minia 1.6088
dsk 1.6066: New formula

DSK is a k-mer counting software, similar to Jellyfish. Jellyfish is
very fast but limited to large-memory servers and k ≤ 32. In contrast,
DSK supports large values of k, and runs with (almost-)arbitrarily low
memory usage and reasonably low temporary disk usage. DSK can count
k-mers of large Illumina datasets on laptops and desktop computers.
spades 3.0
sga 0.10.13

No longer fails to build with clang.
sailfish 0.6.2: New formula

Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads
using Lightweight Algorithms
http://arxiv.org/abs/1308.3700
insighttoolkit: cleanup python usage.
lp_solve: cleanup python usage.
opencv: cleanup python usage.
qgis: cleanup python usage.
shogun: cleanup python usage.
vtk: cleanup python usage.
bedtools 2.18.2

Closes #611
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/