bcbd536e3f
gnu: Update samtools to 1.11.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
2020-10-29 16:55:07 +01:00
04a49b4143
gnu: Update bcftools to 1.11.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
2020-10-29 16:55:03 +01:00
f40add4dbb
gnu: Update htslib to 1.11.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
2020-10-29 16:54:55 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
b31c364467
gnu: r-maldiquant: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here...
* gnu/packages/cran.scm (r-maldiquant): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:59:12 +02:00
30aaee3306
gnu: r-seqminer: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-seqminer): Move from here...
* gnu/packages/cran.scm (r-seqminer): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:59:07 +02:00
66a8e62070
gnu: r-qtl2: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-qtl2): Move from here...
* gnu/packages/cran.scm (r-qtl2): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:59:03 +02:00
496a52dc41
gnu: r-qtl: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-qtl): Move from here...
* gnu/packages/cran.scm (r-qtl): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:58:58 +02:00
66be746dc0
gnu: Move r-bisquerna.
...
* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ...
* gnu/packages/cran.scm: ... here.
2020-09-10 16:38:43 +02:00
0f8db4dc88
Revert "gnu: Add r-loomr."
...
This reverts commit 1f56ec08af
2020-09-09 18:14:48 +02:00
0574446be8
gnu: Add r-bisquerna.
...
* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
2020-09-09 17:02:55 +02:00
1f56ec08af
gnu: Add r-loomr.
...
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
2020-09-09 16:56:02 +02:00
44f93ed6ed
gnu: seqmagick: Update to 0.8.0.
...
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
2020-09-05 22:32:33 +02:00
319de44a09
gnu: delly: Update to 0.8.3.
...
* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3.
[inputs]: Order alphabetically.
2020-08-30 22:55:48 +03:00
e8bbb29b59
gnu: vcflib: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom
'install phase to add vcflib.pc.
2020-08-27 18:18:55 +03:00
6d8dd5bad7
gnu: vcflib: Use shared libraries.
...
* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add
snippet to adjust files for new locations.
[inputs]: Add fastahack, smithwaterman, tabixpp, xz.
[native-inputs]: Add pkg-config. Remove the package-source of fastahack,
fsom, smithwaterman, tabixpp.
[arguments]: Remove make-flags. Add custom phase to add the output lib
directory to the rpath. Adjust custom 'unpack-submodule-sources for the
change in native-inputs. Adjust custom 'install phase to also install
libraries and headers.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2020-08-27 18:18:55 +03:00
4bbcbe93cd
gnu: fastahack: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom
'install phase to add fastahack.pc.
2020-08-27 18:09:28 +03:00
f075bf09bd
gnu: fastahack: Build and install shared library and headers.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to
build PIE objects. Add custom phase to build dynamic library. Adjust
custom 'install phase to install shared library and headers.
2020-08-27 18:08:13 +03:00
5c78997188
gnu: smithwaterman: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust
custom 'install phase to add smithwaterman.pc file.
2020-08-27 18:06:25 +03:00
afa352223f
gnu: smithwaterman: Build and install shared library and headers.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom
phase to build PIE objects. Add custom 'build-dynamic phase to build
dynamic library. Adjust custom 'install phase to install shared library
and headers.
2020-08-27 18:05:20 +03:00
261bc778b6
gnu: tabixpp: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'install phase to add tabixpp.pc file.
2020-08-27 18:03:13 +03:00
35cb1bc527
gnu: tabixpp: Build and install shared library and headers.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'build phase to build shared library. Adjust custom 'install phase to
install libraries and header.
2020-08-27 18:02:16 +03:00
4e0acfe5e7
gnu: r-complexheatmap: Update to 2.4.3.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
2020-08-20 21:25:34 +02:00
e9d2cab0bf
gnu: r-gage: Update to 2.38.3.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
2020-08-20 21:25:34 +02:00
9da4a25b33
gnu: r-annotationhub: Update to 2.20.2.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
2020-08-20 21:25:34 +02:00
67f8477fb5
gnu: r-delayedarray: Update to 0.14.1.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
2020-08-20 21:25:33 +02:00
b414add3d1
gnu: r-annotationdbi: Update to 1.50.3.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
2020-08-20 21:25:33 +02:00
e9128480d4
gnu: r-biocviews: Update to 1.56.2.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
2020-08-20 21:25:33 +02:00
6e5be7ffad
gnu: pigx-chipseq: Update to 0.0.43.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
2020-08-19 12:12:42 +02:00
346ea4b5fc
gnu: bowtie1: Add missing Python input.
...
Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
2020-08-18 12:38:38 +02:00
4d55432fd0
gnu: pigx-bsseq: Update to 0.1.2.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2.
[inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
2020-08-16 15:57:27 +02:00
Roel Janssen
Ludovic Courtès
Ricardo Wurmus
Mădălin Ionel Patrașcu
Nicolas Goaziou
zimoun
Andreas Enge
Efraim Flashner