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2015-08-14gnu: shogun: Move package to machine-learning.scm....* gnu/packages/bioinformatics.scm (shogun): Move from here... * gnu/packages/machine-learning.scm (shogun): ...to here. Ricardo Wurmus
2015-07-25gnu: bedtools: Add patch to fix compilation on 32 bit systems....* gnu/packages/patches/bedtools-32bit-compilation.patch: New file. * gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch. * gnu-system.am (dist_patch_DATA): Register patch. Signed-off-by: Andreas Enge <andreas@enge.fr> Ben Woodcroft
2015-07-25gnu: bedtools: Update to 2.24.0....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0. Ben Woodcroft
2015-07-21gnu: Add aragorn....* gnu/packages/bioinformatics.scm (aragorn): New variable. Ben Woodcroft
2015-07-19gnu: metabat: Minor tweaks....* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in 'fix-includes' phase. [license]: Fix misspelling. Mark H Weaver
2015-07-19gnu: Add metabat....* gnu/packages/bioinformatics.scm (metabat): New variable. Ben Woodcroft
2015-07-09gnu: preseq: Move "use-samtools-headers" phase....* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase "use-samtools-headers" after "enter-dir" phase. Ricardo Wurmus
2015-07-08gnu: Add preseq....* gnu/packages/bioinformatics.scm (preseq): New variable. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file. * gnu-system.am (dist_patch_DATA): Add them. Ricardo Wurmus
2015-07-08gnu: samtools: Install headers....* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase "install-headers" to install header files. Ricardo Wurmus
2015-07-07gnu: samtools: Update to 1.2....* gnu/packages/bioinformatics.scm (samtools): Update to 1.2. Ricardo Wurmus
2015-07-05gnu: Add prodigal....* gnu/packages/bioinformatics.scm (prodigal): New variable. Ben Woodcroft
2015-07-04gnu: shogun: Build with install RPATH....* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to build with install RPATH. Ricardo Wurmus
2015-07-02gnu: Add WarpedLMM....* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable. Ricardo Wurmus
2015-06-29gnu: Add Blast+....* gnu/packages/bioinformatics.scm (blast+): New variable. Ricardo Wurmus
2015-06-29gnu: Add plink....* gnu/packages/bioinformatics.scm (plink): New variable. * gnu/packages/patches/plink-1.07-unclobber-i.patch: New file. Ricardo Wurmus
2015-06-24gnu: Add hmmer....* gnu/packages/bioinformatics.scm (hmmer): New variable. Ben Woodcroft
2015-06-23gnu: star: Update to 2.4.2a....* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a. Ricardo Wurmus
2015-06-23gnu: miso: Install executables....* 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". Ricardo Wurmus
2015-06-23gnu: Add idr....* gnu/packages/bioinformatics.scm (idr): New variable. Ricardo Wurmus
2015-06-21gnu: Add fasttree....* gnu/packages/bioinformatics.scm (fasttree): New variable. Ben Woodcroft
2015-06-17gnu: Add diamond....* gnu/packages/bioinformatics.scm (diamond): New variable. Ben Woodcroft
2015-06-17gnu: miso: Use HTTPS URL....* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for downloading the source tarball. Ricardo Wurmus
2015-06-17gnu: bedops: Update to 2.4.14....* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14. Ricardo Wurmus
2015-06-15gnu: orfm: Update to 0.4.1....* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1. Ricardo Wurmus
2015-06-12gnu: Add OrfM....* gnu/packages/bioinformatics.scm (orfm): New variable. Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> Ben Woodcroft
2015-06-12gnu: Add Couger....* gnu/packages/bioinformatics.scm (couger): New variable. Ricardo Wurmus
2015-06-12gnu: ngs-sdk: Update to version 1.1.1....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1. Ricardo Wurmus
2015-06-02gnu: Add HTSlib....* gnu/packages/bioinformatics.scm (htslib): New variable. Ricardo Wurmus
2015-06-02gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name....* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on i686. Ricardo Wurmus
2015-05-27gnu: Add edirect....* gnu/packages/bioinformatics.scm (edirect): New variable. Ricardo Wurmus
2015-05-27gnu: shogun: Remove non-free source files....* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove non-free sources. Ricardo Wurmus
2015-05-22gnu: Add rsem....* gnu/packages/bioinformatics.scm (rsem): New variable. * gnu/packages/patches/rsem-makefile.patch: New file. Ricardo Wurmus
2015-05-05gnu: vcftools: Remove "-m64" from CFLAGS....* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to remove "-m64" flag. Ricardo Wurmus
2015-05-04gnu: bamtools: Set rpath via LDFLAGS....* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase setting $LDFLAGS to set the rpath to $out/lib/bamtools. Ricardo Wurmus
2015-05-04gnu: Add samtools-0.1.19....* gnu/packages/bioinformatics.scm (samtools-0.1): New variable. Ricardo Wurmus
2015-05-04gnu: samtools: Install libbam.a library....* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase "install-library" to install the libbam.a library. Ricardo Wurmus
2015-05-04gnu: samtools: Remove patch-makefile-curses phase....* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove patch-makefile-curses phase, use make-flags instead. Ricardo Wurmus
2015-04-27gnu: flexbar: Enable tests....* gnu/packages/bioinformatics.scm (flexbar): Enable tests. Ricardo Wurmus
2015-04-21gnu: Add eXpress....* gnu/packages/bioinformatics.scm (express): New variable. Ricardo Wurmus
2015-04-21gnu: Add bamtools....* gnu/packages/bioinformatics.scm (bamtools): New variable. Ricardo Wurmus
2015-04-21gnu: Add subread....* gnu/packages/bioinformatics.scm (subread): New variable. Ricardo Wurmus
2015-04-20gnu: Add sra-tools....* gnu/packages/bioinformatics.scm (sra-tools): New variable. Ricardo Wurmus
2015-04-20gnu: Add NCBI VDB....* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable. Ricardo Wurmus
2015-04-20gnu: Add NGS Java bindings....* gnu/packages/bioinformatics.scm (ngs-java): New variable. Ricardo Wurmus
2015-04-20gnu: Add NGS SDK....* gnu/packages/bioinformatics.scm (ngs-sdk): New variable. Ricardo Wurmus
2015-04-20gnu: Add Biopython....* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New variables. Ricardo Wurmus
2015-04-16gnu: Add FASTX Toolkit....* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable. Ricardo Wurmus
2015-04-13gnu: rseqc: Update hash....* gnu/packages/bioinformatics.scm (rseqc): Update hash. Ricardo Wurmus
2015-04-10gnu: Add GRIT....* gnu/packages/bioinformatics.scm (grit): New variable. Ricardo Wurmus
2015-04-09gnu: Add Shogun....* gnu/packages/bioinformatics.scm (shogun): New variable. Ricardo Wurmus
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