* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.

* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.

* 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/packages/bioinformatics.scm (bedtools): Update to 2.24.0.

* gnu/packages/bioinformatics.scm (aragorn): New variable.

* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
  'fix-includes' phase.
  [license]: Fix misspelling.

* gnu/packages/bioinformatics.scm (metabat): New variable.

* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
  "use-samtools-headers" after "enter-dir" phase.

* 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/packages/bioinformatics.scm (samtools)[arguments]: Add phase
  "install-headers" to install header files.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.

* gnu/packages/bioinformatics.scm (prodigal): New variable.

* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
  build with install RPATH.

* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.

* gnu/packages/bioinformatics.scm (blast+): New variable.

* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.

* gnu/packages/bioinformatics.scm (hmmer): New variable.

* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.

* 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/packages/bioinformatics.scm (idr): New variable.

* gnu/packages/bioinformatics.scm (fasttree): New variable.

* gnu/packages/bioinformatics.scm (diamond): New variable.

* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
  downloading the source tarball.

* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.

* gnu/packages/bioinformatics.scm (orfm): New variable.

Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>

* gnu/packages/bioinformatics.scm (couger): New variable.

* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.

* gnu/packages/bioinformatics.scm (htslib): New variable.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
  "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
  i686.

* gnu/packages/bioinformatics.scm (edirect): New variable.

* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
  non-free sources.

* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.

* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
  remove "-m64" flag.

* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase
  setting $LDFLAGS to set the rpath to $out/lib/bamtools.

* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.

* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
  "install-library" to install the libbam.a library.

* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
  patch-makefile-curses phase, use make-flags instead.

* gnu/packages/bioinformatics.scm (flexbar): Enable tests.

* gnu/packages/bioinformatics.scm (express): New variable.