opencv: switch eigen and openexr to optional

Eigen and OpenEXR are special-case (interoperability) libraries and
are not needed for general purpose usage of OpenCV.

Closes #874.
igraph 0.7.1

Closes #878.
gmt: add full mirror list.

Adding all available mirrors to gmt formula, since
people are experiencing download problems from the main
site.

Closes #876.
openni: fix typo in pkg-config file path

Closes #882.
openni: use checksummed patches
tabix: conflicts with htslib
barrnap 0.4
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