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2293 commits

Author SHA1 Message Date
Ricardo Wurmus
545e12f40d
gnu: Add variant-tools. 
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
 2020-04-28 12:23:28 +02:00
Ricardo Wurmus
9c726c485a
gnu: r-hdf5array: Update to 1.14.4. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
 2020-04-28 08:44:04 +02:00
Ricardo Wurmus
cda0683295
gnu: r-seurat: Update to 3.1.5. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
 2020-04-28 08:44:04 +02:00
Roel Janssen
78799a6fdc
gnu: Update minimap2 to 2.17. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
 2020-04-27 21:34:10 +02:00
Roel Janssen
ccf70a80a1
gnu: Add python-deeptools. 
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
 2020-04-27 13:43:05 +02:00
Roel Janssen
c43edf6f30
gnu: Add python-deeptoolsintervals. 
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
 2020-04-27 13:39:25 +02:00
Efraim Flashner
ee8de73814
gnu: python-scanpy: Update to 1.4.6. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
 2020-04-26 15:03:50 +03:00
Ricardo Wurmus
974bf81776
gnu: python-pygenometracks: Update to 3.3. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3.
[arguments]: Add phase "relax-requirements"; disable tests.
[propagated-inputs]: Remove python-configparser and python-hicexplorer; add
python-gffutils, python-pysam, and python-tqdm.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
d8fce2362b
gnu: Add python-hicmatrix. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
c55beaecd8
gnu: python-cooler: Update to 0.8.7. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7.
[propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and
python-simplejson.
[native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add
python-pytest.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
4a085ffc16
gnu: python-pybigwig: Update to 0.3.17. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
1971d11db9
gnu: r-delayedarray: Update to 0.12.3. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.
 2020-04-14 16:41:00 +02:00
Ricardo Wurmus
679609e179
gnu: r-s4vectors: Update to 0.24.4. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
 2020-04-14 16:41:00 +02:00
Ricardo Wurmus
fba62f8e92
gnu: pigx-chipseq: Update to 0.0.42. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
 2020-04-14 14:07:57 +02:00
Vagrant Cascadian
7cc83f43c9
gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to 
"efficiently obtains".

* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
 2020-04-12 14:59:48 -07:00
Vagrant Cascadian
f49369fad2
gnu: r-qtl: Fix grammar "allows to estimate" to "estimates". 
* gnu/packages/bioinformatics (r-qtl): Fix grammar.
 2020-04-12 14:43:50 -07:00
Marius Bakke
bdb56513e7
gnu: minimap2: Fix cond expression for Guile 3 compatibility. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
 2020-04-09 20:04:43 +02:00
Jakub Kądziołka
7fe746e071
gnu: python-intervaltree: Update to 3.0.2. 
* 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
Ricardo Wurmus
0be3cc7f89
gnu: r-biomart: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
 2020-04-01 11:15:26 +02:00
Ricardo Wurmus
c5c6719f92
gnu: r-genomeinfodb: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
 2020-04-01 11:15:26 +02:00
Roel Janssen
79c395dde3
gnu: Update sambamba to 0.7.1. 
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
  Remove unneeded undead input.
 2020-03-26 18:08:27 +01:00
Ricardo Wurmus
c649d31957
gnu: r-tximport: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Efraim Flashner
10d3fbf051
gnu: edirect: Install more programs. 
* 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
Efraim Flashner
7d13a94215
gnu: Add edirect-go-programs. 
* 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
Ricardo Wurmus
57f6ac8d90
gnu: pigx-scrnaseq: Update to 1.1.4. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
 2020-03-17 20:29:19 +01:00
Ricardo Wurmus
bc6bf142d3
gnu: star: Update to 2.7.3a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
 2020-03-16 13:59:20 +01:00
Efraim Flashner
0c08e4bfa1
gnu: edirect: Update to 13.3.20200128. 
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
 2020-03-12 16:50:23 +02:00
Ricardo Wurmus
0b692ef2c6
gnu: r-qtl: Update to 1.46-2. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
 2020-03-12 15:15:02 +01:00
Efraim Flashner
d9a2a255f9
gnu: python-pybedtools: Update to 0.8.1. 
* 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
Efraim Flashner
173053790c
gnu: python-pyfaidx: Update to 0.5.8. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
 2020-03-11 15:45:33 +02:00
Efraim Flashner
ea2822d7d6
gnu: Add python2-pyfaidx. 
* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
 2020-03-11 15:43:50 +02:00
Björn Höfling
ec11dcfe69
gnu: java-forester-1.005: Update source URI. 
* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
 2020-03-10 23:35:13 +01:00
Roel Janssen
c0f6446579
gnu: Fix build of python-velocyto. 
* 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
Ricardo Wurmus
830eac9c27
gnu: ngless: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
 2020-03-08 23:37:09 +01:00
Ricardo Wurmus
46a864e7c1
gnu: taxtastic: Update to 0.8.11. 
* 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
Ricardo Wurmus
d56553edc3
gnu: r-methylkit: Add r-knitr. 
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
 2020-03-07 19:42:34 +01:00
Ricardo Wurmus
3b7c644569
gnu: r-vsn: Add r-knitr. 
* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
 2020-03-07 19:31:46 +01:00
Ricardo Wurmus
858e642e4c
gnu: python-scanpy: Update to 1.4.5.1. 
* 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
Ricardo Wurmus
4d5d07f75c
gnu: gess: Use WRAP-SCRIPT. 
* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
 2020-03-03 11:33:58 +01:00
Ricardo Wurmus
9309fe355e
gnu: gess: Override PYTHONPATH. 
* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
 2020-03-03 11:33:58 +01:00
Ricardo Wurmus
1284df4ef6
gnu: r-seqminer: Update to 8.0. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
 2020-03-02 21:53:48 +01:00
Ricardo Wurmus
f73b75e00c
gnu: r-hdf5array: Update to 1.14.3. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
 2020-03-01 23:37:58 +01:00
Ricardo Wurmus
6c1f5a1b7e
gnu: r-rsamtools: Update to 2.2.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
 2020-03-01 23:37:52 +01:00
Ricardo Wurmus
9bbf3f9de2
gnu: r-edger: Update to 3.28.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
 2020-03-01 23:37:40 +01:00
Ricardo Wurmus
e3eb7ee474
gnu: r-seurat: Update to 3.1.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
 2020-03-01 23:21:17 +01:00
Ricardo Wurmus
643d90bf74
gnu: infernal: Update to 1.1.3. 
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
 2020-02-27 18:18:34 +01:00
Ricardo Wurmus
e6cc426fbb
gnu: vcftools: Update to 0.1.16. 
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
 2020-02-27 18:18:34 +01:00
Ricardo Wurmus
6c32e9b4dc
gnu: bedtools: Update to 2.29.2. 
* 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
Ricardo Wurmus
d24b3b0213
gnu: rseqc: Update to 3.0.1. 
* 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
Ricardo Wurmus
146430ea0e
gnu: proteinortho: Update to 6.0.14. 
* 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