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* Merge branch 'core-updates'Ludovic Courtès2015-09-26
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| * Merge branch 'master' into core-updatesMark H Weaver2015-09-22
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| * \ Merge branch 'master' into core-updatesLudovic Courtès2015-09-13
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| * | | gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.Ludovic Courtès2015-08-29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | | | gnu: Add seqmagick.Ben Woodcroft2015-09-25
| |_|/ |/| | | | | | | | * gnu/packages/bioinformatics.scm (seqmagick): New variable.
* | | gnu: Add R/qtl.Andreas Enge2015-09-20
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-qtl): New variable. Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
* | | gnu: Add bioruby.Pjotr Prins2015-09-19
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bioruby): New variable.
* | | gnu: Add mafft.Ben Woodcroft2015-09-16
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (mafft): New variable.
* | | gnu: Add bio-locus.Pjotr Prins2015-09-14
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bio-locus): New variable.
* | | Revert "gnu: Add bio-locus."David Thompson2015-09-14
| | | | | | | | | | | | This reverts commit b429c4fbb06299ce10ecc113a7818bf777c63a6e.
* | | gnu: Add bio-locus.Pjotr Prins2015-09-14
| |/ |/| | | | | * gnu/packages/bioinformatics.scm (bio-locus): New variable.
* | gnu: Add deeptools.Ricardo Wurmus2015-09-02
|/ | | | * gnu/packages/bioinformatics.scm (deeptools): New variable.
* gnu: Add BioPerl.Ricardo Wurmus2015-08-26
| | | | * gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
* gnu: shogun: Move package to machine-learning.scm.Ricardo Wurmus2015-08-14
| | | | | * gnu/packages/bioinformatics.scm (shogun): Move from here... * gnu/packages/machine-learning.scm (shogun): ...to here.
* gnu: bedtools: Add patch to fix compilation on 32 bit systems.Ben Woodcroft2015-07-25
| | | | | | | | * 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>
* gnu: bedtools: Update to 2.24.0.Ben Woodcroft2015-07-25
| | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
* gnu: Add aragorn.Ben Woodcroft2015-07-21
| | | | * gnu/packages/bioinformatics.scm (aragorn): New variable.
* gnu: metabat: Minor tweaks.Mark H Weaver2015-07-19
| | | | | | * gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in 'fix-includes' phase. [license]: Fix misspelling.
* gnu: Add metabat.Ben Woodcroft2015-07-19
| | | | * gnu/packages/bioinformatics.scm (metabat): New variable.
* gnu: preseq: Move "use-samtools-headers" phase.Ricardo Wurmus2015-07-09
| | | | | * gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase "use-samtools-headers" after "enter-dir" phase.
* gnu: Add preseq.Ricardo Wurmus2015-07-08
| | | | | | | * 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.
* gnu: samtools: Install headers.Ricardo Wurmus2015-07-08
| | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase "install-headers" to install header files.
* gnu: samtools: Update to 1.2.Ricardo Wurmus2015-07-07
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
* gnu: Add prodigal.Ben Woodcroft2015-07-05
| | | | * gnu/packages/bioinformatics.scm (prodigal): New variable.
* gnu: shogun: Build with install RPATH.Ricardo Wurmus2015-07-04
| | | | | * gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to build with install RPATH.
* gnu: Add WarpedLMM.Ricardo Wurmus2015-07-02
| | | | * gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
* gnu: Add Blast+.Ricardo Wurmus2015-06-29
| | | | * gnu/packages/bioinformatics.scm (blast+): New variable.
* gnu: Add plink.Ricardo Wurmus2015-06-29
| | | | | * gnu/packages/bioinformatics.scm (plink): New variable. * gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
* gnu: Add hmmer.Ben Woodcroft2015-06-24
| | | | * gnu/packages/bioinformatics.scm (hmmer): New variable.
* gnu: star: Update to 2.4.2a.Ricardo Wurmus2015-06-23
| | | | * gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
* gnu: miso: Install executables.Ricardo Wurmus2015-06-23
| | | | | | | * 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".
* gnu: Add idr.Ricardo Wurmus2015-06-23
| | | | * gnu/packages/bioinformatics.scm (idr): New variable.
* gnu: Add fasttree.Ben Woodcroft2015-06-21
| | | | * gnu/packages/bioinformatics.scm (fasttree): New variable.
* gnu: Add diamond.Ben Woodcroft2015-06-17
| | | | * gnu/packages/bioinformatics.scm (diamond): New variable.
* gnu: miso: Use HTTPS URL.Ricardo Wurmus2015-06-17
| | | | | * gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for downloading the source tarball.
* gnu: bedops: Update to 2.4.14.Ricardo Wurmus2015-06-17
| | | | * gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
* gnu: orfm: Update to 0.4.1.Ricardo Wurmus2015-06-15
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
* gnu: Add OrfM.Ben Woodcroft2015-06-12
| | | | | | * gnu/packages/bioinformatics.scm (orfm): New variable. Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
* gnu: Add Couger.Ricardo Wurmus2015-06-12
| | | | * gnu/packages/bioinformatics.scm (couger): New variable.
* gnu: ngs-sdk: Update to version 1.1.1.Ricardo Wurmus2015-06-12
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
* gnu: Add HTSlib.Ricardo Wurmus2015-06-02
| | | | * gnu/packages/bioinformatics.scm (htslib): New variable.
* gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name.Ricardo Wurmus2015-06-02
| | | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on i686.
* gnu: Add edirect.Ricardo Wurmus2015-05-27
| | | | * gnu/packages/bioinformatics.scm (edirect): New variable.
* gnu: shogun: Remove non-free source files.Ricardo Wurmus2015-05-27
| | | | | * gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove non-free sources.
* gnu: Add rsem.Ricardo Wurmus2015-05-22
| | | | | * gnu/packages/bioinformatics.scm (rsem): New variable. * gnu/packages/patches/rsem-makefile.patch: New file.
* gnu: vcftools: Remove "-m64" from CFLAGS.Ricardo Wurmus2015-05-05
| | | | | * gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to remove "-m64" flag.
* gnu: bamtools: Set rpath via LDFLAGS.Ricardo Wurmus2015-05-04
| | | | | * gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase setting $LDFLAGS to set the rpath to $out/lib/bamtools.
* gnu: Add samtools-0.1.19.Ricardo Wurmus2015-05-04
| | | | * gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
* gnu: samtools: Install libbam.a library.Ricardo Wurmus2015-05-04
| | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase "install-library" to install the libbam.a library.
* gnu: samtools: Remove patch-makefile-curses phase.Ricardo Wurmus2015-05-04
| | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove patch-makefile-curses phase, use make-flags instead.
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