me/guix
Archived
1
0
Fork 0
Code Activity
62460 commits 1 branch 0 tags 410 MiB
Commit graph

2412 commits

Author SHA1 Message Date
Ricardo Wurmus
261d931406
gnu: r-bamsignals: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
8f08457f05
gnu: r-rhtslib: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
52ce0d299d
gnu: r-zlibbioc: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.34.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
239ca0f3bd
gnu: r-motifrg: Update to 1.31.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.31.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
40ba4e8466
gnu: r-seqlogo: Update to 1.54.3. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.54.3.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
837e7634d9
gnu: r-genomation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
2d537b5afc
gnu: r-seqpattern: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.20.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
e6df69a84d
gnu: r-impute: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.62.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
d9b23ec47c
gnu: r-bsgenome: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.56.0.
[propagated-inputs]: Add r-matrixstats.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
543fd63c2e
gnu: r-topgo: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.40.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
a285314e29
gnu: r-genomicfeatures: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
f85794edb8
gnu: r-rtracklayer: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.48.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
58613ca1e5
gnu: r-genomicalignments: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.24.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
87c98cf701
gnu: r-summarizedexperiment: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
46e103a1b5
gnu: r-delayedarray: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.0.
[propagated-inputs]: Remove r-biocparallel.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
1f9c87a442
gnu: r-rsamtools: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.4.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
d3491d4dad
gnu: r-biostrings: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm ( r-biostrings): Update to 2.56.0.
[propagated-inputs]: Add r-crayon.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
cb486f16da
gnu: r-biocparallel: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
e87e6cc89d
gnu: r-biomart: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
920224771f
gnu: r-annotationdbi: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
7d91e3bed4
gnu: r-biobase: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.48.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
087a97f8df
gnu: r-genomicranges: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
e0d40fa275
gnu: r-xvector: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
49c766d0bb
gnu: r-limma: Update to 3.44.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
cdd83b2e22
gnu: r-variantannotation: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
c14d59d9ad
gnu: r-edger: Update to 3.30.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
506735eea6
gnu: r-genomeinfodb: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
8a38b676da
gnu: r-iranges: Update to 2.22.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
f189f536be
gnu: r-s4vectors: Update to 0.26.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
1a9de6cfe8
gnu: r-bioccheck: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
9f416be83d
gnu: r-biocstyle: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
1ca88fb8e9
gnu: r-biocviews: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
5de96ae98b
gnu: r-grohmm: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
bb18d11d85
gnu: r-systempiper: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0.
[propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and
r-stringr; remove r-biocgenerics.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
681cca95b3
gnu: r-shortread: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
3d2899dab5
gnu: r-gostats: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
be414286bc
gnu: r-category: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
a8613ff861
gnu: r-gseabase: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
7d8b96e24b
gnu: r-rbgl: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
397568dbca
gnu: r-annotationforge: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
db5addba2c
gnu: r-dexseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
3d7de4ed82
gnu: r-deseq2: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1.
[propagated-inputs]: Remove r-hmisc.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
5fdea056c9
gnu: r-genefilter: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
a620d22ea8
gnu: r-gprofiler: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here...
* gnu/packages/cran.scm (r-gprofiler): ...to here.
 2020-06-13 01:19:38 +02:00
Marius Bakke
fa7bd13e5b
gnu: rcas-web: Use guile2.2 version of Guile-Redis. 
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change from GUILE-REDIS
to GUILE2.2-REDIS.  While at it, rename the GUILE input to "guile" instead
of "guile-next".
 2020-06-06 15:35:40 +02:00
Ricardo Wurmus
0266094531
gnu: python-pypairix: Update to 0.3.7 and build programs. 
* gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.7.
[source]: Fetch from github.
[arguments]: Add phases "build-programs" and "install-programs".
 2020-06-04 11:56:31 +02:00
Ricardo Wurmus
2f49007dd0
gnu: Add python-pairtools. 
* gnu/packages/bioinformatics.scm (python-pairtools): New variable.
 2020-06-03 15:01:19 +02:00
Ricardo Wurmus
6742a84c63
gnu: Remove bedtools-2.26. 
* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable.
 2020-06-03 14:07:58 +02:00
Ricardo Wurmus
08542026ea
gnu: python-pybedtools: Disable unreliable test. 
* gnu/packages/bioinformatics.scm (python-pybedtools)[arguments]: Disable
test_intron_exon_reads test; run tests verbosely.

test_intron_exon_reads
 2020-06-03 14:07:48 +02:00
Nicolas Goaziou
98d6edb621
gnu: blast+: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (blast+)[home-page]: Use HTTPS URI.
 2020-05-27 01:48:37 +02:00