qgis: Modernize formula and fix a few bugs.

- Remove subformulae bison, qwt
  (they are separate deps now and they seem to work)
- Fix issue that a brewed Python framework was not found by cmake
- Move PyQt availablilty-check to a Requirement
- Remove custom accessor functions "grass?". We have now build.with?
- Expat is a dependency qgis searches for (and uses)
- grass and postgis support is :optional (→ auto generated --with-grass)
- Install qgis into Frameworks and not lib as it provides Frameworks.
- Fixes #23 by adding -F to the Qt Framework
beagle: Add Framework location for CUDA

- Fixed typo in handling of opencl option
- Changed --with-cuda to a Requirement
- Adding nvcc to the ENV['PATH']
- See discussion in
  https://github.com/Homebrew/homebrew-science/issues/67
niftilib: 2.0.0

I/O library for the NIFTI file format for MRI and fMRI brain images
http://niftilib.sourceforge.net
pymol: 1.5.0.1

* Make mono install as default (put stereo behind option)
* use ":freetype" as dependency
* GUI render test to "--gui" option
pmw: 1.3.3 (a dep of Pymol)
bowtie2: updated version to 2.0.6
bowtie: updated version to 0.12.9
FastTree 2.1.7

Still: Test fails with clang (though build is fine)
Closes #96
gmap-gsnap: 2013-02-05
mira 3.4.1.1

The patch is no longer necessary.
galib: 2.4.7

galib is a c++ library for working with genetic algorithms. It is
currently not included neither in homebrew/master nor in
homebrew/homebrew-science.

Added a 'make test' call just before the installation step. The test
should end in about 15s on a fast machine.
galib: ENV.deparallelize
wcslib.rb: audit fix
CoinUtils: 2.8.8

CoinUtils installs basic tools used by other COIN-OR projects.
See www.coin-or.org.
velvet: sha1 update & option to support long kmers

Velvet is usually built to support a maximum kmer size of either 31 or 63
and this patch adds a '--with-63mer' option to build the latter.

-  option to support longer kmers (alternate)
   Uses the values of the MAXKMERLENGTH env. var.

Closes #76
metis4: Formula for METIS v4.

METIS v4 used to be in Homebrew-Core and disappeared in
favor of METIS v5. However, certain libraries, such as SuiteSparse,
do not compile properly with METIS v5.

See also https://github.com/mxcl/homebrew/issues/15537.
mira: Fix a compiler error on OS X 10.8