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Author SHA1 Message Date
Ricardo Wurmus d71078bc75
gnu: Add ngless. 
* gnu/packages/bioinformatics.scm (ngless): New variable.
 2018-10-05 23:59:27 +02:00
Christopher Baines 357450dca0
gnu: bioruby: Update to 1.5.2. 
This works with Ruby 2.5.

* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
 2018-10-05 21:25:39 +01:00
Ricardo Wurmus a6798218be
gnu: samtools-0.1: Adjust to match changes in samtools. 
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make
flags.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus 8e72f0f319
gnu: deeptools: Update to 3.1.2. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2.
[source]: Fetch from git.
[arguments]: Delete reset-gzip-timestamps phase.
[inputs]: Add python-plotly.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus 939882f734
gnu: python-pysam: Update to 0.15.1. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.15.1.
[source]: Fetch from git.
[arguments]: Delete tests requiring internet access; use "invoke".
[inputs]: Add curl.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus f79b59e311
gnu: bcftools: Update to 1.9. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus 4ae4a15232
gnu: samtools: Update to 1.9. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.9.
[origin]: Remove bundled htslib sources.
[arguments]: Remove obsolete make-flags.
 2018-10-05 09:21:54 +02:00
Ricardo Wurmus bd5f5eece9
gnu: htslib: Update to 1.9. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
 2018-10-05 09:21:50 +02:00
pimi 0f1622220a
gnu: Add r-absfiltergsea. 
* gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
 2018-10-02 16:23:49 -04:00
pimi 3f0f49d708
gnu: Add poretools. 
* gnu/packages/bioinformatics.scm (poretools): New variable.
 2018-10-02 16:05:14 -04:00
pimi f2bc53af70
gnu: Add porechop. 
* gnu/packages/bioinformatics.scm (porechop): New variable.
 2018-09-30 14:09:48 -04:00
Ricardo Wurmus e72702475d
gnu: Add r-bseqsc. 
* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
 2018-09-24 13:31:20 +02:00
Ricardo Wurmus 28829c040f
gnu: Add r-cssam. 
* gnu/packages/bioinformatics.scm (r-cssam): New variable.
 2018-09-24 13:31:20 +02:00
Ricardo Wurmus a434730f2e
gnu: Add r-xbioc. 
* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
 2018-09-24 13:31:20 +02:00
Ben Woodcroft 05fb1e0017
gnu: hmmer: Update to 3.2.1. 
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-22 09:16:47 +10:00
pimi 7e27393f82
gnu: Add r-pore. 
* gnu/packages/bioinformatics.scm (r-pore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-21 17:04:37 +02:00
Ricardo Wurmus 89ee8a6edf
gnu: rsem: Update to 1.3.1. 
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-20 17:55:26 +02:00
Ricardo Wurmus 1dd153b3aa
gnu: Add python-hic2cool. 
* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
 2018-09-14 09:15:49 +02:00
Leo Famulari 875d068176
Adjust all users of (gnu packages ldc) to use (gnu packages dlang). 
This is a followup to commit 98d6543f86.

* gnu/packages/bioinformatics.scm, guix/build-system/dub.scm: Adjust
accordingly.
 2018-09-10 15:44:32 -04:00
Ricardo Wurmus 5bfa7510d1
gnu: Add python-pygenometracks. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1189c7f1b0
gnu: Add python-hicexplorer. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 5bb9e0af8d
gnu: Add python-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 80f4db91b1
gnu: Add python-pyfaidx. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1f41f01c14
gnu: Add python-pypairix. 
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a9d496b353
gnu: Add python-intervaltree. 
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus ab50580a9d
gnu: r-annotationhub: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus d53aeeafcc
Add missing use-modules clause. 
This is a follow-up to commit 5dfe491290.
Sorry!

* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
 2018-09-06 04:53:32 +02:00
Ricardo Wurmus 00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc. 
* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
 2018-09-05 20:03:09 +02:00
Ricardo Wurmus 5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor. 
* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
 2018-09-05 20:03:08 +02:00
Ricardo Wurmus f077174178
gnu: r-scran: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus 8e44ff0c0d
gnu: r-scater: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
 2018-09-05 20:03:05 +02:00
Ricardo Wurmus e69c07e61a
gnu: r-hdf5array: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 16527f1cbc
gnu: r-ggbio: Update to 1.28.5. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 70daf9362b
gnu: r-biovizbase: Update to 1.28.2. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3c55304688
gnu: r-edaseq: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 6f6aef80e3
gnu: r-seurat: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.4.
[source]: Remove snippet.
[arguments]: Remove.
[native-inputs]: Remove.
[propagated-inputs]: Remove r-caret, r-diffusionmap, r-fnn, r-gdata, r-ranger,
r-stringr, r-tclust, and rvgam; add r-httr.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 07bd90ce90
gnu: r-msnbase: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 4ee8c37cca
gnu: r-maldiquant: Update to 1.18. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.18.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 48b21f8b6b
gnu: r-seqminer: Update to 6.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.1.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus ad2ed8d01f
gnu: r-genomicfeatures: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus f2e79823c6
gnu: r-rtracklayer: Update to 1.40.6. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus aea1b6fb8a
gnu: r-delayedarray: Update to 0.6.5. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.5.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 3e61c2a8b1
gnu: r-rsamtools: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.3.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus a02340058c
gnu: r-biocparallel: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.2.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 1d56c79f86
gnu: r-genomicranges: Update to 1.32.6. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.6.
 2018-09-05 20:03:04 +02:00
Ricardo Wurmus 688cb08527
gnu: r-limma: Update to 3.36.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 33a103a543
gnu: r-variantannotation: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.1.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 1adf4596a6
gnu: r-edger: Update to 3.22.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 5728d9c6c0
gnu: r-iranges: Update to 2.14.11. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.11.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 3c04375614
gnu: r-biocviews: Update to 1.48.3. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.3.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus ce0e762bf9
gnu: r-annotationforge: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.2.
 2018-09-05 20:03:03 +02:00
Ricardo Wurmus 8afdeb8751
gnu: python-pybigwig: Update to 0.3.12. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.12.
[propagated-inputs]: Add python-numpy.
 2018-09-05 12:01:23 +02:00
Ricardo Wurmus 0d7974c376
gnu: libbigwig: Update to 0.4.2. 
* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.2.
[source]: Fetch from git.
[arguments]: Disable tests; remove build phases "disable-curl-test" and
"create-target-dirs".
[native-inputs]: Add python-2.
 2018-09-05 12:01:23 +02:00
Efraim Flashner 647465ace9
gnu: jellyfish: Update to 2.2.10. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.10.
[supported-systems]: Add aarch64-linux, mips64el-linux.
 2018-09-03 08:32:33 +03:00
pimi 4f9355c360
gnu: Add gffcompare. 
gnu/packages/bioinformatics.scm (gffcompare): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-08-29 14:13:49 -04:00
Ricardo Wurmus c7fe888b42
gnu: Add python-scanpy. 
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
 2018-08-29 17:06:13 +02:00
Ricardo Wurmus 079cdd9c15
gnu: Add find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): New variable.
 2018-08-24 11:20:19 +02:00
Ricardo Wurmus 689aacc12f
gnu: Add gffread. 
* gnu/packages/bioinformatics.scm (gffread): New variable.
 2018-08-14 12:48:14 +02:00
Ricardo Wurmus 242519ce70
gnu: Add r-circus. 
* gnu/packages/bioinformatics.scm (r-circus): New variable.
 2018-08-14 11:29:17 +02:00
Tobias Geerinckx-Rice 9aba9b1278
Migrate search.cpan.org home pages to metacpan.org. 
The venerable search.cpan.org has retired[0].

[0]: https://log.perl.org/2018/05/goodbye-search-dot-cpan-dot-org.html

* guix/import/cpan.scm (cpan-home): Generate metacpan.org home page URIs.
Update all previously generated ones in (gnu packages) to their
canonical new homes.
 2018-08-11 17:22:31 +02:00
Ricardo Wurmus 78933bffb7
gnu: pigx-scrnaseq: Update to 0.0.7. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.7.
[inputs]: Add samtools.
 2018-08-03 15:24:40 +02:00
Ben Woodcroft 3f8c82e6d3
gnu: taxtastic: Add missing propagated-inputs. 
* gnu/packages/bioinformatics.scm (taxtastic)[propagated-inputs]: Add
python-psycopg2, python-fastalite, python-pyyaml, python-six, python-jinja2,
python-dendropy.
 2018-07-29 22:53:10 +10:00
Ben Woodcroft 9e0c135c39
gnu: python-dendropy: Update to 4.4.0. 
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy):
Update to 4.4.0.
[source]: Use GitHub URI. Remove patch.
[properties]: Remove field.
(python2-dendropy)[arguments]: Run tests with setup.py.
[native-inputs]: Remove 'python2-nose.
* gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Delete it.
 2018-07-29 22:53:10 +10:00
Ben Woodcroft 5d5a02dd4c
gnu: Add python-fastalite. 
* gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite):
New variables.
 2018-07-29 21:58:00 +10:00
Ricardo Wurmus 26fd7b24ec
gnu: pigx-scrnaseq: Disable another expensive test. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc
test.
 2018-07-27 15:44:23 +02:00
Ricardo Wurmus ed2dfe3955
gnu: Add snakemake-4. 
* gnu/packages/python.scm (snakemake-4): New variable.
* gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq,
pigx-chipseq)[inputs]: Use it.
 2018-07-27 15:30:38 +02:00
Gábor Boskovits d60772dcdd
gnu: java-picard: Fix manifest. 
* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Adjust phase
'edit-classpath-in-manifest for the new manifest generation code.
 2018-07-26 12:46:50 +02:00
Ricardo Wurmus ffe8d21490
gnu: macs: Update to 2.1.1.20160309. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.1.20160309.
 2018-07-09 13:28:53 +02:00
Ricardo Wurmus 5149aeb7e6
gnu: pigx: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.3.
 2018-07-05 16:02:48 +02:00
Ricardo Wurmus aec7d6be70
gnu: r-getopt: Move from bioinformatics to cran. 
* gnu/packages/bioinformatics.scm (r-getopt): Move from here...
* gnu/packages/cran.scm (r-getopt): ...to here.
 2018-07-05 15:08:44 +02:00
Ricardo Wurmus 08d1a8b138
gnu: pigx-scrnaseq: Update to 0.0.6. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6.
[arguments]: Remove "wrap-executable" phase.
 2018-07-05 00:52:31 +02:00
Ricardo Wurmus fab43c6b84
gnu: Add r-loomr. 
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
 2018-07-03 17:58:55 +02:00
Ricardo Wurmus 13f5eb3494
gnu: pigx-bsseq: Update to 0.0.10. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.10.
[arguments]: Remove "wrap-executable" phase.
 2018-07-03 17:33:51 +02:00
Ricardo Wurmus c7d5cd6ca5
gnu: pigx-rnaseq: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.4.
[arguments]: Remove "wrap-executable" phase.
 2018-07-03 16:20:28 +02:00
Ricardo Wurmus 29cbf8178f
gnu: pigx-chipseq: Update to 0.0.20. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
 2018-07-03 16:20:28 +02:00
Tobias Geerinckx-Rice eeb8b0e631
gnu: Use more HTTPS. 
* gnu/packages/admin.scm (net-base, wakelan, pam-krb5)
[home-page]: Use HTTPS.
(dfc, libpcap, tcpdump, wpa-supplicant-minimal, libcap-ng, audit)
[source, home-page]: Likewise.
* gnu/packages/algebra.scm (eigen)[home-page]: Likewise.
(gp2c, pari-gp)[source, home-page]: Likewise.
* gnu/packages/animation.scm (etl, synfig, synfigstudio, papagayo)
[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (tadbit)[home-page]: Likewise.
 2018-06-22 22:00:24 +02:00
Ricardo Wurmus c57e50b2b9
gnu: pigx-chipseq: Update to 0.0.17. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.17.
[arguments]: Remove "wrap-executable" phase.
 2018-06-22 11:40:27 +02:00
Ludovic Courtès 6fe419743d
Do not record store file name in bioinformatics.scm. 
* gnu/packages/bioinformatics.scm (dropseq-tools): Replace full store
file name with ellipses.
 2018-06-22 10:23:31 +02:00
Ricardo Wurmus 1f73fd017c
gnu: r-complexheatmap: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.1.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus a1c7016498
gnu: r-delayedarray: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.1.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus eafd35bad5
gnu: r-optparse: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.0.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus 1e2b2f41d7
gnu: r-biocviews: Update to 1.48.2. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.2.
 2018-06-21 10:31:22 +02:00
Ricardo Wurmus 901bcb7815
gnu: pigx-chipseq: Update to 0.0.16. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
 2018-06-16 12:11:09 +02:00
Ricardo Wurmus 53131eab2d
gnu: Add minimap2. 
* gnu/packages/bioinformatics.scm (minimap2): New variable.
 2018-06-14 13:51:15 +02:00
Ricardo Wurmus ce573b1128
gnu: pigx-bsseq: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
 2018-06-14 12:56:49 +02:00
Ricardo Wurmus 844cc1c8f3
gnu: pigx-scrnaseq: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5.
[inputs]: Add python-magic.
 2018-06-13 22:30:55 +02:00
Ricardo Wurmus 13b8dcf589
gnu: r-seurat: Update to 2.3.2. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2.
[propagated-inputs]: Add r-hdf5r.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5b2a339e19
gnu: r-s4vectors: Update to 0.18.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus 5b730eba3e
gnu: r-biocviews: Update to 1.48.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
 2018-06-13 15:14:37 +02:00
Ricardo Wurmus cbc1c27b67
gnu: rcas-web: Update to 0.0.5. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
 2018-06-08 17:39:24 +02:00
Ricardo Wurmus bcc2e0ed2e
gnu: r-rcas: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
 2018-06-07 22:51:00 +02:00
Ricardo Wurmus 6d095c4cab
gnu: star: Update to 2.6.0c. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
 2018-06-07 11:09:54 +02:00
Ricardo Wurmus ca8de35e90
Merge branch 'master' into core-updates 2018-06-05 23:44:11 +02:00
Ricardo Wurmus 909301591d
gnu: Add sjcount. 
* gnu/packages/bioinformatics.scm (sjcount): New variable.
 2018-06-05 15:42:44 +02:00
Ricardo Wurmus e53152c72d
gnu: dropseq-tools: Remove failing phase. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 13:12:13 +02:00
Ricardo Wurmus 9cc66d75a2
gnu: pigx-scrnaseq: Use only one variant of Picard. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
 2018-06-05 11:26:34 +02:00
Ricardo Wurmus 1f94ba9408
gnu: java-picard: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
 2018-06-05 11:26:08 +02:00
Ricardo Wurmus a993ad833e
gnu: java-picard-1.113: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
 2018-06-05 11:15:21 +02:00
Ricardo Wurmus e847f402c1
gnu: java-picard-2.10.3: Delete failing build phase. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
 2018-06-05 11:14:38 +02:00
Ricardo Wurmus d7e6fb6d7e
Merge branch 'master' into core-updates 2018-06-05 11:09:39 +02:00
Ricardo Wurmus 71c495c941
gnu: r-rtracklayer: Update to 1.40.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus d19e0690b9
gnu: r-methylkit: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus 0da6afa286
gnu: r-bamsignals: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
 2018-06-05 10:40:42 +02:00
Ricardo Wurmus e0f8970357
Merge branch 'master' into core-updates 2018-06-02 13:44:43 +02:00
Ricardo Wurmus 92963798a6
gnu: r-scater: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0.
[propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove
r-matrixstats and r-biomart.
 2018-06-02 13:42:05 +02:00
Ricardo Wurmus d7e3299987
gnu: r-scran: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
 2018-06-02 13:39:13 +02:00
Ricardo Wurmus 8ec56b2956
gnu: r-delayedmatrixstats: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d99e0938fa
gnu: r-singlecellexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fd613234b7
gnu: r-beachmat: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e9c417361e
gnu: r-rhdf5lib: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 0840352835
gnu: r-hdf5array: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 5cd725d002
gnu: r-qvalue: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus c6c619c179
gnu: r-hitc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 4dedecbe70
gnu: r-fithic: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 8db6256f4b
gnu: r-sushi: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 2d3c172b72
gnu: r-gwascat: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus fecbbac286
gnu: r-gviz: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 6929b97583
gnu: r-gqtlstats: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0.
[propagated-inputs]: Add r-homo-sapiens; remove r-ldblock.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 45c29a6e5c
gnu: r-ldblock: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus 9b0b108ed9
gnu: r-erma: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0.
[propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and
r-iranges.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus d26f95d079
gnu: r-snpstats: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus dcd1f0236c
gnu: r-gqtlbase: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0.
 2018-06-02 13:39:12 +02:00
Ricardo Wurmus e214a6e6ff
gnu: r-ggbio: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 34cc18d4de
gnu: r-biovizbase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 94ae875c0a
gnu: r-organismdbi: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bbcd19fb4d
gnu: r-ensembldb: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1.
[propagated-inputs]: Remove r-annotationhub.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 19adb89854
gnu: r-dirichletmultinomial: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d3fb2ad834
gnu: r-complexheatmap: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus d1463f1b0c
gnu: r-genomicfiles: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 1ba126e0e4
gnu: r-gage: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 419e438d52
gnu: r-keggrest: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 15cc1a6867
gnu: r-fastseg: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 646439c7e3
gnu: r-annotationhub: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 420415b057
gnu: r-interactivedisplaybase: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus a67dd4c5e9
gnu: r-edaseq: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 749b712677
gnu: r-deseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus 0ebd7a4c9f
gnu: r-aroma-light: Update to 3.10.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0.
 2018-06-02 13:39:11 +02:00
Ricardo Wurmus bdc8b40af2
gnu: r-msnid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 250d78eac9
gnu: r-msnbase: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1.
[propagated-inputs]: Add r-mass and r-scales.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 0f773b90db
gnu: r-pcamethods: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 7bd2582971
gnu: r-mzid: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus af8710624d
gnu: r-vsn: Update to 3.48.1. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 5837f1835b
gnu: r-affy: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0.
[inputs]: Add zlib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 82589f7430
gnu: r-affyio: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 39cc491790
gnu: r-mzr: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0.
[inputs]: Add zlib.
[propagated-inputs]: Add r-rhdf5lib.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus a02b82088f
gnu: r-protgenerics: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 9547dd8613
gnu: r-sva: Update to 3.28.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 19ad568e79
gnu: r-methylkit: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus aae4f716da
gnu: r-copywriter: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 8f94487da7
gnu: r-chipseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus 62509bbc81
gnu: r-annotationfilter: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus d73c5728f3
gnu: r-rhdf5: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0.
[arguments]: Remove.
[propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib.
[inputs]: Remove perl.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus c76e8baf9e
gnu: r-tximport: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0.
 2018-06-02 13:39:10 +02:00
Ricardo Wurmus b6c2c8f781
gnu: r-mutationalpatterns: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 72f11ff9c5
gnu: r-bamsignals: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 1a08bb8a17
gnu: r-rhtslib: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1.
[native-inputs]: Remove autoconf.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2c480bb012
gnu: r-zlibbioc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 7e6537e257
gnu: r-motifrg: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 8217c2d0bc
gnu: r-seqlogo: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 17d35de73f
gnu: r-genomation: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 5229cedf57
gnu: r-seqpattern: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 25d1df5764
gnu: r-impute: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 89ef133ebd
gnu: r-bsgenome: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus f2eb2e453e
gnu: r-topgo: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 2f66fecd89
gnu: r-graph: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus b4ad4ec6b4
gnu: r-genomicfeatures: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0.
[propagated-inputs]: Remove r-rmysql.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus a30df29768
gnu: r-rtracklayer: Update to 1.40.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2.
[native-inputs]: Add pkg-config.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 90102bd06b
gnu: r-genomicalignments: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0.
 2018-06-02 13:39:09 +02:00
Ricardo Wurmus 9bf4110ea1
gnu: r-summarizedexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 82f593f378
gnu: r-delayedarray: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0.
[propagated-inputs]: Add r-biocparallel.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d2367a89dd
gnu: r-rsamtools: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 942655add1
gnu: r-biostrings: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e6eac58d4c
gnu: r-biocparallel: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 1763cba80e
gnu: r-biomart: Update to 2.36.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 77f66feee7
gnu: r-annotationdbi: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 6fd71f1b6a
gnu: r-biobase: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus e51afc63b7
gnu: r-genomicranges: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus c2401d06c5
gnu: r-xvector: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 0a465e5694
gnu: r-limma: Update to 3.36.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus d358a5a0c1
gnu: r-variantannotation: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 4639025284
gnu: r-edger: Update to 3.22.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 953c8b18f8
gnu: r-genomeinfodb: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 8b44c28f5d
gnu: r-iranges: Update to 2.14.10. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 33cd15fa84
gnu: r-s4vectors: Update to 0.18.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2.
 2018-06-02 13:39:08 +02:00
Ricardo Wurmus 607acf3194
gnu: r-dnacopy: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 3679a2fec4
gnu: r-bioccheck: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus dc6c168ac1
gnu: r-biocstyle: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5f52b692a
gnu: r-biocviews: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 97af51ef40
gnu: r-biocinstaller: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus e5907a44e1
gnu: r-biocgenerics: Update to 0.26.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9370b8ee9f
gnu: r-grohmm: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 712fe39680
gnu: r-systempiper: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus eabe78faca
gnu: r-shortread: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9da8e275ca
gnu: r-gostats: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus d8410d6610
gnu: r-category: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus f1094f50a7
gnu: r-gseabase: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 9177ac2295
gnu: r-rbgl: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 5516db9e70
gnu: r-annotationforge: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 16da69b5e6
gnu: r-dexseq: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 51c1f96ebc
gnu: r-deseq2: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0.
 2018-06-02 13:39:07 +02:00
Ricardo Wurmus 41657b15f4
gnu: r-genefilter: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 4d70c8c486
gnu: r-geneplotter: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 14e9235f0c
gnu: r-copynumber: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 02be818044
gnu: r-annotate: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 59f87b44da
Merge branch 'master' into core-updates 2018-05-31 13:23:49 +02:00
Ricardo Wurmus ce8b9e3b1c
gnu: r-seurat: Update to 2.3.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.1.
[propagated-inputs]: Remove r-gridextra; add r-reticulate.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 3ca317359c
gnu: r-vegan: Update to 2.5-2. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-2.
 2018-05-31 13:21:31 +02:00
Mark H Weaver 1640f16e78
Merge branch 'master' into core-updates 2018-05-27 01:26:09 -04:00
Ricardo Wurmus a1b802454a
gnu: Add fastp. 
* gnu/packages/bioinformatics.scm (fastp): New variable.
 2018-05-24 17:49:32 +02:00
Mark H Weaver 9d10a63402
Merge branch 'master' into core-updates 2018-05-24 02:34:08 -04:00
Ricardo Wurmus a4ab65ee79
gnu: pigx-scrnaseq: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.4.
 2018-05-23 15:27:32 +02:00
Ricardo Wurmus 0f5ad3a1bc
gnu: bismark: Patch bismark2report before installing. 
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Patch file before
installing it.
 2018-05-22 16:05:41 +02:00
Mark H Weaver 0661758e13
Merge branch 'master' into core-updates 2018-05-21 13:22:32 -04:00
Tobias Geerinckx-Rice c61d822621
gnu: f-seq: Factorise ‘install’ phase. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Let-bind more.
 2018-05-19 05:30:11 +02:00
Tobias Geerinckx-Rice 4ca9581119
gnu: multiqc: Fix build. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Add a
‘relax-requirements’ phase to fix building with python-matplotlib@2.2.
 2018-05-17 23:08:30 +02:00
Mark H Weaver 539bf8f2c0
Merge branch 'master' into core-updates 2018-05-17 01:00:50 -04:00
Ben Woodcroft 2c5289b263
gnu: diamond: Update to 0.9.22. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.22.
 2018-05-12 11:01:21 +10:00
Ricardo Wurmus 126c9e3ff7
gnu: bismark: Update to 0.19.1. 
* gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1.
[source]: Fetch from git; remove non-free software in snippet.
[arguments]: Update install phase.
 2018-05-09 18:37:33 +02:00
Ricardo Wurmus f895a7a4d4
gnu: trim-galore: Update to 0.4.5. 
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.4.5.
[source]: Fetch from git.
[arguments]: Remove custom unpack phase.
 2018-05-09 18:37:33 +02:00
Marius Bakke 12bd588346
Merge branch 'master' into core-updates 2018-05-06 15:56:24 +02:00
Tobias Geerinckx-Rice a2cfe19041
gnu: Use HTTPS for www.boost.org. 
* gnu/packages/bioinformatics.scm (libgff)[license]: Use HTTPS.
* gnu/packages/boost.scm (boost-sync)[license]: Likewise.
(boost)[license]: Likewise.
[home-page]: Likewise, and use canonical ‘www’ subdomain.
 2018-05-01 06:51:15 +02:00
Mark H Weaver 3d5ad159b3
Merge branch 'master' into core-updates 2018-04-30 04:03:54 -04:00
Roel Janssen dad9556c5d
gnu: roary: Update to 3.12.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0.
 2018-04-28 01:52:52 +02:00
Roel Janssen d36d5229ed
gnu: star: Update to 2.6.0a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a.
 2018-04-28 01:24:10 +02:00
Roel Janssen 457fd268ff
gnu: multiqc: Update to 1.5. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5.
 2018-04-28 01:10:24 +02:00
Roel Janssen 4b93efec28
gnu: express: Link with shared protobuf library. 
* gnu/packages/bioinformatics.scm (express): Link with shared protobuf
  library.
 2018-04-28 01:07:15 +02:00
Roel Janssen 4ffa085875
gnu: bamtools: Update to 2.5.1. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1.
 2018-04-28 00:56:59 +02:00
Roel Janssen d0c75e73d4
gnu: taxtastic: Update to 0.8.5. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5.
 2018-04-28 00:43:16 +02:00
Ben Woodcroft 53ec1b7e8b
gnu: vsearch: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0.
 2018-04-27 23:20:00 +10:00
Ben Woodcroft 171cf56c2f
gnu: diamond: Update to 0.9.21. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21.
 2018-04-27 23:20:00 +10:00
Roel Janssen b43a9eb361
gnu: bedops: Update to 2.4.33. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33.
 2018-04-27 01:11:57 +02:00
Roel Janssen c829c5ea85
gnu: samtools: Update to 1.8. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.8.
 2018-04-27 01:11:47 +02:00
Roel Janssen cbd9f91c32
gnu: bcftools: Update to 1.8. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8.
* gnu/local.mk: Remove patch.
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
 2018-04-27 01:11:42 +02:00
Roel Janssen 8df0267ad4
gnu: htslib: Update to 1.8. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.8.
 2018-04-27 01:11:24 +02:00
Ricardo Wurmus 3d7f9cbe75
gnu: pigx-chipseq: Update to 0.0.15. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15.
 2018-04-22 23:00:51 +02:00
Ricardo Wurmus c36ce47635
gnu: r-seurat: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.0.
[propagated-inputs]: Add r-cluster, r-dosnow, r-fitdistrplus, r-foreach,
r-lmtest, r-png, and r-rann.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus aeca5f0c5b
gnu: r-scran: Update to 1.6.9. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 80323c3c13
gnu: r-hitc: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus b6d7deca55
gnu: r-ldblock: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus fb1dcfac46
gnu: r-erma: Update to 0.10.1. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 8defca1d94
gnu: r-gprofiler: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus fc6d3e2606
gnu: r-ggbio: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 0bd5c7b859
gnu: r-genomicalignments: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 4207770218
gnu: r-dexseq: Update to 1.24.4. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 3db5d04ccc
gnu: r-vegan: Update to 2.5-1. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
 2018-04-21 23:07:52 +02:00
Mark H Weaver f89aa1521a
Merge branch 'master' into core-updates 2018-04-10 00:42:22 -04:00
Ricardo Wurmus 482959ffa4
gnu: sambamba: Update to 0.6.7-10-g223fa20. 
* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
 2018-04-06 17:12:15 +02:00
Ricardo Wurmus 262ee8eae2
gnu: htslib-for-sambamba: Fix build. 
* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
 2018-04-06 17:12:07 +02:00
Roel Janssen fdc306879b
gnu: Add delly. 
* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-03-30 10:48:01 -04:00
Ben Woodcroft f38ac742e6
gnu: mash: Update to 2.0. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft c7a8aa131d
gnu: mafft: Update to 7.394. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft 9a40b8d9b2
gnu: diamond: Update to 0.9.19. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
 2018-03-30 12:18:35 +10:00
Marius Bakke 5576cfabf3
Merge branch 'master' into core-updates 2018-03-29 17:34:41 +02:00
Roel Janssen e086d2f68b
gnu: r-mutationalpatterns: Update to 1.4.3. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
  [propagated-inputs]: Remove r-gridextra.
 2018-03-29 15:50:44 +02:00
Roel Janssen 53e42694e5
gnu: kaiju: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
  [inputs]: Add zlib.
 2018-03-29 15:40:52 +02:00
Mark H Weaver e3cfef22c4
gnu: Use invoke and return #t from all builders. 
* gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm,
gnu/packages/avr.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm,
gnu/packages/certs.scm, gnu/packages/check.scm, gnu/packages/code.scm,
gnu/packages/commencement.scm, gnu/packages/dictionaries.scm,
gnu/packages/docbook.scm, gnu/packages/emacs.scm, gnu/packages/embedded.scm,
gnu/packages/fonts.scm, gnu/packages/games.scm, gnu/packages/gnome.scm,
gnu/packages/gnu-doc.scm, gnu/packages/guile.scm, gnu/packages/hurd.scm,
gnu/packages/javascript.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/mate.scm,
gnu/packages/pkg-config.scm, gnu/packages/qt.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/statistics.scm,
gnu/packages/syncthing.scm, gnu/packages/tex.scm, gnu/packages/web.scm,
gnu/packages/wine.scm, gnu/packages/xfce.scm: In the builders of packages
using 'trivial-build-system', use invoke where appropriate, raise exceptions
on errors, and otherwise return #t.
 2018-03-27 21:35:41 -04:00
Tobias Geerinckx-Rice 904c3a4e99
gnu: r-annotate: Update to 1.56.2. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
 2018-03-25 00:36:31 +01:00
Ricardo Wurmus 618050a126
gnu: r-bookdown: Do not propagate ghc-pandoc. 
This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.

* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
 2018-03-22 17:07:15 +01:00
Ricardo Wurmus 363ee7a3f4
gnu: pigx-chipseq: Update to 0.0.10. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
 2018-03-21 11:52:56 +01:00
Ricardo Wurmus d7a11f1a8d
gnu: pigx-chipseq: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
 2018-03-20 19:47:37 +01:00
Mark H Weaver ac21be848a
Merge branch 'master' into core-updates 2018-03-20 14:22:06 -04:00
Ricardo Wurmus 4f1e4f33a0
gnu: pigx-bsseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
 2018-03-20 14:56:44 +01:00
Ricardo Wurmus 616446ffbf
gnu: pigx-rnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
 2018-03-20 12:20:51 +01:00
Mark H Weaver 647888845c
Merge branch 'master' into core-updates 2018-03-20 00:49:05 -04:00
Ricardo Wurmus 9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
 2018-03-19 21:06:51 +01:00
Ricardo Wurmus 096589035e
gnu: bismark: Fix references to gunzip. 
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
 2018-03-19 21:06:51 +01:00
Ricardo Wurmus 51237011bf
gnu: pigx-scrnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
 2018-03-19 21:06:50 +01:00
Ricardo Wurmus d8f08c85ad
gnu: pigx: Update to 0.0.2. 
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
 2018-03-19 16:55:43 +01:00
Ricardo Wurmus d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1. 
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 16:55:43 +01:00
Ricardo Wurmus 32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus fd757a8f21
gnu: pigx-chipseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 11:07:54 +01:00
Mark H Weaver 9f388b1ee1
Merge branch 'master' into core-updates 2018-03-17 01:18:37 -04:00
Ricardo Wurmus c1c9cc664b
gnu: Add pigx. 
* gnu/packages/bioinformatics.scm (pigx): New variable.
 2018-03-16 15:40:31 +01:00
Ricardo Wurmus fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
 2018-03-16 15:40:31 +01:00
Mark H Weaver 6cbee49d66
gnu: All snippets report errors using exceptions, else return #t. 
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
 2018-03-16 09:08:31 -04:00
Ricardo Wurmus 46264c73a6
gnu: Add pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
 2018-03-16 11:15:04 +01:00
Ricardo Wurmus b44437c549
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:01:07 +01:00
Ricardo Wurmus 80420f114c
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:00:31 +01:00
Leo Famulari 32cbbac11a
gnu: Add Diversitree. 
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
 2018-03-15 10:57:51 -04:00
Ricardo Wurmus 8c72ed923d
Merge branch 'master' into core-updates 2018-03-14 17:37:20 +01:00
Ludovic Courtès 189be331ac
build-system/gnu: Add 'bootstrap' phase. 
This factorizes what has become a widespread idiom.

* guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable.
(bootstrap): New procedure.
(%standard-phases): Add it after 'unpack'.
* guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap.
* guix/build/asdf-build-system.scm (%standard-phases/source)
(%standard-phases): Likewise.
* guix/build/cargo-build-system.scm (%standard-phases): Likewise.
* guix/build/cmake-build-system.scm (%standard-phases): Likewise.
* guix/build/dub-build-system.scm (%standard-phases): Likewise.
* guix/build/emacs-build-system.scm (%standard-phases): Likewise.
* guix/build/font-build-system.scm (%standard-phases): Likewise.
* guix/build/go-build-system.scm (%standard-phases): Likewise.
* guix/build/haskell-build-system.scm (%standard-phases): Likewise.
* guix/build/minify-build-system.scm (%standard-phases): Likewise.
* guix/build/ocaml-build-system.scm (%standard-phases): Likewise.
* guix/build/perl-build-system.scm (%standard-phases): Likewise.
* guix/build/python-build-system.scm (%standard-phases): Likewise.
* guix/build/r-build-system.scm (%standard-phases): Likewise.
* guix/build/ruby-build-system.scm (%standard-phases): Likewise.
* guix/build/scons-build-system.scm (%standard-phases): Likewise.
* guix/build/texlive-build-system.scm (%standard-phases): Likewise.
* guix/build/waf-build-system.scm (%standard-phases): Likewise.
* gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap.
(soundtouch, cuetools, bluez-alsa): Remove 'arguments'.
(cava)[arguments]: Replace 'bootstrap.
* gnu/packages/backup.scm (rdup): Remove 'bootstrap.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Replace
'bootstrap.
* gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove
'arguments'.
* gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'.
* gnu/packages/crypto.scm (libb2): Remove #:phases.
* gnu/packages/databases.scm (guile-wiredtiger): Likewise.
* gnu/packages/debug.scm (stress-make): Remove 'bootstrap'.
* gnu/packages/documentation.scm (asciidoc): Likewise.
* gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'.
* gnu/packages/ftp.scm (weex): Remove 'arguments'.
* gnu/packages/game-development.scm (ois): Remove 'arguments'.
* gnu/packages/games.scm (pioneer): Remove 'bootstrap.
* gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap.
(arc-theme): Remove 'arguments'.
(faba-icon-theme): Remove 'bootstrap.
(arc-icon-theme): Remove 'arguments'.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/gtk.scm (guile-rsvg): Likewise.
* gnu/packages/guile.scm (mcron2): Remove 'bootstrap.
(guile-bash): Remove #:phases.
(guile-git): Remove 'bootstrap.
(guile-syntax-highlight): Remove 'arguments'.
(guile-sjson): Likewise.
* gnu/packages/java.scm (classpath-devel): Remove 'bootstrap.
* gnu/packages/kodi.scm (libdvdnav/kodi)
(libdvdread/kodi, libdvdcss/kodi): Likewise.
* gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'.
* gnu/packages/libusb.scm (hidapi): Likewise.
* gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to
'patch-stuff'; move it before 'bootstrap', without autoreconf
invocation.
(eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh'
invocation; move it before 'bootstrap.
(gpm): Replace 'bootstrap'.
(f2fs-tools): Remove 'arguments'.
(rng-tools): Remove #:phases.
* gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to
'copy-intltool-makefile'; remove "autoreconf" invocation and move before
'bootstrap'.
(libmesode): Remove 'arguments'.
(libstrophe): Likewise.
* gnu/packages/microcom.scm (microcom): Likewise.
* gnu/packages/networking.scm (libnet): Remove 'bootstrap.
* gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'.
* gnu/packages/package-management.scm (guix): Replace 'bootstrap.
* gnu/packages/sawfish.scm (librep): Remove 'arguments'.
* gnu/packages/version-control.scm (findnewest): Likewise.
* gnu/packages/video.scm (liba52, handbrake, motion): Replace
'bootstrap.
* gnu/packages/web.scm (fcgiwrap): Remove #:phases.
(tidy): Replace 'bootstrap.
(gumbo-parser): Remove #:phases.
* gnu/packages/wget.scm (wget2): Replace 'bootstrap.
* gnu/packages/wm.scm (i3lock-color): Remove #:phases.
* gnu/packages/xdisorg.scm (xclip): Likewise.
* gnu/packages/xml.scm (libxls): Replace 'bootstrap'.
* gnu/packages/xorg.scm (xf86-video-freedreno)
(xf86-video-intel): Remove #:phases.
* gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
 2018-03-11 22:04:40 +01:00
Ricardo Wurmus fb94174fc3
gnu: Add pigx-bsseq. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus 531afc8a89
gnu: Add pigx-chipseq. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus a539ad867d
gnu: r-rhdf5lib: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
 2018-03-09 11:40:59 +01:00
Ricardo Wurmus 22a0c65969
gnu: Add r-phangorn. 
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
 2018-03-08 23:31:56 +01:00
Ricardo Wurmus 53cc59a1d8
gnu: r-ape: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
 2018-03-08 23:31:55 +01:00
Ricardo Wurmus 84c195e505
gnu: r-dropbead: Update to 0-2.d746c6f. 
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
 2018-03-08 18:53:49 +01:00
Ricardo Wurmus 0bdd5b8ab7
gnu: Add pigx-rnaseq. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
 2018-03-07 23:25:36 +01:00
Ricardo Wurmus c072cf57b9
gnu: samtools: Update to 1.7. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus 727d847980
gnu: htslib: Update to 1.7. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus e325c89076
gnu: r-rhdf5: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
 2018-03-06 16:03:04 +01:00
Efraim Flashner da49d13710
gnu: piranha: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner d9a069c2d9
gnu: libdivsufsort: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner 5110672474
gnu: seek: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner b1d4026dfb
gnu: r-dropbead: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
 2018-03-04 12:05:10 +02:00
Ricardo Wurmus 1adeef3194
gnu: Add dropseq-tools. 
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
 2018-03-03 21:28:05 +01:00
Ricardo Wurmus 72299db9fe
gnu: Add java-picard-2.10.3. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
 2018-03-03 21:28:02 +01:00
Ricardo Wurmus 719fa958f3
gnu: Add java-htsjdk-2.10.1. 
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
 2018-03-03 21:27:59 +01:00
Ricardo Wurmus 9a599c17b7
gnu: Add java-htsjdk-latest. 
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
 2018-03-03 21:27:57 +01:00
Ricardo Wurmus 9ac7db1830
gnu: Add java-biojava-alignment-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
 2018-03-03 21:27:56 +01:00
Ricardo Wurmus 5528f9e8f0
gnu: Add java-biojava-phylo-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
 2018-03-03 21:27:53 +01:00
Ricardo Wurmus e44da58c16
gnu: Add java-biojava-core-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
 2018-03-03 21:27:51 +01:00
Ricardo Wurmus 22c09c335b
gnu: Add java-biojava-alignment. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
 2018-03-03 21:27:48 +01:00
Ricardo Wurmus b28c803708
gnu: Add java-biojava-phylo. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
 2018-03-03 21:27:46 +01:00
Ricardo Wurmus 10645b9212
gnu: Add java-forester-1.005. 
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
 2018-03-03 21:27:44 +01:00
Ricardo Wurmus f09d16e594
gnu: Add java-forester. 
* gnu/packages/bioinformatics.scm (java-forester): New variable.
 2018-03-03 21:27:41 +01:00
Ricardo Wurmus 5fef15e506
gnu: Add java-biojava-core. 
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
 2018-03-03 21:27:36 +01:00
Ricardo Wurmus bd975831c6
gnu: Add fastqc. 
* gnu/packages/bioinformatics.scm (fastqc): New variable.
 2018-03-03 21:21:48 +01:00
Ricardo Wurmus 3ede1550e8
gnu: cutadapt: Update to 1.16. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
 2018-03-02 23:44:16 +01:00
Ricardo Wurmus 9aaf2813e2
gnu: r-scran: Update to 1.6.8. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 6a0e13906b
gnu: r-wgcna: Update to 1.63. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 61cbd49b30
gnu: r-topgo: Update to 2.30.1. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 535014ce60
gnu: r-genomicranges: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus eb8971b742
gnu: r-limma: Update to 3.34.9. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 22d96920d3
gnu: r-edger: Update to 3.20.9. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 99e4b11d81
gnu: r-shortread: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus b180893289
gnu: r-dexseq: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
 2018-03-01 21:28:52 +01:00
Ricardo Wurmus 65c9d25739
gnu: r-qtl: Update to 1.42-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
 2018-02-22 11:18:03 +01:00
Ricardo Wurmus 79c6af13d0
gnu: r-delayedmatrixstats: Update to 1.0.3. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus 59b2864d6c
gnu: r-scater: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus d578278e35
gnu: r-gviz: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus ca7855fcd2
gnu: r-gprofiler: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 8877ab432e
gnu: r-ensembldb: Update to 2.2.2. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus ebec98ae1d
gnu: r-seurat: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1.
[propagated-inputs]: Remove r-nmf; add r-metap.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 3118b28644
gnu: r-qtl: Update to 1.42-7. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 824c200475
gnu: r-genomicranges: Update to 1.30.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus e8484711c6
gnu: r-getopt: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 9800f7d9e8
gnu: r-bookdown: Update to 0.7. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7.
[propagated-inputs]: Add r-tinytex.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus ff9d1a2f0c
Merge branch 'master' into core-updates 2018-02-18 00:39:25 +01:00
Ben Woodcroft 369eee8763
gnu: vsearch: Update to 2.7.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.1.
 2018-02-17 12:44:29 +10:00
Mark H Weaver 150062f190
Merge branch 'master' into core-updates 2018-02-16 13:14:26 -05:00
Ben Woodcroft 5ebc8e7f41
gnu: diamond: Update to 0.9.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
 2018-02-16 08:13:24 +10:00
Ricardo Wurmus 152d30c346
gnu: Add python-loompy. 
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
 2018-02-15 17:19:00 +01:00
Ricardo Wurmus 3082de04c2
gnu: Add r-dropbead. 
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
 2018-02-15 17:18:54 +01:00
Ricardo Wurmus 05f7296012
gnu: Add r-delayedmatrixstats. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
 2018-02-15 17:18:52 +01:00
Mark H Weaver 932c98326d
Merge branch 'master' into core-updates 2018-02-14 03:40:08 -05:00
Ben Woodcroft 119c09c219
gnu: vsearch: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
 2018-02-14 07:43:19 +10:00
Mark H Weaver 288b8fd5e9
Merge branch 'master' into core-updates 2018-02-13 13:17:15 -05:00
Ricardo Wurmus 97bf74076c
gnu: r-gprofiler: Update to 0.6.3. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 169942368f
gnu: r-ensembldb: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 34d077b8bc
gnu: r-gage: Update to 2.28.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus f5f9442703
gnu: r-keggrest: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
 2018-02-13 16:18:43 +01:00