14bba460ab
gnu: r-biocgenerics: Move to bioconductor.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
2019-01-13 13:04:18 +01:00
7097c7009d
gnu: r-annotate: Move to bioconductor.
...
* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.
2019-01-13 13:04:18 +01:00
c80fb90f4a
gnu: r-vegan: Move from bioinformatics to cran.
...
* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.
2019-01-13 13:04:18 +01:00
c476edc2cd
gnu: r-rtracklayer: Update to 1.42.1.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
2019-01-12 23:35:18 +01:00
1e107b0960
gnu: r-scater: Update to 1.10.1.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
0f268bb275
gnu: r-singlecellexperiment: Update to 1.4.1.
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* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
2019-01-12 23:35:18 +01:00
a0224bd4f6
gnu: r-rhdf5lib: Update to 1.4.2.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
2019-01-12 23:35:18 +01:00
40561d0249
gnu: r-hdf5array: Update to 1.10.1.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
ad10b3979d
gnu: r-qvalue: Update to 2.14.1.
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* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
2019-01-12 23:35:18 +01:00
19cacb5a2d
gnu: r-gviz: Update to 1.26.4.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
2019-01-12 23:35:18 +01:00
c80595935d
gnu: r-biovizbase: Update to 1.30.1.
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* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
2019-01-12 23:35:18 +01:00
27194effd7
gnu: r-ensembldb: Update to 2.6.3.
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* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
2019-01-12 23:35:18 +01:00
43931ff72f
gnu: r-dirichletmultinomial: Update to 1.24.1.
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* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
2019-01-12 23:35:18 +01:00
15d89fe9f8
gnu: r-gage: Update to 2.32.1.
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* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
2019-01-12 23:35:18 +01:00
4615cf9f1a
gnu: r-annotationhub: Update to 2.14.2.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
2019-01-12 23:35:18 +01:00
ab4a862ab8
gnu: r-edaseq: Update to 2.16.3.
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* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.
2019-01-12 23:35:18 +01:00
3bdc41b352
gnu: r-deseq: Update to 1.34.1.
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* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
2019-01-12 23:35:18 +01:00
9abf344f8b
gnu: r-msnid: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
2019-01-12 23:35:17 +01:00
880ed11e9f
gnu: r-msnbase: Update to 2.8.3.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
2019-01-12 23:35:17 +01:00
6451af78e1
gnu: r-mzid: Update to 1.20.1.
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* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
2019-01-12 23:35:17 +01:00
a4f038dc97
gnu: r-mzr: Update to 2.16.1.
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* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
2019-01-12 23:35:17 +01:00
46508c3a92
gnu: r-sva: Update to 3.30.1.
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* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
2019-01-12 23:35:17 +01:00
c20426ec5c
gnu: r-methylkit: Update to 1.8.1.
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* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
2019-01-12 23:35:17 +01:00
5c72ebafeb
gnu: r-copywriter: Update to 2.14.1.
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* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
2019-01-12 23:35:17 +01:00
86162c767e
gnu: r-rhdf5: Update to 2.26.2.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
2019-01-12 23:35:17 +01:00
4c7b9222dd
gnu: r-tximport: Update to 1.10.1.
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* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
2019-01-12 23:35:17 +01:00
4bfde52178
gnu: r-genomicalignments: Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
2019-01-12 23:35:17 +01:00
1fa12b2f06
gnu: r-biostrings: Update to 2.50.2.
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* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
2019-01-12 23:35:17 +01:00
d4fc834cf7
gnu: r-biocparallel: Update to 1.16.5.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
2019-01-12 23:35:17 +01:00
52c977a05b
gnu: r-limma: Update to 3.38.3.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
2019-01-12 23:35:17 +01:00
3fd48846eb
gnu: r-variantannotation: Update to 1.28.8.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
2019-01-12 23:35:17 +01:00
a619850930
gnu: r-edger: Update to 3.24.3.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
2019-01-12 23:35:17 +01:00
00f105fe20
gnu: r-biocviews: Update to 1.50.10.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
2019-01-12 23:35:16 +01:00
9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
2019-01-12 23:35:16 +01:00
3b8c884285
gnu: r-rbgl: Update to 1.58.1.
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* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
2019-01-12 23:35:16 +01:00
ffe16ef33c
gnu: r-dexseq: Update to 1.28.1.
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* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
2019-01-12 23:35:16 +01:00
f7e95c50b8
gnu: r-deseq2: Update to 1.22.2.
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* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
2019-01-12 23:35:16 +01:00
feb561f721
gnu: r-scran: Update to 1.10.2.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
2019-01-12 23:35:16 +01:00
80c4e75b87
gnu: r-seqminer: Update to 7.1.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
2019-01-12 23:35:16 +01:00
3bc0667f3c
gnu: r-bookdown: Update to 0.9.
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* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
2019-01-12 23:35:16 +01:00
24155bf40d
gnu: Move Java compression packages to new module.
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* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.
2019-01-12 12:14:28 +01:00
e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
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* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
6fd2ed23ac
gnu: mantis: Limit to x86_64-linux.
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* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
e942813aac
gnu: Add mantis.
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* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07 11:56:18 +01:00
8894668cd2
gnu: discrover: Comment on attempt of minimal texlive-union.
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* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
texlive-union.
2018-12-20 12:07:40 +01:00
2f3977b9a7
gnu: gess: Don't hardcode python version.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
2018-12-17 12:08:05 +02:00
9718265eec
gnu: mash: Use C++ 14.
...
I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,
tweak the compilation to allow it to build with 0.7. The package also builds
with the current version of capnproto. I got the idea of changing the c++
version from here [1].
1: https://github.com/marbl/Mash/issues/98
* gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
2018-12-05 20:29:12 +00:00
42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
2018-12-04 16:21:50 +01:00
4b2d1dc4dc
gnu: bless: Adjust to zlib static output.
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* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
2018-11-24 19:32:48 +01:00
f028823c0f
gnu: mosaik: Fix FTBFS from b90289dadc.
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* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-24 15:57:56 +01:00
Ricardo Wurmus