raxml 8.0.5

Updates raxml to version 8.0.5. Also fixes old broken pthreads compile and automatically compiles vectorized versions based on detected CPU capabilities.

Closes #667.
ucsc-genome-browser: Patch makefile
kmergenie 1.6213
nonpareil: New formula

Nonpareil allows the estimation of average coverage in
metagenomic datasets and the projection to larger sequencing
efforts.

Closes 655.
igv 2.3.25

Closes #621.
opencascade: New formula

opencascade.org (3D modeling & numerical simulation)

Closes #624.
oce: New formula

OpenCascade Community Edition

Closes #629.
bedtools 2.19.0

Closes #669.
mathgl: 2.2.1

This new version fixes the build with recent gsl versions.
Conditionally enable OpenMP.
Streamline build options.

Closes #588. Closes #661.
insighttoolkit: Disable python wrappings

Added message that python binaries can be found in a private tap.

Closes #649.
ann: Fix compilation in mavericks

Closes #425.
viennarna 2.1.6
wcslib 4.20

Closes #606.
vtk 6.1

Removed the patches which were merged for the 6.1 release.
Removed freetype, fails with latest freetype versions.

Closes #641.
ucsc-genome-browser 295
lammps 2014.02.12

Closes #675.
New Formula: graph-tool 2.2.29.1. HEAD

Closes #565.
mafft 7.130
libgpkg 0.9.15 (new formula)

SQLite3 extension for OGC GeoPackage implementation
see: http://www.ogcnetwork.net/geopackage

Closes #599.
libgpkg: fix missing spaces in caveats