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283 Commits

Author SHA1 Message Date
Ricardo Wurmus 4714d521e3
gnu: Add r-bsgenome-mmusculus-ucsc-mm10. 
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
  variable.
 2016-06-15 17:08:08 +02:00
Ben Woodcroft e4a44a6aa5
gnu: Add ruby-bio-kseq. 
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
 2016-06-14 07:57:09 +10:00
Ricardo Wurmus 883302daf2
gnu: piranha: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
 2016-06-13 11:53:38 +02:00
Hartmut Goebel 698bd29799
gnu: Use full SHA1 commit ids. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik,
  smithlab-cpp, piranha): Use full SHA1 commit ids.
* gnu/packages/ci.scm (hydra): Likewise.
* gnu/packages/compression.scm (sfarkxtc): Likewise.
* gnu/packages/emacs.scm (emacs-ob-ipython): Likewise.
* gnu/packages/games.scm (mars, emulation-station): Likewise.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/music.scm (non-sequencer): Likewise.
* gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise.
* gnu/packages/xorg.scm (xf86-video-intel): Likewise.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-06-05 00:05:38 +02:00
Ben Woodcroft 6ac0a0fbe7
gnu: diamond: Update to 0.8.5. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
 2016-06-04 09:28:54 +10:00
Ricardo Wurmus 64efa3078a
gnu: Add r-genomationdata. 
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
 2016-05-31 16:29:37 +02:00
Ben Woodcroft 9fcc3509a7 gnu: Update diamond to 0.8.3. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
 2016-05-28 23:44:16 +10:00
Ricardo Wurmus 0783787436 gnu: Add ParDRe. 
* gnu/packages/bioinformatics.scm (pardre): New variable.
 2016-05-23 12:55:09 +02:00
Ricardo Wurmus 7740f58128
gnu: r-genomation: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d7420566a9
gnu: r-biocparallel: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 73af676feb
gnu: r-annotationdbi: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 679e670b36
gnu: r-variantannotation: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 186ed87337
gnu: r-genomeinfodb: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
 2016-05-20 15:18:23 +02:00
Ben Woodcroft 7c544991dc gnu: diamond: Do not specify target architecture. 
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
 2016-05-18 21:25:06 +10:00
Ricardo Wurmus e62ffce538 gnu: Add Piranha. 
* gnu/packages/bioinformatics.scm (piranha): New variable.
 2016-05-18 11:59:34 +02:00
Ben Woodcroft 849485f5a0 gnu: sortmerna: Update to 2.1b. 
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
 2016-05-17 21:45:49 +10:00
Ben Woodcroft daaeed765a gnu: vsearch: Update to 1.11.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
 2016-05-17 21:36:46 +10:00
Ben Woodcroft 122395f9fc gnu: diamond: Update to 0.8.1. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
 2016-05-17 21:07:00 +10:00
Ricardo Wurmus 96101b6718
gnu: r-zlibbioc: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
 2016-05-16 20:59:50 +02:00
Ricardo Wurmus a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
 2016-05-16 20:59:38 +02:00
Ricardo Wurmus 1f5786a918
gnu: r-seqlogo: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
 2016-05-16 20:59:27 +02:00
Ricardo Wurmus 8adc3b628d
gnu: r-genomation: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
 2016-05-16 20:59:14 +02:00
Ricardo Wurmus 7555817c2b
gnu: r-seqpattern: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
 2016-05-16 20:59:04 +02:00
Ricardo Wurmus d1bff89d26
gnu: r-impute: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
 2016-05-16 20:58:49 +02:00
Ricardo Wurmus 5190ed1751
gnu: r-bsgenome: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
 2016-05-16 20:58:35 +02:00
Ricardo Wurmus e48e88c217
gnu: r-topgo: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
 2016-05-16 20:58:24 +02:00
Ricardo Wurmus 0c56023557
gnu: r-graph: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
 2016-05-16 20:58:08 +02:00
Ricardo Wurmus c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
 2016-05-16 20:57:55 +02:00
Ricardo Wurmus d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
 2016-05-16 20:57:43 +02:00
Ricardo Wurmus 3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
 2016-05-16 20:57:30 +02:00
Ricardo Wurmus d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
 2016-05-16 20:57:21 +02:00
Ricardo Wurmus b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
 2016-05-16 20:57:10 +02:00
Ricardo Wurmus 2477d9773a
gnu: r-biostrings: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
 2016-05-16 20:56:58 +02:00
Ricardo Wurmus 6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
 2016-05-16 20:56:39 +02:00
Ricardo Wurmus 63cea37234
gnu: r-biomart: Update to 2.28.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
 2016-05-16 20:56:29 +02:00
Ricardo Wurmus c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
 2016-05-16 20:56:19 +02:00
Ricardo Wurmus 4466a02c9f
gnu: r-biobase: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
 2016-05-16 20:56:09 +02:00
Ricardo Wurmus 828980cad6
gnu: r-genomicranges: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
 2016-05-16 20:55:58 +02:00
Ricardo Wurmus e782ca3e97
gnu: r-xvector: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
 2016-05-16 20:55:46 +02:00
Ricardo Wurmus 052ee32b24
gnu: r-variantannotation: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
  1.18.0.
 2016-05-16 20:55:32 +02:00
Ricardo Wurmus d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
 2016-05-16 20:55:20 +02:00
Ricardo Wurmus 952ff8c862
gnu: r-iranges: Update to 2.6.0. 
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
 2016-05-16 20:55:11 +02:00
Ricardo Wurmus 3654a61146
gnu: r-s4vectors: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
 2016-05-16 20:54:59 +02:00
Ricardo Wurmus a936bf59ea
gnu: r-dnacopy: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
 2016-05-16 20:54:37 +02:00
Ricardo Wurmus dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
 2016-05-16 20:53:48 +02:00
Efraim Flashner a83e604662
gnu: hmmer: Update urls. 
* gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to
eddylab, with their downloads.
[home-page]: Update to new homepage.
 2016-05-16 14:28:53 +03:00
Mark H Weaver 99828fa788
gnu: Update module imports for asciidoc and doxygen. 
This is a followup to commit 0573a923de.

* gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm,
gnu/packages/fcitx.scm, gnu/packages/fish.scm,
gnu/packages/freedesktop.scm, gnu/packages/game-development.scm,
gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm,
gnu/packages/kodi.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/messaging.scm,
gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm,
gnu/packages/serialization.scm, gnu/packages/version-control.scm,
gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or
(gnu packages doxygen) to (gnu packages documentation).
 2016-05-12 20:18:15 -04:00
Ricardo Wurmus 83b84fa812 gnu: edirect: Update to 4.10. 
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
 2016-05-04 16:45:43 +02:00