Eliminate global methods
suite-sparse: update to 4.2.0

Update suite-sparse to the new 4.2.0. This should fix the recent Octave
build problems.

Also change the metis dependency to use the metis4 formula instead of metis,
since SuiteSparse is not compatible with Metix 5.x.

Now uses built-in Mac make script.

Use :recommend and :option for dependencies

closes #128, closes #132, closes #139, closes #146, closes #153

Signed-off-by: Derek Thomas <derekathomas@gmail.com>
OpenCV 2.4.5

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
blast 2.2.28

Closes #156.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
metis: support universal builds

Closes #149.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
cd-hit 4.6.1

Closes #130.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
abyss: The GitHub repository moved to bcgsc/abyss
bwa 0.7.4
suite-sparse: fix audit warning
bioawk: New formula
abyss; New option --enable-maxk
bowtie2 2.1.0

Closes #164
bowtie 1.0.0

Closes #163
jellyfish 1.1.10: New formula

Closes #150
lastz: new formula: LASTZ 1.02

Pairwise aligner for DNA sequences, designed to handle sequences the size
of human chromosomes and from different species.
lastz 1.03.34

Closes #115
sickle: new formula
sickle 1.2

Closes #31
mrfast 2.6.0.1

Closes #166
bam-readcount 0.4.4: New formula