Fix for karyotype sorting multifasta genomes.

Some of the UCSC style genomes are in multifasta format, which
was not being split into individual chromosomes before
being karyotype sorted. This fixes that issue.
Skip creating the STAR index if the GTF file is not found.
Generalize dbSNP preparation script.
Update featureCounts to 64 bit version. Support OSX installs.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Fix for string formatting issue.
Provide downloads for annotated repeat regions for human SNP indel and structural variant calling: low complexity regions from Heng Li and telomeres/centromeres from delly
Fix for homebrew causing a failedOSX installation.

This checks for homebrew first before trying to install it
again. Fixes #155. Partial progres on chapmanb/bcbio-nextgen#396.
Fix Tophat installation on OSX.
Add directory to search for find(1).

OSX find(1) needs this set explicitly:

rory@clotho:~$ find -name "foo"
find: illegal option -- n
Remove pbgzip which fails to compile on Mac and is not currently used. Add samblaster and speedseq builds for lumpy SV calls
Remove use of -r sed flag for snpEff; fix for MacOSX. Remove unused builds that have been moved over to homebrew
Add camFam3 dbSNP resource to automatic downloads. Swap mm10 to use bgzipped and tabix indexed files
Readd samtools custom build used in gemini installation. Fixes arq5x/gemini#279
Correct flag value to install_brew() automated=True.

That's what I REALLY meant in 6375737108abc4de5a529685930f4de7c5a131bf.
Merge pull request #162 from glebkuznetsov/master

Correct flag value to install_brew() automated=True.
Do not fail on missing version information, instead re-install (chapmanb/bcbio-nextgen#405). Use custom version of delly exclusion file compatible with lumpy
Avoid estscan install which is problematic on Ubuntu 14.04. Fixes #163
Swap Pyrex to Pyrex-real.

Looks like the Pyrex pypi repository is dead and has moved to
Pyrex-real.
Remove gnuplot-py, it is missing from pypi at the moment.