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Author SHA1 Message Date
Ricardo Wurmus c098c49b3e
gnu: sailfish: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
 2018-11-08 08:53:54 +01:00
Ricardo Wurmus 4031e7f1ec
gnu: ngs-sdk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus 6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus 3398dfb764
gnu: ncbi-vdb: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
 2018-11-08 08:53:53 +01:00
Ricardo Wurmus e0f1aa2d2b
gnu: tadbit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
 2018-11-08 08:53:50 +01:00
Ricardo Wurmus f3f34b132c
gnu: filevercmp: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
 2018-11-07 23:17:36 +01:00
Ricardo Wurmus 3b888065da
gnu: ritornello: Update to 2.0.1. 
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
 2018-11-07 23:17:36 +01:00
Ricardo Wurmus 7145f4e519
gnu: ritornello: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus e0a8fc85dd
gnu: snap-aligner: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 6236524409
gnu: sortmerna: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 273df99d7d
gnu: vsearch: Fetch source from git. 
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 67caa4b773
gnu: preseq: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 37e285be43
gnu: preseq: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 63f3255e13
gnu: seqtk: Update to 1.3. 
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 019fcdf20a
gnu: seqtk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus b9d0c3564b
gnu: raxml: Update to 8.2.12. 
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus d9ba126d17
gnu: python2-biom-format: Fix build. 
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 4715d4af17
gnu: raxml: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 5e242b02c3
gnu: pyicoteo: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 2b773a9273
gnu: sra-tools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 55698df260
gnu: libgff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 4257c10ad2
gnu: kentutils: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 1a20bcadf3
gnu: r-seqgl: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus a2b9d6a8d0
gnu: pplacer: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 6052264b56
gnu: minced: Update to 0.3.2. 
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 9d94ca0ebf
gnu: minced: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus b58d9e4aa2
gnu: metabat: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 5c1f35e71b
gnu: mash: Update to 2.1. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 497fc04d8f
gnu: mash: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 2dc28391f3
gnu: kaiju: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
 2018-11-07 20:47:22 +01:00
Ricardo Wurmus 6fe323bf2e
gnu: kaiju: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
 2018-11-07 20:46:36 +01:00
Ricardo Wurmus f0731591a5
gnu: idr: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
 2018-11-07 20:41:58 +01:00
Ricardo Wurmus b8a6230df3
gnu: java-htsjdk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
 2018-11-07 20:36:07 +01:00
Ricardo Wurmus 57be690d91
gnu: hisat2: Use versioned source URL. 
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
 2018-11-07 20:32:29 +01:00
Ricardo Wurmus c8f02c1dcb
gnu: grit: Update to 2.0.5. 
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
 2018-11-07 20:30:44 +01:00
Ricardo Wurmus 8d75adbf03
gnu: grit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
 2018-11-07 20:27:10 +01:00
Ricardo Wurmus 152bebd9e0
gnu: gemma: Update to 0.98. 
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
 2018-11-07 20:26:46 +01:00
Ricardo Wurmus b113f39019
gnu: gemma: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
 2018-11-07 20:26:45 +01:00
Ricardo Wurmus 91b71cfbba
gnu: fxtract: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
 2018-11-07 19:55:50 +01:00
Ricardo Wurmus 7ca49ab57a
gnu: ribodiff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
 2018-11-07 19:48:21 +01:00
Ricardo Wurmus 239716fb0b
gnu: python-biom-format: Update to 2.1.7. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
 2018-11-07 19:47:07 +01:00
Ricardo Wurmus 007a81d5cf
gnu: python-biom-format: Fetch source from git. 
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
 2018-11-07 19:10:36 +01:00
Ricardo Wurmus 383cb7b8e6
gnu: bioawk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
 2018-11-07 19:06:30 +01:00
Ricardo Wurmus 20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
 2018-11-07 18:52:46 +01:00
Ricardo Wurmus 8e58319c45
gnu: bamtools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
 2018-11-07 18:44:30 +01:00
Ricardo Wurmus 21335fdbec
gnu: ngless: Install links to required tools. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
 2018-11-07 17:19:53 +01:00
Ricardo Wurmus fff67cc8a7
gnu: prodigal: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
 2018-11-07 17:19:53 +01:00
Ricardo Wurmus 9255198423
gnu: r-mzr: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8e48d36f26
gnu: r-hdf5array: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 611a255d2b
gnu: r-rhdf5: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus a1c2bf8e54
gnu: r-rcas: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 70a3a76ba7
gnu: r-scran: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 48f2791496
gnu: r-scater: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 3c833608f3
gnu: r-beachmat: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus edb91244c3
gnu: r-qvalue: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus d055f199a9
gnu: r-hitc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8023912934
gnu: r-fithic: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 7468a76480
gnu: r-sushi: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 85b16c05e8
gnu: r-gwascat: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus d57445c9b2
gnu: r-gviz: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus ea55326dc7
gnu: r-gqtlstats: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus da679b5202
gnu: r-ldblock: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 4b91335566
gnu: r-erma: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 220ac15e3f
gnu: r-snpstats: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 181a843143
gnu: r-gqtlbase: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus f20c766413
gnu: r-ggbio: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus e7a0bc1ccf
gnu: r-biovizbase: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus cdab2dcfea
gnu: r-organismdbi: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus e8e78c4966
gnu: r-ensembldb: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 0c96e4b290
gnu: r-dirichletmultinomial: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 5ae5a8ebfc
gnu: r-complexheatmap: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.20.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus d78c6aca55
gnu: r-genomicfiles: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.18.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 122e099e72
gnu: r-gage: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 4984212786
gnu: r-keggrest: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.22.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 95df764c01
gnu: r-fastseg: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.28.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 147633d4c1
gnu: r-annotationhub: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.1.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus d7ea34bf99
gnu: r-interactivedisplaybase: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.20.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus b03951f26b
gnu: r-edaseq: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 7812e6b82e
gnu: r-deseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 800954eba4
gnu: r-aroma-light: Update to 3.12.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.12.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus 675d91a035
gnu: r-msnid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 762aca7270
gnu: r-msnbase: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 73d7475246
gnu: r-pcamethods: Update to 1.74.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.74.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2c4311dc7c
gnu: r-mzid: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 0e16fc4699
gnu: r-vsn: Update to 3.50.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.50.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2b085484c0
gnu: r-affy: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.60.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 511abd7add
gnu: r-affyio: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.52.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 691ce09fd3
gnu: r-protgenerics: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.14.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 8af8688339
gnu: r-sva: Update to 3.30.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 18604a76e4
gnu: r-methylkit: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 739a856db8
gnu: r-copywriter: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2e9d8116fb
gnu: r-chipseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.32.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus cec8f0920b
gnu: r-annotationfilter: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.6.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus d2b60be596
gnu: r-tximport: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus ad90921ddc
gnu: r-mutationalpatterns: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.8.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 338f860cc6
gnu: r-bamsignals: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.14.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 48196899cd
gnu: r-rhtslib: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 7d7c702c03
gnu: r-zlibbioc: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.28.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2919fefe12
gnu: r-motifrg: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.26.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 34f1c60c78
gnu: r-seqlogo: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.48.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus c5b0815c44
gnu: r-genomation: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.14.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 45ba2caedb
gnu: r-seqpattern: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.14.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus d11bc259a8
gnu: r-impute: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.56.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 78ecdbc00a
gnu: r-bsgenome: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.50.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 44fa14dfa3
gnu: r-topgo: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.34.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 8a0d57d26e
gnu: r-genomicfeatures: Update to 1.34.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.1.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus c5f1d1ce80
gnu: r-rtracklayer: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 52b95337e8
gnu: r-genomicalignments: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 9fd4350e5a
gnu: r-summarizedexperiment: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.12.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus de4c38f80b
gnu: r-delayedarray: Update to 0.8.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.8.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 7f3778eb06
gnu: r-rsamtools: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 4804c59227
gnu: r-biostrings: Update to 2.50.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus cd8828918f
gnu: r-biocparallel: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 3359d44210
gnu: r-biomart: Update to 2.38.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.38.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 3986e0dee5
gnu: r-annotationdbi: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.44.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 5b82e12a99
gnu: r-biobase: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.42.0.
 2018-11-07 12:27:13 +01:00
Ricardo Wurmus 8d3906a95f
gnu: r-genomicranges: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.34.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus fb10fb72ba
gnu: r-xvector: Update to 0.22.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.22.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 78d2ffdc73
gnu: r-limma: Update to 3.38.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.2.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus ca2945c316
gnu: r-variantannotation: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.1.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 08cd2d5b59
gnu: r-edger: Update to 3.24.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 12871693fe
gnu: r-genomeinfodb: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 9a8dd51979
gnu: r-iranges: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.16.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus a037453554
gnu: r-s4vectors: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 70f2758f71
gnu: r-dnacopy: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.56.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus a127d3522a
gnu: r-bioccheck: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.18.0.
[propagated-inputs]: Add r-knitr and r-biocmanager; remove r-biocinstaller.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 6087f5ce37
gnu: r-biocstyle: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.10.0.
[propagated-inputs]: Add biocmanager.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus c8dbb5fa7f
gnu: r-biocviews: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.1.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 36d7d823a4
gnu: r-biocinstaller: Update to 1.32.1. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.32.1.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 2f28ffd81d
gnu: r-biocgenerics: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.28.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 5c996cab4c
gnu: r-grohmm: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.16.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus bf25930cf6
gnu: r-systempiper: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 9adf78c21e
gnu: r-shortread: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.40.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 4a4b5b8537
gnu: r-gostats: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.48.0.
 2018-11-07 12:27:12 +01:00
Ricardo Wurmus 95ae5acc89
gnu: r-category: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 6dfb0b25ae
gnu: r-gseabase: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.44.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 19a6149190
gnu: r-rbgl: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 2ff6604a53
gnu: r-annotationforge: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.24.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 856444a0a1
gnu: r-dexseq: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus b5c552e654
gnu: r-deseq2: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.1.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 85fb33a051
gnu: r-genefilter: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.64.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus f4a95a0d15
gnu: r-geneplotter: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.60.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus dadd682c53
gnu: r-copynumber: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.22.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 090d4c0159
gnu: r-annotate: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.60.0.
 2018-11-07 12:26:34 +01:00
Ricardo Wurmus 6b451c0801
gnu: r-gprofiler: Update to 0.6.7. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.7.
 2018-10-30 21:42:48 +01:00
Ricardo Wurmus 4fc6609a0c
gnu: r-keggrest: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.2.
 2018-10-30 21:42:39 +01:00
Ricardo Wurmus 67cfb83ff1
gnu: r-msnbase: Update to 2.6.4. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.4.
 2018-10-30 21:42:31 +01:00
Ricardo Wurmus 807d961cc9
gnu: r-methylkit: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.3.
 2018-10-30 21:42:20 +01:00
Ricardo Wurmus ac0166450d
gnu: r-wgcna: Update to 1.66. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.66.
 2018-10-30 21:42:09 +01:00
Ricardo Wurmus 1182460750
gnu: r-go-db: Update to 3.6.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.6.0.
 2018-10-30 21:42:00 +01:00
Ricardo Wurmus 466bf3af89
gnu: r-genomicfeatures: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.3.
 2018-10-30 21:41:12 +01:00
Ricardo Wurmus dd0216e0e7
gnu: r-delayedarray: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.6.
 2018-10-30 21:40:57 +01:00
Ricardo Wurmus 72408357fa
gnu: r-genomicranges: Update to 1.32.7. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.7.
 2018-10-30 21:40:48 +01:00
Ricardo Wurmus 9dad1957ab
gnu: r-limma: Update to 3.36.5. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.5.
 2018-10-30 21:40:40 +01:00
Ricardo Wurmus 57cf6a14f0
gnu: r-edger: Update to 3.22.5. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.5.
 2018-10-30 21:40:32 +01:00
Ricardo Wurmus eb890466fa
gnu: r-genomeinfodbdata: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.1.0.
 2018-10-30 21:40:22 +01:00
Ricardo Wurmus e563acb96b
gnu: r-iranges: Update to 2.14.12. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.12.
 2018-10-30 21:40:12 +01:00
Ricardo Wurmus 192c19f484
gnu: r-vegan: Update to 2.5-3. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-3.
 2018-10-30 21:40:00 +01:00
Ricardo Wurmus f8ee22fc8b
gnu: flexbar: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0.
[source]: Fetch from git.
[arguments]: Adjust check and install phases.
[home-page]: Update to new home at Github.
[license]: Change to bsd-3.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 4d93a9a36c
gnu: seqan: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0.
[native-inputs]: Replace bzip2 with xz.
(seqan-1): New variable.
(tophat)[inputs]: Use seqan-1.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 4b8f4536ce
gnu: khmer: Update to 2.1.2. 
* gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2.
[source]: Fetch from git; remove bundled libraries in snippet.
[arguments]: Remove "set-paths" phase; remove "post-install-check" phase;
remove "reset-gzip-timestamps" phase.
[native-inputs]: Remove seqan and python-nose; add python-cython,
python-pytest, and python-pytest-runner.
[inputs]: Remove gcc-4.9.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 50e33c3a8c
gnu: python-screed: Update to 1.0. 
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.0.
[arguments]: Run tests after installation.
[native-inputs]: Add python-pytest, python-pytest-cov, and
python-pytest-runner; remove python-nose.
 2018-10-21 23:06:47 +02:00
Ricardo Wurmus 0db75f7a79
gnu: fasttree: Use INVOKE. 
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify
install phase.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 38622ccd14
gnu: express-beta-diversity: Update to 1.0.8. 
* gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8.
[source]: Fetch from git.
[arguments]: Use INVOKE; remove "exit-source" build phase; simplify.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus c96ca68f31
gnu: edirect: Update to 10.2.20181018. 
* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018.
[arguments]: Add simple check phase; simplify other phases.
[inputs]: Add perl-xml-simple.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 949fa34b84
gnu: eigensoft: Update to 7.2.1. 
* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 5748fe5fcc
gnu: discrover: Fetch from git. 
* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 1c06399358
gnu: diamond: Fetch from git. 
* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 7a1e62ca67
gnu: delly: Update to 0.7.9. 
* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9.
[source]: Fetch from git.
[arguments]: Add phase install-templates; use default install phase.
[native-inputs]: Remove python-2.
[home-page]: Use new home page.
* gnu/packages/patches/delly-use-system-libraries.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 4d494a4fa3
gnu: deeptools: Update to 3.1.3. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 42643fc24d
gnu: python-dendropy: Fetch from git. 
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
 2018-10-21 23:06:46 +02:00
Ricardo Wurmus 6b31040ae6
gnu: python-py2bit: Update to 0.3.0. 
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 6b7260bad1
gnu: cutadapt: Update to 1.18. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus a5b0038cbd
gnu: Add python-dnaio. 
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 7321920cd3
gnu: crossmap: Update to 0.2.9. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 8640f9ec91
gnu: python-twobitreader: Update to 3.1.6. 
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus f5cec0068a
gnu: Add python-bx-python. 
* gnu/packages/bioinformatics.scm (python-bx-python): New variable.
(python2-bx-python): Define in terms of python-bx-python.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 2ba2d62c69
gnu: python2-bx-python: Update to 0.8.2. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2.
[source]: Remove obsolete snippet.
[inputs]: Move python2-numpy from here...
[propagated-inputs]: ...to here; add python2-six.
[native-inputs]: Add python2-lzo and python2-cython.
[home-page]: Update to new home at Github.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 1d18ee6dfd
gnu: bwa-pssm: Fetch from git. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
 2018-10-21 23:06:45 +02:00
Ricardo Wurmus 9a6808e0c0
gnu: tophat: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2018-10-21 23:06:45 +02:00
Ben Woodcroft 617c478506
gnu: python2-dendropy: Disable failing test. 
* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
 2018-10-21 22:31:56 +10:00
Ricardo Wurmus 21c837405a
gnu: bowtie: Update to 2.3.4.3. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus f45093429c
gnu: blast+: Use INVOKE and return #T unconditionally. 
* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus f8b697a385
gnu: bedops: Update to 2.4.35. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus 337d72fb44
gnu: bedops: Use INVOKE. 
* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus c793f4d8fb
gnu: bamm: Fetch from git and use INVOKE. 
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
 2018-10-20 23:37:34 +02:00
Ricardo Wurmus 95758e2faf
gnu: aragorn: Use invoke and simplify. 
* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus 8b4102b903
gnu: clipper: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Add fix-typo phase.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus 895cf8278a
gnu: python-pybedtools: Update to 0.7.10. 
* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10.
[arguments]: Disable broken tests.
[propagated-inputs]: Replace bedtools with bedtools-2.26; add
python-matplotlib, python-pysam, and python-pyyaml.
[native-inputs]: Remove python-pyyaml; add kentutils, python-numpy,
python-pandas, and python-six.
(python-pybedtools): New variable.
 2018-10-20 23:37:33 +02:00
Ricardo Wurmus 129363b762
gnu: Add bedtools-2.26. 
* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
 2018-10-20 23:37:28 +02:00
Ricardo Wurmus e8a7eab169
gnu: kallisto: Update to 0.44.0. 
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.44.0.
[source]: Fetch from git.
[arguments]: Add build phase to use htslib from Guix.
[inputs]: Add htslib.
 2018-10-11 16:12:11 +02:00
pimi b6bd8b108a
gnu: Add filtlong. 
* gnu/packages/bioinformatics.scm (filtlong): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2018-10-08 18:32:42 +02:00
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