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1525 commits

Author SHA1 Message Date
Ricardo Wurmus
079cdd9c15
gnu: Add find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): New variable.
 2018-08-24 11:20:19 +02:00
Ricardo Wurmus
689aacc12f
gnu: Add gffread. 
* gnu/packages/bioinformatics.scm (gffread): New variable.
 2018-08-14 12:48:14 +02:00
Ricardo Wurmus
242519ce70
gnu: Add r-circus. 
* 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. 
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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6.
[arguments]: Remove "wrap-executable" phase.
 2018-07-05 00:52:31 +02:00
Ricardo Wurmus
fab43c6b84
gnu: Add r-loomr. 
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
 2018-07-03 17:58:55 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Tobias Geerinckx-Rice
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
Ricardo Wurmus
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
Ludovic Courtès
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
53131eab2d
gnu: Add minimap2. 
* gnu/packages/bioinformatics.scm (minimap2): New variable.
 2018-06-14 13:51:15 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
13b8dcf589
gnu: r-seurat: Update to 2.3.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2.
[propagated-inputs]: Add r-hdf5r.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus
5b2a339e19
gnu: r-s4vectors: Update to 0.18.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus
5b730eba3e
gnu: r-biocviews: Update to 1.48.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus
cbc1c27b67
gnu: rcas-web: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
 2018-06-08 17:39:24 +02:00
Ricardo Wurmus
bcc2e0ed2e
gnu: r-rcas: Update to 1.6.0. 
* 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
Ricardo Wurmus
6d095c4cab
gnu: star: Update to 2.6.0c. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus
ca8de35e90
Merge branch 'master' into core-updates 2018-06-05 23:44:11 +02:00
Ricardo Wurmus
909301591d
gnu: Add sjcount. 
* gnu/packages/bioinformatics.scm (sjcount): New variable.
 2018-06-05 15:42:44 +02:00
Ricardo Wurmus
e53152c72d
gnu: dropseq-tools: Remove failing phase. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 13:12:13 +02:00
Ricardo Wurmus
9cc66d75a2
gnu: pigx-scrnaseq: Use only one variant of Picard. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
 2018-06-05 11:26:34 +02:00
Ricardo Wurmus
1f94ba9408
gnu: java-picard: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 11:26:08 +02:00
Ricardo Wurmus
a993ad833e
gnu: java-picard-1.113: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
 2018-06-05 11:15:21 +02:00
Ricardo Wurmus
e847f402c1
gnu: java-picard-2.10.3: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
 2018-06-05 11:14:38 +02:00
Ricardo Wurmus
d7e6fb6d7e
Merge branch 'master' into core-updates 2018-06-05 11:09:39 +02:00
Ricardo Wurmus
71c495c941
gnu: r-rtracklayer: Update to 1.40.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus
d19e0690b9
gnu: r-methylkit: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus
0da6afa286
gnu: r-bamsignals: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus
e0f8970357
Merge branch 'master' into core-updates 2018-06-02 13:44:43 +02:00
Ricardo Wurmus
92963798a6
gnu: r-scater: Update to 1.8.0. 
* 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
Ricardo Wurmus
d7e3299987
gnu: r-scran: Update to 1.8.2. 
* 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
Ricardo Wurmus
8ec56b2956
gnu: r-delayedmatrixstats: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
d99e0938fa
gnu: r-singlecellexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
fd613234b7
gnu: r-beachmat: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
0840352835
gnu: r-hdf5array: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
5cd725d002
gnu: r-qvalue: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
c6c619c179
gnu: r-hitc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
4dedecbe70
gnu: r-fithic: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
8db6256f4b
gnu: r-sushi: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
2d3c172b72
gnu: r-gwascat: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
fecbbac286
gnu: r-gviz: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
6929b97583
gnu: r-gqtlstats: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
45c29a6e5c
gnu: r-ldblock: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
9b0b108ed9
gnu: r-erma: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
d26f95d079
gnu: r-snpstats: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
dcd1f0236c
gnu: r-gqtlbase: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus
e214a6e6ff
gnu: r-ggbio: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
34cc18d4de
gnu: r-biovizbase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
94ae875c0a
gnu: r-organismdbi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
bbcd19fb4d
gnu: r-ensembldb: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1.
[propagated-inputs]: Remove r-annotationhub.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
19adb89854
gnu: r-dirichletmultinomial: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
d3fb2ad834
gnu: r-complexheatmap: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
d1463f1b0c
gnu: r-genomicfiles: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
1ba126e0e4
gnu: r-gage: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
419e438d52
gnu: r-keggrest: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
15cc1a6867
gnu: r-fastseg: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
646439c7e3
gnu: r-annotationhub: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
420415b057
gnu: r-interactivedisplaybase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
a67dd4c5e9
gnu: r-edaseq: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
749b712677
gnu: r-deseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
0ebd7a4c9f
gnu: r-aroma-light: Update to 3.10.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus
bdc8b40af2
gnu: r-msnid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
250d78eac9
gnu: r-msnbase: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
0f773b90db
gnu: r-pcamethods: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
7bd2582971
gnu: r-mzid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
af8710624d
gnu: r-vsn: Update to 3.48.1. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
5837f1835b
gnu: r-affy: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
82589f7430
gnu: r-affyio: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
39cc491790
gnu: r-mzr: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
a02b82088f
gnu: r-protgenerics: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
9547dd8613
gnu: r-sva: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
19ad568e79
gnu: r-methylkit: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
aae4f716da
gnu: r-copywriter: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
8f94487da7
gnu: r-chipseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
62509bbc81
gnu: r-annotationfilter: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
d73c5728f3
gnu: r-rhdf5: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
c76e8baf9e
gnu: r-tximport: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus
b6c2c8f781
gnu: r-mutationalpatterns: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
72f11ff9c5
gnu: r-bamsignals: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
1a08bb8a17
gnu: r-rhtslib: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
2c480bb012
gnu: r-zlibbioc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
7e6537e257
gnu: r-motifrg: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
8217c2d0bc
gnu: r-seqlogo: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
17d35de73f
gnu: r-genomation: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
5229cedf57
gnu: r-seqpattern: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
25d1df5764
gnu: r-impute: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
89ef133ebd
gnu: r-bsgenome: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
f2eb2e453e
gnu: r-topgo: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
2f66fecd89
gnu: r-graph: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
b4ad4ec6b4
gnu: r-genomicfeatures: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
a30df29768
gnu: r-rtracklayer: Update to 1.40.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
90102bd06b
gnu: r-genomicalignments: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus
9bf4110ea1
gnu: r-summarizedexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
82f593f378
gnu: r-delayedarray: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
d2367a89dd
gnu: r-rsamtools: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
942655add1
gnu: r-biostrings: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
e6eac58d4c
gnu: r-biocparallel: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
1763cba80e
gnu: r-biomart: Update to 2.36.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
77f66feee7
gnu: r-annotationdbi: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
6fd71f1b6a
gnu: r-biobase: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
e51afc63b7
gnu: r-genomicranges: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
c2401d06c5
gnu: r-xvector: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
0a465e5694
gnu: r-limma: Update to 3.36.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
d358a5a0c1
gnu: r-variantannotation: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
4639025284
gnu: r-edger: Update to 3.22.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
953c8b18f8
gnu: r-genomeinfodb: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
8b44c28f5d
gnu: r-iranges: Update to 2.14.10. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
33cd15fa84
gnu: r-s4vectors: Update to 0.18.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus
607acf3194
gnu: r-dnacopy: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
3679a2fec4
gnu: r-bioccheck: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
dc6c168ac1
gnu: r-biocstyle: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
e5f52b692a
gnu: r-biocviews: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
97af51ef40
gnu: r-biocinstaller: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
e5907a44e1
gnu: r-biocgenerics: Update to 0.26.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
9370b8ee9f
gnu: r-grohmm: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
712fe39680
gnu: r-systempiper: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
eabe78faca
gnu: r-shortread: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
9da8e275ca
gnu: r-gostats: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
d8410d6610
gnu: r-category: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
f1094f50a7
gnu: r-gseabase: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
9177ac2295
gnu: r-rbgl: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
5516db9e70
gnu: r-annotationforge: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
16da69b5e6
gnu: r-dexseq: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
51c1f96ebc
gnu: r-deseq2: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus
41657b15f4
gnu: r-genefilter: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus
4d70c8c486
gnu: r-geneplotter: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus
14e9235f0c
gnu: r-copynumber: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus
02be818044
gnu: r-annotate: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus
59f87b44da
Merge branch 'master' into core-updates 2018-05-31 13:23:49 +02:00
Ricardo Wurmus
ce8b9e3b1c
gnu: r-seurat: Update to 2.3.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.1.
[propagated-inputs]: Remove r-gridextra; add r-reticulate.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus
3ca317359c
gnu: r-vegan: Update to 2.5-2. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-2.
 2018-05-31 13:21:31 +02:00
Mark H Weaver
1640f16e78
Merge branch 'master' into core-updates 2018-05-27 01:26:09 -04:00
Ricardo Wurmus
a1b802454a
gnu: Add fastp. 
* gnu/packages/bioinformatics.scm (fastp): New variable.
 2018-05-24 17:49:32 +02:00
Mark H Weaver
9d10a63402
Merge branch 'master' into core-updates 2018-05-24 02:34:08 -04:00
Ricardo Wurmus
a4ab65ee79
gnu: pigx-scrnaseq: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.4.
 2018-05-23 15:27:32 +02:00
Ricardo Wurmus
0f5ad3a1bc
gnu: bismark: Patch bismark2report before installing. 
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Patch file before
installing it.
 2018-05-22 16:05:41 +02:00
Mark H Weaver
0661758e13
Merge branch 'master' into core-updates 2018-05-21 13:22:32 -04:00
Tobias Geerinckx-Rice
c61d822621
gnu: f-seq: Factorise ‘install’ phase. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Let-bind more.
 2018-05-19 05:30:11 +02:00
Tobias Geerinckx-Rice
4ca9581119
gnu: multiqc: Fix build. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Add a
‘relax-requirements’ phase to fix building with python-matplotlib@2.2.
 2018-05-17 23:08:30 +02:00
Mark H Weaver
539bf8f2c0
Merge branch 'master' into core-updates 2018-05-17 01:00:50 -04:00
Ben Woodcroft
2c5289b263
gnu: diamond: Update to 0.9.22. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.22.
 2018-05-12 11:01:21 +10:00
Ricardo Wurmus
126c9e3ff7
gnu: bismark: Update to 0.19.1. 
* gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1.
[source]: Fetch from git; remove non-free software in snippet.
[arguments]: Update install phase.
 2018-05-09 18:37:33 +02:00
Ricardo Wurmus
f895a7a4d4
gnu: trim-galore: Update to 0.4.5. 
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.4.5.
[source]: Fetch from git.
[arguments]: Remove custom unpack phase.
 2018-05-09 18:37:33 +02:00
Marius Bakke
12bd588346
Merge branch 'master' into core-updates 2018-05-06 15:56:24 +02:00
Tobias Geerinckx-Rice
a2cfe19041
gnu: Use HTTPS for www.boost.org. 
* gnu/packages/bioinformatics.scm (libgff)[license]: Use HTTPS.
* gnu/packages/boost.scm (boost-sync)[license]: Likewise.
(boost)[license]: Likewise.
[home-page]: Likewise, and use canonical ‘www’ subdomain.
 2018-05-01 06:51:15 +02:00
Mark H Weaver
3d5ad159b3
Merge branch 'master' into core-updates 2018-04-30 04:03:54 -04:00
Roel Janssen
dad9556c5d
gnu: roary: Update to 3.12.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0.
 2018-04-28 01:52:52 +02:00
Roel Janssen
d36d5229ed
gnu: star: Update to 2.6.0a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a.
 2018-04-28 01:24:10 +02:00
Roel Janssen
457fd268ff
gnu: multiqc: Update to 1.5. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5.
 2018-04-28 01:10:24 +02:00
Roel Janssen
4b93efec28
gnu: express: Link with shared protobuf library. 
* gnu/packages/bioinformatics.scm (express): Link with shared protobuf
  library.
 2018-04-28 01:07:15 +02:00
Roel Janssen
4ffa085875
gnu: bamtools: Update to 2.5.1. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1.
 2018-04-28 00:56:59 +02:00
Roel Janssen
d0c75e73d4
gnu: taxtastic: Update to 0.8.5. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5.
 2018-04-28 00:43:16 +02:00
Ben Woodcroft
53ec1b7e8b
gnu: vsearch: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0.
 2018-04-27 23:20:00 +10:00
Ben Woodcroft
171cf56c2f
gnu: diamond: Update to 0.9.21. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21.
 2018-04-27 23:20:00 +10:00
Roel Janssen
b43a9eb361
gnu: bedops: Update to 2.4.33. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33.
 2018-04-27 01:11:57 +02:00
Roel Janssen
c829c5ea85
gnu: samtools: Update to 1.8. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.8.
 2018-04-27 01:11:47 +02:00
Roel Janssen
cbd9f91c32
gnu: bcftools: Update to 1.8. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8.
* gnu/local.mk: Remove patch.
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
 2018-04-27 01:11:42 +02:00
Roel Janssen
8df0267ad4
gnu: htslib: Update to 1.8. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.8.
 2018-04-27 01:11:24 +02:00
Ricardo Wurmus
3d7f9cbe75
gnu: pigx-chipseq: Update to 0.0.15. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15.
 2018-04-22 23:00:51 +02:00
Ricardo Wurmus
c36ce47635
gnu: r-seurat: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.0.
[propagated-inputs]: Add r-cluster, r-dosnow, r-fitdistrplus, r-foreach,
r-lmtest, r-png, and r-rann.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
aeca5f0c5b
gnu: r-scran: Update to 1.6.9. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
80323c3c13
gnu: r-hitc: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
b6d7deca55
gnu: r-ldblock: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
fb1dcfac46
gnu: r-erma: Update to 0.10.1. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
8defca1d94
gnu: r-gprofiler: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
fc6d3e2606
gnu: r-ggbio: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
0bd5c7b859
gnu: r-genomicalignments: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
4207770218
gnu: r-dexseq: Update to 1.24.4. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus
3db5d04ccc
gnu: r-vegan: Update to 2.5-1. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
 2018-04-21 23:07:52 +02:00
Mark H Weaver
f89aa1521a
Merge branch 'master' into core-updates 2018-04-10 00:42:22 -04:00
Ricardo Wurmus
482959ffa4
gnu: sambamba: Update to 0.6.7-10-g223fa20. 
* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
 2018-04-06 17:12:15 +02:00
Ricardo Wurmus
262ee8eae2
gnu: htslib-for-sambamba: Fix build. 
* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
 2018-04-06 17:12:07 +02:00
Roel Janssen
fdc306879b
gnu: Add delly. 
* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-03-30 10:48:01 -04:00
Ben Woodcroft
f38ac742e6
gnu: mash: Update to 2.0. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft
c7a8aa131d
gnu: mafft: Update to 7.394. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft
9a40b8d9b2
gnu: diamond: Update to 0.9.19. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
 2018-03-30 12:18:35 +10:00
Marius Bakke
5576cfabf3
Merge branch 'master' into core-updates 2018-03-29 17:34:41 +02:00
Roel Janssen
e086d2f68b
gnu: r-mutationalpatterns: Update to 1.4.3. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
  [propagated-inputs]: Remove r-gridextra.
 2018-03-29 15:50:44 +02:00
Roel Janssen
53e42694e5
gnu: kaiju: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
  [inputs]: Add zlib.
 2018-03-29 15:40:52 +02:00
Mark H Weaver
e3cfef22c4
gnu: Use invoke and return #t from all builders. 
* gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm,
gnu/packages/avr.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm,
gnu/packages/certs.scm, gnu/packages/check.scm, gnu/packages/code.scm,
gnu/packages/commencement.scm, gnu/packages/dictionaries.scm,
gnu/packages/docbook.scm, gnu/packages/emacs.scm, gnu/packages/embedded.scm,
gnu/packages/fonts.scm, gnu/packages/games.scm, gnu/packages/gnome.scm,
gnu/packages/gnu-doc.scm, gnu/packages/guile.scm, gnu/packages/hurd.scm,
gnu/packages/javascript.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/mate.scm,
gnu/packages/pkg-config.scm, gnu/packages/qt.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/statistics.scm,
gnu/packages/syncthing.scm, gnu/packages/tex.scm, gnu/packages/web.scm,
gnu/packages/wine.scm, gnu/packages/xfce.scm: In the builders of packages
using 'trivial-build-system', use invoke where appropriate, raise exceptions
on errors, and otherwise return #t.
 2018-03-27 21:35:41 -04:00