abyss: use spec deps
beast: use spec deps
bowtie2: move conditional into method
bpel2owfn: use spec deps
fastx_toolkit: use spec deps
genet: use spec deps
hmmer: use spec deps
lola: use spec deps
mtl: use spec deps
ray: use spec deps
insighttoolkit: remove trailing whitespace
vtk: fix file permissions
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.