snpeff 3.6c

Closes #935.
paml 4.8
graph-tool: fix dep; flag changes; add test

Build failure fixed by requiring Python on Boost dependency.

Sparsehash dependency is recommended offically. Since the sparsehash
installation problem on 10.9.2 is now fixed (Homebrew/homebrew#27652),
it should be enabled by default.

Add option to drop Cairo dependency.

Add test based on the official quick start example
(http://graph-tool.skewed.de/static/doc/quickstart.html).

Closes #917.
nlopt 2.4.2

Closes #937.
cminpack 1.3.4

Closes #936.
bowtie2 2.2.3
cppad 20140000.3
hmmer: add make check
bowtie2: use test from examples
libpll 1.0.0 (new formula)

PLL is a highly optimized, parallized software library to ease the
development of new software tools dealing with phylogenetic inference.
(http://www.libpll.org)

Closes #901.
openimageio 1.4.8

Closes #921.
data-science-toolbox 077c94f
bowtie: add test suite, fails with gcc-4.8

Refactor for tests, switch to more complete package archive.

Closes #885.
pykep 1.1.3 (new formula)

Closes #194.
spades 3.1.0
lightstringgraph 0.1.0: New formula

Lightweight String Graph Construction
spades: use --test for test

Closes #934.
README: update links
cube: Add qt to recommended dependencies