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2550 Commits

Author SHA1 Message Date
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
Marius Bakke
87a027243f
Merge branch 'master' into staging 2020-11-23 23:39:47 +01:00
Efraim Flashner
964bc9e5fe
gnu: Add cwltool. 
* gnu/packages/bioinformatics.scm (cwltool): New variable.
 2020-11-23 15:43:38 +02:00
Efraim Flashner
7face25953
gnu: Add python-schema-salad. 
* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
 2020-11-23 15:43:37 +02:00
Marius Bakke
4e5e05d409
Merge branch 'master' into staging 2020-11-15 23:45:34 +01:00
Ricardo Wurmus
e1fa3ea9fe
gnu: methyldackel: Update to 0.5.1. 
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1.
[arguments]: Link with libbigwig.
[inputs]: Add curl and libbigwig; replace htslib with htslib-1.9.
 2020-11-15 23:31:35 +01:00
Roel Janssen
37ba374a53
gnu: Fix build for python-pysam. 
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9,
  samtools-1.9, and bcftools-1.9.
 2020-11-13 16:16:43 +01:00
Roel Janssen
ecc309c142
gnu: Add bcftools-1.9. 
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
 2020-11-13 16:14:01 +01:00
Roel Janssen
c3232fcc77
gnu: bedtools: Use samtools-1.9. 
The build for bedtools with samtools 1.11 triggers a testsuite
failure which is reported here:
https://github.com/arq5x/bedtools2/issues/814

* gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
 2020-11-13 14:49:31 +01:00
Roel Janssen
da4a38edad
gnu: Add samtools-1.9. 
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
 2020-11-13 14:49:27 +01:00
Roel Janssen
3ede804f6d
gnu: Add htslib-1.9. 
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
 2020-11-13 14:49:20 +01:00
Marius Bakke
a9a0d34874
Merge branch 'master' into staging 2020-11-11 00:02:32 +01:00
Efraim Flashner
4b3a535770
gnu: macs: Remove generated code. 
* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove
cython generated code.
[native-inputs]: Add python-cython.
 2020-11-09 11:34:08 +02:00
Efraim Flashner
4dcd19d3ff
gnu: macs: Update check phase. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check
phase before using custom 'check phase.
 2020-11-09 11:34:08 +02:00
Efraim Flashner
fa82adb5e0
gnu: macs: Update source, home-page URIs. 
* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update
URIs to new location.
 2020-11-09 11:34:08 +02:00
Marius Bakke
32787d6524
Merge branch 'master' into staging 
Conflicts:
	gnu/local.mk
	gnu/packages/gdb.scm
	gnu/packages/lisp-xyz.scm
	gnu/packages/web-browsers.scm
 2020-11-07 21:33:32 +01:00
Roel Janssen
bcbd536e3f
gnu: Update samtools to 1.11. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
 2020-10-29 16:55:07 +01:00
Roel Janssen
04a49b4143
gnu: Update bcftools to 1.11. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
 2020-10-29 16:55:03 +01:00
Roel Janssen
f40add4dbb
gnu: Update htslib to 1.11. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
 2020-10-29 16:54:55 +01:00
Ludovic Courtès
c9a656a5d0
gnu: imp: Update to 2.13.0. 
* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
 2020-10-23 16:35:38 +02:00
Marius Bakke
997abda92b
gnu: Remove redundant MariaDB inputs. 
For well-behaved build systems, including the "dev" output suffices.

* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Remove MARIADB:LIB.
* gnu/packages/cran.scm (r-rmysql)[inputs]: Likewise.
* gnu/packages/databases.scm (python-mysqlclient, soci)[inputs]: Likewise.
* gnu/packages/qt.scm (qt-4, qtbase): Likewise.
* gnu/packages/ruby.scm (ruby-mysql2)[inputs]: Likewise.
 2020-10-13 23:48:16 +02:00
Marius Bakke
f7175626ff
Merge branch 'master' into staging 2020-10-13 23:39:27 +02:00
Roel Janssen
fb0037af8c
gnu: htslib: Enable support for custom URI schemes. 
* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
 2020-10-07 15:33:28 +02:00