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* gnu: r-go-db: Add missing input.Ricardo Wurmus2016-01-141-0/+2
| | | | | * gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
* gnu: bowtie: Update to 2.2.6.Ricardo Wurmus2016-01-141-22/+16
| | | | | | | | | | * 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 Woodcroft2016-01-141-3/+7
| | | | | | * 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 Wurmus2016-01-131-27/+12
| | | | | | | * 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 Woodcroft2016-01-121-0/+66
| | | | * gnu/packages/bioinformatics.scm (fxtract): New variable.
* gnu: bedtools: Update to 2.25.0.Ben Woodcroft2016-01-111-14/+3
| | | | | | | | | * 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 Woodcroft2016-01-111-19/+19
| | | | * gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
* gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin2016-01-081-0/+1
| | | | | * gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
* gnu: Add genomation.Ricardo Wurmus2016-01-071-0/+43
| | | | * gnu/packages/bioinformatics.scm (r-genomation): New variable.
* gnu: Add seqPattern.Ricardo Wurmus2016-01-071-0/+26
| | | | * gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
* gnu: Add impute.Ricardo Wurmus2016-01-071-0/+20
| | | | * gnu/packages/bioinformatics.scm (r-impute): New variable.
* gnu: Add BSgenome.Ricardo Wurmus2016-01-071-0/+30
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
* gnu: Add topGO.Ricardo Wurmus2016-01-071-0/+29
| | | | * gnu/packages/bioinformatics.scm (r-topgo): New variable.
* gnu: Add GO.db.Ricardo Wurmus2016-01-071-0/+20
| | | | * gnu/packages/bioinformatics.scm (r-go-db): New variable.
* gnu: Add GenomicFeatures.Ricardo Wurmus2016-01-071-0/+41
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
* gnu: Add rtracklayer.Ricardo Wurmus2016-01-071-0/+45
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
* gnu: Add GenomicAlignments.Ricardo Wurmus2016-01-071-0/+33
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
* gnu: Add SummarizedExperiment.Ricardo Wurmus2016-01-071-0/+29
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
* gnu: Add Rsamtools.Ricardo Wurmus2016-01-071-0/+44
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
* gnu: Add Biostrings.Ricardo Wurmus2016-01-071-0/+26
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): New variable.
* gnu: Add BiocParallel.Ricardo Wurmus2016-01-071-0/+24
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
* gnu: Add biomaRt.Ricardo Wurmus2016-01-071-0/+30
| | | | * gnu/packages/bioinformatics.scm (r-biomart): New variable.
* gnu: Add AnnotationDbi.Ricardo Wurmus2016-01-071-0/+27
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
* gnu: Add Biobase.Ricardo Wurmus2016-01-071-0/+22
| | | | * gnu/packages/bioinformatics.scm (r-biobase): New variable.
* gnu: edirect: Update to 3.50.Ricardo Wurmus2016-01-071-5/+3
| | | | | * gnu/packages/bioinformatics.scm (edirect): Update to 3.50. [native-inputs]: Remove "unzip".
* gnu: Add and use default IcedTea.Ricardo Wurmus2016-01-061-2/+2
| | | | | | | | | | | * 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 Wurmus2016-01-061-0/+50
| | | | * gnu/packages/bioinformatics.scm (jellyfish): New variable.
* gnu: Add fraggenescan.Ben Woodcroft2015-12-291-0/+81
| | | | * gnu/packages/bioinformatics.scm (fraggenescan): New variable.
* gnu: Add GenomicRanges.Ricardo Wurmus2015-12-211-0/+28
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
* gnu: Add XVector.Ricardo Wurmus2015-12-211-0/+37
| | | | * gnu/packages/bioinformatics.scm (r-xvector): New variable.
* gnu: Add GenomeInfoDb.Ricardo Wurmus2015-12-211-0/+27
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
* gnu: Add IRanges.Ricardo Wurmus2015-12-211-0/+30
| | | | * gnu/packages/bioinformatics.scm (r-iranges): New variable.
* gnu: Add S4Vectors.Ricardo Wurmus2015-12-211-0/+28
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
* gnu: Add BiocGenerics.Ricardo Wurmus2015-12-211-0/+21
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
* gnu: Add r-acsnminer.Ricardo Wurmus2015-12-211-0/+26
| | | | * gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
* gnu: mafft: Update to 7.267.Ben Woodcroft2015-12-211-3/+20
| | | | | | | * 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 Woodcroft2015-12-111-0/+37
| | | | * gnu/packages/bioinformatics.scm (snap-aligner): New variable.
* gnu: python-biopython, python2-biopython: Update to 1.66.Ben Woodcroft2015-12-101-5/+4
| | | | | * 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 Wurmus2015-11-201-25/+18
| | | | | | | | | | | * 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.
* gnu: Add smithlab-cpp.Ricardo Wurmus2015-11-201-0/+53
| | | | * gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
* gnu: edirect: Update home page.Ricardo Wurmus2015-11-201-1/+1
| | | | | * gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing slash to home page.
* gnu: sra-tools: Update to 2.5.4.Ricardo Wurmus2015-11-201-2/+2
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
* gnu: ncbi-vdb: Update to 2.5.4.Ricardo Wurmus2015-11-201-16/+2
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
* gnu: ngs-java: Update to 1.2.2.Ricardo Wurmus2015-11-201-20/+2
| | | | | * gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2. [arguments]: Remove build phase "fix-java-symlink-installation".
* gnu: ngs-sdk: Update to 1.2.2.Ricardo Wurmus2015-11-201-2/+2
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
* gnu: bless: Build only for x86_64.Ricardo Wurmus2015-11-201-0/+1
| | | | * gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
* gnu: htseq: Propagate numpy.Ricardo Wurmus2015-11-201-3/+5
| | | | | | * gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy from here ... [propagated-inputs]: ... to here.
* gnu: mosaik: Build only on x86_64.Ricardo Wurmus2015-11-121-0/+1
| | | | | * gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add field.
* gnu: bless: Correct indentation and home-page.Ricardo Wurmus2015-11-061-3/+3
| | | | | * gnu/packages/bioinformatics.scm (bless): Fix indentation. [home-page]: Replace broken URL.
* gnu: Add BLESS.Ricardo Wurmus2015-11-061-0/+83
| | | | | | * gnu/packages/bioinformatics.scm (bless): New variable. Co-authored-by: Diane Trout <diane@ghic.org>
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