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1035 Commits

Author SHA1 Message Date
Roel Janssen
b9bf2b8985 gnu: Update r-mutationalpatterns to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.2.
 2017-12-22 12:23:06 +01:00
Ricardo Wurmus
b9e8a5c594 gnu: r-biomart: Update to 2.34.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1.
[propagated-inputs]: Add r-httr.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
11e42209a8 gnu: r-gviz: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
2ccd850192 gnu: r-gqtlstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
28d25d037e gnu: r-rtracklayer: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus
d41f678420 gnu: r-limma: Update to 3.34.4. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
ab0dd8ac10 gnu: r-edger: Update to 3.20.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
7665fb39f5 gnu: r-biocstyle: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
756ac7254c gnu: r-dexseq: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus
8d11ef4470 gnu: r-vegan: Update to 2.4-5. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
 2017-12-19 20:35:02 +01:00
Ricardo Wurmus
f1a2b1cb20 gnu: r-seurat: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0.
[propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica,
r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr,
r-rcppeigen, r-fastica.
 2017-12-18 12:01:35 +01:00
Ricardo Wurmus
8271b8d22a gnu: r-seurat: Fix ModularityOptimizer.jar. 
* gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class
attribute in manifest.
 2017-12-18 12:01:34 +01:00
Ben Woodcroft
6098a386a9 gnu: bedtools: Update to 2.27.1. 
* gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
 2017-12-15 13:56:51 +10:00
Ben Woodcroft
4e0b3583ea gnu: diamond: Update to 0.9.14. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
 2017-12-14 22:50:10 +10:00
Christopher Baines
9cf5f134d5 gnu: Switch to using the version-major procedure. 
* gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major.
  (hmmer)[source]: Switch to using version-major.
  (pidgin)[native-search-paths]: Switch to using version-major.
  (r-minimal)[source]: Switch to using version-major.
 2017-12-11 19:12:33 +00:00
Ricardo Wurmus
83b9d121a7 gnu: bedtools-2.18: Fix build. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom
install phase.

Reported by Mark H Weaver <mhw@netris.org>.
 2017-12-09 13:01:15 +01:00
Ricardo Wurmus
0d9824cc12 gnu: bedtools: Update to 2.27.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
[arguments]: Remove custom "install" phase; specify prefix.
 2017-12-06 19:13:35 +01:00
Ricardo Wurmus
d112e5a8c2 gnu: Add kallisto. 
* gnu/packages/bioinformatics.scm (kallisto): New variable.
 2017-12-03 18:38:58 +01:00
Ricardo Wurmus
117d8cc40e gnu: jellyfish: Update to 2.2.7. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7.
[native-inputs]: Add pkg-config.
[inputs]: Add htslib.
 2017-11-30 17:38:36 +01:00
Ricardo Wurmus
9b8d02011f gnu: r-annotationhub: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
 2017-11-30 17:28:24 +01:00
Ricardo Wurmus
87e91a9fff gnu: r-msnid: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus
439492654b gnu: r-maldiquant: Update to 1.17. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus
06e8e0fc6c gnu: r-genomicalignments: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus
1ce5d32b49 gnu: r-limma: Update to 3.34.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus
8131cf4162 gnu: r-variantannotation: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
 2017-11-30 17:28:21 +01:00
Ricardo Wurmus
d2081a17ed gnu: r-getopt: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus
4220ab0c81 gnu: r-gseabase: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus
d259932ca8 gnu: r-dexseq: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
 2017-11-30 17:28:19 +01:00
Ricardo Wurmus
058644c0f2 gnu: r-deseq2: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
 2017-11-30 17:28:18 +01:00
Ricardo Wurmus
654c29aceb gnu: r-annotate: Update to 1.56.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
 2017-11-30 17:28:18 +01:00
Arun Isaac
9364a520ce gnu: metabat: Use scons-build-system. 
* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
 2017-11-30 18:19:32 +05:30
Roel Janssen
1fd904fb38 gnu: Update r-mutationalpatterns to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
 2017-11-29 14:56:28 +01:00
Roel Janssen
efa6a1ddb5 gnu: Add r-copynumber. 
* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
 2017-11-29 12:46:17 +01:00
Ricardo Wurmus
d7f24778de gnu: Add java-picard-1.113. 
* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
 2017-11-27 12:12:41 +01:00
Ricardo Wurmus
d7fed31ad2 gnu: Add java-picard. 
* gnu/packages/bioinformatics.scm (java-picard): New variable.
 2017-11-27 12:12:40 +01:00
Ricardo Wurmus
bd94b6f850 gnu: java-htsjdk: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0.
[arguments]: Build with JDK 8.
[inputs]: Add java-ngs, java-snappy, java-commons-compress,
java-commons-logging-minimal, java-commons-jexl-2, and java-xz.
[native-inputs]: Add java-testng.
 2017-11-27 12:12:40 +01:00
Ricardo Wurmus
35e78aaa25 gnu: r-rhdf5: Fix build phase. 
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Fix "unpack-smallhdf5"
phase.
 2017-11-27 12:11:52 +01:00
Ricardo Wurmus
e6debcaf02 gnu: subread: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (subread): Update to 1.6.0.
 2017-11-23 13:16:12 +01:00
Ricardo Wurmus
aa33cc29ca gnu: idr: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (idr): Update to 2.0.3.
[source]: Add snippet to remove generated code.
 2017-11-21 23:17:43 +01:00
Ricardo Wurmus
40590caf3b gnu: idr: Correct license. 
* gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
 2017-11-21 23:17:43 +01:00
Ricardo Wurmus
261b38a978 gnu: r-genomeinfodbdata: Update to 0.99.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 0.99.1.
 2017-11-18 11:18:41 +01:00
Ricardo Wurmus
592f4a9434 gnu: r-go-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.5.0.
 2017-11-18 11:18:41 +01:00
Ricardo Wurmus
e4664290ce gnu: r-org-ce-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.5.0.
 2017-11-18 11:18:40 +01:00
Ricardo Wurmus
19fc299f68 gnu: r-org-dm-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.5.0.
 2017-11-18 11:18:40 +01:00
Ricardo Wurmus
f3569f5218 gnu: r-org-mm-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.5.0.
 2017-11-18 11:18:40 +01:00
Ricardo Wurmus
57dc9b58db gnu: r-genomationdata: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
 2017-11-18 11:18:39 +01:00
Ricardo Wurmus
90dbd984f8 gnu: Remove duplicate from (gnu packages bioinformatics). 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
 2017-11-18 11:18:39 +01:00
Ricardo Wurmus
676507e388 gnu: r-org-hs-eg-db: Clarify description. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
 2017-11-18 11:18:38 +01:00
Ricardo Wurmus
d595fed33d gnu: r-org-hs-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.
 2017-11-18 11:18:37 +01:00
Ricardo Wurmus
ccedfd3a43 gnu: r-org-hs-eg-db: Remove duplicate package definition. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.
 2017-11-18 11:18:37 +01:00