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Author SHA1 Message Date
zimoun
728369634f
gnu: r-rhtslib: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
b0d85e36f1
gnu: r-zlibbioc: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.36.0.
 2020-12-09 12:12:40 +01:00
zimoun
329879b70c
gnu: r-seqlogo: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.56.0.
 2020-12-09 12:12:40 +01:00
zimoun
2a70c96e3d
gnu: r-genomation: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun
44bf116f03
gnu: r-seqpattern: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun
a180744b37
gnu: r-impute: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.64.0.
 2020-12-09 12:12:40 +01:00
zimoun
e2e11f095f
gnu: r-bsgenome: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.58.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen
6a7de43a58
gnu: r-topgo: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.42.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen
26e2184fc1
gnu: r-genomicfeatures: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.1.
 2020-12-09 12:12:40 +01:00
zimoun
92377e7fea
gnu: r-rtracklayer: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.50.0.
 2020-12-09 12:12:39 +01:00
zimoun
077e813657
gnu: r-genomicalignments: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.26.0.
 2020-12-09 12:12:39 +01:00
zimoun
3ca5b05474
gnu: r-variantannotation: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.36.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:39 +01:00
zimoun
8607a5394b
gnu: r-summarizedexperiment: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.20.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:39 +01:00
zimoun
9168ab0911
gnu: r-rsamtools: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.6.0.
 2020-12-09 12:12:39 +01:00
zimoun
5d60273b77
gnu: r-biostrings: Update to 2.58.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.58.0.
 2020-12-09 12:12:39 +01:00
Roel Janssen
444b101dc2
gnu: r-biocparallel: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.24.1.
 2020-12-09 12:12:39 +01:00
zimoun
4fac3fe67d
gnu: r-biomart: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.0.
 2020-12-09 12:12:39 +01:00
zimoun
f517365cef
gnu: r-annotationdbi: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.52.0.
 2020-12-09 12:12:39 +01:00
zimoun
9103041d13
gnu: r-biobase: Update to 2.50.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.50.0.
 2020-12-09 12:12:38 +01:00
zimoun
7641dba3e6
gnu: r-genomicranges: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.42.0.
 2020-12-09 12:12:38 +01:00
zimoun
d972ab690e
gnu: r-limma: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.46.0.
 2020-12-09 12:12:38 +01:00
zimoun
5996929b36
gnu: r-edger: Update to 3.32.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.0.
 2020-12-09 12:12:38 +01:00
zimoun
cde7fcedf9
gnu: r-genomeinfodb: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.0.
 2020-12-09 12:12:38 +01:00
zimoun
2ae3b7db24
gnu: r-bioccheck: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.26.0.
 2020-12-09 12:12:38 +01:00
zimoun
1160c83caf
gnu: r-biocstyle: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.0.
 2020-12-09 12:12:38 +01:00
zimoun
182a080127
gnu: r-biocviews: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.0.
 2020-12-09 12:12:38 +01:00
zimoun
16a4822a07
gnu: r-grohmm: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.24.0.
 2020-12-09 12:12:37 +01:00
Roel Janssen
5598f53497
gnu: r-systempiper: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.2.
[propagated-inputs]: Add r-iranges.
 2020-12-09 12:12:37 +01:00
zimoun
a05bb428e4
gnu: r-shortread: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.48.0.
 2020-12-09 12:12:37 +01:00
zimoun
74204b48eb
gnu: r-gostats: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.56.0.
 2020-12-09 12:12:37 +01:00
zimoun
afbc8e1433
gnu: r-category: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.56.0.
 2020-12-09 12:12:37 +01:00
zimoun
03312f052a
gnu: r-gseabase: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.0.
 2020-12-09 12:12:37 +01:00
zimoun
7a57b229b6
gnu: r-rbgl: Update to 1.66.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.66.0.
 2020-12-09 12:12:37 +01:00
zimoun
4451918e3a
gnu: r-annotationforge: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.32.0.
 2020-12-09 12:12:37 +01:00
zimoun
a323c1e9b4
gnu: r-dexseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.36.0.
 2020-12-09 12:12:37 +01:00
zimoun
936227f144
gnu: r-deseq2: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.30.0.
 2020-12-09 12:12:37 +01:00
zimoun
64cf667e98
gnu: r-genefilter: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.0.
 2020-12-09 12:12:36 +01:00
zimoun
fafa94b065
gnu: r-delayedarray: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.0.
[propagated-inputs]: Add r-matrixgenerics; remove r-matrixstats.
 2020-12-09 12:12:36 +01:00
zimoun
cf6033ee6e
gnu: r-iranges: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.0.
 2020-12-09 12:12:35 +01:00
zimoun
57820475db
gnu: r-s4vectors: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.0.
 2020-12-09 12:12:35 +01:00
zimoun
724b770678
gnu: r-xvector: Update to 0.30.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.30.0.
 2020-12-09 12:12:35 +01:00
zimoun
1e536c307c
gnu: Update r-msnbase to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.0.
 2020-12-09 12:12:27 +01:00
Efraim Flashner
3832704aff
gnu: minimap2: Fix build on aarch64-linux. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust
configure-flags to be better per-architecture.
[source]: Add patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2020-12-07 12:48:07 +02:00
Efraim Flashner
f48cd014f3
gnu: minimap2: Prepare for cross compilation. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Use
cc-for-target.
 2020-12-07 12:48:01 +02:00
Ricardo Wurmus
555677fdf7
gnu: java-picard-1.113: Use ant/java8. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use
ant/java8.
[inputs]: Replace ant with ant/java8.
 2020-12-01 13:30:34 +01:00
Ricardo Wurmus
80fbad4fe6
gnu: pigx-chipseq: Update to 0.0.51. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.51.
[inputs]: Add r-corrplot, r-deseq2, r-dt, r-ggrepel, r-gprofiler2, r-pheatmap,
and r-rsubread.
 2020-11-30 22:39:34 +01:00
Ricardo Wurmus
d3c1b5f66d
gnu: pigx-scrnaseq: Update to 1.1.7. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.7.
 2020-11-30 22:39:34 +01:00
Marius Bakke
bff94a5a53
Merge branch 'master' into staging 2020-11-26 01:08:35 +01:00
Maxim Cournoyer
4efbf56e53
gnu: tadbit: Update to 1.0.1. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1.
[arguments]: Remove #:tests? and #:python arguments.
[phases]{fix-problems-with-setup.py}: Remove no longer needed steps.
{check}: Override phase.
[native-inputs]: Add glib and pkg-config.
[inputs]: Add python-future and python-h5py.
 2020-11-24 02:20:32 -05:00
Maxim Cournoyer
e7e73f750f
gnu: imp: Migrate to Python 3. 
* gnu/packages/bioinformatics.scm (imp)
[arguments]: Enable tests by removing the #:tests? argument.
Specify the arguments to pass to the ctest test running via the
 #:configure-flags argument.
[inputs]: Add cgal and opencv.  Remove python-2.  Move swig to...
[native-inputs]: ...here.  Add python-wrapper.
[propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas,
python2-scikit-learn and python2-networkx by python-numpy, python-scipy,
python-pandas, python-scikit-learn and python-networkx, respectively.
 2020-11-24 02:20:31 -05:00