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Author SHA1 Message Date
Efraim Flashner
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
Efraim Flashner
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
Pierre Langlois
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
Pierre Langlois
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
Pierre Langlois
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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