8d59c262ad
Merge branch 'master' into core-updates
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Conflicts:
gnu/local.mk
gnu/packages/algebra.scm
gnu/packages/bioinformatics.scm
gnu/packages/curl.scm
gnu/packages/docbook.scm
gnu/packages/emacs-xyz.scm
gnu/packages/maths.scm
gnu/packages/plotutils.scm
gnu/packages/python-web.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/readline.scm
gnu/packages/tls.scm
gnu/packages/xml.scm
gnu/packages/xorg.scm
2021-06-06 21:16:32 +02:00
b65c02e2d3
gnu: freebayes: Update to 1.3.5.
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* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-06-06 12:13:28 +03:00
d1e7b50dbf
gnu: python-cooler: Update to 0.8.11.
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* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
2021-06-06 08:33:21 +02:00
f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
2021-06-05 09:12:39 +02:00
7382aa00b8
gnu: python-scanpy: Update to 1.7.2.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04 23:51:35 +02:00
b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'.
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* gnu/packages/bioinformatics.scm
(nanopolish)[arguments]<#:phases>{wrap-programs}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'.
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* gnu/packages/bioinformatics.scm
(gess)[arguments]<#:phases>{install}
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'.
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* gnu/packages/bioinformatics.scm
(prinseq)[arguments]<#:phases>{install}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'.
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* gnu/packages/bioinformatics.scm
(proteinortho)[arguments]<#:phases>{wrap-programs}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
d06ae05808
gnu: Add pigx-sars-cov2-ww.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
2021-06-04 12:57:08 +02:00
0928e55266
gnu: Add fit-sne.
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* gnu/packages/bioinformatics.scm (fit-sne): New variable.
2021-06-03 12:22:29 +02:00
011d586c2c
gnu: Add biobambam2.
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* gnu/packages/bioinformatics.scm (biobambam2): New variable.
2021-06-02 13:54:15 +02:00
18e0081045
gnu: Add libmaus2.
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* gnu/packages/bioinformatics.scm (libmaus2): New variable.
2021-06-02 13:54:15 +02:00
7ae2b1f2dc
gnu: Add bamutils.
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* gnu/packages/bioinformatics.scm (bamutils): New variable.
2021-06-01 13:14:38 +02:00
f463f376e9
gnu: bits: Use git-version and git-file-name.
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* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:10:20 +02:00
d1e1c02e28
gnu: piranha: Use git-version.
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* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
2021-05-31 16:10:00 +02:00
8c033085cc
gnu: r-chipkernels: Use git-version and git-file-name.
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* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:09:35 +02:00
3acfbd4811
gnu: f-seq: Use git-version and git-file-name.
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* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:09:07 +02:00
09b50a6ec2
gnu: bismark: Use git-file-name.
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* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
2021-05-31 16:08:47 +02:00
f383f9e311
gnu: filevercmp: Use git-version.
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* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
2021-05-31 16:08:12 +02:00
a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
2021-05-31 15:53:20 +02:00
b0ecd6cea9
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.
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* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 15:46:30 +02:00
c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
2021-05-31 15:39:49 +02:00
7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
2021-05-31 15:39:49 +02:00
36cb01066c
gnu: r-copyhelper: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31 15:39:47 +02:00
31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
2021-05-31 15:39:00 +02:00
0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
2021-05-31 15:39:00 +02:00
cc1dbea883
gnu: r-annotationfilter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
2021-05-31 15:39:00 +02:00
67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
2021-05-31 15:39:00 +02:00
b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
2021-05-31 15:39:00 +02:00
bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
2021-05-31 15:39:00 +02:00
7360dea624
gnu: r-rcas: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
2021-05-31 15:39:00 +02:00
45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
2021-05-31 15:38:59 +02:00
043c309d15
gnu: r-rhtslib: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
2021-05-31 15:38:59 +02:00
e0c81584ea
gnu: r-zlibbioc: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
2021-05-31 15:38:58 +02:00
0006a66415
gnu: r-seqlogo: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
2021-05-31 15:38:21 +02:00
c2a18aee16
gnu: r-motifrg: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
2021-05-31 15:38:00 +02:00
621aa3b442
gnu: r-sva: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
2021-05-31 15:38:00 +02:00
900ef8fb1e
gnu: r-protgenerics: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
2021-05-31 15:38:00 +02:00
720d2694a5
gnu: r-mzr: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
2021-05-31 15:38:00 +02:00
88cf24febb
gnu: r-ensembldb: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
2021-05-31 15:37:59 +02:00
fea33b9d1e
gnu: r-biovizbase: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
2021-05-31 15:37:59 +02:00
8d4311bb8e
gnu: r-vsn: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
2021-05-31 15:37:59 +02:00
96ae9822c4
gnu: r-affyio: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
2021-05-31 15:37:59 +02:00
8182e6a6fd
gnu: r-organismdbi: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
2021-05-31 15:37:59 +02:00
d1ea2b7c8b
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
2021-05-31 15:37:59 +02:00
0b5b41c561
gnu: r-genomicfiles: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
2021-05-31 15:37:59 +02:00
ff65fa90d2
gnu: r-complexheatmap: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
2021-05-31 15:37:59 +02:00
84019edf38
gnu: r-gage: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
2021-05-31 15:37:59 +02:00
d0a5503752
gnu: r-keggrest: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
2021-05-31 15:37:58 +02:00
Marius Bakke
Efraim Flashner
Mădălin Ionel Patrașcu
Ricardo Wurmus
Roel Janssen
Maxime Devos
zimoun