Ricardo Wurmus
d53aeeafcc
Add missing use-modules clause.
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This is a follow-up to commit 5dfe491290
2018-09-06 04:53:32 +02:00
Ricardo Wurmus
00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
Ricardo Wurmus
c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
Ricardo Wurmus
7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
Ricardo Wurmus
ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
Ricardo Wurmus
dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.
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* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
2018-09-05 20:03:09 +02:00
Ricardo Wurmus
5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor.
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* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
2018-09-05 20:03:08 +02:00
Ricardo Wurmus
f077174178
gnu: r-scran: Update to 1.8.4.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
2018-09-05 20:03:05 +02:00
Ricardo Wurmus
8e44ff0c0d
gnu: r-scater: Update to 1.8.4.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
2018-09-05 20:03:05 +02:00
Ricardo Wurmus
e69c07e61a
gnu: r-hdf5array: Update to 1.8.1.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
16527f1cbc
gnu: r-ggbio: Update to 1.28.5.
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* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
70daf9362b
gnu: r-biovizbase: Update to 1.28.2.
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* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1.
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* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
3c55304688
gnu: r-edaseq: Update to 2.14.1.
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* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
6f6aef80e3
gnu: r-seurat: Update to 2.3.4.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
07bd90ce90
gnu: r-msnbase: Update to 2.6.3.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
4ee8c37cca
gnu: r-maldiquant: Update to 1.18.
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* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
48b21f8b6b
gnu: r-seqminer: Update to 6.1.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
a02340058c
gnu: r-biocparallel: Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
1d56c79f86
gnu: r-genomicranges: Update to 1.32.6.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus
688cb08527
gnu: r-limma: Update to 3.36.3.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
2018-09-05 20:03:03 +02:00
Ricardo Wurmus
33a103a543
gnu: r-variantannotation: Update to 1.26.1.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
2018-09-05 20:03:03 +02:00
Ricardo Wurmus
1adf4596a6
gnu: r-edger: Update to 3.22.3.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
2018-09-05 20:03:03 +02:00
Ricardo Wurmus
5728d9c6c0
gnu: r-iranges: Update to 2.14.11.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
2018-09-05 20:03:03 +02:00
Ricardo Wurmus
3c04375614
gnu: r-biocviews: Update to 1.48.3.
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* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
2018-09-05 20:03:03 +02:00
Ricardo Wurmus
ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2.
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* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
2018-09-05 20:03:03 +02:00
Ricardo Wurmus
8afdeb8751
gnu: python-pybigwig: Update to 0.3.12.
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* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
2018-09-05 12:01:23 +02:00
Ricardo Wurmus
0d7974c376
gnu: libbigwig: Update to 0.4.2.
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* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
2018-09-05 12:01:23 +02:00
Efraim Flashner
647465ace9
gnu: jellyfish: Update to 2.2.10.
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* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
2018-09-03 08:32:33 +03:00
pimi
4f9355c360
gnu: Add gffcompare.
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gnu/packages/bioinformatics.scm (gffcompare): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2018-08-29 14:13:49 -04:00
Ricardo Wurmus
c7fe888b42
gnu: Add python-scanpy.
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* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
2018-08-29 17:06:13 +02:00
Ricardo Wurmus
079cdd9c15
gnu: Add find-circ.
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* gnu/packages/bioinformatics.scm (find-circ): New variable.
2018-08-24 11:20:19 +02:00
Ricardo Wurmus
689aacc12f
gnu: Add gffread.
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* gnu/packages/bioinformatics.scm (gffread): New variable.
2018-08-14 12:48:14 +02:00
Ricardo Wurmus
242519ce70
gnu: Add r-circus.
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* gnu/packages/bioinformatics.scm (r-circus): New variable.
2018-08-14 11:29:17 +02:00
Tobias Geerinckx-Rice
9aba9b1278
Migrate search.cpan.org home pages to metacpan.org.
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The venerable search.cpan.org has retired[0].
[0]: https://log.perl.org/2018/05/goodbye-search-dot-cpan-dot-org.html
* guix/import/cpan.scm (cpan-home): Generate metacpan.org home page URIs.
Update all previously generated ones in (gnu packages) to their
canonical new homes.
2018-08-11 17:22:31 +02:00
Ricardo Wurmus
78933bffb7
gnu: pigx-scrnaseq: Update to 0.0.7.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.7.
[inputs]: Add samtools.
2018-08-03 15:24:40 +02:00
Ben Woodcroft
3f8c82e6d3
gnu: taxtastic: Add missing propagated-inputs.
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* gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add
python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2,
python-dendropy.
2018-07-29 22:53:10 +10:00
Ben Woodcroft
9e0c135c39
gnu: python-dendropy: Update to 4.4.0.
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* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy):
Update to 4.4.0.
[source]: Use GitHub URI. Remove patch.
[properties]: Remove field.
(python2-dendropy)[arguments]: Run tests with setup.py.
[native-inputs]: Remove 'python2-nose.
* gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Delete it.
2018-07-29 22:53:10 +10:00
Ben Woodcroft
5d5a02dd4c
gnu: Add python-fastalite.
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* gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite):
New variables.
2018-07-29 21:58:00 +10:00
Ricardo Wurmus
26fd7b24ec
gnu: pigx-scrnaseq: Disable another expensive test.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc
test.
2018-07-27 15:44:23 +02:00
Ricardo Wurmus
ed2dfe3955
gnu: Add snakemake-4.
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* gnu/packages/python.scm (snakemake-4): New variable.
* gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq,
pigx-chipseq)[inputs]: Use it.
2018-07-27 15:30:38 +02:00
Gábor Boskovits
d60772dcdd
gnu: java-picard: Fix manifest.
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* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Adjust phase
'edit-classpath-in-manifest for the new manifest generation code.
2018-07-26 12:46:50 +02:00
Ricardo Wurmus
ffe8d21490
gnu: macs: Update to 2.1.1.20160309.
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* gnu/packages/bioinformatics.scm (macs): Update to 2.1.1.20160309.
2018-07-09 13:28:53 +02:00
Ricardo Wurmus
5149aeb7e6
gnu: pigx: Update to 0.0.3.
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* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.3.
2018-07-05 16:02:48 +02:00
Ricardo Wurmus
aec7d6be70
gnu: r-getopt: Move from bioinformatics to cran.
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* gnu/packages/bioinformatics.scm (r-getopt): Move from here...
* gnu/packages/cran.scm (r-getopt): ...to here.
2018-07-05 15:08:44 +02:00
Ricardo Wurmus
08d1a8b138
gnu: pigx-scrnaseq: Update to 0.0.6.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6.
[arguments]: Remove "wrap-executable" phase.
2018-07-05 00:52:31 +02:00
