7cc83f43c9
gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to
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"efficiently obtains".
* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
2020-04-12 14:59:48 -07:00
f49369fad2
gnu: r-qtl: Fix grammar "allows to estimate" to "estimates".
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* gnu/packages/bioinformatics (r-qtl): Fix grammar.
2020-04-12 14:43:50 -07:00
bdb56513e7
gnu: minimap2: Fix cond expression for Guile 3 compatibility.
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* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
2020-04-09 20:04:43 +02:00
7fe746e071
gnu: python-intervaltree: Update to 3.0.2.
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* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
2020-04-05 20:43:17 +02:00
0be3cc7f89
gnu: r-biomart: Update to 2.42.1.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
2020-04-01 11:15:26 +02:00
c5c6719f92
gnu: r-genomeinfodb: Update to 1.22.1.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
2020-04-01 11:15:26 +02:00
79c395dde3
gnu: Update sambamba to 0.7.1.
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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
Remove unneeded undead input.
2020-03-26 18:08:27 +01:00
c649d31957
gnu: r-tximport: Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
2020-03-24 11:06:00 +01:00
10d3fbf051
gnu: edirect: Install more programs.
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* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
2020-03-22 09:53:57 +02:00
7d13a94215
gnu: Add edirect-go-programs.
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* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
2020-03-22 09:53:57 +02:00
57f6ac8d90
gnu: pigx-scrnaseq: Update to 1.1.4.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
2020-03-17 20:29:19 +01:00
bc6bf142d3
gnu: star: Update to 2.7.3a.
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* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
2020-03-16 13:59:20 +01:00
0c08e4bfa1
gnu: edirect: Update to 13.3.20200128.
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* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
2020-03-12 16:50:23 +02:00
0b692ef2c6
gnu: r-qtl: Update to 1.46-2.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
2020-03-12 15:15:02 +01:00
d9a2a255f9
gnu: python-pybedtools: Update to 0.8.1.
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* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
2020-03-11 16:31:33 +02:00
173053790c
gnu: python-pyfaidx: Update to 0.5.8.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
2020-03-11 15:45:33 +02:00
ea2822d7d6
gnu: Add python2-pyfaidx.
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* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
2020-03-11 15:43:50 +02:00
ec11dcfe69
gnu: java-forester-1.005: Update source URI.
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* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
2020-03-10 23:35:13 +01:00
c0f6446579
gnu: Fix build of python-velocyto.
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* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
2020-03-09 14:34:41 +01:00
830eac9c27
gnu: ngless: Update to 1.1.0.
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* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
2020-03-08 23:37:09 +01:00
46a864e7c1
gnu: taxtastic: Update to 0.8.11.
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* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
2020-03-08 22:50:16 +01:00
d56553edc3
gnu: r-methylkit: Add r-knitr.
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* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07 19:42:34 +01:00
3b7c644569
gnu: r-vsn: Add r-knitr.
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* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
2020-03-07 19:31:46 +01:00
858e642e4c
gnu: python-scanpy: Update to 1.4.5.1.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
2020-03-06 09:16:48 +01:00
4d5d07f75c
gnu: gess: Use WRAP-SCRIPT.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
2020-03-03 11:33:58 +01:00
9309fe355e
gnu: gess: Override PYTHONPATH.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
2020-03-03 11:33:58 +01:00
1284df4ef6
gnu: r-seqminer: Update to 8.0.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
2020-03-02 21:53:48 +01:00
f73b75e00c
gnu: r-hdf5array: Update to 1.14.3.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
2020-03-01 23:37:58 +01:00
6c1f5a1b7e
gnu: r-rsamtools: Update to 2.2.3.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
2020-03-01 23:37:52 +01:00
9bbf3f9de2
gnu: r-edger: Update to 3.28.1.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
2020-03-01 23:37:40 +01:00
e3eb7ee474
gnu: r-seurat: Update to 3.1.4.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
2020-03-01 23:21:17 +01:00
643d90bf74
gnu: infernal: Update to 1.1.3.
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* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
2020-02-27 18:18:34 +01:00
e6cc426fbb
gnu: vcftools: Update to 0.1.16.
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* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
2020-02-27 18:18:34 +01:00
6c32e9b4dc
gnu: bedtools: Update to 2.29.2.
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* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
2020-02-27 17:38:17 +01:00
d24b3b0213
gnu: rseqc: Update to 3.0.1.
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* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
2020-02-27 17:38:17 +01:00
146430ea0e
gnu: proteinortho: Update to 6.0.14.
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* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
2020-02-26 14:07:32 +01:00
9207575669
gnu: diamond: Update to 0.9.30.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
2020-02-26 14:07:32 +01:00
b38dd34f40
gnu: crossmap: Update to 0.3.8.
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* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
2020-02-26 14:07:32 +01:00
640d910427
gnu: macs: Update to 2.2.6.
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* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6.
[source]: Fetch from git.
[arguments]: Enable tests, build with default Python.
[inputs]: Replace python2-numpy with python-numpy.
[native-inputs]: Add python-pytest.
2020-02-26 12:53:23 +01:00
59c5f85d06
gnu: Remove python-loompy-for-pigx-scrnaseq.
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* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
2020-02-26 08:59:11 +01:00
4f19106770
gnu: pigx-scrnaseq: Update to 1.1.3.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
2020-02-26 08:58:06 +01:00
788de3aec8
gnu: jamm: Update to 1.0.7.6.
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* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
2020-02-25 15:37:27 +01:00
f55084b782
gnu: r-scran: Update to 1.14.6.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
2020-02-19 23:00:58 +01:00
9374f550e6
gnu: r-hdf5array: Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
2020-02-19 23:00:53 +01:00
f2b9f41234
gnu: r-gviz: Update to 1.30.3.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
2020-02-19 23:00:48 +01:00
3f4f3a7822
gnu: r-rhtslib: Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
2020-02-19 23:00:42 +01:00
f0e330d68b
gnu: r-genomicfeatures: Update to 1.38.2.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
2020-02-19 23:00:36 +01:00
154babb9c4
gnu: r-rsamtools: Update to 2.2.2.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
2020-02-19 23:00:31 +01:00
e0ca7b3a14
gnu: r-limma: Update to 3.42.2.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
2020-02-19 23:00:25 +01:00
0f72b7abd8
gnu: r-shortread: Update to 1.44.3.
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* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
2020-02-19 23:00:20 +01:00
Vagrant Cascadian
Marius Bakke
Jakub Kądziołka
Ricardo Wurmus
Roel Janssen
Efraim Flashner
Björn Höfling