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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
2015-11-20gnu: Add smithlab-cpp.•••* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable. Ricardo Wurmus
2015-11-20gnu: edirect: Update home page.•••* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing slash to home page. Ricardo Wurmus
2015-11-20gnu: sra-tools: Update to 2.5.4.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4. Ricardo Wurmus
2015-11-20gnu: ncbi-vdb: Update to 2.5.4.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4. Ricardo Wurmus
2015-11-20gnu: ngs-java: Update to 1.2.2.•••* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2. [arguments]: Remove build phase "fix-java-symlink-installation". Ricardo Wurmus
2015-11-20gnu: ngs-sdk: Update to 1.2.2.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2. Ricardo Wurmus
2015-11-20gnu: bless: Build only for x86_64.•••* gnu/packages/bioinformatics.scm (bless): Add supported-systems field. Ricardo Wurmus
2015-11-20gnu: htseq: Propagate numpy.•••* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy from here ... [propagated-inputs]: ... to here. Ricardo Wurmus
2015-11-12gnu: mosaik: Build only on x86_64.•••* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add field. Ricardo Wurmus
2015-11-06gnu: bless: Correct indentation and home-page.•••* gnu/packages/bioinformatics.scm (bless): Fix indentation. [home-page]: Replace broken URL. Ricardo Wurmus
2015-11-06gnu: Add BLESS.•••* gnu/packages/bioinformatics.scm (bless): New variable. Co-authored-by: Diane Trout <diane@ghic.org> Ricardo Wurmus
2015-11-02gnu: hisat: Disable build on non-x86_64.•••* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field. Ricardo Wurmus
2015-11-02gnu: Add express-beta-diversity.•••* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Ben Woodcroft
2015-10-28gnu: pbtranscript-tofu: Update to 2.2.3.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3. [source]: Remove bundled Cython sources in a snippet. Replace ".tar.gz" extension in file-name field with "-checkout". [arguments]: Replace "enter-directory-and-clean-up" phase with "enter-directory" phase, and add "patch-setuppy" phase. [inputs]: Add python2-h5py. Move python2-cython ... [native-inputs]: ... to this field. Ricardo Wurmus
2015-10-27gnu: subread: Use SSE optimizations on x86_64 only.•••* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and CCFLAGS conditionally dependent on target system. Ricardo Wurmus
2015-10-27gnu: crossmap: Update to 0.2.1.•••* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1. Ricardo Wurmus
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