bd978be3ae
gnu: r-annotationdbi: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1.
2020-07-02 12:45:53 +02:00
3d5334c390
gnu: blast+: Update to 2.10.1.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1.
2020-06-30 18:49:11 +02:00
5e5bcba295
gnu: r-qtl2: Update synopsis, description.
...
* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's
synopsis.
[description]: Same.
2020-06-28 10:18:47 +03:00
54bb476670
gnu: r-qtl2: Update to 0.22-8.
...
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8.
[source]: Download from cran.
2020-06-28 10:15:21 +03:00
fb4804d03d
gnu: r-scater: Update to 1.16.2.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2.
2020-06-28 05:46:19 +02:00
e66f81cf63
gnu: r-biocviews: Update to 1.56.1.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1.
2020-06-28 05:46:19 +02:00
fa7871af77
gnu: r-dexseq: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1.
2020-06-28 05:46:19 +02:00
de0f36f0aa
gnu: miniasm: Make sure all phases return #t.
...
* gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom
'install phase return #t.
2020-06-23 16:04:51 +03:00
896f18210b
gnu: miniasm: Don't use unstable tarball.
...
* gnu/packages/bioinformatics.scm (miniasm)[source]: Download using
git-fetch.
2020-06-23 16:04:04 +03:00
6e31d6f3c4
gnu: python-plotly: Update to 4.8.1.
...
But keep version 2.4.1 around for packages that still need it and for python2
support.
* gnu/packages/graph.scm (python-plotly): Update to 4.8.1.
[source]: Use git-fetch so that tests are also included.
[arguments]: Enable tests.
[home-page]: Follow redirect.
(python-plotly-2.4.1): New variable.
(python2-plotly): Inherit from python-plotly-2.4.1.
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on
python-plotly-2.4.1.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22 15:44:16 +02:00
20b545f768
gnu: python-pandas: Update to 1.0.5.
...
But also keep version 0.25.3 around for packages requiring an earlier
versions, as well as version 0.24.2 for a version with python2.
* gnu/packages/python-science.scm (python-pandas): Update to 1.0.5.
[arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not
delete tests that depend on "moto", they are skipped automatically.
[propagated-inputs]: Add python-jinja2.
[inputs]: Add xsel and xclip.
[native-inputs]: Add xorg-server-for-tests so we can test clipboard support.
(python-pandas-0.24): New variable.
(python2-pandas): Inherit from python-pandas-0.25.
* gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]:
Switch to python-pandas-0.25.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22 15:44:08 +02:00
3a79adab41
gnu: deeptools: Deprecate in favor of python-deeptools.
...
And make sure python-deeptools's tests are running.
* gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git.
[native-inputs]: Add python-mock and python-nose.
(deeptools): Mark as deprecated.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22 15:43:59 +02:00
ebcebc59ab
gnu: r-hdf5array: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1.
2020-06-22 12:15:49 +02:00
b07e53bb09
gnu: r-rhdf5: Update to 2.32.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.1.
2020-06-22 12:15:49 +02:00
f65d5e84de
gnu: r-biomart: Update to 2.44.1.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1.
2020-06-22 12:15:49 +02:00
55401384dc
gnu: r-genomeinfodb: Update to 1.24.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.2.
2020-06-22 12:15:49 +02:00
acba72b914
gnu: express: Update to 1.5.3.
...
* gnu/packages/bioinformatics.scm (express): Update to 1.5.3.
[source]: Fetch from Github.
[arguments]: Add phase "remove-update-check".
2020-06-22 09:07:51 +02:00
8b00728144
gnu: r-limma: Update to 3.44.3.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3.
2020-06-15 12:00:21 +02:00
9ae4bd0b77
gnu: r-mzr: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.22.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:20:02 +02:00
a3b55161c7
gnu: r-delayedmatrixstats: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:47 +02:00
47c7670c43
gnu: r-scran: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.16.0.
[propagated-inputs]: Add r-iranges.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:47 +02:00
7039b53945
gnu: r-scater: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.1.
[propagated-inputs]: Add r-rlang.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
9e7acf2f14
gnu: r-singlecellexperiment: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
16dd6bacaa
gnu: r-beachmat: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
87d5444d9f
gnu: r-rhdf5lib: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.0.
[source]: Update snippet.
[arguments]: Replace ZLIB variables in Makevars.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
cf907680e8
gnu: r-hdf5array: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0.
2020-06-13 01:19:46 +02:00
46f188d1df
gnu: r-hitc: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0.
2020-06-13 01:19:46 +02:00
6be25cc2db
gnu: r-fithic: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.14.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
a811751f49
gnu: r-sushi: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0.
2020-06-13 01:19:46 +02:00
ddef43a29d
gnu: r-gwascat: Update to 2.20.1.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.20.1.
[propagated-inputs]: Remove r-homo-sapiens; add r-ggplot2.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
522da60b29
gnu: r-gviz: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.32.0.
[propagated-inputs]: Add r-ensembldb.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
a97897bc3d
gnu: r-gqtlstats: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.20.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
6caad43c18
gnu: r-ldblock: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.18.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
87772ab4dd
gnu: r-erma: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.4.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
aab0e28fc1
gnu: r-snpstats: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
2020-06-13 01:19:45 +02:00
42d8cd9f97
gnu: r-gqtlbase: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
7038aeb210
gnu: r-ggbio: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.36.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
07518c3a34
gnu: r-biovizbase: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0.
2020-06-13 01:19:45 +02:00
7c26687871
gnu: r-organismdbi: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0.
2020-06-13 01:19:45 +02:00
39da6fbc40
gnu: r-ensembldb: Update to 2.12.1.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.12.1.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
7a9e7e4844
gnu: r-dirichletmultinomial: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.30.0.
2020-06-13 01:19:45 +02:00
ca5c92c0c7
gnu: r-complexheatmap: Update to 2.4.2.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.2.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
8323ff3376
gnu: r-genomicfiles: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.24.0.
2020-06-13 01:19:45 +02:00
817e4c8b68
gnu: r-gage: Update to 2.37.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.37.0.
2020-06-13 01:19:45 +02:00
d80a6cacaf
gnu: r-keggrest: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.28.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
3422533bd9
gnu: r-fastseg: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.34.0.
2020-06-13 01:19:44 +02:00
5fce232977
gnu: r-annotationhub: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
334e8d7b79
gnu: r-interactivedisplaybase: Update to 1.26.3.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.26.3.
[propagated-inputs]: Add r-dt.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
15990617eb
gnu: r-edaseq: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.22.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
c9059a3b0e
gnu: r-deseq: Update to 1.39.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.39.0.
2020-06-13 01:19:44 +02:00
019bc36732
gnu: r-aroma-light: Update to 3.18.0.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.18.0.
2020-06-13 01:19:44 +02:00
f6ddf20891
gnu: r-msnid: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.22.0.
2020-06-13 01:19:44 +02:00
10a7ee2609
gnu: r-msnbase: Update to 2.14.2.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.14.2.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
7b4fc6ae0a
gnu: r-pcamethods: Update to 1.80.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.80.0.
2020-06-13 01:19:44 +02:00
8eb579883d
gnu: r-mzid: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.26.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
8e0d11d88b
gnu: r-vsn: Update to 3.56.0.
...
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.56.0.
2020-06-13 01:19:44 +02:00
736f6cfe66
gnu: r-affy: Update to 1.66.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.66.0.
2020-06-13 01:19:44 +02:00
d93af7d632
gnu: r-affyio: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.58.0.
2020-06-13 01:19:43 +02:00
157eb89707
gnu: r-protgenerics: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.20.0.
2020-06-13 01:19:43 +02:00
d95a1cb10e
gnu: r-sva: Update to 3.36.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.36.0.
[propagated-inputs]: Add r-edger.
2020-06-13 01:19:43 +02:00
c336d54d5f
gnu: r-methylkit: Update to 1.14.2.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.14.2.
2020-06-13 01:19:43 +02:00
3475ad075b
gnu: r-copywriter: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.20.0.
2020-06-13 01:19:43 +02:00
6a25fb9b6c
gnu: r-chipseq: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.38.0.
2020-06-13 01:19:43 +02:00
43dec928d2
gnu: r-annotationfilter: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.12.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:43 +02:00
05716c1b1c
gnu: r-rhdf5: Update to 2.32.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:43 +02:00
876e05bfce
gnu: r-tximport: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.16.1.
2020-06-13 01:19:43 +02:00
40a4772f09
gnu: r-mutationalpatterns: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 2.0.0.
2020-06-13 01:19:43 +02:00
3c53617efc
gnu: r-rcas: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.14.0.
[propagated-inputs]: Remove r-annotationdbi, r-biomart, r-dbi, r-knitr,
r-motifrg, r-org-hs-eg-db, and r-topgo; add r-bsgenome, r-gprofiler2,
r-iranges, and r-ranger.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:43 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2f49007dd0
gnu: Add python-pairtools.
...
* gnu/packages/bioinformatics.scm (python-pairtools): New variable.
2020-06-03 15:01:19 +02:00
6742a84c63
gnu: Remove bedtools-2.26.
...
* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable.
2020-06-03 14:07:58 +02:00
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
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
f41f882272
gnu: bbmap: Use HTTPS home page URI.
...
* gnu/packages/bioinformatics.scm (bbmap)[home-page]: Use HTTPS URI.
2020-05-27 01:45:21 +02:00
9dc50c8c47
gnu: sra-tools: Update to 2.10.6.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6.
[arguments]: Replace CC variable in utf8proc Makefile.
[inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
2020-05-19 12:42:01 +02:00
68de995674
gnu: ncbi-vdb: Update to 2.10.6.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6.
2020-05-19 12:42:01 +02:00
6437c598e7
gnu: ngs-sdk: Update to 2.10.5.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5.
2020-05-19 12:42:01 +02:00
87a40d7203
Merge branch 'master' into core-updates
2020-05-05 20:43:21 +02:00
31def9a9df
gnu: Add grocsvs.
...
* gnu/packages/bioinformatics.scm (grocsvs): New variable.
* gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2020-05-05 10:06:28 +03:00
8bf8cd9b85
Merge branch 'master' into core-updates
...
Conflicts:
gnu/local.mk
gnu/packages/backup.scm
gnu/packages/emacs-xyz.scm
gnu/packages/guile.scm
gnu/packages/lisp.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/web.scm
gnu/packages/xorg.scm
2020-04-30 23:47:49 +02:00
eca648b65b
gnu: Add miniasm.
...
* gnu/packages/bioinformatics.scm (miniasm): New variable.
2020-04-30 15:30:16 +02:00
4a148c6da3
gnu: python2-warpedlmm: Fix build.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
2020-04-30 13:08:33 +02:00
545e12f40d
gnu: Add variant-tools.
...
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
2020-04-28 12:23:28 +02:00
9c726c485a
gnu: r-hdf5array: Update to 1.14.4.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
2020-04-28 08:44:04 +02:00
cda0683295
gnu: r-seurat: Update to 3.1.5.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
2020-04-28 08:44:04 +02:00
78799a6fdc
gnu: Update minimap2 to 2.17.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
2020-04-27 21:34:10 +02:00
ccf70a80a1
gnu: Add python-deeptools.
...
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
2020-04-27 13:43:05 +02:00
c43edf6f30
gnu: Add python-deeptoolsintervals.
...
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
2020-04-27 13:39:25 +02:00
ee8de73814
gnu: python-scanpy: Update to 1.4.6.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
2020-04-26 15:03:50 +03:00
7abe35febe
Merge branch 'master' into core-updates
2020-04-19 16:53:01 +02:00
974bf81776
gnu: python-pygenometracks: Update to 3.3.
...
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3.
[arguments]: Add phase "relax-requirements"; disable tests.
[propagated-inputs]: Remove python-configparser and python-hicexplorer; add
python-gffutils, python-pysam, and python-tqdm.
2020-04-17 15:53:03 +02:00
d8fce2362b
gnu: Add python-hicmatrix.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
2020-04-17 15:53:03 +02:00
c55beaecd8
gnu: python-cooler: Update to 0.8.7.
...
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7.
[propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and
python-simplejson.
[native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add
python-pytest.
2020-04-17 15:53:03 +02:00
4a085ffc16
gnu: python-pybigwig: Update to 0.3.17.
...
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
2020-04-17 15:53:03 +02:00
bd21acf6c3
Merge branch 'master' into core-updates
2020-04-15 19:26:55 +02:00
1971d11db9
gnu: r-delayedarray: Update to 0.12.3.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.
2020-04-14 16:41:00 +02:00
679609e179
gnu: r-s4vectors: Update to 0.24.4.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
2020-04-14 16:41:00 +02:00
fba62f8e92
gnu: pigx-chipseq: Update to 0.0.42.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
2020-04-14 14:07:57 +02:00
fc58cb5bd2
Merge branch 'master' into core-updates
2020-04-13 20:26:21 +02:00
7cc83f43c9
gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to
...
"efficiently obtains".
* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
2020-04-12 14:59:48 -07:00
f49369fad2
gnu: r-qtl: Fix grammar "allows to estimate" to "estimates".
...
* gnu/packages/bioinformatics (r-qtl): Fix grammar.
2020-04-12 14:43:50 -07:00
bdb90df764
Merge branch 'master' into core-updates
2020-04-11 00:10:23 +02:00
bdb56513e7
gnu: minimap2: Fix cond expression for Guile 3 compatibility.
...
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
2020-04-09 20:04:43 +02:00
2778302399
Merge branch 'master' into core-updates
...
Conflicts:
etc/news.scm
gnu/local.mk
gnu/packages/check.scm
gnu/packages/cross-base.scm
gnu/packages/gimp.scm
gnu/packages/java.scm
gnu/packages/mail.scm
gnu/packages/sdl.scm
gnu/packages/texinfo.scm
gnu/packages/tls.scm
gnu/packages/version-control.scm
2020-04-08 13:00:50 +02:00
7fe746e071
gnu: python-intervaltree: Update to 3.0.2.
...
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
2020-04-05 20:43:17 +02:00
Ricardo Wurmus
Efraim Flashner
Pierre Langlois
Marius Bakke
Nicolas Goaziou
Marius Bakke
Roel Janssen
Vagrant Cascadian
Jakub Kądziołka