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2015-05-27gnu: Add edirect.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (edirect): New variable.
2015-05-27gnu: shogun: Remove non-free source files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove non-free sources.
2015-05-22gnu: Add rsem.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rsem): New variable. * gnu/packages/patches/rsem-makefile.patch: New file.
2015-05-05gnu: vcftools: Remove "-m64" from CFLAGS.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to remove "-m64" flag.
2015-05-04gnu: bamtools: Set rpath via LDFLAGS.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase setting $LDFLAGS to set the rpath to $out/lib/bamtools.
2015-05-04gnu: Add samtools-0.1.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
2015-05-04gnu: samtools: Install libbam.a library.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase "install-library" to install the libbam.a library.
2015-05-04gnu: samtools: Remove patch-makefile-curses phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove patch-makefile-curses phase, use make-flags instead.
2015-04-27gnu: flexbar: Enable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
2015-04-21gnu: Add eXpress.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (express): New variable.
2015-04-21gnu: Add bamtools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): New variable.
2015-04-21gnu: Add subread.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread): New variable.
2015-04-20gnu: Add sra-tools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): New variable.
2015-04-20gnu: Add NCBI VDB.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
2015-04-20gnu: Add NGS Java bindings.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
2015-04-20gnu: Add NGS SDK.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
2015-04-20gnu: Add Biopython.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New variables.
2015-04-16gnu: Add FASTX Toolkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
2015-04-13gnu: rseqc: Update hash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rseqc): Update hash.
2015-04-10gnu: Add GRIT.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (grit): New variable.
2015-04-09gnu: Add Shogun.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (shogun): New variable.
2015-04-01gnu: Add clustal omega.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
2015-03-31gnu: pbtranscript-tofu: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing runtime inputs.
2015-03-31gnu: pbtranscript-tofu: Delete pre-built libraries.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete "build" directory and any shared objects after unpacking.
2015-03-31gnu: Add vcftools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcftools): New variable.
2015-03-31gnu: Add cutadapt.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cutadapt): New variable.
2015-03-24gnu: Add pbtranscript-tofu.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
2015-03-24gnu: Add python2-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
2015-03-24gnu: Add python2-pbcore.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.
2015-03-17gnu: Add MISO.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (miso): New variable.
2015-03-17gnu: Add bwa.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa): New variable.
2015-03-10gnu: Add htsjdk.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htsjdk): New variable.
2015-03-04Merge branch 'core-updates'.Ludovic Courtès
2015-03-02gnu: Add crossmap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (crossmap): New variable. * gnu/packages/patches/crossmap-allow-system-pysam.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2015-03-02gnu: Add CLIPper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clipper): New variable.
2015-03-02gnu: Add MACS.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs): New variable.
2015-03-02gnu: Add pybedtools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
2015-02-28gnu: Add 'file-name' fields for github source tarballs without a name.Mark H Weaver
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb), gnu/packages/audio.scm (jack-2, lvtk), gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie), gnu/packages/game-development.scm (tiled), gnu/packages/games.scm (minetest-data, minetest, retroarch), gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson), gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask), gnu/packages/mail.scm (offlineimap, libetpan), gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja), gnu/packages/nutrition.scm (gourmet), gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf), gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add 'file-name' field to origin.
2015-02-27gnu: Remove now unneeded 'unpack' phases for unzip.Ludovic Courtès
This is a followup to commit cd0385b. * gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove 'unpack' phase. * gnu/packages/image.scm (freeimage): Likewise. * gnu/packages/python.scm (python2-cssutils): Likewise.
2015-02-20gnu: Add HTSeq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq): New variable.
2015-02-19gnu: Add RSeQC.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rseqc): New variable.
2015-02-13gnu: Add bedops.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): New variable.
2015-02-12gnu: hisat: fix build on non-x86_64.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to make-flags on architectures other than x86_64.
2015-02-10gnu: Add STAR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): New variable.
2015-02-10gnu: Add HISAT.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat): New variable.
2015-02-09gnu: Add flexbar.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flexbar): New variable.
2015-02-09gnu: Add seqan.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqan): New variable.
2015-01-30gnu: bowtie: fix build errorsRicardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and add Makefile patch. * gnu/packages/patches/bowtie-fix-makefile.patch: New file. * gnu-system.am (dist_patch_DATA): Add it.
2014-12-19gnu: Add bowtieRicardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16gnu: Add bedtoolsRicardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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