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
metis 5.1.0

Closes #315
Upgrade OpenBLAS to 2.8.

This also removes the download of Lapack since OpenBlas now ships lapack
as part of the tar file and repo see
https://github.com/xianyi/OpenBLAS/blob/master/Changelog.txt

This also separates the tests for easier inspection.

Closes #398
Upgrade GLPK to 4.52.

In addition, make tests separately for easier inspection.
yaha 0.1.79: New formula

yaha is a split-read aligner.

Yaha currently only supports a linux binary. The goal of this package is
to encourage use on Linux/Linuxbrew to advocate for a source code or
MacOSX-specific upstream release.

Closes #389
lumpy-sv 0.1.5: New formula

This structural variation caller supports integration of multiple
structural variant detection approaches, including split and paired
end reads.

Closes #388
gmap-gsnap 2013-10-15
fasta 36.3.6d
cap3 2007-12-21: New formula
pcap 2005-06-07: New formula
qualimap 0.7.1: New formula

Qualimap: Evaluating next generation sequencing alignment data

Qualimap is a platform-independent application written in Java and R
that provides both a Graphical User Inteface (GUI) and a command-line
interface to facilitate the quality control of alignment sequencing
data.

Closes #387