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1426 Commits

Author SHA1 Message Date
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