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2017-08-15Merge branch 'master' into core-updatesMark H Weaver
2017-08-14gnu: Add bismark.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark): New variable.
2017-08-14gnu: Add r-dexseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
2017-08-09Merge branch 'master' into core-updatesMark H Weaver
2017-08-09gnu: r-wgcna: Update to 1.61.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61. [propagated-inputs]: Add r-rcpp, r-robust, r-survival.
2017-08-09gnu: Add reference to (gnu packages graph).Ricardo Wurmus
This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3.
2017-08-07Merge branch 'master' into core-updatesMark H Weaver
2017-08-07gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Restore hash from before the tarball changed in place. It changed back. This reverts commit fd4085793818ab2aea28dfeeb2728f6f02416c4c.
2017-08-06Merge branch 'master' into core-updatesMark H Weaver
2017-08-05gnu: perl: Work around more "dotless @INC" build issues.Ludovic Courtès
* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path' phase. * gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment 'configure' phase to set PERL5LIB. * gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
2017-08-03gnu: bioinformatics.scm: Use (gnu packages cran) module.Efraim Flashner
This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
2017-08-03gnu: r-seqminer: Update to 6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
2017-08-03gnu: r-wgcna: Update to 1.60.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
2017-08-03gnu: r-qtl: Update to 1.41-6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
2017-08-03gnu: r-seqinr: Update to 3.4-5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
2017-08-03gnu: r-optparse: Update to 1.4.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
2017-08-03gnu: r-bookdown: Update to 0.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
2017-08-03gnu: htseq: Use PyPI URI.Ben Woodcroft
This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
2017-08-03gnu: htseq: Update to 0.9.1.Ben Woodcroft
* 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.
2017-08-02gnu: r-deseq2: Update to 1.16.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
2017-08-02gnu: r-annotationforge: Update to 1.18.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
2017-08-02gnu: r-category: Update to 2.42.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
2017-08-02gnu: r-biocstyle: Update to 2.4.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
2017-08-02gnu: r-dnacopy: Update to 1.50.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
2017-08-02gnu: r-iranges: Update to 2.10.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
2017-08-02gnu: r-genomeinfodb: Update to 1.12.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
2017-08-02gnu: r-variantannotation: Update to 1.22.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
2017-08-02gnu: r-limma: Update to 3.32.5.Roel Janssen
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
2017-08-02gnu: r-biobase: Update to 2.36.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
2017-08-02gnu: r-annotationdbi: Update to 1.38.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
2017-08-02gnu: r-biomart: Update to 2.32.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
2017-08-02gnu: r-biocparallel: Update to 1.10.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
2017-08-02gnu: r-biostrings: Update to 2.44.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
2017-08-02gnu: r-delayedarray: Update to 0.2.7.Roel Janssen
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
2017-08-02gnu: r-summarizedexperiment: Update to 1.6.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
2017-08-02gnu: r-genomicalignments: Update to 1.12.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
2017-08-02gnu: r-rtracklayer: Update to 1.36.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
2017-08-02gnu: r-genomicfeatures: Update to 1.28.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
2017-08-02gnu: r-copywriter: Update to 2.8.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
2017-08-02gnu: r-sva: Update to 3.24.4.Roel Janssen
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
2017-08-01Merge branch 'master' into core-updatesMarius Bakke
2017-08-01gnu: metabat: Limit to x86_64 and i686 only.Efraim Flashner
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
2017-07-29gnu: metabat: Update to 2.11.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
2017-07-23gnu: metabat: Fix boost-related compilation issue.Ben Woodcroft
Reported by Leo Famulari. * gnu/packages/patches/metabat-fix-boost-issue.patch: New file. * gnu/packages/bioinformatics.scm (metabat): Use it. * gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23gnu: metabat: Update to 2.11.1.Ben Woodcroft
* 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.
2017-07-23gnu: python-plastid: Update to 0.4.8.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
2017-07-23gnu: bcftools: Update to 1.5.Ben Woodcroft
* 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.
2017-07-23gnu: samtools: Update to 1.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
2017-07-23gnu: htslib: Update to 1.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
2017-07-23gnu: python-pysam: Update to 0.11.2.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
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