bedtools 2.18.2

Closes #611
update pymol to 1.7
circos 0.64: New formula

Circos is a software package for visualizing data and information. It
visualizes data in a circular layout — this makes Circos ideal for
exploring relationships between objects or positions.
ray 2.3.0

Fails to build with clang, llvm and gcc-4.2. Builds with gcc-4.8.
ray: Add HEAD

Requires RayPlatform.
https://github.com/sebhtml/RayPlatform
snpeff 3.4i

Closes #584
beetl 0.9.0: New formula

BEETL: Burrows-Wheeler Extended Tool Library

Markus J. Bauer, Anthony J. Cox and Giovanna Rosone
Lightweight BWT Construction for Very Large String Collections.
Proceedings of CPM 2011, pp.219-231
ropebwt 20130801: New formula

RopeBWT is the predecessor of ropeBWT2. The old version implements
three separate algorithms: in-memory BCR, single-string incremental
FM-index on top of a B+ tree and single-string incremental FM-index on
top of a red-black tree. BCR is later extended to support RLO and RCLO
as well.

https://github.com/lh3/ropebwt2#ropebwt2-vs-ropebwt
ropebwt2 r132: New formula

RopeBWT2 is an experimental tool for constructing the FM-index for a
collection of DNA sequences.

https://github.com/lh3/ropebwt2#introduction
geneid 1.4.4: New formula

geneid is a program to predict genes in anonymous genomic sequences
designed with a hierarchical structure.

http://genome.crg.es/software/geneid/
genewise 2.4.1: New formula

Wise2's key programs are genewise, a program for aligning proteins or
protein HMMs to DNA, and dynamite a rather cranky "macro language"
which automates the production of dynamic programming.

http://www.ebi.ac.uk/~birney/wise2/
cegma 2.4.010312: New formula

CEGMA (Core Eukaryotic Genes Mapping Approach) is for building a
highly reliable set of gene annotations in the absence of experimental
data.

http://korflab.ucdavis.edu/datasets/cegma/
Update ASL to 20140131.
Add a new formula for PSPP

PSPP is the GNU reimplementation of SPSS, a package for doing
statistical analysis. This formula adds support for the GUI and
command-line pspp tools.

Closes #539.
augustus 3.0.1: New formula

AUGUSTUS is a program that predicts genes in eukaryotic genomic
sequences.
ogdraw 1.1.1: New formula

OGDRAW - Quickly draw high-quality graphical maps of organellar
genomes (And other circular DNA molecules, if you like).
hmmer 3.1b1: Promote devel to stable

repeatmasker requires hmmer 3.1 for nhmmer.
hmmer 3.1b1 was released 2013-May.
trf 4.07b: New formula

Tandem Repeats Finder is a program to locate and display tandem
repeats in DNA sequences.
repeatmasker 4.0.3: New formula

RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences.
snap 2013-11-29: New formula

SNAP - Semi-HMM-based Nucleic Acid Parser