lumpy-sv 0.2.2.2

Closes #898.
wcslib 4.23

Closes #903.
root: cocoa as default, :x11 optional

* fix building without XCode
* disable old workaround
* refactor argument list

Closes #889.
lammps: fix path to gfortran

gfortran formula was removed in favor of gcc.

Full path to libgfortran currently:
/usr/local/opt/gcc/lib/gcc/x86_64-apple-darwin13.2.0/4.8.2/

Fixes #904.
bwa 0.7.9a
gmap-gsnap 2014-05-15

Add DOI
maker 2.31.5
pbsuite 14.5.13: New formula

Software for Long-Read Sequencing Data from PacBio
PBJelly - the genome upgrading tool
PBHoney - the structural variation discovery tool
root: tab -> spaces
genometools: Add head and DOI
bedtools: Add DOI
samtools: add vcfutils.pl to without-bcftools

vcfutils.pl is now included in the latest bcftools release candidate
(rc8) so conflicts when installed alongside samtools. This removes the
conflict when passing --without-bcftools. chapmanb/bcbio-nextgen#426

Closes #910.
root: patch not required with HEAD

Patch is only required for non-HEAD users at or before 5.34.18
without XCode installed.

Closes #905.
spatialite-gis: fix compilation with wxWidgets 3

See also https://github.com/Homebrew/homebrew/commit/b31227d6ef602142ea399b04211d306eaaea674c

Closes #298.
Closes #456.
galib: fix clang error with undeclared identifiers

Closes #908.
mummer: Add DOI
netcdf: patch to fix hdf5 1.8.13 missing symbols

HDF5 1.8.13 removes symbols related to MPI POSIX VFD, leading to
errors when linking hdf5 and netcdf5 such as "undefined reference to
`_H5Pset_fapl_mpiposix’".

The patch has already been added to netcdf, and will be included
in the next release.

Fixes #911.
Closes #916.
armadillo 4.300.3

Copy examples/ directory to prefix.

Closes #912.