paml 4.7

paml 4.6 was stable and 4.7 was devel.
Update stable to 4.7 and remove devel.
Closes #226
cgns: style update
CoinMP: use :fortran
CoinUtils: use :fortran
hopdm: use :fortran
galib: style update
prank: fix indents
mrbayes: remove :using
octave: use :fortran

Also remove comment about building with -O2.
opencv: specify Python executable

Shield against wrong python installations.

Explicitly specify the python executable to use in the CMake call to prevent
picking up python executables not related to the specified library.

Closes #233.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
viennarna 2.1.2

Closes #232.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
build isn't allowed in test methods

'build' isn't currently set up for test methods, so comment out
these tests for now.
fasta 36.3.5e: New formula

Bioinformatics tool for sequence alignment
http://faculty.virginia.edu/wrpearson/fasta/
vcftools 0.1.11

Closes #234
mrbayes: fix optional dep
trilinos: use optional deps
mathgl 2.1.3.1

Closes #236.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
hmmer 3.1b1: Add --devel and --HEAD

Closes #235
Cufflinks: still fails with clang 425
soapdenovo: Specify the version explicitly

The version number is incorrectly identified as `V1.05.src`.