bedops 2.3.0

Add devel 2.4.1-rc1
bedops 2.4.0

Closes #666
circos: gd requires --with-freetype

Closes #684
mitofy: Add instructions to use the Mitofy web app
libgpkg 0.9.16

Closes #687.
root 5.34.15

Closes #682.
root: make Cocoa default, add --with-x11 option

On OSX >= 10.8 ROOT now uses Cocoa backend by default instead of X11.
This replaces --with-cocoa option with --with-x11 option.

Closes #690.
maker 2.31: New formula

MAKER is a portable and easily configurable genome annotation
pipeline.
itk 4.5.1

Closes #679.
circos: add GD::Polyline caveat
snpeff 3.5
snpeff: fix version 3.5b
repeatmasker 4.0.5
igv 2.3.8
gmap-gsnap 2014-02-18
Revert "igv 2.3.8"
bwa 0.7.6a
circos: Add instructions to install gd and circos

Also add useful, non-trivial tests

Closes #684
ray 2.3.1

No longer fails to build with clang.
bwa: Install README.md and NEWS to doc