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path: root/gnu/packages/bioinformatics.scm
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2015-09-13Merge branch 'master' into core-updatesLudovic Courtès
2015-09-02gnu: Add deeptools.•••* gnu/packages/bioinformatics.scm (deeptools): New variable. Ricardo Wurmus
2015-08-29gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.•••* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools, plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'. * gnu/packages/check.scm (catch-framework): Likewise. * gnu/packages/code.scm (global): Likewise. * gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools): Likewise. * gnu/packages/engineering.scm (fastcap, fasthenry): Likewise. * gnu/packages/gnuzilla.scm (nss): Likewise. * gnu/packages/guile.scm (guile-minikanren): Likewise. * gnu/packages/java.scm (swt): Likewise. * gnu/packages/make-bootstrap.scm (%static-binaries): Likewise. * gnu/packages/maths.scm (lpsolve): Likewise. * gnu/packages/mp3.scm (mpc123): Likewise. * gnu/packages/ninja.scm (ninja): Likewise. * gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise. * gnu/packages/screen.scm (dtach): Likewise. * gnu/packages/synergy.scm (synergy): Likewise. * gnu/packages/textutils.scm (utf8proc): Likewise. * gnu/packages/version-control.scm (git-test-sequence): Likewise. * gnu/packages/wicd.scm (wicd): Likewise. Ludovic Courtès
2015-08-26gnu: Add BioPerl.•••* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable. Ricardo Wurmus
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
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