mrfast 2.6.0.1

Closes #166
bam-readcount 0.4.4: New formula
blast: Support recent versions of gnutls

Add an upstream patch to support recent versions of gnutls.
Add an optional build dependency on gnutls.
Add configure --without-debug --with-mt as recommended by upstream.
Closes #161, closes #170.
ROOT: use builtin GLEW

Closes #19724.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
vtk: fixes for 10.8 and 10.6 with python wrapping

For 10.8 : https://github.com/mxcl/homebrew/issues/16646
For 10.6 : https://github.com/mxcl/homebrew/issues/14871

Closes #180.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
sratoolkit 2.3.2-4: New formula
viennarna 2.1.1

Remove the patch. Fixed upstream. Closes #162
mafft 7.037

Closes #172
R 3.0.1

Announcement at https://stat.ethz.ch/pipermail/r-announce/2013/000563.html.

Closes #19900.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
mafft: Add a test
AMOS: New formula
amos: Add dependencies

Closes #39
analysis 0.8.3: New formula

Closes #92
bedops 2.0.0b: New formula

Highly scalable genomic feature operations.
bedops is a BED/GFF/VCF manipulation package similar to bedtools.
Closes #111
seqdb 0.2.0: New formula

A file format, compressor and storage tool for the raw data produced by
Next-Generation Sequencing platforms.
Closes #117
CoinUtils 2.9.0
populations 1.2.33-2: New formula

Closes #34
bamutil 1.0.7: New formula

http://genome.sph.umich.edu/wiki/BamUtil
velvet: add contributed scripts for shuffle sequence

closes #118
wcslib: fix download

fixes #138