89ee8a6edf
gnu: rsem: Update to 1.3.1.
...
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-20 17:55:26 +02:00
1dd153b3aa
gnu: Add python-hic2cool.
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* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
2018-09-14 09:15:49 +02:00
875d068176
Adjust all users of (gnu packages ldc) to use (gnu packages dlang).
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This is a followup to commit 98d6543f86
2018-09-10 15:44:32 -04:00
5bfa7510d1
gnu: Add python-pygenometracks.
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* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
2018-09-10 16:50:26 +02:00
1189c7f1b0
gnu: Add python-hicexplorer.
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* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
2018-09-10 16:50:26 +02:00
5bb9e0af8d
gnu: Add python-cooler.
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* gnu/packages/bioinformatics.scm (python-cooler): New variable.
2018-09-10 16:50:26 +02:00
80f4db91b1
gnu: Add python-pyfaidx.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
2018-09-10 16:50:26 +02:00
1f41f01c14
gnu: Add python-pypairix.
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* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
2018-09-10 16:50:26 +02:00
a9d496b353
gnu: Add python-intervaltree.
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* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
2018-09-10 16:50:26 +02:00
ab50580a9d
gnu: r-annotationhub: Update to 2.12.1.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
2018-09-09 22:26:02 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
689aacc12f
gnu: Add gffread.
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* gnu/packages/bioinformatics.scm (gffread): New variable.
2018-08-14 12:48:14 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
fab43c6b84
gnu: Add r-loomr.
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* gnu/packages/bioinformatics.scm (r-loomr): New variable.
2018-07-03 17:58:55 +02:00
13f5eb3494
gnu: pigx-bsseq: Update to 0.0.10.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.10.
[arguments]: Remove "wrap-executable" phase.
2018-07-03 17:33:51 +02:00
c7d5cd6ca5
gnu: pigx-rnaseq: Update to 0.0.4.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.4.
[arguments]: Remove "wrap-executable" phase.
2018-07-03 16:20:28 +02:00
29cbf8178f
gnu: pigx-chipseq: Update to 0.0.20.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
2018-07-03 16:20:28 +02:00
eeb8b0e631
gnu: Use more HTTPS.
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* gnu/packages/admin.scm (net-base, wakelan, pam-krb5)
[home-page]: Use HTTPS.
(dfc, libpcap, tcpdump, wpa-supplicant-minimal, libcap-ng, audit)
[source, home-page]: Likewise.
* gnu/packages/algebra.scm (eigen)[home-page]: Likewise.
(gp2c, pari-gp)[source, home-page]: Likewise.
* gnu/packages/animation.scm (etl, synfig, synfigstudio, papagayo)
[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (tadbit)[home-page]: Likewise.
2018-06-22 22:00:24 +02:00
c57e50b2b9
gnu: pigx-chipseq: Update to 0.0.17.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.17.
[arguments]: Remove "wrap-executable" phase.
2018-06-22 11:40:27 +02:00
6fe419743d
Do not record store file name in bioinformatics.scm.
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* gnu/packages/bioinformatics.scm (dropseq-tools): Replace full store
file name with ellipses.
2018-06-22 10:23:31 +02:00
1f73fd017c
gnu: r-complexheatmap: Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.1.
2018-06-21 10:31:22 +02:00
a1c7016498
gnu: r-delayedarray: Update to 0.6.1.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.1.
2018-06-21 10:31:22 +02:00
eafd35bad5
gnu: r-optparse: Update to 1.6.0.
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* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.0.
2018-06-21 10:31:22 +02:00
1e2b2f41d7
gnu: r-biocviews: Update to 1.48.2.
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* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.2.
2018-06-21 10:31:22 +02:00
901bcb7815
gnu: pigx-chipseq: Update to 0.0.16.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
2018-06-16 12:11:09 +02:00
53131eab2d
gnu: Add minimap2.
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* gnu/packages/bioinformatics.scm (minimap2): New variable.
2018-06-14 13:51:15 +02:00
ce573b1128
gnu: pigx-bsseq: Update to 0.0.9.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
2018-06-14 12:56:49 +02:00
844cc1c8f3
gnu: pigx-scrnaseq: Update to 0.0.5.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5.
[inputs]: Add python-magic.
2018-06-13 22:30:55 +02:00
13b8dcf589
gnu: r-seurat: Update to 2.3.2.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2.
[propagated-inputs]: Add r-hdf5r.
2018-06-13 15:14:37 +02:00
5b2a339e19
gnu: r-s4vectors: Update to 0.18.3.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
2018-06-13 15:14:37 +02:00
5b730eba3e
gnu: r-biocviews: Update to 1.48.1.
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* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
2018-06-13 15:14:37 +02:00
cbc1c27b67
gnu: rcas-web: Update to 0.0.5.
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* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
2018-06-08 17:39:24 +02:00
bcc2e0ed2e
gnu: r-rcas: Update to 1.6.0.
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* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
2018-06-07 22:51:00 +02:00
6d095c4cab
gnu: star: Update to 2.6.0c.
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* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
2018-06-07 11:09:54 +02:00
ca8de35e90
Merge branch 'master' into core-updates
2018-06-05 23:44:11 +02:00
909301591d
gnu: Add sjcount.
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* gnu/packages/bioinformatics.scm (sjcount): New variable.
2018-06-05 15:42:44 +02:00
e53152c72d
gnu: dropseq-tools: Remove failing phase.
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* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
2018-06-05 13:12:13 +02:00
9cc66d75a2
gnu: pigx-scrnaseq: Use only one variant of Picard.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
2018-06-05 11:26:34 +02:00
1f94ba9408
gnu: java-picard: Delete failing build phase.
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* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
2018-06-05 11:26:08 +02:00
a993ad833e
gnu: java-picard-1.113: Delete failing build phase.
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* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
2018-06-05 11:15:21 +02:00
e847f402c1
gnu: java-picard-2.10.3: Delete failing build phase.
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* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
2018-06-05 11:14:38 +02:00
d7e6fb6d7e
Merge branch 'master' into core-updates
2018-06-05 11:09:39 +02:00
71c495c941
gnu: r-rtracklayer: Update to 1.40.3.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
2018-06-05 10:40:42 +02:00
d19e0690b9
gnu: r-methylkit: Update to 1.6.1.
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* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
2018-06-05 10:40:42 +02:00
0da6afa286
gnu: r-bamsignals: Update to 1.12.1.
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* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
2018-06-05 10:40:42 +02:00
e0f8970357
Merge branch 'master' into core-updates
2018-06-02 13:44:43 +02:00
92963798a6
gnu: r-scater: Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0.
[propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove
r-matrixstats and r-biomart.
2018-06-02 13:42:05 +02:00
d7e3299987
gnu: r-scran: Update to 1.8.2.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
2018-06-02 13:39:13 +02:00
8ec56b2956
gnu: r-delayedmatrixstats: Update to 1.2.0.
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* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
2018-06-02 13:39:12 +02:00
d99e0938fa
gnu: r-singlecellexperiment: Update to 1.2.0.
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* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
2018-06-02 13:39:12 +02:00
fd613234b7
gnu: r-beachmat: Update to 1.2.1.
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* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
2018-06-02 13:39:12 +02:00
e9c417361e
gnu: r-rhdf5lib: Update to 1.2.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
2018-06-02 13:39:12 +02:00
0840352835
gnu: r-hdf5array: Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
2018-06-02 13:39:12 +02:00
Ricardo Wurmus