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Author SHA1 Message Date
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
Roel Janssen
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
Ricardo Wurmus
0f8db4dc88
Revert "gnu: Add r-loomr." 
This reverts commit 1f56ec08af.

This package is not free software.
 2020-09-09 18:14:48 +02:00
Roel Janssen
0574446be8
gnu: Add r-bisquerna. 
* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
 2020-09-09 17:02:55 +02:00
Roel Janssen
1f56ec08af
gnu: Add r-loomr. 
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
 2020-09-09 16:56:02 +02:00
Andreas Enge
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
6f5530b9bc
gnu: pigx-scrnaseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
ac6eba4eb4
gnu: pigx-bsseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
c0ad6dc976
gnu: pigx-chipseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
2cb9f0f2a6
gnu: pigx-rnaseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
19afa4d58f
gnu: r-rcas: Use pandoc instead of ghc-pandoc. 
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Replace
ghc-pandoc with pandoc.
 2020-08-16 15:57:25 +02:00
Ricardo Wurmus
e6bdc6949b
gnu: hisat2: Use pandoc instead of ghc-pandoc. 
* gnu/packages/bioinformatics.scm (hisat2)[native-inputs]: Replace ghc-pandoc
with pandoc.
 2020-08-15 10:10:39 +02:00
Ricardo Wurmus
bcdc61bfa1
gnu: tophat: Hide default GCC. 
* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
 2020-08-12 21:55:06 +02:00
Ricardo Wurmus
8ca7141c02
gnu: r-seurat: Update to 3.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.2.0.
[propagated-inputs]: Remove r-tsne; add r-jsonlite, r-miniui, r-shiny, r-spatstat, and r-tibble.
 2020-08-12 13:57:10 +02:00
Ricardo Wurmus
a62aadf216
gnu: Add phast. 
* gnu/packages/bioinformatics.scm (phast): New variable.
 2020-08-10 21:58:38 +02:00
Ricardo Wurmus
92b34df789
gnu: clipper: Update to 2.0. 
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.
[source]: Remove snippet.
[arguments]: Build with Python 3; remove phase "fix-typo", add phase
"make-files-writable".
[inputs]: Replace all Python 2 variants with Python 3 variants.
[native-inputs]: Add python-setuptools-git.
 2020-08-07 12:53:23 +02:00
Jakub Kądziołka
6a7bdbfa2d
gnu: paml: Fix build. 
* gnu/packages/bioinformatics.scm (paml)[snippet]: Fix permissions
  before repacking the source tarball.
 2020-07-30 03:48:50 +02:00
Jakub Kądziołka
56f12a65a0
gnu: r-rhdf5lib: Fix libsz substitution. 
This is a follow-up to commit b7f051db14 -
in the new version, some of the format strings being replaced gained
quotes. This commit fixes build of dependents of r-rhdf5lib, such as
r-hdf5array.

* gnu/packages/bioinformatics (r-rhdf5lib): Remove all instances of libsz.a.
 2020-07-19 15:54:48 +02:00
Tobias Geerinckx-Rice
fe39c70195
gnu: Use HTTPS for mdc-berlin.de home pages. 
* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq)
(pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice
c980589260
gnu: Use HTTPS for biojava.org home pages. 
* gnu/packages/bioinformatics.scm (java-biojava-core)
(java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0)
(java-biojava-alignment-4.0)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Ricardo Wurmus
b7f051db14
gnu: r-rhdf5lib: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
82eafe32a2
gnu: r-qtl2: Update to 0.22-11. 
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
16e16586d2
gnu: r-genomicfeatures: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
02f3a622e2
gnu: r-summarizedexperiment: Update to 1.18.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
b80f141f86
gnu: r-delayedmatrixstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
 2020-07-16 10:08:03 +02:00