picard-tools 1.103

Closes #500
bowtie: Install documents and scripts
bowtie: Fails with clang

error: reference to 'lock_guard' is ambiguous

Closes #476
tophat 2.0.10

 * patches from 2.0.9 are still necessary and still apply
 * added test step based on example at http://tophat.cbcb.umd.edu/tutorial.shtml#ref
 * added recommended dependency to bowtie2 as it is required to execute tophat

Closes #496
plink: Fails with clang

sets.cpp:771:37: error: redefinition of 'i' with a different type:
'vector<Individual *>::iterator' (aka '__wrap_iter<pointer>') vs 'int'
      vector<Individual*>::iterator i = PP->sample.begin();
                                    ^
sets.cpp:703:12: note: previous definition is here
  for (int i=0; i<snpset.size(); i++)
           ^

Closes #492
Add mirror and checks to NetCDF formula.

Added NetCDF mirror because Unidata's servers are not responding so well lately
Add checks.

Closes #498.
trinity: Fix the build on OS X

Closes #374
Update voro++.rb to solve Mavericks build issues

See https://github.com/Homebrew/homebrew-science/issues/404

Closes #431.
Move libgtextutils from core
trinity r20131110

The patch to fix building on a case insensitive file system is no
longer necessary.
Upgrade CoinMP to 1.7.3.

- add head ref
- add tests
- remove hack.

Fixes #460.
cufflinks: Fails with clang 500

./hits.h:829:10: error: unknown type name 'shared_ptr'
        MateHit(shared_ptr<ReadGroupProperties const> rg_props,

Closes #509
gmap-gsnap 2013-11-22
stacks: Fails with clang 500

error: 'tr1/unordered_map' file not found
stacks 1.07
stacks 1.08
stacks 1.09
Fix VTK issue on mavericks

Closes #410.
Corrected sha1 for hdf5-1.8.12.tar.bz2

Closes #513.
sga: Fails with clang 500