opencv: make jasper dependency optional

Closes #875.
prokka 1.9
barrnap 0.4.2
bamtools: use checksummed patch
root: Fix compilation error with X11 backend

ROOT compilation with X11 backend may fail if there is a clash between
homebrewed freetype>=2.5.1 in /usr/local/include/freetype and XQuartz
freetype<2.5.1. This patch rises XQuartz'es includes priority so that
clang doesn't try to halfbreed freetype headers.

Closes #853.
Closes #868.
hmmer: Add DOI
hmmer2 2.3.2: New formula
sga: Add DOI
smrtanalysis 2.2.0.133377: New formula
blasr 2.1: Fails to build with clang and gcc-4.2
exonerate 2.2.0: Add DOI and a test
maker: Make most dependencies optional
Add DOI
openni: fix patch shasums

Closes #888.
htslib 0.2.0-rc8

Closes #881.
bcftools 0.2.0-rc8

Closes #880.
mcl 14-136

Closes #890.
mcl 14-137

Closes #895.
netcdf 4.3.2

Closes #892.
hdf5 1.8.13

Closes #893.