ensembl-tools: update shasum
fcgene: update shasum
mira: Remove dependency on homebrew/dupes/zlib

Closes #1037
Vips: update to 7.40.3

update vips.rb to latest stable, list of changes here:

http://libvips.blogspot.co.uk/2014/06/new-stable-version-740.html

add the new libgsf-1 optional dep

reorder the formula to get all recommended and all optional deps listed
together

Closes #1035.
igv 2.3.34

Closes #1048.
nextflow 0.8.3: New formula

Closes #1039
gmsh: update to 2.8.5

Closes #1052.
ASL: upgrade to 20140704

Fixes #1056.
kmerstream 1.0: New formula

KmerStream: Streaming algorithms for k-mer abundance estimation
bowtie: fix build with gcc-4.8
ucsc-genome-browser 302
openblas 0.2.9

Add --devel 0.2.10-rc2.

Closes #1038.
tbl2asn 23.6
Use patch DSL
emboss: add mirror
gmt4: update gshhg resource
gmt: update gshhg resource
getdp: update to 2.4.4

Removed the library fix (line 55) because now also corrected upstream

Closes #1061.
R 3.1.1

Release notes: https://stat.ethz.ch/pipermail/r-announce/2014/000575.html

Closes #1058.
arpack: fix symlink overwriting pkgconfig directory

Closes #1059.