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* gnu: bioinformatics.scm: Use (gnu packages cran) module.Efraim Flashner2017-08-03
| | | | | | This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
* gnu: r-seqminer: Update to 6.0.Ricardo Wurmus2017-08-03
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
* gnu: r-wgcna: Update to 1.60.Ricardo Wurmus2017-08-03
| | | | * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
* gnu: r-qtl: Update to 1.41-6.Ricardo Wurmus2017-08-03
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
* gnu: r-seqinr: Update to 3.4-5.Ricardo Wurmus2017-08-03
| | | | * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
* gnu: r-optparse: Update to 1.4.4.Ricardo Wurmus2017-08-03
| | | | * gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
* gnu: r-bookdown: Update to 0.4.Ricardo Wurmus2017-08-03
| | | | * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
* gnu: htseq: Use PyPI URI.Ben Woodcroft2017-08-03
| | | | | | This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
* gnu: htseq: Update to 0.9.1.Ben Woodcroft2017-08-03
| | | | | | | | | | * gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1. [arguments]: Use python-3 by removing field. [native-inputs]: Add 'python-cython'. [propagated-inputs]: Use python3 numpy package. [inputs]: Use python3 pysam package. Add 'python-matplotlib'. (python2-htseq): New variable. (clipper)[inputs]: Use it.
* gnu: r-deseq2: Update to 1.16.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
* gnu: r-annotationforge: Update to 1.18.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
* gnu: r-category: Update to 2.42.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
* gnu: r-biocstyle: Update to 2.4.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
* gnu: r-dnacopy: Update to 1.50.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
* gnu: r-iranges: Update to 2.10.2.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
* gnu: r-genomeinfodb: Update to 1.12.2.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
* gnu: r-variantannotation: Update to 1.22.3.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
* gnu: r-limma: Update to 3.32.5.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
* gnu: r-biobase: Update to 2.36.2.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
* gnu: r-annotationdbi: Update to 1.38.2.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
* gnu: r-biomart: Update to 2.32.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
* gnu: r-biocparallel: Update to 1.10.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
* gnu: r-biostrings: Update to 2.44.2.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
* gnu: r-delayedarray: Update to 0.2.7.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
* gnu: r-summarizedexperiment: Update to 1.6.3.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
* gnu: r-genomicalignments: Update to 1.12.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
* gnu: r-rtracklayer: Update to 1.36.4.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
* gnu: r-genomicfeatures: Update to 1.28.4.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
* gnu: r-copywriter: Update to 2.8.1.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
* gnu: r-sva: Update to 3.24.4.Roel Janssen2017-08-02
| | | | * gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
* gnu: metabat: Limit to x86_64 and i686 only.Efraim Flashner2017-08-01
| | | | * gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
* gnu: metabat: Update to 2.11.2.Ben Woodcroft2017-07-29
| | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
* gnu: metabat: Update to 2.11.1.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: python-plastid: Update to 0.4.8.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
* gnu: bcftools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.5. [origin]: Remove fix-makefile patch. [arguments]: Add configure flags, add LIBS make flag. Do not delete configure phase. * gnu/packages/patches/bcftools-fix-makefile.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: samtools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
* gnu: htslib: Update to 1.5.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
* gnu: python-pysam: Update to 0.11.2.2.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
* gnu: bamm: Use htslib-1.3.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics (htslib-1.3): New variable. (bamm)[inputs]: Replace htslib with htslib-1.3.
* gnu: bcftools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1. [arguments]: Move Makefile modifications from here ... [source]: ... to added patch. Adjust patch for update to 1.4. * gnu/packages/patches/bcftools-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
* gnu: samtools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1. [arguments]: Add '--with-htslib=system' configure flag. [inputs]: Add htslib.
* gnu: htslib: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1. [inputs]: Add curl, openssl.
* gnu: samtools: Use "modify-phases" syntax.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax.
* gnu: r-s4vectors: Update to 0.14.3.Ricardo Wurmus2017-07-22
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
* gnu: r-genomicranges: Update to 1.28.4.Ricardo Wurmus2017-07-22
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
* gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.Ricardo Wurmus2017-07-19
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Update hash because the tarball changed in place.
* gnu: sortmerna: Limit support to x86_64 and i686 only.Efraim Flashner2017-07-19
| | | | * gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
* gnu: raxml: Limit to x86_64 and i686 only.Efraim Flashner2017-07-18
| | | | * gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
* gnu: bowtie: Use 'modify-phases'.Ben Woodcroft2017-07-14
| | | | | * gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases' syntax.
* gnu: bowtie: Update to 2.3.2.Ben Woodcroft2017-07-14
| | | | | * gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2. [inputs]: Add zlib.
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