Upgrade GLPK to 4.52.

In addition, make tests separately for easier inspection.
Updates to Scalapack formula

- always run tests
- make openblas optional instead of recommended.
New formula for IPOPT.
New formula for CppAD.
Update ceres-solver.rb to version 1.8.0

1. Fix Mavericks breakage.
2. Add the ability run test (on by default) (thanks @dpo)
Update MUMPS formula for Mavericks.
Update ceres-solver to 1.8.0

- Fix for Mavericks
- Add tests
- Build shared libs.
Merge pull request #489 from dpo/mumps

Update MUMPS formula for Mavericks.
New formula for ASL.

ASL is the AMPL Solver Library and allows optimization solvers to
interact with models written in the AMPL modeling language
(www.ampl.com), one of the most common modeling languages used in the
optimization community.
Merge pull request #393 from dpo/asl

New formula for ASL.
Merge pull request #416 from dpo/ipopt

New formula for IPOPT.
Merge pull request #440 from dpo/cppad

New formula for CppAD.
Merge pull request #399 from dpo/glpk

Upgrade GLPK to 4.52.
Merge pull request #412 from dpo/scalapack

Updates to Scalapack formula
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.