6f5cbac67d
gnu: pigx-sars-cov-2: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
2022-05-06 15:34:31 +02:00
f550c0ccb0
gnu: Add pigx-sars-cov-2.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable.
(pigx-sars-cov2-ww): Deprecate this package in favor of the former.
2022-05-06 15:34:31 +02:00
39d6c13fda
gnu: python-hic2cool: Fix build.
...
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
2022-05-02 17:33:31 +02:00
b1dd32d8e3
gnu: htslib-for-stringtie: Inherit from htslib-1.12.
...
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
2022-05-02 14:35:26 +02:00
5caad9f252
gnu: python-cooler: Use more recent cytoolz.
...
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
2022-05-02 13:33:16 +02:00
33fe027f91
gnu: Add r-giotto.
...
* gnu/packages/bioinformatics.scm (r-giotto): New variable.
2022-04-26 09:48:14 +02:00
ffb616b69d
gnu: vcflib: Update to 1.0.3.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3.
[source]: Remove trailing #t.
[arguments]: Remove trailing #t from phases.
2022-04-19 21:56:50 +03:00
7034746e15
gnu: scregseg: Remove cythonized file.
...
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
2022-04-14 22:55:33 +03:00
c8a6e4abbc
gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).
...
* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
2022-04-14 13:35:22 +02:00
6413d0898b
gnu: Add r-copykat.
...
* gnu/packages/bioinformatics.scm (r-copykat): New variable.
2022-04-11 16:11:45 +02:00
96a132809f
gnu: smithwaterman: Fix cross-compiling.
...
The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences.
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More
closely match the 'ar' and 'ld' commands when substituting them.
2022-04-10 20:49:33 +03:00
e3e3381fdb
gnu: Add r-rnaseqdtu.
...
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-06 11:43:46 +02:00
df2dc0c416
gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.
...
This is needed since the update of python-loompy.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename
'set-PYTHONPATH to 'set-additional-environment-variables and set
NUMBA_CACHE_DIR.
2022-04-05 18:40:48 +02:00
e721122069
gnu: pigx-scrnaseq: Use new inputs style.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
2022-04-05 18:40:48 +02:00
5d1c9fcdcf
gnu: pigx-scrnaseq: Update to 1.1.8.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
[patches]: Remove.
[native-inputs]: Remove.
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-04-05 18:40:48 +02:00
345f79b2cf
gnu: freebayes: Fix test suite.
...
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
2022-04-04 22:58:25 +03:00
c1fc65ecb6
gnu: smithwaterman: Use new style for phases.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
2022-04-04 22:45:37 +03:00
855c8d9d41
gnu: smithwaterman: Fix cross-compiling.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add
make-flag to use cxx-for-target. Adjust custom 'patch-source and
'build-dynamic phases to use cross toolchain binaries when cross
compiling. Remove trailing #t from phases.
2022-04-04 22:41:54 +03:00
05e68f31ba
gnu: python-velocyto: Set cache directory for Numba.
...
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
2022-03-31 16:02:21 +02:00
8f3dc994bb
gnu: wfmash: Enable test suite.
...
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
2022-03-31 16:29:34 +03:00
1ca9d9e194
gnu: Add wfmash.
...
* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:53 +03:00
7d331dd203
gnu: htslib: Add bzip2 and xz to inputs.
...
htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31 16:14:52 +03:00
a69a44bf59
gnu: python-loompy: Update to 3.0.7.
...
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
2022-03-31 14:37:58 +02:00
591007f7d1
gnu: r-signac: Update to 1.6.0-2.458e647.
...
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 17:40:17 +02:00
977a33139e
gnu: plink-ng: Update to 2.00a3-20220315.
...
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
2022-03-29 15:33:55 +02:00
d710f01957
gnu: Add r-cytobackbone.
...
* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29 14:03:44 +02:00
6d5964e804
gnu: pigx-sars-cov2-ww: Update to 0.0.5.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
847acc3206
gnu: pigx-rnaseq: Update to 0.0.20.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29 13:52:16 +02:00
ca588fdfde
gnu: Add r-scopeloomr.
...
* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
2022-03-09 11:35:59 +01:00
e5dbda5abc
gnu: texlive-latex-pgf: Rename to "texlive-pgf".
...
Suggested by Ricardo Wurmus.
* gnu/packages/tex.scm (texlive-latex-pgf): Rename to...
(texlive-pgf): ... this. Change 'name' accordingly.
(texlive-latex-pgf): Define as deprecated.
(texlive-beamer)[propagated-inputs]: Use the new name.
(texlive-todonotes)[propagated-inputs]: Likewise.
(texlive-adjustbox)[propagated-inputs]: Likewise.
(texlive-tcolorbox)[propagated-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
2022-03-02 19:26:16 +01:00
a6867b2d98
gnu: minimap2: Update to 2.24.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
2022-02-27 11:42:30 +02:00
3fb78caa55
gnu: Add r-dyngen.
...
* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
2022-02-22 18:48:30 +01:00
b5d472ef5d
gnu: python-gffutils: Update to 0.10.1.
...
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1.
[arguments]: Remove obsolete phase. Respect TESTS? in check phase while at
it.
2022-02-15 00:21:16 +01:00
7fc8a6faf6
gnu: Add scvelo.
...
* gnu/packages/bioinformatics.scm (scvelo): New variable.
2022-01-31 16:07:40 +01:00
cd4bf5ecb4
gnu: python-louvain-0.6: Update to 0.7.1.
...
* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1.
[arguments]: Add build phases 'find-igraph and 'pretend-version.
[native-inputs]: Add python-setuptools-scm and python-wheel.
Rename this variable...
(python-louvain-0.7): ...to this, naturally.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update
reference to python-louvain-0.6.
2022-01-31 16:07:39 +01:00
9ce1fd24e3
gnu: bwa-meth: Remove trailing #T from build phase.
...
* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
2022-01-31 16:07:39 +01:00
f32a49fceb
gnu: bwa-meth: Update to 0.2.3.
...
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
2022-01-31 16:07:39 +01:00
f00ed43653
gnu: pigx-sars-cov2-ww: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set
PYTHONPATH variable in new build phase.
2022-01-27 22:15:25 +01:00
aa649ae231
gnu: pigx-scrnaseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
f4cbf11c65
gnu: pigx-bsseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
f127bce3ec
gnu: pigx-chipseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
c6bf89cff0
gnu: pigx-rnaseq: Fix Python module capture.
...
The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
2022-01-27 22:15:25 +01:00
ed9ca97409
gnu: cwltool: Update to 3.1.20220119140128.
...
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20220119140128.
[propagated-inputs]: Change from PYTHON-RDFLIB-5 to PYTHON-RDFLIB.
[native-inputs]: Remove PYTHON-RDFLIB-JSONLD.
2022-01-22 10:23:01 +01:00
af473726b2
gnu: python-pyvcf: Build with old setuptools.
...
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add
PYTHON-SETUPTOOLS.
2022-01-22 10:23:01 +01:00
ce291b193c
gnu: Add r-scseqcomm.
...
* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
2022-01-21 15:53:18 +01:00
dac6b53c7e
gnu: Add r-icellnet.
...
* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
2022-01-21 15:53:18 +01:00
d99e42d7f6
gnu: samtools-0.1: Install headers and library.
...
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases
'install-library and 'install-headers.
2022-01-20 15:25:56 +01:00
61d7da5a1f
gnu: Add r-doubletfinder.
...
* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
2022-01-20 12:00:03 +01:00
2a4c271e61
gnu: python-rdflib: Update to 6.1.1.
...
* gnu/packages/rdf.scm (python-rdflib): Update to 6.1.1.
[arguments]: Remove #:tests. Add #:phases.
[native-inputs]: Change from PYTHON-NOSE to PYTHON-PYTEST.
(python-rdflib-5): New variable.
(python2-rdflib): Inherit from PYTHON-RDFLIB-5.
* gnu/packages/python-xyz.scm (python-prov): Change from PYTHON-RDFLIB to
PYTHON-RDFLIB-5.
* gnu/packages/bioinformatics.scm (cwltool): Likewise.
2022-01-18 19:35:55 +01:00
276f40fdc3
Merge branch 'version-1.4.0'
...
With resolved conflicts in:
gnu/packages/gnome.scm
gnu/packages/openstack.scm
gnu/packages/python-xyz.scm
2022-01-17 11:47:09 -05:00
Ricardo Wurmus
Efraim Flashner
zimoun
Hong Li
Arun Isaac
Mădălin Ionel Patrașcu
Ludovic Courtès
Marius Bakke
Maxim Cournoyer