0971f8bd88
gnu: Remove r-biocinstaller.
...
It requires R < 3.6 and is no longer supported.
* gnu/packages/bioinformatics.scm (r-biocinstaller): Define as
deprecated in favour of r-biocmanager.
2019-07-08 16:13:11 +02:00
1042e3481d
gnu: r-xbioc: Update to 0.1.16-1.6ff0670.
...
This is needed to deprecate r-biocinstaller, which is no longer
distributed.
* gnu/packages/bioinformatics.scm (r-xbioc): Update to 0.1.16-1.6ff0670.
[propagated-inputs]: Replace deprecated r-biocinstaller with
r-biocmanager.
2019-07-08 16:11:55 +02:00
b35af24938
gnu: nanopolish: Update to 0.11.1-1.6331dc4.
...
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
2019-07-05 15:10:38 +02:00
c7b1d06024
gnu: pigx-rnaseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
2019-07-04 12:42:38 +02:00
5b86bcfa68
gnu: r-phangorn: Update to 2.5.5.
...
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
2019-06-29 01:34:43 +02:00
7f17e60ab7
gnu: r-tximport: Update to 1.12.3.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
2019-06-29 01:34:43 +02:00
dafd290d21
gnu: r-genomicfeatures: Update to 1.36.3.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
2019-06-29 01:34:43 +02:00
c40bba2b36
gnu: r-genomicalignments: Update to 1.20.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
2019-06-29 01:34:43 +02:00
888085c36c
gnu: r-biomart: Update to 2.40.1.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
2019-06-29 01:34:43 +02:00
f0c244229a
gnu: r-edger: Update to 3.26.5.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
2019-06-29 01:34:43 +02:00
0253b5d881
gnu: r-systempiper: Update to 1.18.2.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
2019-06-29 01:34:42 +02:00
bae0f8af21
gnu: pigx-scrnaseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
2019-06-27 23:23:29 +02:00
b556abe416
gnu: khmer: Update to 3.0.0a3.
...
* gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3.
[source]: Remove patch; remove seqan in snippet.
[inputs]: Add seqan-1.
* gnu/packages/patches/khmer-use-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2019-06-21 11:41:54 +02:00
28618b05f0
gnu: pigx-rnaseq: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7.
[inputs]: Add coreutils and sed.
2019-06-20 22:29:43 +02:00
30adfd3600
gnu: ngs-sdk: Update to 2.9.6.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
2019-06-20 14:33:57 +02:00
20874b7044
gnu: sra-tools: Update to 2.9.6.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
2019-06-20 14:33:57 +02:00
7cb44fb571
gnu: ncbi-vdb: Update to 2.9.6.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6.
[arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
2019-06-20 14:33:57 +02:00
a6f2ced34b
gnu: Add tbsp.
...
* gnu/packages/bioinformatics.scm (tbsp): New variable.
2019-06-17 20:22:38 +02:00
42df44f645
gnu: r-seurat: Update to 3.0.2.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
2019-06-17 04:55:03 +02:00
6dc3c58728
gnu: r-tximport: Update to 1.12.1.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
2019-06-17 04:54:56 +02:00
7bbd06ed59
gnu: r-systempiper: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1.
2019-06-17 04:54:51 +02:00
bc70516bba
gnu: Remove r-loomr.
...
The loomR package is actually non-free software according to its author. See
https://github.com/mojaveazure/loomR/pull/24 .
* gnu/packages/bioinformatics.scm (r-loomr): Remove variable.
2019-06-14 17:32:04 +02:00
6054c823ae
gnu: pigx-rnaseq: Update to 0.0.6.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.6.
[inputs]: Remove bedtools.
2019-06-12 13:12:00 +02:00
944cb87a33
gnu: Add r-psiplot.
...
* gnu/packages/bioinformatics.scm (r-psiplot): New variable.
2019-06-11 13:39:50 +02:00
823e23fffe
gnu: r-msnbase: Update to 2.10.1.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.1.
2019-06-09 15:19:58 +02:00
85e067161a
gnu: r-iranges: Update to 2.18.1.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.1.
2019-06-09 15:19:58 +02:00
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
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
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
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
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
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
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
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
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
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
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
bf70490223
gnu: umi-tools: Fix typo "containing".
...
* gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
2019-05-22 18:09:35 -07:00
df5fb3ca28
gnu: r-gage: Fix typo "functions".
...
* gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
2019-05-22 18:09:32 -07:00
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
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
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
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
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
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
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
44323e63a3
gnu: Add ataqv.
...
* gnu/packages/bioinformatics.scm (ataqv): New variable.
2019-05-14 16:15:19 +02:00
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
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
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
Tobias Geerinckx-Rice