suite-sparse: Update the sha1
Revert "suite-sparse: Update the sha1"

This reverts commit 05b80fd0d3f033f2c6db1262b0a46bc3b187c25a.
Closes #373
agalma: upgraded to 0.3.4
trinity: workaround for issues with superenv
oma 0.99t: new Formula

Identification of Orthologs from Complete Genome Data
R 3.0.2

Announcement at https://stat.ethz.ch/pipermail/r-announce/2013/000567.html

Announced md5 fingerprint (f9a8374736e7650e4848f33e2e3bbee3) checked
and replaced by sha1.

Closes #357
rml-mmc: simplify finding smlnj

Closes #367.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
trinity: Fails with clang build 500
trinity r2013_08_14
pastix 5.2.1: New formula for PaStiX

PaStiX (Parallel Sparse matriX package) is a scientific library that
provides a high performance parallel solver for very large sparse
linear systems based on direct methods.

Closes #365
igv 2.3.20: New formula

The Integrative Genomics Viewer (IGV) is a high-performance
visualization tool for interactive exploration of large, integrated
genomic datasets. It supports a wide variety of data types, including
array-based and next-generation sequence data, and genomic
annotations.
blasr: New formula
opencv: optional dep on ffmpeg, fix linking if not

Closes #366.

Signed-off-by: Misty De Meo <mistydemeo@gmail.com>
VTK: update version to 6.0.0
vtk: Fix rpath libdir
blasr 2.1
InsightToolkit : 4.4.2 and added python wrapping

- Added vtk dependency
- Added itkv3 compatibility option
- Changed the compiler to llvm-gcc
- Added a patch for ITK 4.4.2, so it can build with VTK 6.0.0 while ITKVtkGlue is set to ON
insighttoolkit: Try to remove llvm-gcc
samtools: Add test
novoalign: Use `OS.mac?` rather than `MACOS`

Closes #395
Closes #397