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2016-02-02gnu: Update sortmerna to 2.1.•••* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1. Ben J. Woodcroft
2016-01-26gnu: sra-tools: Update to 2.5.7.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7. Ben Woodcroft
2016-01-26gnu: ncbi-vdb: Update to 2.5.7.•••gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7. Ben Woodcroft
2016-01-26gnu: ngs-sdk: Update to 1.2.3.•••gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3. Ben Woodcroft
2016-01-25gnu: Add sortmerna.•••* gnu/packages/bioinformatics.scm (sortmerna): New variable. Ben Woodcroft
2016-01-23gnu: Add cufflinks.•••* gnu/packages/bioinformatics.scm (cufflinks): New variable. Ricardo Wurmus
2016-01-23gnu: Add TopHat.•••* 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. Ricardo Wurmus
2016-01-23gnu: star: Update to 2.5.1b.•••* 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". Ricardo Wurmus
2016-01-23gnu: star: Use "modify-phases" syntax.•••* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax. Ricardo Wurmus
2016-01-21gnu: r-qtl: Update to 1.38-4.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4. Pjotr Prins
2016-01-16gnu: samtools-0.1: Adapt to changes in "samtools" variable.•••* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add "LIBCURSES" make flag; delete "configure" phase; disable tests outside of "substitute-keyword-arguments". Ricardo Wurmus
2016-01-14gnu: r-go-db: Add missing input.•••* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi". Ricardo Wurmus
2016-01-14gnu: bowtie: Update to 2.2.6.•••* 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. Ricardo Wurmus
2016-01-14gnu: orfm: Update to 0.5.3.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas. Ben Woodcroft
2016-01-13gnu: samtools: Update to 1.3.•••* 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. Ricardo Wurmus
2016-01-12gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable. Ben Woodcroft
2016-01-11gnu: bedtools: Update to 2.25.0.•••* 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. Ben Woodcroft
2016-01-11gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases. Ben Woodcroft
2016-01-08gnu: Add missing (gnu packages gcc) import.•••* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'. Mathieu Lirzin
2016-01-07gnu: Add genomation.•••* gnu/packages/bioinformatics.scm (r-genomation): New variable. Ricardo Wurmus
2016-01-07gnu: Add seqPattern.•••* gnu/packages/bioinformatics.scm (r-seqpattern): New variable. Ricardo Wurmus
2016-01-07gnu: Add impute.•••* gnu/packages/bioinformatics.scm (r-impute): New variable. Ricardo Wurmus
2016-01-07gnu: Add BSgenome.•••* gnu/packages/bioinformatics.scm (r-bsgenome): New variable. Ricardo Wurmus
2016-01-07gnu: Add topGO.•••* gnu/packages/bioinformatics.scm (r-topgo): New variable. Ricardo Wurmus
2016-01-07gnu: Add GO.db.•••* gnu/packages/bioinformatics.scm (r-go-db): New variable. Ricardo Wurmus
2016-01-07gnu: Add GenomicFeatures.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable. Ricardo Wurmus
2016-01-07gnu: Add rtracklayer.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable. Ricardo Wurmus
2016-01-07gnu: Add GenomicAlignments.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable. Ricardo Wurmus
2016-01-07gnu: Add SummarizedExperiment.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable. Ricardo Wurmus
2016-01-07gnu: Add Rsamtools.•••* gnu/packages/bioinformatics.scm (r-rsamtools): New variable. Ricardo Wurmus
2016-01-07gnu: Add Biostrings.•••* gnu/packages/bioinformatics.scm (r-biostrings): New variable. Ricardo Wurmus
2016-01-07gnu: Add BiocParallel.•••* gnu/packages/bioinformatics.scm (r-biocparallel): New variable. Ricardo Wurmus
2016-01-07gnu: Add biomaRt.•••* gnu/packages/bioinformatics.scm (r-biomart): New variable. Ricardo Wurmus
2016-01-07gnu: Add AnnotationDbi.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable. Ricardo Wurmus
2016-01-07gnu: Add Biobase.•••* gnu/packages/bioinformatics.scm (r-biobase): New variable. Ricardo Wurmus
2016-01-07gnu: edirect: Update to 3.50.•••* gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip". Ricardo Wurmus
2016-01-06gnu: Add and use default IcedTea.•••* 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". Ricardo Wurmus
2016-01-06gnu: Add Jellyfish.•••* gnu/packages/bioinformatics.scm (jellyfish): New variable. Ricardo Wurmus
2015-12-29gnu: Add fraggenescan.•••* gnu/packages/bioinformatics.scm (fraggenescan): New variable. Ben Woodcroft
2015-12-21gnu: Add GenomicRanges.•••* gnu/packages/bioinformatics.scm (r-genomicranges): New variable. Ricardo Wurmus
2015-12-21gnu: Add XVector.•••* gnu/packages/bioinformatics.scm (r-xvector): New variable. Ricardo Wurmus
2015-12-21gnu: Add GenomeInfoDb.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable. Ricardo Wurmus
2015-12-21gnu: Add IRanges.•••* gnu/packages/bioinformatics.scm (r-iranges): New variable. Ricardo Wurmus
2015-12-21gnu: Add S4Vectors.•••* gnu/packages/bioinformatics.scm (r-s4vectors): New variable. Ricardo Wurmus
2015-12-21gnu: Add BiocGenerics.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable. Ricardo Wurmus
2015-12-21gnu: Add r-acsnminer.•••* gnu/packages/bioinformatics.scm (r-acsnminer): New variable. Ricardo Wurmus
2015-12-21gnu: mafft: Update to 7.267.•••* 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. Ben Woodcroft
2015-12-11gnu: Add snap-aligner.•••* gnu/packages/bioinformatics.scm (snap-aligner): New variable. Ben Woodcroft
2015-12-10gnu: python-biopython, python2-biopython: Update to 1.66.•••* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66. [source]: Use PyPi instead of biopython.org. Ben Woodcroft
2015-11-20gnu: preseq: Update to 2.0.•••* 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. Ricardo Wurmus
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