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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.
2015-12-21gnu: Add S4Vectors.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
2015-12-21gnu: Add BiocGenerics.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
2015-12-21gnu: Add r-acsnminer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
2015-12-21gnu: mafft: Update to 7.267.Ben Woodcroft
* 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.
2015-12-11gnu: Add snap-aligner.Ben Woodcroft
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
2015-12-10gnu: python-biopython, python2-biopython: Update to 1.66.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66. [source]: Use PyPi instead of biopython.org.
2015-11-20gnu: preseq: Update to 2.0.Ricardo Wurmus
* 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.
2015-11-20gnu: Add smithlab-cpp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
2015-11-20gnu: edirect: Update home page.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing slash to home page.
2015-11-20gnu: sra-tools: Update to 2.5.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
2015-11-20gnu: ncbi-vdb: Update to 2.5.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
2015-11-20gnu: ngs-java: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2. [arguments]: Remove build phase "fix-java-symlink-installation".
2015-11-20gnu: ngs-sdk: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
2015-11-20gnu: bless: Build only for x86_64.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
2015-11-20gnu: htseq: Propagate numpy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy from here ... [propagated-inputs]: ... to here.
2015-11-12gnu: mosaik: Build only on x86_64.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add field.
2015-11-06gnu: bless: Correct indentation and home-page.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bless): Fix indentation. [home-page]: Replace broken URL.
2015-11-06gnu: Add BLESS.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bless): New variable. Co-authored-by: Diane Trout <diane@ghic.org>
2015-11-02gnu: hisat: Disable build on non-x86_64.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
2015-11-02gnu: Add express-beta-diversity.Ben Woodcroft
* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2015-10-28gnu: pbtranscript-tofu: Update to 2.2.3.Ricardo Wurmus
* 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.
2015-10-27gnu: subread: Use SSE optimizations on x86_64 only.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and CCFLAGS conditionally dependent on target system.
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