blasr: Specify the path to hdf5

Closes #932
sundials: add features

- add serial tests for C bindings
- add patches from mailing list since 2.5.0 release
- add openblas support
- add Fortran support
- add serial Fortran tests
- add mpi support
- add parallel tests for C bindings
- add parallel tests for Fortran bindings
- add patches (submitted upstream) to fix additioanl bugs
- add Argonne PETSc project mirror

Closes #962.
Healpix version 3.11

See http://healpix.jpl.nasa.gov/

HEALPix is an acronym for Hierarchical Equal Area isoLatitude
Pixelization of a sphere. As suggested in the name, this pixelization
produces a subdivision of a spherical surface in which each pixel
covers the same surface area as every other pixel.  Healpix is used
extensively in astronomy to produce maps of data on the sky.

Closes #169.
qcl: 0.6.4: a language for quantum computers

Wikipedia lists QCL as one of the first quantum programming languages. This formula downloads and installs the latest version of QCL from the maintainer's website. In addition, the formula copies the standard QCL library so that the interpreter is able to run properly.

Closes #288.
mafft: fix build error on 10.6

Closes #313.
ropebwt2 r181

Add a link to the PDF on arXiv.
Sara: 1.13 - Deciding reachability for Petri nets

Sara is a tool for solving the reachability problem for Petri nets. Given a
low-level Petri net, i.e. sets of places and transitions with weighted arcs
between them, and an initial and a final marking, Sara tries to determine
whether the final marking can be reached from the initial marking by firing a
sequence of transitions in the Petri net. While the initial marking must be a
map from the places to non-negative integers, that means one single marking,
the final marking can be somewhat generalized. It is possible -- for each place
on its own -- to declare that the given number must be reached exactly (as for
the initial marking), covered (a higher value is allowed), or bounded (a lower
value is permissible). In addition, more general constraints may be formulated
which the final marking must fulfill. Such a constraint can be any linear
(in)equation built from places and transitions.

As a by-product, also problems of form ``given a Petri net, an initial marking,
and a transition multiset, is the multiset realizable?'' can be solved.
Realizable means that there is a firing sequence in the Petri net that contains
each transition exactly as often as the transition multiset dictates.

If Sara can compute the problem given, it should either tell the user that
there is a solution and present a firing sequence proving this, or it should
tell that the problem is infeasible. In the latter case, Sara might provide
additional information that gives some insight into why the problem is
infeasible.

Closes #349.
PNAPI: 4.03 - A C++ Petri Net API

The Petri Net API is a C++ library of Petri net-related functions. It is
currently used in more than a dozen Petri net tools, ranging from compilers
to verification tools.

Closes #353.
Migrate vtk5 back from homebrew-versions
vtk: use patch DSL
Mira: upgrade to 4.0.2.

The Boost libraries aren't discovered unless they are passed to make.

Closes #968.
Upgrade asl to v20140617.

Closes #978.
version 6.7.1

Closes #972.
delly 0.5.5

Closes #974.
sratoolkit: version 2.3.5-2

Closes #965.
Ipopt: upgrade to 3.11.8
Scotch: build shared libs and run tests.

Include a patch to fix the ptcheck tests and to correct an omission
in the tests Makefile.
asl 20140618

Closes #981.
New formula: getdp 2.4.3

Closes #945.
vecLibFort 0.2: new formula

Closes #765.