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2530 Commits

Author SHA1 Message Date
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
Ricardo Wurmus
73a2fe4ab7
gnu: r-gqtlbase: Update to 1.20.4. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.
 2020-10-06 13:23:38 +02:00
Ricardo Wurmus
906c79d1a3
gnu: r-rhdf5: Update to 2.32.3. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
 2020-10-06 13:23:38 +02:00
Ricardo Wurmus
78d9fbd2fd
gnu: r-biocstyle: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.
 2020-10-06 13:23:38 +02:00
Guillaume Le Vaillant
87c079d9b5
Merge branch 'master' into staging 2020-10-05 14:17:25 +02:00
Mădălin Ionel Patrașcu
0990d61193
gnu: mafft: Update to 7.471. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.471.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-09-25 14:12:13 +02:00
Guillaume Le Vaillant
2374443561
Merge branch 'staging' into wip-lisp 2020-09-23 14:50:19 +02:00
Nicolas Goaziou
d27ec8db70
gnu: mafft: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI.
 2020-09-22 11:12:52 +02:00
zimoun
3292f6eda0
gnu: r-fithic: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-fithic): Move from here...
* gnu/packages/bioconductor.scm (r-fithic): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:40:15 +02:00
zimoun
7df42d3774
gnu: r-hitc: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-hitc): Move from here...
* gnu/packages/bioconductor.scm (r-hitc): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:40:15 +02:00
zimoun
63b75c01c2
gnu: r-hdf5array: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here...
* gnu/packages/bioconductor.scm (r-hdf5array): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:40:10 +02:00
zimoun
c61268c1b7
gnu: r-rhdf5lib: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:33 +02:00
zimoun
8863c14cd8
gnu: r-beachmat: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-beachmat): Move from here...
* gnu/packages/bioconductor.scm (r-beachmat): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:30 +02:00
zimoun
916a3e59ab
gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here...
* gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:27 +02:00
zimoun
6b1946b334
gnu: r-scater: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-scater): Move from here...
* gnu/packages/bioconductor.scm (r-scater): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:24 +02:00
zimoun
1193b77e60
gnu: r-scran: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-scran): Move from here...
* gnu/packages/bioconductor.scm (r-scran): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:22 +02:00
zimoun
8c7c6db408
gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here...
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:19 +02:00
zimoun
d4e2ec1b8a
gnu: r-absfiltergsea: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here...
* gnu/packages/cran.scm (r-absfiltergsea): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:23 +02:00
zimoun
77c7394086
gnu: r-diversitree: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-diversitree): Move from here...
* gnu/packages/cran.scm (r-diversitree): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:23 +02:00
zimoun
415aa8a583
gnu: r-phangorn: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-phangorn): Move from here...
* gnu/packages/cran.scm (r-phangorn): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:21 +02:00
zimoun
f9c0b2e05a
gnu: r-seurat: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-seurat): Move from here...
* gnu/packages/cran.scm (r-seurat): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:17 +02:00