Commit Graph

1822 Commits (01307bba9c00ada07f8a39bd8de7031beef12afd)

Author SHA1 Message Date
Ricardo Wurmus 58d8225ddb
gnu: trim-galore: Add pigz.
* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz.
[arguments]: Embed reference to pigz.
2019-03-27 11:32:08 +01:00
Ricardo Wurmus 5f1e31094d
gnu: trim-galore: Fix test for Python.
* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace
"configure" phase to skip ill-advised test for Python.
2019-03-27 11:28:38 +01:00
Ricardo Wurmus dfe420ee46
gnu: r-rhdf5lib: Update to 1.4.3.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3.
2019-03-27 09:33:50 +01:00
Ricardo Wurmus 3b6c77445b
gnu: r-genomicfeatures: Update to 1.34.7.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7.
2019-03-27 09:33:50 +01:00
Ricardo Wurmus 28d32817d8
gnu: python-scanpy: Update to 1.4.
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.
[source]: Fetch from git.
[arguments]: Disable broken tests.
[native-inputs]: Add python-pytest.
[home-page]: Use HTTPS.
2019-03-26 18:06:35 +01:00
Ricardo Wurmus fdc316f374
gnu: trim-galore: Update to 0.6.1.
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1.
[arguments]: Adjust patching.
2019-03-26 16:40:42 +01:00
Ricardo Wurmus 9ac17c6242
gnu: cutadapt: Update to 2.1.
* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1.
[source]: Fetch from pypi.
[native-inputs]: Add python-setuptools-scm.
2019-03-26 16:40:42 +01:00
Ricardo Wurmus 80eb01c776
gnu: r-gkmsvm: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here...
* gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.
2019-03-25 14:34:41 +01:00
Ricardo Wurmus c5a2b518ad
gnu: r-wgcna: Move to (gnu packages cran).
* gnu/packages/bioinformatics.scm (r-wgcna): Move from here...
* gnu/packages/cran.scm (r-wgcna): ...to here.
2019-03-25 14:05:09 +01:00
Ricardo Wurmus 72a216a9d0
gnu: r-optparse: Move to (gnu packages cran).
* gnu/packages/bioinformatics.scm (r-optparse): Move from here...
* gnu/packages/cran.scm (r-optparse): ...to here.
2019-03-25 14:04:19 +01:00
Ricardo Wurmus 0ef062b338
gnu: r-bookdown: Move to (gnu packages cran).
* gnu/packages/bioinformatics.scm (r-bookdown): Move from here...
* gnu/packages/cran.scm (r-bookdown): ...to here.
2019-03-25 14:03:21 +01:00
Ricardo Wurmus 469fb43891
gnu: r-sparql: Move to (gnu packages cran).
* gnu/packages/bioinformatics.scm (r-sparql): Move from here...
* gnu/packages/cran.scm (r-sparql): ...to here.
2019-03-25 14:01:56 +01:00
Ricardo Wurmus c4d521ba2c
gnu: r-seqinr: Move to (gnu packages cran).
* gnu/packages/bioinformatics.scm (r-seqinr): Move from here...
* gnu/packages/cran.scm (r-seqinr): ...to here.
2019-03-24 23:44:13 +01:00
Ricardo Wurmus 49a48c496f
gnu: r-acsnminer: Move to (gnu packages cran).
* gnu/packages/bioinformatics.scm (r-acsnminer): Move from here...
* gnu/packages/cran.scm (r-acsnminer): ...to here.
2019-03-24 23:44:13 +01:00
Ricardo Wurmus 9ebb7f8181
gnu: r-phangorn: Update to 2.5.3.
* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.3.
2019-03-24 20:36:51 +01:00
Ricardo Wurmus adfbda0fb0
gnu: r-gqtlstats: Update to 1.14.1.
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.1.
2019-03-24 20:36:51 +01:00
Ricardo Wurmus 7a73c247b2
gnu: r-rbgl: Update to 1.58.2.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.2.
2019-03-24 20:36:51 +01:00
Ricardo Wurmus fdfaba9032
gnu: Add starlong.
* gnu/packages/bioinformatics.scm (starlong): New variable.
2019-03-22 16:17:01 +01:00
Ricardo Wurmus c2b45ac578
gnu: r-diversitree: Update to 0.9-11.
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
2019-03-21 00:02:49 +01:00
Ricardo Wurmus db39269c89
gnu: r-maldiquant: Update to 1.19.2.
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
2019-03-21 00:02:49 +01:00
Ricardo Wurmus 28d0eb2565
gnu: r-diversitree: Fix typo.
* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo
in package labels.
2019-03-21 00:02:48 +01:00
Ricardo Wurmus 933cc19684
gnu: r-annotationhub: Update to 2.14.5.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
2019-03-20 22:32:37 +01:00
Ricardo Wurmus e49d5d34ed
gnu: r-genomicfeatures: Update to 1.34.6.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
2019-03-20 22:32:32 +01:00
Ricardo Wurmus 2b83d218d8
gnu: r-variantannotation: Update to 1.28.13.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
2019-03-20 22:32:25 +01:00
Ricardo Wurmus 0adb6f207b
gnu: r-category: Update to 2.48.1.
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
2019-03-20 22:32:17 +01:00
Ricardo Wurmus e014dc78f0
gnu: r-dexseq: Update to 1.28.3.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
2019-03-20 22:32:11 +01:00
Ricardo Wurmus 35f9c6628f
gnu: Add adapterremoval.
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
2019-03-20 12:19:55 +01:00
Ricardo Wurmus c5542196d5
gnu: nanopolish: Use python-wrapper.
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with
"python-wrapper" as scripts require "python" executable.
2019-03-19 13:30:41 +01:00
Ricardo Wurmus 7c1685e9d8
gnu: nanopolish: Remove bundled library sources.
* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove
bundled htslib sources.
2019-03-19 13:30:41 +01:00
Ricardo Wurmus 9e1d9a0a46
gnu: python-biom-format: Fix build.
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove
generated C files.
[arguments]: Disable second broken test.
2019-03-18 23:46:27 +01:00
Ricardo Wurmus 6e42cef0ab
gnu: Add bbmap.
* gnu/packages/bioinformatics.scm (bbmap): New variable.
2019-03-18 21:35:57 +01:00
Ricardo Wurmus ee4ca57809
gnu: blasr: Add home page.
Reported by Efraim Flashner <efraim@flashner.co.il> on IRC.

* gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
2019-03-18 16:02:30 +01:00
Ricardo Wurmus 19bd7f2e79
gnu: Add arriba.
* gnu/packages/bioinformatics.scm (arriba): New variable.
2019-03-18 16:00:30 +01:00
Ricardo Wurmus f88bdc5ff9
gnu: Add blasr.
* gnu/packages/bioinformatics.scm (blasr): New variable.
2019-03-18 14:47:49 +01:00
Ricardo Wurmus 6a6cd48cf0
gnu: Add blasr-libcpp.
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
2019-03-18 14:47:45 +01:00
Ricardo Wurmus 55154c5f40
gnu: Add pbbam.
* gnu/packages/bioinformatics.scm (pbbam): New variable.
2019-03-18 14:47:26 +01:00
Ricardo Wurmus 07c8b558e3
gnu: Add bwa-meth.
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
2019-03-15 11:36:56 +01:00
Ricardo Wurmus fd4c7a098a
gnu: Add python-velocyto.
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
2019-03-13 22:48:53 +01:00
Ricardo Wurmus 55a0a3c853
gnu: python-loompy: Update to 2.0.17.
* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
2019-03-13 22:48:52 +01:00
Ricardo Wurmus 0b5d12ccdf
gnu: Add tetoolkit.
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
2019-03-13 15:14:10 +01:00
Ricardo Wurmus 4dc2ecc279
gnu: r-qvalue: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-qvalue): Move from here...
* gnu/packages/bioconductor.scm (r-qvalue): ...to here.
2019-03-12 22:47:56 +01:00
Ricardo Wurmus 8b6acb1f20
gnu: blast+: Update to 2.7.1.
* gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1.
[inputs]: Add lmdb.
[source]: Remove obsolete patch.
* gnu/package/patches/blast+-fix-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2019-03-08 23:00:07 +01:00
Ricardo Wurmus 183b6575e7
gnu: r-mzr: Update to 2.16.2.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2.
[inputs]: Replace "boost" with "boost-for-mysql".
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 6453d7aecc
gnu: r-gviz: Update to 1.26.5.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 101dcc29d3
gnu: r-ensembldb: Update to 2.6.7.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus d3713237c5
gnu: r-annotationhub: Update to 2.14.4.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 53e7f028ed
gnu: r-rhtslib: Update to 1.14.1.
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus d86b9eca56
gnu: r-genomicfeatures: Update to 1.34.4.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus d493043daf
gnu: r-rtracklayer: Update to 1.42.2.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 57f40dc220
gnu: r-rsamtools: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
2019-03-08 09:14:00 +01:00