masurca: Fix No rule to make target `src/masurca'

Closes #94
Tophat: upgrade to 2.0.12.

Closes #963.
htslib 0.2.0-rc10
bcftools: Remove dependency on htslib/version.h

See #1015
bcftools 0.2.0-rc10
ucsc-genome-browser 301
bedtools 2.20.1
Symphony: Add readline support.
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.