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Author SHA1 Message Date
Efraim Flashner 61bce4d143
gnu: python-mappy: Move to (gnu packages bioinformatics). 
* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
 2021-06-08 09:50:55 +03:00
Ricardo Wurmus 4a01e00a13
gnu: pigx-rnaseq: Update to 0.0.17. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
 2021-06-08 00:53:06 +02:00
Ricardo Wurmus be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus bb38287570
gnu: salmon: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 9875dae429
gnu: macs: Update to 2.2.7.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 1ace395f9c
gnu: libgff: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 176513f5f3
gnu: jellyfish: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 1ac8f05103
gnu: multiqc: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
 2021-06-07 10:53:16 +02:00
Mădălin Ionel Patrașcu a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3. 
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Marius Bakke 8d59c262ad
Merge branch 'master' into core-updates 
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
Efraim Flashner b65c02e2d3
gnu: freebayes: Update to 1.3.5. 
* 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
Mădălin Ionel Patrașcu d1e7b50dbf
gnu: python-cooler: Update to 0.8.11. 
* 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
Ricardo Wurmus f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13. 
* 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
Roel Janssen 7382aa00b8
gnu: python-scanpy: Update to 1.7.2. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
 2021-06-04 23:51:35 +02:00
Maxime Devos b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'. 
* 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
Maxime Devos 2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'. 
* 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
Maxime Devos c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'. 
* 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
Maxime Devos fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'. 
* 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
Ricardo Wurmus d06ae05808
gnu: Add pigx-sars-cov2-ww. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
 2021-06-04 12:57:08 +02:00
Ricardo Wurmus 0928e55266
gnu: Add fit-sne. 
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
 2021-06-03 12:22:29 +02:00
Ricardo Wurmus 011d586c2c
gnu: Add biobambam2. 
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
 2021-06-02 13:54:15 +02:00
Ricardo Wurmus 18e0081045
gnu: Add libmaus2. 
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
 2021-06-02 13:54:15 +02:00
Roel Janssen 7ae2b1f2dc
gnu: Add bamutils. 
* gnu/packages/bioinformatics.scm (bamutils): New variable.
 2021-06-01 13:14:38 +02:00
Ricardo Wurmus f463f376e9
gnu: bits: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:10:20 +02:00
Ricardo Wurmus d1e1c02e28
gnu: piranha: Use git-version. 
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
 2021-05-31 16:10:00 +02:00
Ricardo Wurmus 8c033085cc
gnu: r-chipkernels: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:09:35 +02:00
Ricardo Wurmus 3acfbd4811
gnu: f-seq: Use git-version and git-file-name. 
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
 2021-05-31 16:09:07 +02:00
Ricardo Wurmus 09b50a6ec2
gnu: bismark: Use git-file-name. 
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
 2021-05-31 16:08:47 +02:00
Ricardo Wurmus f383f9e311
gnu: filevercmp: Use git-version. 
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
 2021-05-31 16:08:12 +02:00
Ricardo Wurmus a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor). 
* 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
Ricardo Wurmus b0ecd6cea9
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1. 
* 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
zimoun c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor). 
* 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
zimoun 7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor). 
* 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
zimoun 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
zimoun 31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor). 
* 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
zimoun 0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor). 
* 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
zimoun 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
zimoun 67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor). 
* 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
zimoun b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor). 
* 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
zimoun bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). 
* 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
zimoun 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
zimoun 45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor). 
* 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 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
zimoun 22cda2e432
gnu: r-affy: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 32ae36e96f
gnu: r-fastseg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 9644745692
gnu: r-annotationhub: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun dfe6224f5f
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun f6f43a2d40
gnu: r-edaseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun ef954bb488
gnu: r-deseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun bb118f20fe
gnu: r-aroma-light: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 7756e08b44
gnu: r-mzid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun ad46c8aa7f
gnu: r-pcamethods: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
 2021-05-31 15:37:57 +02:00
zimoun d7fa9c1ffd
gnu: r-genomationdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:37:55 +02:00
zimoun f8fe5497c7
gnu: r-genomation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
 2021-05-31 15:36:32 +02:00
zimoun f3b50aa4fd
gnu: r-go-db: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
 2021-05-31 15:35:53 +02:00
zimoun 14fb30e5f6
gnu: r-seqpattern: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
 2021-05-31 15:35:30 +02:00
zimoun b832fddbfc
gnu: r-impute: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
 2021-05-31 15:34:45 +02:00
zimoun 4f030cc0db
gnu: r-msnbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 8c7c78bfce
gnu: r-msnid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 537d48d869
gnu: r-bsgenome: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 90bbab5cff
gnu: r-topgo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun f78ff75b41
gnu: r-genomicfeatures: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun a88230a1bc
gnu: r-rtracklayer: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun ca1a015777
gnu: r-genomicalignments: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
 2021-05-31 15:34:39 +02:00
Ricardo Wurmus e3cde9aaf8
gnu: Add mosaicatcher. 
* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-29 07:26:15 +02:00
Christopher Baines 6417b97c7e
Revert "gnu: Add mosaicatcher." 
mosaicatcher-unbundle-htslib.patch is missing.

This reverts commit b1ae0f30d8.
 2021-05-29 01:21:14 +01:00
Ricardo Wurmus b1ae0f30d8
gnu: Add mosaicatcher. 
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-28 23:00:47 +02:00
Roel Janssen 87c9f63fce
gnu: Add python-pyega3. 
* gnu/packages/bioinformatics.scm (python-pyega3): New variable.
 2021-05-27 23:01:35 +02:00
Roel Janssen a30e616ccc
gnu: Add python-htsget. 
* gnu/packages/bioinformatics.scm (python-htsget): New variable.
 2021-05-27 22:50:46 +02:00
Efraim Flashner c5f7203e3e
gnu: minimap2: Install more files. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules.
Adjust custom 'install phase to also install library, headers and a
pkg-config file.
 2021-05-26 15:22:10 +03:00
Efraim Flashner 36a90d0637
gnu: minimap2: Update to 2.18. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.18.
[source]: Remove patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-05-26 15:22:10 +03:00
Roel Janssen af163badb4
gnu: Add r-phantompeakqualtools. 
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable.
 2021-05-26 09:34:37 +02:00
Roel Janssen b1fee8a003
gnu: Add r-spp. 
* gnu/packages/bioinformatics.scm (r-spp): New variable.
 2021-05-26 09:29:01 +02:00
Marius Bakke 4ea6852c5f
Merge branch 'master' into core-updates 2021-05-22 17:21:57 +02:00
Ricardo Wurmus 7ff515aa51
gnu: r-rhdf5filters: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Update to 1.2.1.
 2021-05-20 14:43:34 +02:00
Ricardo Wurmus 48b8a5e701
gnu: pigx-chipseq: Update to 0.0.52. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.52.
 2021-05-17 18:45:55 +02:00
Ludovic Courtès 25487c3fe6
Merge branch 'master' into core-updates 2021-05-15 22:55:24 +02:00
Ricardo Wurmus 848126d008
gnu: prinseq: Fix references to perl executable. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Embed concrete
references to the "perl" executable.
 2021-05-14 17:11:52 +02:00
Marius Bakke f034264204
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/bioinformatics.scm
	gnu/packages/django.scm
	gnu/packages/gtk.scm
	gnu/packages/llvm.scm
	gnu/packages/python-web.scm
	gnu/packages/python.scm
	gnu/packages/tex.scm
	guix/build-system/asdf.scm
	guix/build/emacs-build-system.scm
	guix/profiles.scm
 2021-05-09 21:29:46 +02:00
Ricardo Wurmus 9b99b6d947
gnu: Add ensembl-vep. 
* gnu/packages/bioinformatics.scm (ensembl-vep): New variable.
 2021-05-07 08:52:49 +02:00
Ricardo Wurmus ce7b202f9b
gnu: Add perl-bio-db-hts. 
* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable.
 2021-05-06 18:56:24 +02:00
Ricardo Wurmus da7f89c737
gnu: python-pybedtools: Update to 0.8.2. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2.
[arguments]: Remove outdated substitutions; simplify check phase.
 2021-05-05 16:18:13 +02:00
Ricardo Wurmus 7694acebd1
gnu: r-summarizedexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here...
* gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here.
 2021-05-04 10:11:34 +02:00
Ricardo Wurmus d4051161e7
gnu: r-ensembldb: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 7072dc8c53
gnu: r-gage: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 3b002a49d4
gnu: r-annotationhub: Update to 2.22.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1.
 2021-05-04 09:47:36 +02:00
Roel Janssen f09e4dd8ea
gnu: Add pbgzip. 
* gnu/packages/bioinformatics.scm (pbgzip): New variable.
 2021-04-30 18:44:46 +02:00
Roel Janssen 7540f6915c
gnu: Update bedtools to 2.30.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
  [inputs]: Use latest samtools.
 2021-04-29 12:14:06 +02:00
Roel Janssen 558d11c3a8
gnu: Update samtools to 1.12. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
 2021-04-29 12:14:02 +02:00
Roel Janssen b904bb89a0
gnu: Update bcftools to 1.12. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
 2021-04-29 12:13:56 +02:00
Roel Janssen 241994230b
gnu: htslib: Update to 1.12. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
 2021-04-29 12:13:46 +02:00
Ricardo Wurmus e7707d5262
gnu: pigx-bsseq: Update to 0.1.3. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3.
[inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
 2021-04-28 21:58:05 +02:00
Ricardo Wurmus 01e33a031e
gnu: Add lofreq. 
* gnu/packages/bioinformatics.scm (lofreq): New variable.
 2021-04-28 17:41:47 +02:00
Ricardo Wurmus f01b3cd063
gnu: kraken2: Replace references to rsync. 
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
 2021-04-28 14:50:50 +02:00
Ricardo Wurmus 5ea5ea6066
gnu: Add python-pyliftover. 
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
 2021-04-28 10:52:12 +02:00
Vinicius Monego 76fb1a5cf2
gnu: Add python-louvain 0.15. 
* gnu/packages/graph.scm (python-louvain): Rename variable to
python-louvain-0.6.
(python-louvain): New variable.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Use
python-louvain-0.6.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2021-04-25 14:49:57 -04:00
Ricardo Wurmus f1f17c7bba
gnu: Add shorah. 
* gnu/packages/bioinformatics.scm (shorah): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus c9371b698d
gnu: Add r-shinycell. 
* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus 92032d8081
gnu: Add kraken2. 
* gnu/packages/bioinformatics.scm (kraken2): New variable.
 2021-04-22 08:31:17 +02:00
Roel Janssen c3926120ba
gnu: Update blast+ to 2.11.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.11.0.
 2021-04-16 20:56:43 +02:00
Efraim Flashner fcc39864db
Merge remote-tracking branch 'origin/master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/boost.scm
	gnu/packages/chez.scm
	gnu/packages/compression.scm
	gnu/packages/crates-io.scm
	gnu/packages/docbook.scm
	gnu/packages/engineering.scm
	gnu/packages/gcc.scm
	gnu/packages/gl.scm
	gnu/packages/gtk.scm
	gnu/packages/nettle.scm
	gnu/packages/python-check.scm
	gnu/packages/python-xyz.scm
	gnu/packages/radio.scm
	gnu/packages/rust.scm
	gnu/packages/sqlite.scm
	guix/build-system/node.scm
 2021-04-16 14:39:48 +03:00
Arun Isaac 563e4bd884
gnu: cwltool: Update to 3.0.20210319143721. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.0.20210319143721.
[arguments]: In the loosen-version-restrictions phase, relax pytest version
restriction. In the modify-tests phase, delete file tests/test_content_type.py
since it contains tests that require network access.
 2021-04-14 22:39:54 +05:30
Arun Isaac 12e210d907
gnu: python-schema-salad: Update to 7.1.20210316164414. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
7.1.20210316164414.
[arguments]: Add skip-failing-tests phase.
 2021-04-14 22:39:54 +05:30
Tobias Geerinckx-Rice e5852655b8
gnu: sortmerna: Mark up description. 
* gnu/packages/bioinformatics.scm (sortmerna)[description]: Use @acronym{}.
 2021-04-10 14:11:26 +02:00
Ricardo Wurmus 5f0c3535aa
gnu: r-genomicfeatures: Update to 1.42.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3.
 2021-04-08 13:28:24 +02:00
zimoun 23686ba3eb
Revert "Revert some commits that caused `guix pull` to fail." 
This reverts commit 8ec0ca8faf.
 2021-03-31 21:23:45 +02:00
Efraim Flashner 04ba7a196a
gnu: plink-ng: Build prettify binary. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to also build prettify.
 2021-03-31 14:33:42 +03:00
Efraim Flashner 5f3f2a7cc8
gnu: plink-ng: Remove custom install phase. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags and remove custom 'install phase.
 2021-03-31 14:33:34 +03:00
Efraim Flashner 977ea2c0a3
gnu: plink-ng: Sort inputs alphabetically. 
* gnu/packages/bioinformatics.scm (plink-ng)[inputs]: Sort
alphabetically.
 2021-03-31 14:32:43 +03:00
Efraim Flashner 58e9e0e142
gnu: plink-ng: Update to 2.00a2.3. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a2.3.
[arguments]: Adjust make-flags.
 2021-03-31 14:32:43 +03:00
Efraim Flashner 2aab587f84
Merge remote-tracking branch 'origin/master' into core-updates 2021-03-24 20:50:44 +02:00
Hong Li ee4fc3b662
gnu: Add r-signac. 
* gnu/packages/bioinformatics.scm (r-signac): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-03-22 14:27:17 +01:00
Mark H Weaver 1a265842e6
gnu: Use PACKAGE/INHERIT in more places. 
* gnu/packages/algebra.scm (fftwf, fftw-openmpi),
gnu/packages/audio.scm (ztoolkit-rsvg),
gnu/packages/bioinformatics.scm (python2-dendropy),
gnu/packages/boost.scm (boost-with-python2),
gnu/packages/check.scm (python2-mock, python2-pytest-mock),
gnu/packages/cups.scm (hplip-minimal),
gnu/packages/freedesktop.scm (libinput-minimal),
gnu/packages/gettext.scm (gnu-gettext),
gnu/packages/glib.scm (python2-pygobject),
gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi),
gnu/packages/groff.scm (groff-minimal),
gnu/packages/jami.scm (ffmpeg-jami),
gnu/packages/libcanberra.scm (libcanberra/gtk+-2),
gnu/packages/lirc.scm (python2-lirc),
gnu/packages/llvm.scm (clang-runtime-3.5),
gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple),
gnu/packages/node.scm (libnode),
gnu/packages/onc-rpc.scm (libtirpc/hurd),
gnu/packages/python-compression.scm (bitshuffle-for-snappy),
gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography)
(python2-cryptography, python2-m2crypto),
gnu/packages/python-web.scm (python2-html2text, python2-tornado)
(python2-terminado, python2-ndg-httpsclient, python2-websocket-client)
(python2-rauth, python2-url, python2-s3transfer),
gnu/packages/python-xyz.scm (python2-psutil, python2-serpent)
(python2-humanfriendly, python2-empy, python2-parse-type, python2-polib)
(python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc)
(python2-ipyparallel, python2-traitlets, python2-dbus)
(python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse)
(python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal)
(python2-contextlib2, python2-promise, python2-anyjson, python2-amqp)
(python2-kombu, python2-billiard, python2-celery, python2-whoosh)
(python2-jellyfish, python-rope, ptpython-2, python2-binaryornot)
(python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort)
(python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash)
(python2-cloudpickle, python2-reparser),
gnu/packages/python.scm (python2-called-python),
gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt)
(python-qscintilla, python-pyqt+qscintilla),
gnu/packages/scanner.scm (sane-backends),
gnu/packages/sdl.scm (guile3.0-sdl2),
gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc)
(python-sepolgen, policycoreutils),
gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack),
gnu/packages/simulation.scm (fenics),
gnu/packages/statistics.scm (python2-statsmodels),
gnu/packages/texinfo.scm (info-reader),
gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1),
gnu/packages/xml.scm (xmlsec-nss),
gnu/packages/xorg.scm (uim-gtk, uim-qt),
guix/build-system/python.scm (package-with-explicit-python)
(strip-python2-variant): Use PACKAGE/INHERIT.
 2021-03-17 03:58:10 -04:00
Ricardo Wurmus fcf8c6c565
gnu: hisat2: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.
 2021-03-16 11:12:01 +01:00
Leo Famulari 8ec0ca8faf
Revert some commits that caused `guix pull` to fail. 
This reverts commits 821e643921 through
8f9fd9b70c.

Specifically, these commits caused the build failure of
guix-package-cache.drv like this:

------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
 2021-03-15 19:52:34 -04:00
zimoun d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun adf45daae9
gnu: r-rsamtools: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 821e643921
gnu: r-limma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
 2021-03-15 23:30:26 +01:00
Ricardo Wurmus 14204d696c
gnu: r-genomicfeatures: Update to 1.42.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus f10f2745eb
gnu: r-delayedarray: Update to 0.16.2. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
 2021-03-15 15:03:08 +01:00
zimoun bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
 2021-03-15 14:06:24 +01:00
zimoun 082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
 2021-03-15 14:06:16 +01:00
zimoun 35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
 2021-03-15 14:05:56 +01:00
zimoun 8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
 2021-03-15 14:05:47 +01:00
zimoun 9949f459bf
gnu: r-iranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
 2021-03-15 14:05:37 +01:00
zimoun d64e3a487b
gnu: r-s4vectors: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
 2021-03-15 14:05:27 +01:00
zimoun 852fa82d4c
gnu: r-bioccheck: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
 2021-03-15 14:05:22 +01:00