bowtie2 2.2.2
hotspot 4.1.0

Closes #827
ucsc-genome-browser 298
scarpa 0.241: New formula

Scarpa is a stand-alone scaffolding tool for NGS data. It can be used
together with virtually any genome assembler and any NGS read mapper
that supports SAM format.
snpeff 3.5h
igvtools 2.3.32
R: link with Accelerate framework

By default R should link against the Accelerate framework.

Closes #825.
field3d 1.4.3
lammps: install examples dir

Closes #808.
orocos-kdl 1.2.2 (new formula)

Closes #415.
sais 2.4.1: New formula

An implementation of the induced sorting algorithm

sais is a very simple and small library that provides an
implementation of the induced sorting [1] based suffix array
construction algorithm. The algorithm runs in O(n) worst-case time,
and MAX(2n, 4k) worst-case extra working space, where n and k are the
length of the input string and the number of alphabets.
Fix audit warnings
openbr 0.4.1 (new formula)

OpenBR is an open source framework, supplying face recognition and
related functionality.  OpenBR is a a communal biometrics framework
supporting the development of open algorithms and reproducible evaluations.
OpenBR is supported on Windows, Mac OS X, and Debian Linux. The project is
licensed under Apache 2.0 and releases follow the Semantic Versioning
convention. Internally the code base uses the CMake build system and
requires Qt and OpenCV.

Closes #494.
opencv: Add --with-cuda, require -stdlib=libstdc++ when enabled

Closes #305.
picard-tools 1.112

Closes #840.
r-gui 1.64 (new formula)

New formula for the R Mac GUI.

The following restrictions hold (based on the `INSTALL` instructions):
> Only Mac OS X 10.6 and higher are supported, and only 64-bit R

R.app is linked against the installed version of R (in opt).

HEAD version works via SVN repo (employs a minor hack due to the build
scripts requiring the SVN version).

Closes #831.
barrnap 0.3: New formula

Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes
in Bacterial and Archaeal genome sequences. It takes FASTA DNA
sequence as input, and write GFF3 as output.
prokka: Depends on barrnap
prodigal: Add DOI
prokka: Add DOI