netcdf 4.3.2

Closes #892.
hdf5 1.8.13

Closes #893.
octave 3.8.1: optional GUI & JIT

Squashed these commits:
Support suite-sparse built with metis4
Removed X11 dependancy
Removed X11 dependancy, we don’t need it for Mac at all, because we
build with native Qt. (+9 squashed commits)
Squashed commits:
[c0d9779] Fixes X11 Problem

Remove hack with X11 lib, because homebrew removes it anyway.
https://github.com/Homebrew/homebrew-science/pull/723#issuecomment-42023
408

Added regular x11 depends_on
[f32ba8e] Moved the X11 replacement to the proper place
[85d53b3] Added X11 lib path fix back in
[2364e7e] Further remove unnecessary link dependencies in mkoctfile.
[f5ec7bd] Removed the keyboard patch for HEAD builds; added mkoctfile patch, pstoedit/epstool dependencies
[3050c2a] EXPERIMENT: stripping out extra link dependencies in mkoctfile, to see if it fixes the pkg problems.
[ac7b8eb] X11/TeX fixes
[c72b81f] Fix for odd mkoctfile dependency issues
[a671276] octave 3.8.1: optional GUI & JIT

Closes #723.
moab 4.6.2

Also use --libdir=libexec/lib

Closes #891.
Mathgl 2.2.2.1
Add tetgen
alembic: update url, add HEAD
alembic: use hg release tag

Google Code seems to generate differing tag archives each download.
Fix audit warnings
cmor 2.9.1 (new formula)

CMOR is Climate Model Output Rewriter, which is a standard tool for
transforming climate model output data into standard form. For more
information, see http://www2-pcmdi.llnl.gov/cmor.

Closes #860.
tetgen 1.5.0

TetGen is a program to generate tetrahedral meshes of any 3D
polyhedral domains.

Closes #899.
gmsh 2.8.4

Gmsh is a 3D finite element grid generator with a build-in CAD engine
and post-processor.

Closes #872.
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