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* gnu: Update sortmerna to 2.1.Ben J. Woodcroft2016-02-02
| | | | * gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
* gnu: sra-tools: Update to 2.5.7.Ben Woodcroft2016-01-26
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
* gnu: ncbi-vdb: Update to 2.5.7.Ben Woodcroft2016-01-26
| | | | gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
* gnu: ngs-sdk: Update to 1.2.3.Ben Woodcroft2016-01-26
| | | | gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
* gnu: Add sortmerna.Ben Woodcroft2016-01-25
| | | | * gnu/packages/bioinformatics.scm (sortmerna): New variable.
* gnu: Add cufflinks.Ricardo Wurmus2016-01-23
| | | | * gnu/packages/bioinformatics.scm (cufflinks): New variable.
* gnu: Add TopHat.Ricardo Wurmus2016-01-23
| | | | | | * 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.
* gnu: star: Update to 2.5.1b.Ricardo Wurmus2016-01-23
| | | | | | | * 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".
* gnu: star: Use "modify-phases" syntax.Ricardo Wurmus2016-01-23
| | | | | * gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax.
* gnu: r-qtl: Update to 1.38-4.Pjotr Prins2016-01-21
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
* gnu: samtools-0.1: Adapt to changes in "samtools" variable.Ricardo Wurmus2016-01-16
| | | | | | * gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add "LIBCURSES" make flag; delete "configure" phase; disable tests outside of "substitute-keyword-arguments".
* gnu: r-go-db: Add missing input.Ricardo Wurmus2016-01-14
| | | | | * gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
* gnu: bowtie: Update to 2.2.6.Ricardo Wurmus2016-01-14
| | | | | | | | | | * 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.
* gnu: orfm: Update to 0.5.3.Ben Woodcroft2016-01-14
| | | | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas.
* gnu: samtools: Update to 1.3.Ricardo Wurmus2016-01-13
| | | | | | | * 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.
* gnu: Add fxtract.Ben Woodcroft2016-01-12
| | | | * gnu/packages/bioinformatics.scm (fxtract): New variable.
* gnu: bedtools: Update to 2.25.0.Ben Woodcroft2016-01-11
| | | | | | | | | * 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.
* gnu: bedtools: Use modify-phases.Ben Woodcroft2016-01-11
| | | | * gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
* gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin2016-01-08
| | | | | * gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
* gnu: Add genomation.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomation): New variable.
* gnu: Add seqPattern.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
* gnu: Add impute.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-impute): New variable.
* gnu: Add BSgenome.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
* gnu: Add topGO.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-topgo): New variable.
* gnu: Add GO.db.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-go-db): New variable.
* gnu: Add GenomicFeatures.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
* gnu: Add rtracklayer.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
* gnu: Add GenomicAlignments.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
* gnu: Add SummarizedExperiment.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
* gnu: Add Rsamtools.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
* gnu: Add Biostrings.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): New variable.
* gnu: Add BiocParallel.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
* gnu: Add biomaRt.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biomart): New variable.
* gnu: Add AnnotationDbi.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
* gnu: Add Biobase.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biobase): New variable.
* gnu: edirect: Update to 3.50.Ricardo Wurmus2016-01-07
| | | | | * gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip".
* gnu: Add and use default IcedTea.Ricardo Wurmus2016-01-06
| | | | | | | | | | | * 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".
* gnu: Add Jellyfish.Ricardo Wurmus2016-01-06
| | | | * gnu/packages/bioinformatics.scm (jellyfish): New variable.
* gnu: Add fraggenescan.Ben Woodcroft2015-12-29
| | | | * gnu/packages/bioinformatics.scm (fraggenescan): New variable.
* gnu: Add GenomicRanges.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
* gnu: Add XVector.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-xvector): New variable.
* gnu: Add GenomeInfoDb.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
* gnu: Add IRanges.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-iranges): New variable.
* gnu: Add S4Vectors.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
* gnu: Add BiocGenerics.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
* gnu: Add r-acsnminer.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
* gnu: mafft: Update to 7.267.Ben Woodcroft2015-12-21
| | | | | | | * gnu/packages/bioinformatics.scm (mafft): Update to 7.267. [arguments]: Don't include mafft-homologs manpage. [inputs]: Add gawk and grep. [propagated-inputs]: Add coreutils.
* gnu: Add snap-aligner.Ben Woodcroft2015-12-11
| | | | * gnu/packages/bioinformatics.scm (snap-aligner): New variable.
* gnu: python-biopython, python2-biopython: Update to 1.66.Ben Woodcroft2015-12-10
| | | | | * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66. [source]: Use PyPi instead of biopython.org.
* gnu: preseq: Update to 2.0.Ricardo Wurmus2015-11-20
| | | | | | | | | | | * gnu/packages/bioinformatics.scm (preseq): Update to 2.0. [source]: Add file-name field, remove patches. [arguments]: Remove unused build phases, add make flags. [inputs]: Add smithlab-cpp. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove them.
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