545730891e
gnu: r-gostats: Update to 2.52.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0.
2019-12-15 15:39:04 +01:00
f29c9f0d33
gnu: r-shortread: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0.
2019-12-15 15:39:04 +01:00
58fd68b299
gnu: r-systempiper: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.20.0.
2019-12-15 15:39:03 +01:00
f8f815667d
gnu: r-grohmm: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.20.0.
2019-12-15 15:39:03 +01:00
74d59b6748
gnu: r-biocviews: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.54.0.
2019-12-15 15:39:03 +01:00
ef96154433
gnu: r-biocstyle: Update to 2.14.2.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.2.
2019-12-15 15:39:03 +01:00
7758d5205c
gnu: r-bioccheck: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.22.0.
2019-12-15 15:39:03 +01:00
d37daf8929
gnu: r-s4vectors: Update to 0.24.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.1.
2019-12-15 15:39:03 +01:00
d2723484f6
gnu: r-iranges: Update to 2.20.1.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.1.
2019-12-15 15:39:03 +01:00
937f3a46eb
gnu: r-genomeinfodb: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.0.
2019-12-15 15:39:03 +01:00
da03fa3c90
gnu: r-edger: Update to 3.28.0.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.0.
2019-12-15 15:39:03 +01:00
8f5d2c3abc
gnu: r-variantannotation: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.32.0.
2019-12-15 15:39:03 +01:00
eea491e5c6
gnu: r-limma: Update to 3.42.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.0.
2019-12-15 15:39:03 +01:00
da6edb199d
gnu: r-xvector: Update to 0.26.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.26.0.
2019-12-15 15:39:02 +01:00
0202b13e8b
gnu: r-genomicranges: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.38.0.
2019-12-15 15:39:02 +01:00
8d1c3666d7
gnu: r-biobase: Update to 2.46.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.46.0.
2019-12-15 15:39:02 +01:00
de9ae3e7b1
gnu: r-annotationdbi: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.48.0.
2019-12-15 15:39:02 +01:00
68a9d9f26a
gnu: r-biomart: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.0.
[propagated-inputs]: Add r-biocfilecache, r-openssl, and r-rappdirs; remove
r-rcurl.
2019-12-15 15:39:02 +01:00
5854a4a265
gnu: r-biocparallel: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.0.
2019-12-15 15:39:02 +01:00
15cd3f6ef5
gnu: r-biostrings: Update to 2.54.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.54.0.
2019-12-15 15:39:02 +01:00
e1d681e2af
gnu: r-rsamtools: Update to 2.2.1.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.1.
2019-12-15 15:39:02 +01:00
4ada4fb745
gnu: r-delayedarray: Update to 0.12.0.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.0.
2019-12-15 15:39:02 +01:00
264db038c6
gnu: r-summarizedexperiment: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.0.
2019-12-15 15:39:02 +01:00
55e515d206
gnu: r-genomicalignments: Update to 1.22.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.22.1.
2019-12-15 15:39:01 +01:00
15187da9e7
gnu: r-rtracklayer: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.46.0.
2019-12-15 15:39:01 +01:00
9fec340391
gnu: r-genomicfeatures: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.0.
2019-12-15 15:39:01 +01:00
323f42b2ca
gnu: r-topgo: Update to 2.37.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.37.0.
2019-12-15 15:39:01 +01:00
e3a2b96c80
gnu: r-bsgenome: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.54.0.
2019-12-15 15:39:01 +01:00
bca1c45e4e
gnu: r-impute: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.60.0.
2019-12-15 15:39:01 +01:00
b590742362
gnu: r-seqpattern: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.18.0.
2019-12-15 15:39:01 +01:00
e06b34e8c6
gnu: r-genomation: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.18.0.
2019-12-15 15:39:01 +01:00
a9790190d1
gnu: r-seqlogo: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.52.0.
2019-12-15 15:39:01 +01:00
a5f9b30338
gnu: r-motifrg: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.30.0.
2019-12-15 15:39:01 +01:00
2f15045400
gnu: r-zlibbioc: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.32.0.
2019-12-15 15:39:01 +01:00
108c03a8eb
gnu: r-rhtslib: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.0.
[propagated-inputs]: Add curl.
2019-12-15 15:39:01 +01:00
7b6c008960
gnu: r-bamsignals: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.18.0.
2019-12-15 15:39:00 +01:00
f375d74072
gnu: r-rcas: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.12.0.
2019-12-15 15:39:00 +01:00
3964f2c24e
gnu: r-mutationalpatterns: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.12.0.
2019-12-15 15:39:00 +01:00
3a0229eba0
gnu: r-tximport: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.0.
2019-12-15 15:39:00 +01:00
126539d1ae
gnu: r-rhdf5: Update to 2.30.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.30.1.
2019-12-15 15:39:00 +01:00
4e5c217684
gnu: r-pcamethods: Update to 1.78.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.78.0.
2019-12-15 15:39:00 +01:00
589939937d
gnu: r-msnbase: Update to 2.12.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.12.0.
2019-12-15 15:39:00 +01:00
597aeb8a34
gnu: r-msnid: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.20.0.
2019-12-15 15:39:00 +01:00
3ccf1e3c20
gnu: r-aroma-light: Update to 3.16.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.16.0.
2019-12-15 15:39:00 +01:00
783bbe3ace
gnu: r-deseq: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.38.0.
2019-12-15 15:39:00 +01:00
0a6704e226
gnu: r-edaseq: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.20.0.
2019-12-15 15:38:59 +01:00
2beffcb558
gnu: r-interactivedisplaybase: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.24.0.
2019-12-15 15:38:59 +01:00
6339ea22f1
gnu: r-annotationhub: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.18.0.
[propagated-inputs]: Add r-biocversion.
2019-12-15 15:38:59 +01:00
c21bf901e2
gnu: r-fastseg: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.32.0.
2019-12-15 15:38:59 +01:00
fedba48bb5
gnu: r-keggrest: Update to 1.26.1.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.26.1.
2019-12-15 15:38:59 +01:00
b342b20a24
gnu: r-gage: Update to 2.36.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.36.0.
2019-12-15 15:38:59 +01:00
48c7ee93b7
gnu: r-genomicfiles: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.22.0.
2019-12-15 15:38:59 +01:00
dac706c322
gnu: r-complexheatmap: Update to 2.2.0.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.2.0.
2019-12-15 15:38:59 +01:00
2edb116c1c
gnu: r-dirichletmultinomial: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.28.0.
2019-12-15 15:38:59 +01:00
e107f3df54
gnu: r-ensembldb: Update to 2.10.2.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.10.2.
2019-12-15 15:38:59 +01:00
e89032667d
gnu: r-organismdbi: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.28.0.
2019-12-15 15:38:59 +01:00
866810e686
gnu: r-biovizbase: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.34.1.
2019-12-15 15:38:59 +01:00
81600df302
gnu: r-ggbio: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.34.0.
2019-12-15 15:38:58 +01:00
89a41696ab
gnu: r-gqtlbase: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.18.0.
2019-12-15 15:38:58 +01:00
67d4fd523d
gnu: r-erma: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.2.0.
2019-12-15 15:38:58 +01:00
14eb0978a8
gnu: r-snpstats: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.36.0.
2019-12-15 15:38:58 +01:00
6fff104191
gnu: r-ldblock: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.16.0.
[propagated-inputs]: Remove r-go-db and r-homo-sapiens.
2019-12-15 15:38:58 +01:00
cfa93a30b4
gnu: r-gqtlstats: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.18.0.
2019-12-15 15:38:58 +01:00
d57b6b4bae
gnu: r-gviz: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.0.
2019-12-15 15:38:58 +01:00
2e13f10e89
gnu: r-sushi: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.24.0.
2019-12-15 15:38:58 +01:00
28329991b0
gnu: r-gwascat: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.18.0.
2019-12-15 15:38:58 +01:00
0a16021241
gnu: r-hitc: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.30.0.
2019-12-15 15:38:58 +01:00
8db2915900
gnu: r-fithic: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.12.0.
2019-12-15 15:38:58 +01:00
7557bd0cce
gnu: r-hdf5array: Update to 1.14.1.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.1.
[propagated-inputs]: Add r-matrix.
2019-12-15 15:38:57 +01:00
1f5d262cfd
gnu: r-rhdf5lib: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.8.0.
[arguments]: Update patches.
2019-12-15 15:38:57 +01:00
8804e4b48e
gnu: r-beachmat: Update to 2.2.1.
...
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.2.1.
[propagated-inputs]: Add r-matrix.
2019-12-15 15:38:57 +01:00
376f2f35b6
gnu: r-singlecellexperiment: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.8.0.
2019-12-15 15:38:57 +01:00
bf23416fe1
gnu: r-scater: Update to 1.14.5.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.5.
[propagated-inputs]: Remove r-dplyr.
2019-12-15 15:38:57 +01:00
964634fa44
gnu: r-scran: Update to 1.14.5.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.5.
[propagated-inputs]: Remove r-dynamictreecut.
2019-12-15 15:38:57 +01:00
c81ccd3076
gnu: r-delayedmatrixstats: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.8.0.
2019-12-15 15:38:57 +01:00
758dfc61ee
gnu: r-mzid: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.24.0.
2019-12-15 15:38:57 +01:00
dc9d4832b9
gnu: r-vsn: Update to 3.54.0.
...
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.54.0.
2019-12-15 15:38:57 +01:00
af87ac3aa7
gnu: r-annotationfilter: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.10.0.
2019-12-15 15:38:57 +01:00
43058ca656
gnu: r-chipseq: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.36.0.
2019-12-15 15:38:57 +01:00
746e1f062e
gnu: r-copywriter: Update to 2.18.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.18.0.
2019-12-15 15:38:57 +01:00
32f6059635
gnu: r-affy: Update to 1.64.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.64.0.
2019-12-15 15:38:56 +01:00
51ca216bdf
gnu: r-affyio: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.56.0.
2019-12-15 15:38:56 +01:00
065c305ca5
gnu: r-methylkit: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.12.0.
2019-12-15 15:38:56 +01:00
2a6ce98b17
gnu: r-sva: Update to 3.34.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.34.0.
2019-12-15 15:38:56 +01:00
d12328f9fe
gnu: r-protgenerics: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.18.0.
2019-12-15 15:38:56 +01:00
3381dc4b5c
gnu: r-mzr: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.20.0.
2019-12-15 15:38:56 +01:00
5a4aab2193
gnu: Add r-qtl2.
...
* gnu/packages/bioinformatics.scm (r-qtl2): New variable.
2019-12-10 13:11:44 +02:00
88f06fd015
gnu: Really move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.
...
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
javascript module instead of lisp.
2019-12-05 16:23:06 +01:00
d9544d91a6
Revert "gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm."
...
This reverts commit ac1ee30f4f
2019-12-05 15:38:52 +01:00
ac1ee30f4f
gnu: Properly move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.
...
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
javascript module instead of lisp.
2019-12-05 13:48:47 +01:00
33b59c1a3e
Merge branch 'staging'
2019-12-04 20:12:41 +01:00
ec1224a73b
gnu: python-scipy: Move to (gnu packages python-science).
...
* gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from
here...
* gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here.
* gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm,
gnu/packages/statistics.scm: Adjust module imports.
2019-12-02 15:25:17 +01:00
076527c354
Revert "gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm."
...
This reverts commit abf43a67d5
2019-11-28 21:09:24 +01:00
abf43a67d5
gnu: Move lisp libraries to lisp-xyz, uglify-js to javascript and stumpwm to wm.
...
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
2019-11-28 19:36:12 +01:00
0897ad7fac
Merge branch 'master' into staging
2019-11-28 00:38:25 +01:00
3546771cc8
gnu: libdivsufsort: Move to datastructures.scm.
...
* gnu/packages/bioinformatics.scm (libdivsufsort): Move to ...
* gnu/packages/datastructures.scm: ... here.
2019-11-25 14:08:32 +02:00
8b1fd3cafd
gnu: bioperl-minimal: Don't use unstable tarball.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal)[source]: Download
using git-fetch.
2019-11-25 14:08:31 +02:00
b60d2bfff9
Merge branch 'master' into staging
2019-11-21 22:44:15 +01:00
c1637311b6
gnu: ngless: Update to 1.0.1.
...
* gnu/packages/bioinformatics.scm (ngless): Update to 1.0.1.
[arguments]: Add a 'create-Versions.hs' phase that patches the Makefile
and invokes 'make' to generate a required file.
[inputs]: Remove 'ghc-chart', 'ghc-chart-cairo', and
'ghc-conduit-combinators'; add 'ghc-diagrams-core', 'ghc-diagrams-lib',
'ghc-diagrams-svg', and 'ghc-tar-conduit'.
2019-11-20 20:48:54 -05:00
f056553c6b
Merge branch 'master' into staging
2019-11-15 20:11:35 +01:00
Ricardo Wurmus
Efraim Flashner
Pierre Neidhardt
Tobias Geerinckx-Rice
Marius Bakke
Timothy Sample