07bd90ce90
gnu: r-msnbase: Update to 2.6.3.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
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.
...
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
2018-08-29 17:06:13 +02:00
079cdd9c15
gnu: Add find-circ.
...
* gnu/packages/bioinformatics.scm (find-circ): New variable.
2018-08-24 11:20:19 +02:00
689aacc12f
gnu: Add gffread.
...
* gnu/packages/bioinformatics.scm (gffread): New variable.
2018-08-14 12:48:14 +02:00
242519ce70
gnu: Add r-circus.
...
* 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.
...
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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc
test.
2018-07-27 15:44:23 +02:00
ed2dfe3955
gnu: Add snakemake-4.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
2018-07-03 16:20:28 +02:00
eeb8b0e631
gnu: Use more HTTPS.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
2018-06-16 12:11:09 +02:00
53131eab2d
gnu: Add minimap2.
...
* gnu/packages/bioinformatics.scm (minimap2): New variable.
2018-06-14 13:51:15 +02:00
ce573b1128
gnu: pigx-bsseq: Update to 0.0.9.
...
* 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.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5.
[inputs]: Add python-magic.
2018-06-13 22:30:55 +02:00
Ricardo Wurmus