LoLA: Updated to LoLA 2.0

Closes #990.
Symphony: upgrade to 5.5.7.

Closes #873.
JoinX: exit with error message on OSX.

Closes #939.
Revert "htslib: Install version.h"

This reverts commit 71634ba8bebd92719c287f3d5a1d6e085a8a1e76.

Closes #1015
libsequence 1.8.2

Update to latest version of libsequence to fix compile issues on
Mavericks with clang (among other issues). Also changes download
location to github repository releases.

Closes #1029.
healpix: depends on pkg-config

Closes #1013.
swetest 2.00.00

Closes #927.
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.