amos: Fails with clang

genome-complexity-fast.cc:21:54:
error: reference to 'hash' is ambiguous
note: candidate found by name lookup is 'std::__1::hash'
note: candidate found by name lookup is '__gnu_cxx::hash'

Closes #485
ucsc-genome-browser: Fix the mysql include path

Change
"MYSQLINC=#{HOMEBREW_PREFIX}/include"
to
"MYSQLINC=#{HOMEBREW_PREFIX}/include/mysql"
ucsc-genome-browser 292
fastx_toolkit: Add HEAD

Closes #536
beast 1.8.0: Fix directory reference in HEAD

Closes #538
Changed CMake options for enabling Qt support.

Closes #530.
Upate vigra to 10.0.

- Add checks at build time
- Optionally depend on hdf5 and Python.
adding enblend and enfuse 4.1.1

this formula builds both the enblend and and the enfuse tools

Closes #120.
New formula for Arpack.

Closes #188.
Closes #511.
New formula: SNID 5.0

A Supernova Identification package, originally
written by John Tonry to determine redshifts of
Type Ia supernovae. It has since been re-written
and expanded to include type and age determination,
as well as an interactive plotting package.

Closes #167.
vtk: Added new VTK_INSTALL_PYTHON_MODULE_DIR for the python wrappings (HEAD build, in prevision of future vtk 6.1)
Do not use the patch for Head, it was merged

Closes #435.
snid: use proper fortran declaration

Closes #547.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
Fix audit warnings
blast: Fix the error in `stat' Errno::ENOENT

mv gives the error message:
fileutils.rb:1552:in `stat'
Errno::ENOENT: No such file or directory -
$HOMEBREW_PREFIX/Cellar/blast/2.2.28/lib/libaccess-static.a
Does not work: mv Dir[lib / 'lib*.a'], libexec
Works: system "mv #{lib}/lib*.a #{libexec}/"
blast: Add the option --disable-tests
blast: Add a test
blast: Rename --disable-tests to --without-check
abyss: Fails with clang

error: implicit instantiation of undefined template
'std::__1::hash<cstring>'
abyss: Add 512 to the --enable-maxk options
abyss 1.3.7

No longer fails with clang