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2015-06-29gnu: Add Blast+.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blast+): New variable.
2015-06-29gnu: Add plink.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink): New variable. * gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
2015-06-24gnu: Add hmmer.Ben Woodcroft
* gnu/packages/bioinformatics.scm (hmmer): New variable.
2015-06-23gnu: star: Update to 2.4.2a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
2015-06-23gnu: miso: Install executables.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use "setuptools" so that executables are built. * gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock" and "python2-pytz".
2015-06-23gnu: Add idr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (idr): New variable.
2015-06-21gnu: Add fasttree.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fasttree): New variable.
2015-06-17gnu: Add diamond.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): New variable.
2015-06-17gnu: miso: Use HTTPS URL.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for downloading the source tarball.
2015-06-17gnu: bedops: Update to 2.4.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
2015-06-15gnu: orfm: Update to 0.4.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
2015-06-12gnu: Add OrfM.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): New variable. Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
2015-06-12gnu: Add Couger.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (couger): New variable.
2015-06-12gnu: ngs-sdk: Update to version 1.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
2015-06-02gnu: Add HTSlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): New variable.
2015-06-02gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on i686.
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.
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