07c8b558e3
gnu: Add bwa-meth.
...
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
2019-03-15 11:36:56 +01:00
fd4c7a098a
gnu: Add python-velocyto.
...
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
2019-03-13 22:48:53 +01:00
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
0b5d12ccdf
gnu: Add tetoolkit.
...
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
2019-03-13 15:14:10 +01:00
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
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
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
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
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
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
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
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
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
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
58209b1e21
gnu: r-biocparallel: Update to 1.16.6.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
2019-03-08 09:14:00 +01:00
cd43ae3fd6
gnu: r-variantannotation: Update to 1.28.11.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
2019-03-08 09:14:00 +01:00
fff11bccc6
gnu: r-genomeinfodb: Update to 1.18.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
2019-03-08 09:14:00 +01:00
8972989e10
gnu: r-dexseq: Update to 1.28.2.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
2019-03-08 09:14:00 +01:00
3b296475bf
gnu: cd-hit: Support longer sequences.
...
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make
flags.
2019-03-07 13:38:01 +01:00
8035819f4c
gnu: r-org-mm-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): ...to here.
2019-03-06 21:43:33 +01:00
d56df35a25
gnu: r-org-hs-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): ...to here.
2019-03-06 21:42:39 +01:00
f8780e96ff
gnu: r-org-dm-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-dm-eg-db): ...to here.
2019-03-06 21:41:48 +01:00
3a08940e1a
gnu: r-org-ce-eg-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-ce-eg-db): ...to here.
2019-03-06 21:35:20 +01:00
7bc5d1b0e1
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Move from here...
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
...to here.
2019-03-06 21:33:17 +01:00
13dabd6947
gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
...to here.
2019-03-06 21:31:41 +01:00
0c792ffbd1
gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here.
2019-03-06 21:30:30 +01:00
b7d93cf508
gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here.
2019-03-06 21:29:20 +01:00
c3adc83054
gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here.
2019-03-06 21:26:54 +01:00
5acb9052cf
gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here.
2019-03-06 21:25:18 +01:00
fe0b76e215
gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
2019-03-06 21:23:42 +01:00
40a6505711
gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
...to here.
2019-03-06 21:23:20 +01:00
66e35ce63b
gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move
from here...
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to
here.
2019-03-06 21:16:33 +01:00
bfb93b4889
gnu: r-geneplotter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here...
* gnu/packages/bioconductor.scm (r-geneplotter): ...to here.
2019-03-06 21:13:38 +01:00
3d13b448e5
gnu: r-copynumber: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copynumber): Move from here...
* gnu/packages/bioconductor.scm (r-copynumber): ...to here.
2019-03-06 21:07:49 +01:00
38502a7d13
gnu: bismark: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (bismark): Update to 0.20.1.
[source]: Remove obsolete snippet.
[arguments]: Add build phase "replace-plotly.js" and add requried modules;
adjust "install" phase.
[inputs]: Add perl-carp and perl-getopt-long.
[native-inputs]: Add plotly.js and uglify-js.
2019-03-06 16:26:23 +01:00
cb66fb101f
gnu: Add r-scde.
...
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06 15:55:54 +01:00
afeb10a056
gnu: Add bowtie1.
...
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06 15:32:45 +01:00
4fc9b5b1dd
gnu: Add genrich.
...
* gnu/packages/bioinformatics.scm (genrich): New variable.
2019-03-06 13:28:45 +01:00
1fe9a36173
gnu: r-dnacopy: Remove duplicate definition.
...
Reported by Christopher Baines <mail@cbaines.net>.
* gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable.
2019-03-06 10:39:28 +01:00
c335df433f
gnu: pigx-chipseq: Update to 0.0.31.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.31.
2019-03-02 22:05:30 +01:00
a27ca96f10
gnu: Add velvet.
...
* gnu/packages/bioinformatics.scm (velvet): New variable.
2019-03-01 12:55:35 +01:00
0ce256dc79
gnu: discrover: Remove indirect TexLive dependencies.
...
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove
texlive-generic-ifxetex, texlive-latex-oberdiek, texlive-latex-url, and
texlive-latex-xcolor from texlive-union.
2019-03-01 12:55:35 +01:00
8aa1ca85ac
gnu: flexbar: Fix reproducibility bug.
...
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Add phase
"do-not-tune-to-CPU".
2019-02-27 15:40:46 +01:00
cc842b58af
gnu: pigx-chipseq: Update to 0.0.21.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.21.
2019-02-25 15:40:12 +01:00
3ca1d917b6
gnu: discrover: Replace "texlive" with a texlive-union.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"fix-latex-errors"; add build phase "setenv-HOME".
[inputs]: Add rmath-standalone.
[native-inputs]: Replace "texlive" with a texlive-union consisting of
texlive-fonts-cm, texlive-fonts-amsfonts, texlive-generic-ifxetex,
texlive-latex-doi, texlive-latex-examplep, texlive-latex-hyperref,
texlive-latex-ms, texlive-latex-natbib, texlive-bibtex,
texlive-latex-oberdiek, texlive-latex-pgf, texlive-latex-url,
texlive-latex-verbatimbox, and texlive-latex-xcolor.
2019-02-25 15:05:35 +01:00
2e125ece09
gnu: pplacer: Remove the package, which is affected by a CVE on ocaml@4.01.
...
This makes progress towards fixing <https://bugs.gnu.org/27462 >.
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove
variables.
2019-02-19 22:37:02 +01:00
61506fe551
gnu: Remove unneeded uses of python{,2}-minimal.
...
The "python-minimal" package exists mostly to resolve a dependency cycle. To
reduce duplication, packages should prefer the regular Python variants.
* gnu/packages/admin.scm (htop)[native-inputs]: Change PYTHON-MINIMAL-WRAPPER
to PYTHON-WRAPPER.
* gnu/packages/crypto.scm (botan)[native-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Change
PYTHON-MINIMAL to PYTHON.
* gnu/packages/dictionaries.scm (apertium)[native-inputs]: Likewise.
* gnu/packages/databases.scm (mongodb)[native-inputs]: Change PYTHON2-MINIMAL
to PYTHON2.
* gnu/packages/games.scm (openttd-opensfx, openttd-openmsx)[native-inputs]:
Likewise.
* gnu/packages/gnome.scm (deja-dup)[native-inputs]: Likewise.
2019-02-17 18:44:18 +01:00
9846ec0bea
gnu: Add python-pyfit-sne.
...
* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable.
2019-02-15 11:03:26 +01:00
155194d97d
gnu: python-pybedtools: Update to 0.8.0 and fix build.
...
From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 10 Feb 2019 23:39:25 -0500
Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build.
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0.
[phases]{disable-broken-tests}: Do not disable "test_issue_157" and
"test_to_dataframe" tests. Disable the "test_getting_example_beds".
{remove-cython-generated-files}: Add phase.
{generate-cython-extensions}: Add phase.
{check}: Move from python2-pybedtools to here. Add a scripts
subdirectory of the build directory to the PATH, so that the tests can call
them. Invoke pytest rather than nosetests.
[modules]: Move from python2-pybedtools to here.
[propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.26.
[native-inputs]: Replace python-nose by python-pytest and add python-psutil.
2019-02-12 17:16:05 +01:00
385d7546e1
gnu: Add cnvkit.
...
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12 15:41:02 +01:00
Ricardo Wurmus