e87e6cc89d
gnu: r-biomart: Update to 2.44.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.0.
2020-06-13 01:19:41 +02:00
920224771f
gnu: r-annotationdbi: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:41 +02:00
7d91e3bed4
gnu: r-biobase: Update to 2.48.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.48.0.
2020-06-13 01:19:41 +02:00
087a97f8df
gnu: r-genomicranges: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:41 +02:00
e0d40fa275
gnu: r-xvector: Update to 0.28.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
2020-06-13 01:19:41 +02:00
49c766d0bb
gnu: r-limma: Update to 3.44.1.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
2020-06-13 01:19:41 +02:00
cdd83b2e22
gnu: r-variantannotation: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
2020-06-13 01:19:41 +02:00
c14d59d9ad
gnu: r-edger: Update to 3.30.3.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
2020-06-13 01:19:41 +02:00
506735eea6
gnu: r-genomeinfodb: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
2020-06-13 01:19:40 +02:00
8a38b676da
gnu: r-iranges: Update to 2.22.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
2020-06-13 01:19:40 +02:00
f189f536be
gnu: r-s4vectors: Update to 0.26.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
2020-06-13 01:19:40 +02:00
1a9de6cfe8
gnu: r-bioccheck: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:40 +02:00
9f416be83d
gnu: r-biocstyle: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:40 +02:00
1ca88fb8e9
gnu: r-biocviews: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
2020-06-13 01:19:40 +02:00
5de96ae98b
gnu: r-grohmm: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
2020-06-13 01:19:40 +02:00
bb18d11d85
gnu: r-systempiper: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0.
[propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and
r-stringr; remove r-biocgenerics.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:40 +02:00
681cca95b3
gnu: r-shortread: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
2020-06-13 01:19:40 +02:00
3d2899dab5
gnu: r-gostats: Update to 2.54.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
2020-06-13 01:19:40 +02:00
be414286bc
gnu: r-category: Update to 2.54.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
2020-06-13 01:19:40 +02:00
a8613ff861
gnu: r-gseabase: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:40 +02:00
7d8b96e24b
gnu: r-rbgl: Update to 1.64.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
2020-06-13 01:19:39 +02:00
397568dbca
gnu: r-annotationforge: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:39 +02:00
db5addba2c
gnu: r-dexseq: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:39 +02:00
3d7de4ed82
gnu: r-deseq2: Update to 1.28.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1.
[propagated-inputs]: Remove r-hmisc.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:39 +02:00
5fdea056c9
gnu: r-genefilter: Update to 1.70.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:39 +02:00
a620d22ea8
gnu: r-gprofiler: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here...
* gnu/packages/cran.scm (r-gprofiler): ...to here.
2020-06-13 01:19:38 +02:00
fa7bd13e5b
gnu: rcas-web: Use guile2.2 version of Guile-Redis.
...
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change from GUILE-REDIS
to GUILE2.2-REDIS. While at it, rename the GUILE input to "guile" instead
of "guile-next".
2020-06-06 15:35:40 +02:00
0266094531
gnu: python-pypairix: Update to 0.3.7 and build programs.
...
* gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.7.
[source]: Fetch from github.
[arguments]: Add phases "build-programs" and "install-programs".
2020-06-04 11:56:31 +02:00
2f49007dd0
gnu: Add python-pairtools.
...
* gnu/packages/bioinformatics.scm (python-pairtools): New variable.
2020-06-03 15:01:19 +02:00
6742a84c63
gnu: Remove bedtools-2.26.
...
* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable.
2020-06-03 14:07:58 +02:00
08542026ea
gnu: python-pybedtools: Disable unreliable test.
...
* gnu/packages/bioinformatics.scm (python-pybedtools)[arguments]: Disable
test_intron_exon_reads test; run tests verbosely.
test_intron_exon_reads
2020-06-03 14:07:48 +02:00
98d6edb621
gnu: blast+: Use HTTPS home page URI.
...
* gnu/packages/bioinformatics.scm (blast+)[home-page]: Use HTTPS URI.
2020-05-27 01:48:37 +02:00
f41f882272
gnu: bbmap: Use HTTPS home page URI.
...
* gnu/packages/bioinformatics.scm (bbmap)[home-page]: Use HTTPS URI.
2020-05-27 01:45:21 +02:00
9dc50c8c47
gnu: sra-tools: Update to 2.10.6.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6.
[arguments]: Replace CC variable in utf8proc Makefile.
[inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
2020-05-19 12:42:01 +02:00
68de995674
gnu: ncbi-vdb: Update to 2.10.6.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6.
2020-05-19 12:42:01 +02:00
6437c598e7
gnu: ngs-sdk: Update to 2.10.5.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5.
2020-05-19 12:42:01 +02:00
87a40d7203
Merge branch 'master' into core-updates
2020-05-05 20:43:21 +02:00
31def9a9df
gnu: Add grocsvs.
...
* gnu/packages/bioinformatics.scm (grocsvs): New variable.
* gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2020-05-05 10:06:28 +03:00
8bf8cd9b85
Merge branch 'master' into core-updates
...
Conflicts:
gnu/local.mk
gnu/packages/backup.scm
gnu/packages/emacs-xyz.scm
gnu/packages/guile.scm
gnu/packages/lisp.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/web.scm
gnu/packages/xorg.scm
2020-04-30 23:47:49 +02:00
eca648b65b
gnu: Add miniasm.
...
* gnu/packages/bioinformatics.scm (miniasm): New variable.
2020-04-30 15:30:16 +02:00
4a148c6da3
gnu: python2-warpedlmm: Fix build.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
2020-04-30 13:08:33 +02:00
545e12f40d
gnu: Add variant-tools.
...
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
2020-04-28 12:23:28 +02:00
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
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
78799a6fdc
gnu: Update minimap2 to 2.17.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
2020-04-27 21:34:10 +02:00
ccf70a80a1
gnu: Add python-deeptools.
...
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
2020-04-27 13:43:05 +02:00
c43edf6f30
gnu: Add python-deeptoolsintervals.
...
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
2020-04-27 13:39:25 +02:00
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
7abe35febe
Merge branch 'master' into core-updates
2020-04-19 16:53:01 +02:00
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
d8fce2362b
gnu: Add python-hicmatrix.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
2020-04-17 15:53:03 +02:00
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
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
bd21acf6c3
Merge branch 'master' into core-updates
2020-04-15 19:26:55 +02:00
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
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
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
fc58cb5bd2
Merge branch 'master' into core-updates
2020-04-13 20:26:21 +02:00
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
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
bdb90df764
Merge branch 'master' into core-updates
2020-04-11 00:10:23 +02:00
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
2778302399
Merge branch 'master' into core-updates
...
Conflicts:
etc/news.scm
gnu/local.mk
gnu/packages/check.scm
gnu/packages/cross-base.scm
gnu/packages/gimp.scm
gnu/packages/java.scm
gnu/packages/mail.scm
gnu/packages/sdl.scm
gnu/packages/texinfo.scm
gnu/packages/tls.scm
gnu/packages/version-control.scm
2020-04-08 13:00:50 +02:00
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
f12f7a0464
gnu: sailfish: Fix build failure.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to
CPLUS_INCLUDE_PATH instead of overriding it.
2020-04-03 19:11:05 +02:00
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
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
18af687037
Merge branch 'master' into core-updates
...
Conflicts:
gnu/packages/icu4c.scm
gnu/packages/man.scm
gnu/packages/python-xyz.scm
guix/scripts/environment.scm
guix/scripts/pack.scm
guix/scripts/package.scm
guix/scripts/pull.scm
guix/store.scm
2020-03-27 00:12:15 +01:00
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
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
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
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
c4d769d359
Merge branch 'master' into core-updates
2020-03-18 19:41:08 +01:00
961d2ee269
Merge branch 'master' into core-updates
2020-03-14 13:13:40 +01:00
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
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
aaadd6e2e1
gnu: salmon: Adjust for C_INCLUDE_PATH changes.
...
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to
C_INCLUDE_PATH instead of CPATH.
2020-03-13 00:18:57 +01:00
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
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
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
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
ea2822d7d6
gnu: Add python2-pyfaidx.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
2020-02-19 23:00:20 +01:00
f45ada0fc8
gnu: r-seurat: Update to 3.1.3.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3.
[propagated-inputs]: Remove r-sdmtools.
2020-02-19 20:55:00 +01:00
db092c2a90
gnu: r-qtl: Update to 1.45-11.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
2020-02-19 20:54:45 +01:00
01005f4269
gn: edirect: Update to 12.1.20190829.
...
The previous version has disappeared upstream.
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
2020-02-18 13:34:20 +02:00
bf71edd3df
gnu: python2-pbcore: Remove python2-sphinx dependency.
...
* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
2020-02-13 16:47:22 +01:00
94600c3960
gnu: r-gviz: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
2020-01-27 20:48:36 +01:00
c7b98a84d9
gnu: r-genomicfeatures: Update to 1.38.1.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
2020-01-27 20:48:36 +01:00
caf4290bd8
gnu: r-s4vectors: Update to 0.24.3.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
2020-01-27 20:48:36 +01:00
c6b4b4e719
gnu: r-diversitree: Update to 0.9-13.
...
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
2020-01-27 16:33:27 +01:00
87858bc526
gnu: ocaml: Switch to ocaml 4.09 by default.
...
Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.
* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.
2020-01-27 03:56:06 +01:00
a19fb6a436
gnu: Use HTTPS for (gnu packages bioinformatics) home pages.
...
* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
2020-01-21 02:15:32 +01:00
72607005e4
gnu: r-gage: Update home page.
...
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
2020-01-21 02:15:32 +01:00
0388046068
gnu: sra-tools: Update home page.
...
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
2020-01-21 02:15:31 +01:00
0eeaf1ac3c
gnu: raxml: Update home page.
...
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
2020-01-21 02:15:31 +01:00
5832b88c45
gnu: prodigal: Update home page.
...
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
2020-01-21 02:15:31 +01:00
030fe2fb7e
gnu: miso: Update home page.
...
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
2020-01-21 02:15:31 +01:00
b725655fce
gnu: grit: Update home page.
...
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
2020-01-21 02:15:31 +01:00
b56f2b6366
gnu: express-beta-diversity: Update home page.
...
The original is not coming back:
<https://github.com/dparks1134/ExpressBetaDiversity/issues/11 >.
* gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]:
Use source code repository as home page.
2020-01-21 02:15:31 +01:00
568bd2e382
gnu: dendropy: Update home page.
...
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
2020-01-21 02:15:31 +01:00
99db6db7be
gnu: Use HTTPS for bioconductor.org.
...
* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked,
r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno,
r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise.
* gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
2020-01-21 00:43:39 +01:00
f1fa954a7d
gnu: edirect: Use HTTPS home page.
...
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
2020-01-19 06:09:02 +01:00
7699e32289
gnu: kentutils: Build with OpenSSL 1.0.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
2020-01-16 19:20:20 +01:00
d64124df89
gnu: r-delayedarray: Update to 0.12.2.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
2020-01-16 06:53:31 +01:00
f7b5c1a02f
gnu: r-iranges: Update to 2.20.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
2020-01-16 06:53:31 +01:00
fdf69f1ee0
gnu: r-s4vectors: Update to 0.24.2.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
2020-01-16 06:53:31 +01:00
7241b44ad4
gnu: r-biocstyle: Update to 2.14.4.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
2020-01-16 06:53:30 +01:00
2604ecb3a9
gnu: smithwaterman: Update to 0.0.0-2.2610e25.
...
* gnu/packages/bioinformatics.scm (smithwaterman): Update to 0.0.0-2.2610e25.
[arguments]: Add make-flags to build static library. Adjust custom
'install phase to install static library.
2020-01-09 14:30:38 +02:00
0ab7f6c5f4
gnu: vcflib: Update to 1.0.1.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.1.
[source]: Download using url-fetch.
[native-inputs]: Sort alphabetically. Move perl, python ...
[inputs]: ... to here.
[arguments]: Add make-flags. Update custom 'build phase.
(tabixpp-freebayes): Remove variable.
(freebayes)[native-inputs]: Use tabixpp-source over tabixpp-freebayes.
2020-01-09 14:30:38 +02:00
2e3efa6e55
gnu: fastahack: Update to 1.0.0.
...
* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
2020-01-09 14:30:38 +02:00
de933b71ee
gnu: Add intervaltree.
...
* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
2020-01-09 14:30:38 +02:00
612d6a8e5b
gnu: tabixpp: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.0.
[source]: Add snippet to remove vendored library.
[arguments]: Adjust custom 'build phase to fix INCLUDES.
2020-01-09 14:30:37 +02:00
2673620f24
gnu: bwa: Install static library.
...
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static
library.
2020-01-09 14:30:34 +02:00
ba42da245b
gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition.
...
This fixes the bug which prevented uglify-js from being defined properly, and
cascaded back to all Common Lisp packages.
* gnu/packages/bioinformatics.scm: Replace javascript module with lisp-xyz.
* gnu/packages/cran.scm: Use lisp-xyz module.
* gnu/packages/javascript.scm (uglify-js): Move from here...
* gnu/packages/lisp-xyz.scm: ... To here.
* gnu/packages/web.scm: Replace javascript module with lisp-xyz.
* guix/build-system/minify.scm: Find uglify-js in the lisp-xyz module.
2020-01-03 15:03:36 +01:00
04b181cb15
gnu: r-topgo: Update to 2.38.1.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27 21:30:25 +01:00
4997ff5c1b
gnu: r-summarizedexperiment: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27 21:30:25 +01:00
ba17429d67
gnu: r-delayedarray: Update to 0.12.1.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27 21:30:25 +01:00
Ricardo Wurmus
Marius Bakke
Nicolas Goaziou
Marius Bakke
Efraim Flashner
Roel Janssen
Vagrant Cascadian
Jakub Kądziołka
Björn Höfling
Julien Lepiller
Tobias Geerinckx-Rice
Pierre Neidhardt