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* gnu: roary: Update to 3.7.0.Ben Woodcroft2016-11-26
| | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
* gnu: Add proteinortho.Ben Woodcroft2016-11-26
| | | | * gnu/packages/bioinformatics.scm (proteinortho): New variable.
* gnu: diamond: Update to 0.8.27.Ben Woodcroft2016-11-22
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
* gnu: Remove redundancy where mkdir-p <dir> is followed by install-file ↵Petter2016-11-21
| | | | | | | | | | | | | | | | | <file> <dir>. * gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p. (eigensoft)[arguments]: Likewise. (snap-aligner)[arguments]: Likewise. (pardre)[arguments]: Likewise. (piranha)[arguments]: Likewise. * gnu/packages/maths.scm (hypre)[arguments]: Likewise. * gnu/packages/mp3.scm (mpc123)[arguments]: Likewise. * gnu/packages/music.scm (tuxguitar)[arguments]: Likewise. * gnu/packages/pdf.scm (impressive)[arguments]: Likewise. * gnu/packages/qemu.scm (qemu)[arguments]: Likewise. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: hisat: Fix typo.Ricardo Wurmus2016-11-15
| | | | | * gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory name in install phase.
* gnu: r-org-mm-eg-db: Update to 3.4.0.Ricardo Wurmus2016-11-11
| | | | * gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.
* gnu: r-org-dm-eg-db: Update to 3.4.0.Ricardo Wurmus2016-11-11
| | | | * gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.
* gnu: r-org-ce-eg-db: Update to 3.4.0.Ricardo Wurmus2016-11-11
| | | | * gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.
* gnu: r-org-hs-eg-db: Update to 3.4.0.Ricardo Wurmus2016-11-11
| | | | * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.
* gnu: diamond: Update to 0.8.26.Ben Woodcroft2016-11-07
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
* gnu: r-rcas: Update to 1.0.0.Ricardo Wurmus2016-11-03
| | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
* gnu: r-rtracklayer: Update to 1.34.1.Ricardo Wurmus2016-11-03
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
* gnu: r-biocparallel: Update to 1.8.1.Ricardo Wurmus2016-11-03
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
* gnu: r-limma: Update to 3.30.2.Ricardo Wurmus2016-11-03
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
* gnu: r-edger: Update to 3.16.1.Ricardo Wurmus2016-11-03
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
* gnu: python-twobitreader: Update to 3.1.4.Leo Famulari2016-10-28
| | | | | * gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader): Update to 3.1.4.
* gnu: python-twobitreader: Disable the test suite.Leo Famulari2016-10-28
| | | | | | | | The tests were silently skipped with Python 3.4. With Python 3.5, this caused the build of python-twobitreader to fail. * gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader)[arguments]: Disable the tests.
* gnu: Add r-mutationalpatterns.Roel Janssen2016-10-27
| | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
* gnu: r-seqinr: Update to 3.3-3.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
* gnu: bioperl-minimal: Update to 1.7.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
* gnu: r-genomationdata: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
* gnu: r-bamsignals: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
* gnu: r-rhtslib: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0. [native-inputs]: Add autoconf.
* gnu: r-zlibbioc: Update to 1.20.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
* gnu: r-motifrg: Update to 1.18.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
* gnu: r-seqlogo: Update to 1.40.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
* gnu: r-genomation: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | | | * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0. [propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors. [inputs]: Add zlib.
* gnu: r-seqpattern: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0. [propagated-inputs]: Add r-kernsmooth.
* gnu: r-impute: Update to 1.48.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
* gnu: r-bsgenome: Update to 1.42.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
* gnu: r-topgo: Update to 2.26.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi.
* gnu: r-graph: Update to 1.52.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
* gnu: r-go-db: Update to 3.4.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
* gnu: r-genomicfeatures: Update to 1.26.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
* gnu: r-rtracklayer: Update to 1.34.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
* gnu: r-genomicalignments: Update to 1.10.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0.
* gnu: r-summarizedexperiment: Update to 1.4.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0.
* gnu: r-rsamtools: Update to 1.26.1.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
* gnu: r-biostrings: Update to 2.42.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
* gnu: r-biocparallel: Update to 1.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
* gnu: r-biomart: Update to 2.30.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
* gnu: r-annotationdbi: Update to 1.36.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
* gnu: r-biobase: Update to 2.34.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
* gnu: r-genomicranges: Update to 1.26.1.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors.
* gnu: r-xvector: Update to 0.14.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
* gnu: r-limma: Update to 3.30.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
* gnu: r-variantannotation: Update to 1.20.0.Ricardo Wurmus2016-10-26
| | | | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.0. [propagated-inputs]: Add r-biobase, r-biostrings, r-iranges, r-rtracklayer, r-s4vectors, r-xvector.
* gnu: r-edger: Update to 3.16.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit.
* gnu: r-genomeinfodb: Update to 1.10.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
* gnu: r-iranges: Update to 2.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
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