Ricardo Wurmus
|
f53b4a6b77
|
gnu: r-biocviews: Update to 1.52.2.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.2.
[propagated-inputs]: Add r-biocmanager.
|
2019-06-01 23:04:26 +02:00 |
|
Ricardo Wurmus
|
add5ecfd68
|
gnu: r-biocviews: Update to 1.52.1.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.1.
|
2019-05-30 13:41:10 +02:00 |
|
Ricardo Wurmus
|
d37ba98409
|
gnu: r-scran: Update to 1.12.1.
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.1.
|
2019-05-29 00:02:42 +02:00 |
|
Ricardo Wurmus
|
55cd48508e
|
gnu: r-scater: Update to 1.12.2.
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.2.
|
2019-05-29 00:02:37 +02:00 |
|
Ricardo Wurmus
|
102cf9a1ca
|
gnu: r-sva: Update to 3.32.1.
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.1.
|
2019-05-29 00:02:31 +02:00 |
|
Ricardo Wurmus
|
24f46e6e9e
|
gnu: r-genomicfeatures: Update to 1.36.1.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.1.
|
2019-05-29 00:02:25 +02:00 |
|
Ricardo Wurmus
|
4eea449aaa
|
gnu: r-edger: Update to 3.26.4.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.4.
|
2019-05-29 00:02:17 +02:00 |
|
Ricardo Wurmus
|
4929a30f69
|
gnu: r-variantannotation: Update to 1.30.1.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
|
2019-05-29 00:02:10 +02:00 |
|
Ricardo Wurmus
|
164cb4da63
|
gnu: pigx-chipseq: Update to 0.0.41.
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.41.
|
2019-05-26 10:56:52 +02:00 |
|
Marius Bakke
|
9d0c291e3e
|
gnu: Move Sphinx and friends to (gnu packages sphinx).
* gnu/packages/python-xyz.scm (python-sphinxcontrib-websupport,
python2-sphinxcontrib-websupport, python-sphinx, python2-sphinx,
python-sphinx-gallery, python2-sphinx-gallery, python-sphinx-rtd-theme,
python2-sphinx-rtd-theme, python-guzzle-sphinx-theme,
python2-guzzle-sphinx-theme, python-sphinxcontrib-newsfeed,
python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput,
python-sphinx-repoze-interface, python2-sphinx-repoze-interface,
python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme,
python-sphinx-alabaster-theme, python2-sphinx-alabaster-theme,
python-sphinx-me, python-sphinxcontrib-svg2pdfconverter): Move to ...
(gnu):
* gnu/packages/sphinx.scm: ... here. New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
* gnu/packages/admin.scm, gnu/packages/bioinformatics.scm,
gnu/packages/calendar.scm, gnu/packages/cluster.scm,
gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/disk.scm,
gnu/packages/django.scm, gnu/packages/elf.scm, gnu/packages/emacs-xyz.scm,
gnu/packages/emulators.scm, gnu/packages/finance.scm, gnu/packages/image.scm,
gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm,
gnu/packages/openstack.scm, gnu/packages/pdf.scm, gnu/packages/python-web.scm,
gnu/packages/search.scm, gnu/packages/statistics.scm,
gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm,
gnu/packages/tls.scm, gnu/packages/web.scm: Adjust module imports.
|
2019-05-24 21:54:31 +02:00 |
|
Ricardo Wurmus
|
a9150d4c23
|
gnu: salmon: Update to 0.13.1.
* gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1.
[arguments]: Adjust "do-not-look-for-boost" build phase; adjust
"prepare-rapmap" phase; adjust "use-system-libraries" phase.
[inputs]: Remove bwa, jellyfish, spdlog-for-salmon.
[native-inputs]: Add pkg-config.
(spdlog-for-salmon, bwa-for-salmon): Remove variables.
|
2019-05-23 16:32:21 +02:00 |
|
Vagrant Cascadian
|
bf70490223
|
gnu: umi-tools: Fix typo "containing".
* gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
|
2019-05-22 18:09:35 -07:00 |
|
Vagrant Cascadian
|
df5fb3ca28
|
gnu: r-gage: Fix typo "functions".
* gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
|
2019-05-22 18:09:32 -07:00 |
|
Ricardo Wurmus
|
a8a465e816
|
gnu: r-limma: Update to 3.40.2.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.2.
|
2019-05-20 15:06:07 +02:00 |
|
Ricardo Wurmus
|
9c714b9ba9
|
gnu: r-edger: Update to 3.26.3.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.3.
|
2019-05-20 15:06:01 +02:00 |
|
Ricardo Wurmus
|
7a94438130
|
gnu: r-scater: Update to 1.12.1.
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.1.
|
2019-05-20 12:00:38 +02:00 |
|
Ricardo Wurmus
|
461fb28ac5
|
gnu: r-seurat: Update to 3.0.1.
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.1.
|
2019-05-20 12:00:37 +02:00 |
|
Ricardo Wurmus
|
d94c698a13
|
gnu: r-maldiquant: Update to 1.19.3.
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.3.
|
2019-05-20 12:00:37 +02:00 |
|
Ricardo Wurmus
|
7c97f45700
|
gnu: r-edger: Update to 3.26.1.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.1.
|
2019-05-20 12:00:37 +02:00 |
|
Ricardo Wurmus
|
a4ff3255d4
|
gnu: star: Update to 2.7.1a.
* gnu/packages/bioinformatics.scm (star): Update to 2.7.1a.
|
2019-05-16 13:45:23 +02:00 |
|
Ricardo Wurmus
|
44323e63a3
|
gnu: Add ataqv.
* gnu/packages/bioinformatics.scm (ataqv): New variable.
|
2019-05-14 16:15:19 +02:00 |
|
Ricardo Wurmus
|
21ec924868
|
gnu: r-hdf5array: Update to 1.12.1.
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.1.
|
2019-05-11 12:05:35 +02:00 |
|
Ricardo Wurmus
|
3addf736d5
|
gnu: r-systempiper: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.0.
[propagated-inputs]: Replace r-batchjobs with r-batchtools; add r-yaml.
|
2019-05-06 00:14:44 +02:00 |
|
Ricardo Wurmus
|
9bcbca135b
|
gnu: r-rsamtools: Update to 2.0.0.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.0.0.
[propagated-inputs]: Add r-rhtslib.
|
2019-05-06 00:14:44 +02:00 |
|
Ricardo Wurmus
|
82d9340b0c
|
gnu: r-impute: Update to 1.58.0.
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.58.0.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
|
2019-05-06 00:14:44 +02:00 |
|
Ricardo Wurmus
|
2b4ac1d77e
|
gnu: r-rcas: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.0.
[propagated-inputs]: Add ghc-pandoc.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
8322c860f9
|
gnu: r-methylkit: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.10.0.
[propagated-inputs]: Add r-mgcv.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
b173dbe617
|
gnu: r-annotationhub: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.16.0.
[propagated-inputs]: Add r-biocfilecache, r-dplyr, and r-rappdirs.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
a8abc8dd3a
|
gnu: r-fastseg: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.30.0.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
e699e8e599
|
gnu: r-keggrest: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.24.0.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
c798455d87
|
gnu: r-gage: Update to 2.34.0.
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.34.0.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
d4ef1d59cc
|
gnu: r-genomicfiles: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.20.0.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
70a3e4499d
|
gnu: r-complexheatmap: Update to 2.0.0.
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.0.0.
[propagated-inputs]: Add r-clue and r-png.
|
2019-05-06 00:14:43 +02:00 |
|
Ricardo Wurmus
|
e2cb23404c
|
gnu: r-dirichletmultinomial: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.26.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
0af6efa3c5
|
gnu: r-ensembldb: Update to 2.8.0.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.8.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
96f98c5b72
|
gnu: r-organismdbi: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.26.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
a98c3b4ae4
|
gnu: r-biovizbase: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.32.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
d38fbacad1
|
gnu: r-ggbio: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.32.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
623be1a443
|
gnu: r-gqtlbase: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.16.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
ed7de45655
|
gnu: r-snpstats: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.34.0.
|
2019-05-06 00:14:42 +02:00 |
|
Ricardo Wurmus
|
3c5f5b4154
|
gnu: r-erma: Update to 1.0.0.
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.0.0.
|
2019-05-06 00:14:41 +02:00 |
|
Ricardo Wurmus
|
89ba9a7226
|
gnu: r-ldblock: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.0.
|
2019-05-06 00:14:41 +02:00 |
|
Ricardo Wurmus
|
a349d57a46
|
gnu: r-gqtlstats: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.16.0.
|
2019-05-06 00:14:41 +02:00 |
|
Ricardo Wurmus
|
105d9e2cb4
|
gnu: r-gviz: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.28.0.
|
2019-05-06 00:14:41 +02:00 |
|
Ricardo Wurmus
|
1b454f9f69
|
gnu: r-gwascat: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.16.0.
[propagated-inputs]: Remove r-annotationhub, r-ggbio, r-ggplot2, r-gqtlstats,
r-graph, r-gviz, r-snpstats, r-summarizedexperiment, and r-variantannotation.
|
2019-05-06 00:14:41 +02:00 |
|
Ricardo Wurmus
|
256609eb46
|
gnu: r-sushi: Update to 1.22.0.
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.22.0.
|
2019-05-06 00:14:41 +02:00 |
|
Ricardo Wurmus
|
7705165882
|
gnu: r-fithic: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.10.0.
|
2019-05-06 00:14:40 +02:00 |
|
Ricardo Wurmus
|
e998a26e1d
|
gnu: r-hitc: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.28.0.
|
2019-05-06 00:14:40 +02:00 |
|
Ricardo Wurmus
|
65925573be
|
gnu: r-hdf5array: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
|
2019-05-06 00:14:40 +02:00 |
|
Ricardo Wurmus
|
d5625b3a9e
|
gnu: r-rhdf5lib: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.6.0.
|
2019-05-06 00:14:40 +02:00 |
|