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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.
2017-07-23gnu: bamm: Use htslib-1.3.Ben Woodcroft
* gnu/packages/bioinformatics (htslib-1.3): New variable. (bamm)[inputs]: Replace htslib with htslib-1.3.
2017-07-23gnu: bcftools: Update to 1.4.1.Ben Woodcroft
* 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.
2017-07-23gnu: samtools: Update to 1.4.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1. [arguments]: Add '--with-htslib=system' configure flag. [inputs]: Add htslib.
2017-07-23gnu: htslib: Update to 1.4.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1. [inputs]: Add curl, openssl.
2017-07-23gnu: samtools: Use "modify-phases" syntax.Ben Woodcroft
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax.
2017-07-22gnu: r-s4vectors: Update to 0.14.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
2017-07-22gnu: r-genomicranges: Update to 1.28.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
2017-07-19gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Update hash because the tarball changed in place.
2017-07-19gnu: sortmerna: Limit support to x86_64 and i686 only.Efraim Flashner
* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
2017-07-18gnu: raxml: Limit to x86_64 and i686 only.Efraim Flashner
* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
2017-07-14gnu: bowtie: Use 'modify-phases'.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases' syntax.
2017-07-14gnu: bowtie: Update to 2.3.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2. [inputs]: Add zlib.
2017-07-09gnu: deeptools: Update to 2.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1. [arguments]: Remove. [native-inputs]: Use "python-" instead of "python2-" variants. [inputs]: Likewise; add python-py2bit.
2017-07-09gnu: Add python-py2bit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
2017-07-08gnu: blast+: Update to 2.6.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. Add patch. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python. * gnu/packages/patches/blast+-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-07-06Revert "gnu: blast+: Update to 2.6.0."Leo Famulari
This reverts commit 18dea67dc3a42d782b34b551304748346f173184.
2017-07-04gnu: gemma: Fix building on non-Intel architectures.Efraim Flashner
* gnu/packages/patches/gemma-intel-compat.patch: New file. * gnu/packages/bioinformatics.scm (gemma)[source]: Add patch. [arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures. * gnu/local.mk (dist_patch_DATA): Register patch.
2017-07-04gnu: diamond: Update to 0.9.9.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
2017-07-04gnu: blast+: Update to 2.6.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python.
2017-07-01gnu: cd-hit: Update to 4.6.8.Ben Woodcroft
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
2017-07-01gnu: bwa: Update to 0.7.15.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
2017-06-25gnu: Add f-seq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq): New variable.
2017-06-24gnu: orfm: Update to 0.7.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
2017-06-23gnu: orfm: Update to 0.7.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
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