pymol: fix dependencies and HEAD install
trinity: Trinity r2013-02-25

De novo transcriptome assembler for RNA-Seq data
Closes #82
gfan: New Formula

Gfan is a software package for computing Gröbner fans and tropical
varieties.

Closes #109
cddlib: 094g - New formula

The C-library cddlib is a C implementation of the Double Description
Method of Motzkin et al. for generating all vertices (i.e. extreme
points) and extreme rays of a general convex polyhedron in R^d given
by a system of linear inequalities:

   P = { x=(x1, ..., xd)^T :  b - A  x  >= 0 }

where A is a given m x d real matrix, b is a given m-vector
and 0 is the m-vector of all zeros.

Closes #108
mummer: 3.23

Closes #110
resolved conflict in trinity, readded Buttefly.jar