl-http-parser,
perl-plack-middleware-reverseproxy),
* gnu/packages/xorg.scm (xkeyboard-config, mkfontdir, xcursor-theme,
mkfontscale, xinit, font-alias)[description]: Use @code instead of quotes.
2019-03-31 20:51:10 +03:00
e9d4409bab
gnu: Add python-bbknn.
...
* gnu/packages/bioinformatics.scm (python-bbknn): New variable.
2019-03-29 03:55:45 +01:00
58d8225ddb
gnu: trim-galore: Add pigz.
...
* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz.
[arguments]: Embed reference to pigz.
2019-03-27 11:32:08 +01:00
5f1e31094d
gnu: trim-galore: Fix test for Python.
...
* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace
"configure" phase to skip ill-advised test for Python.
2019-03-27 11:28:38 +01:00
dfe420ee46
gnu: r-rhdf5lib: Update to 1.4.3.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.
2019-03-27 09:33:50 +01:00
3b6c77445b
gnu: r-genomicfeatures: Update to 1.34.7.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.
2019-03-27 09:33:50 +01:00
28d32817d8
gnu: python-scanpy: Update to 1.4.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.
[source]: Fetch from git.
[arguments]: Disable broken tests.
[native-inputs]: Add python-pytest.
[home-page]: Use HTTPS.
2019-03-26 18:06:35 +01:00
fdc316f374
gnu: trim-galore: Update to 0.6.1.
...
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1.
[arguments]: Adjust patching.
2019-03-26 16:40:42 +01:00
9ac17c6242
gnu: cutadapt: Update to 2.1.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1.
[source]: Fetch from pypi.
[native-inputs]: Add python-setuptools-scm.
2019-03-26 16:40:42 +01:00
80eb01c776
gnu: r-gkmsvm: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here...
* gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.
2019-03-25 14:34:41 +01:00
c5a2b518ad
gnu: r-wgcna: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-wgcna): Move from here...
* gnu/packages/cran.scm (r-wgcna): ...to here.
2019-03-25 14:05:09 +01:00
72a216a9d0
gnu: r-optparse: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-optparse): Move from here...
* gnu/packages/cran.scm (r-optparse): ...to here.
2019-03-25 14:04:19 +01:00
0ef062b338
gnu: r-bookdown: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-bookdown): Move from here...
* gnu/packages/cran.scm (r-bookdown): ...to here.
2019-03-25 14:03:21 +01:00
469fb43891
gnu: r-sparql: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-sparql): Move from here...
* gnu/packages/cran.scm (r-sparql): ...to here.
2019-03-25 14:01:56 +01:00
c4d521ba2c
gnu: r-seqinr: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-seqinr): Move from here...
* gnu/packages/cran.scm (r-seqinr): ...to here.
2019-03-24 23:44:13 +01:00
49a48c496f
gnu: r-acsnminer: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-acsnminer): Move from here...
* gnu/packages/cran.scm (r-acsnminer): ...to here.
2019-03-24 23:44:13 +01:00
9ebb7f8181
gnu: r-phangorn: Update to 2.5.3.
...
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.3.
2019-03-24 20:36:51 +01:00
adfbda0fb0
gnu: r-gqtlstats: Update to 1.14.1.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.1.
2019-03-24 20:36:51 +01:00
7a73c247b2
gnu: r-rbgl: Update to 1.58.2.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.2.
2019-03-24 20:36:51 +01:00
fdfaba9032
gnu: Add starlong.
...
* gnu/packages/bioinformatics.scm (starlong): New variable.
2019-03-22 16:17:01 +01:00
c2b45ac578
gnu: r-diversitree: Update to 0.9-11.
...
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
2019-03-21 00:02:49 +01:00
db39269c89
gnu: r-maldiquant: Update to 1.19.2.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
2019-03-21 00:02:49 +01:00
28d0eb2565
gnu: r-diversitree: Fix typo.
...
* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo
in package labels.
2019-03-21 00:02:48 +01:00
933cc19684
gnu: r-annotationhub: Update to 2.14.5.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
2019-03-20 22:32:37 +01:00
e49d5d34ed
gnu: r-genomicfeatures: Update to 1.34.6.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
2019-03-20 22:32:32 +01:00
2b83d218d8
gnu: r-variantannotation: Update to 1.28.13.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
2019-03-20 22:32:25 +01:00
0adb6f207b
gnu: r-category: Update to 2.48.1.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
2019-03-20 22:32:17 +01:00
e014dc78f0
gnu: r-dexseq: Update to 1.28.3.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
2019-03-20 22:32:11 +01:00
35f9c6628f
gnu: Add adapterremoval.
...
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
2019-03-20 12:19:55 +01:00
c5542196d5
gnu: nanopolish: Use python-wrapper.
...
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with
"python-wrapper" as scripts require "python" executable.
2019-03-19 13:30:41 +01:00
7c1685e9d8
gnu: nanopolish: Remove bundled library sources.
...
* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove
bundled htslib sources.
2019-03-19 13:30:41 +01:00
9e1d9a0a46
gnu: python-biom-format: Fix build.
...
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove
generated C files.
[arguments]: Disable second broken test.
2019-03-18 23:46:27 +01:00
6e42cef0ab
gnu: Add bbmap.
...
* gnu/packages/bioinformatics.scm (bbmap): New variable.
2019-03-18 21:35:57 +01:00
ee4ca57809
gnu: blasr: Add home page.
...
Reported by Efraim Flashner <efraim@flashner.co.il> on IRC.
* gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
2019-03-18 16:02:30 +01:00
19bd7f2e79
gnu: Add arriba.
...
* gnu/packages/bioinformatics.scm (arriba): New variable.
2019-03-18 16:00:30 +01:00
f88bdc5ff9
gnu: Add blasr.
...
* gnu/packages/bioinformatics.scm (blasr): New variable.
2019-03-18 14:47:49 +01:00
6a6cd48cf0
gnu: Add blasr-libcpp.
...
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
2019-03-18 14:47:45 +01:00
55154c5f40
gnu: Add pbbam.
...
* gnu/packages/bioinformatics.scm (pbbam): New variable.
2019-03-18 14:47:26 +01:00
07c8b558e3
gnu: Add bwa-meth.
...
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
2019-03-15 11:36:56 +01:00
fd4c7a098a
gnu: Add python-velocyto.
...
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
2019-03-13 22:48:53 +01:00
55a0a3c853
gnu: python-loompy: Update to 2.0.17.
...
* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
2019-03-13 22:48:52 +01:00
0b5d12ccdf
gnu: Add tetoolkit.
...
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
2019-03-13 15:14:10 +01:00
4dc2ecc279
gnu: r-qvalue: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-qvalue): Move from here...
* gnu/packages/bioconductor.scm (r-qvalue): ...to here.
2019-03-12 22:47:56 +01:00
8b6acb1f20
gnu: blast+: Update to 2.7.1.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1.
[inputs]: Add lmdb.
[source]: Remove obsolete patch.
* gnu/package/patches/blast+-fix-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2019-03-08 23:00:07 +01:00
183b6575e7
gnu: r-mzr: Update to 2.16.2.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2.
[inputs]: Replace "boost" with "boost-for-mysql".
2019-03-08 09:14:01 +01:00
6453d7aecc
gnu: r-gviz: Update to 1.26.5.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
2019-03-08 09:14:01 +01:00
101dcc29d3
gnu: r-ensembldb: Update to 2.6.7.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus