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2016-02-16gnu: htseq: Add PySam to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
2016-02-16gnu: Add StringTie.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (stringtie): New variable.
2016-02-16gnu: prodigal: Update to 2.6.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
2016-02-15gnu: r-annotationdbi: Update to 1.32.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
2016-02-15gnu: vsearch: Update to 1.10.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0. [origin]: Adapt to changes in bundling of cityhash.
2016-02-12gnu: macs: Update to 2.1.0.20151222.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
2016-02-12gnu: macs: Use "pypi-uri".Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to build source URI.
2016-02-02gnu: Update sortmerna to 2.1.Ben J. Woodcroft
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
2016-01-26gnu: sra-tools: Update to 2.5.7.Ben Woodcroft
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
2016-01-26gnu: ncbi-vdb: Update to 2.5.7.Ben Woodcroft
gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
2016-01-26gnu: ngs-sdk: Update to 1.2.3.Ben Woodcroft
gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
2016-01-25gnu: Add sortmerna.Ben Woodcroft
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
2016-01-23gnu: Add cufflinks.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
2016-01-23gnu: Add TopHat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tophat): New variable. * gnu/packages/patches/tophat-build-with-later-seqan.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2016-01-23gnu: star: Update to 2.5.1b.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b. [source]: Remove bundled htslib sources and pre-built binaries. [arguments]: Add phase "do-not-use-bundled-htslib". [inputs]: Add "htslib".
2016-01-23gnu: star: Use "modify-phases" syntax.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax.
2016-01-21gnu: r-qtl: Update to 1.38-4.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
2016-01-16gnu: samtools-0.1: Adapt to changes in "samtools" variable.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add "LIBCURSES" make flag; delete "configure" phase; disable tests outside of "substitute-keyword-arguments".
2016-01-14gnu: r-go-db: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
2016-01-14gnu: bowtie: Update to 2.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6. [source]: Remove patch; do not set CC and CPP variables. [inputs]: Add "tbb". [arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom "install" phase. * gnu/packages/patches/bowtie-fix-makefile.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove patch file.
2016-01-14gnu: orfm: Update to 0.5.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas.
2016-01-13gnu: samtools: Update to 1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3. [arguments]: Enable tests for all architectures; set ncurses in configure-flags instead of make-flags; simplify "patch-tests" phase; restore "configure" phase.
2016-01-12gnu: Add fxtract.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-11gnu: bedtools: Update to 2.25.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
2016-01-11gnu: bedtools: Use modify-phases.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-08gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
2016-01-07gnu: Add genomation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
2016-01-07gnu: Add seqPattern.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
2016-01-07gnu: Add impute.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-impute): New variable.
2016-01-07gnu: Add BSgenome.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
2016-01-07gnu: Add topGO.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): New variable.
2016-01-07gnu: Add GO.db.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
2016-01-07gnu: Add GenomicFeatures.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
2016-01-07gnu: Add rtracklayer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
2016-01-07gnu: Add GenomicAlignments.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
2016-01-07gnu: Add SummarizedExperiment.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
2016-01-07gnu: Add Rsamtools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
2016-01-07gnu: Add Biostrings.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
2016-01-07gnu: Add BiocParallel.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
2016-01-07gnu: Add biomaRt.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
2016-01-07gnu: Add AnnotationDbi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
2016-01-07gnu: Add Biobase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
2016-01-07gnu: edirect: Update to 3.50.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip".
2016-01-06gnu: Add and use default IcedTea.Ricardo Wurmus
* gnu/packages/java.scm (icedtea): New variable. (swt)[native-inputs]: Replace "icedtea6" with "icedtea". * gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise. (ngs-java)[inputs]: Likewise. * gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with "icedtea". * gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7" with "icedtea".
2016-01-06gnu: Add Jellyfish.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
2015-12-29gnu: Add fraggenescan.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
2015-12-21gnu: Add GenomicRanges.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
2015-12-21gnu: Add XVector.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
2015-12-21gnu: Add GenomeInfoDb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
2015-12-21gnu: Add IRanges.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
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