d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.
...
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 16:55:43 +01:00
32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
2018-03-19 11:07:55 +01:00
2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
fd757a8f21
gnu: pigx-chipseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:54 +01:00
c1c9cc664b
gnu: Add pigx.
...
* gnu/packages/bioinformatics.scm (pigx): New variable.
2018-03-16 15:40:31 +01:00
fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
2018-03-16 15:40:31 +01:00
46264c73a6
gnu: Add pigx-scrnaseq.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
2018-03-16 11:15:04 +01:00
b44437c549
gnu: kentutils: Build with mariadb.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
2018-03-16 10:01:07 +01:00
32cbbac11a
gnu: Add Diversitree.
...
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
2018-03-15 10:57:51 -04:00
fb94174fc3
gnu: Add pigx-bsseq.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
2018-03-11 20:01:53 +01:00
531afc8a89
gnu: Add pigx-chipseq.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
2018-03-11 20:01:53 +01:00
a539ad867d
gnu: r-rhdf5lib: Make build reproducible.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
2018-03-09 11:40:59 +01:00
22a0c65969
gnu: Add r-phangorn.
...
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
2018-03-08 23:31:56 +01:00
53cc59a1d8
gnu: r-ape: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
2018-03-08 23:31:55 +01:00
84c195e505
gnu: r-dropbead: Update to 0-2.d746c6f.
...
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
2018-03-08 18:53:49 +01:00
0bdd5b8ab7
gnu: Add pigx-rnaseq.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
2018-03-07 23:25:36 +01:00
c072cf57b9
gnu: samtools: Update to 1.7.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
2018-03-06 16:03:04 +01:00
727d847980
gnu: htslib: Update to 1.7.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
2018-03-06 16:03:04 +01:00
e325c89076
gnu: r-rhdf5: Make build reproducible.
...
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
2018-03-06 16:03:04 +01:00
da49d13710
gnu: piranha: Declare a source file-name.
...
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
2018-03-04 12:05:13 +02:00
d9a069c2d9
gnu: libdivsufsort: Declare a source file-name.
...
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
2018-03-04 12:05:13 +02:00
5110672474
gnu: seek: Declare a source file-name.
...
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
2018-03-04 12:05:13 +02:00
b1d4026dfb
gnu: r-dropbead: Declare a source file-name.
...
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
2018-03-04 12:05:10 +02:00
1adeef3194
gnu: Add dropseq-tools.
...
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
2018-03-03 21:28:05 +01:00
72299db9fe
gnu: Add java-picard-2.10.3.
...
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
2018-03-03 21:28:02 +01:00
719fa958f3
gnu: Add java-htsjdk-2.10.1.
...
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
2018-03-03 21:27:59 +01:00
9a599c17b7
gnu: Add java-htsjdk-latest.
...
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
2018-03-03 21:27:57 +01:00
9ac7db1830
gnu: Add java-biojava-alignment-4.0.
...
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
2018-03-03 21:27:56 +01:00
5528f9e8f0
gnu: Add java-biojava-phylo-4.0.
...
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
2018-03-03 21:27:53 +01:00
e44da58c16
gnu: Add java-biojava-core-4.0.
...
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
2018-03-03 21:27:51 +01:00
22c09c335b
gnu: Add java-biojava-alignment.
...
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
2018-03-03 21:27:48 +01:00
b28c803708
gnu: Add java-biojava-phylo.
...
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
2018-03-03 21:27:46 +01:00
10645b9212
gnu: Add java-forester-1.005.
...
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
2018-03-03 21:27:44 +01:00
f09d16e594
gnu: Add java-forester.
...
* gnu/packages/bioinformatics.scm (java-forester): New variable.
2018-03-03 21:27:41 +01:00
5fef15e506
gnu: Add java-biojava-core.
...
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
2018-03-03 21:27:36 +01:00
bd975831c6
gnu: Add fastqc.
...
* gnu/packages/bioinformatics.scm (fastqc): New variable.
2018-03-03 21:21:48 +01:00
3ede1550e8
gnu: cutadapt: Update to 1.16.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
2018-03-02 23:44:16 +01:00
9aaf2813e2
gnu: r-scran: Update to 1.6.8.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
2018-03-01 21:28:53 +01:00
6a0e13906b
gnu: r-wgcna: Update to 1.63.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
2018-03-01 21:28:53 +01:00
61cbd49b30
gnu: r-topgo: Update to 2.30.1.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
2018-03-01 21:28:53 +01:00
535014ce60
gnu: r-genomicranges: Update to 1.30.3.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
2018-03-01 21:28:53 +01:00
eb8971b742
gnu: r-limma: Update to 3.34.9.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
2018-03-01 21:28:53 +01:00
22d96920d3
gnu: r-edger: Update to 3.20.9.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
2018-03-01 21:28:53 +01:00
99e4b11d81
gnu: r-shortread: Update to 1.36.1.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
2018-03-01 21:28:53 +01:00
b180893289
gnu: r-dexseq: Update to 1.24.3.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
2018-03-01 21:28:52 +01:00
65c9d25739
gnu: r-qtl: Update to 1.42-8.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
2018-02-22 11:18:03 +01:00
79c6af13d0
gnu: r-delayedmatrixstats: Update to 1.0.3.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
2018-02-19 09:53:05 +01:00
59b2864d6c
gnu: r-scater: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
2018-02-19 09:53:05 +01:00
d578278e35
gnu: r-gviz: Update to 1.22.3.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
2018-02-19 09:53:05 +01:00
ca7855fcd2
gnu: r-gprofiler: Update to 0.6.4.
...
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
2018-02-19 09:53:04 +01:00
8877ab432e
gnu: r-ensembldb: Update to 2.2.2.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
2018-02-19 09:53:04 +01:00
ebec98ae1d
gnu: r-seurat: Update to 2.2.1.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1.
[propagated-inputs]: Remove r-nmf; add r-metap.
2018-02-19 09:53:04 +01:00
3118b28644
gnu: r-qtl: Update to 1.42-7.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
2018-02-19 09:53:04 +01:00
824c200475
gnu: r-genomicranges: Update to 1.30.2.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
2018-02-19 09:53:04 +01:00
e8484711c6
gnu: r-getopt: Update to 1.20.2.
...
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
2018-02-19 09:53:04 +01:00
9800f7d9e8
gnu: r-bookdown: Update to 0.7.
...
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7.
[propagated-inputs]: Add r-tinytex.
2018-02-19 09:53:04 +01:00
ff9d1a2f0c
Merge branch 'master' into core-updates
2018-02-18 00:39:25 +01:00
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
150062f190
Merge branch 'master' into core-updates
2018-02-16 13:14:26 -05:00
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
152d30c346
gnu: Add python-loompy.
...
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
2018-02-15 17:19:00 +01:00
3082de04c2
gnu: Add r-dropbead.
...
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
2018-02-15 17:18:54 +01:00
05f7296012
gnu: Add r-delayedmatrixstats.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
2018-02-15 17:18:52 +01:00
932c98326d
Merge branch 'master' into core-updates
2018-02-14 03:40:08 -05:00
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
288b8fd5e9
Merge branch 'master' into core-updates
2018-02-13 13:17:15 -05:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
7f1d9bef50
gnu: Add r-scran.
...
* gnu/packages/bioinformatics.scm (r-scran): New variable.
2018-02-12 15:29:44 +01:00
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
6fb1dc17a3
gnu: Add r-singlecellexperiment.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable.
2018-02-12 15:29:43 +01:00
9ec0898824
gnu: Add r-beachmat.
...
* gnu/packages/bioinformatics.scm (r-beachmat): New variable.
2018-02-12 15:29:43 +01:00
748e9f163a
gnu: Add r-rhdf5lib.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
2018-02-12 15:29:43 +01:00
aba3e482b9
gnu: Add r-hdf5array.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): New variable.
2018-02-11 11:42:09 +01:00
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
e7ca634912
Merge branch 'master' into core-updates
2018-02-03 22:46:07 -05:00
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
bee7bb315c
Merge branch 'master' into core-updates
2018-02-01 13:18:47 +01:00
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
b89d8a4271
Merge branch 'master' into core-updates
2018-01-26 00:15:26 -05:00
Ricardo Wurmus