Run sequence preparation from UCSC/Ensemble inside a temporary work directory to avoid picking up FASTA files from existing transcript directories
Add scalpel and hall-lab-sv-tools to default bcbio-nextgen install: chapmanb/bcbio-nextgen#432
Update to latest version of snpEff, GEMINI and VEP. Prefer brew installs for snpEff and VEP, maintaining old snpEff for short-term back-compatibility
Include additional perl libraries in local install required by VEP
Provide download target for dbNSFP to support use with VEP. Add additional required perl library for proxy-friendly downloads from VEP
Replace CDN url where SGE is retrieved from during CloudMan config; include novnc into CloudMan config
CloudMan now handles editing /etc/exports when managing file systems so don't bake all the file system into the image
Update virtualenv-burrito install command as per the docs
Add additional perl libraries required by VEP installer
Ensure we correctly mark comments when tabix indexing dbNSFP with recent versions of tabix
Improve dbNSFP download: enable continues and use same file directory instead of global /tmp to avoid space issues
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Update Tophat to grab from the new JHU URL.

Closes chapmanb/bcbio-nextgen#447
Remove source builds for cufflinks and tophat which are no longer maintained
sacCer2 to sacCer3
Move INDEX_FNs so outside packages can get a list of supported indexes.
updated yaml; sacCer2 => sacCer3
Remove automatic uploading to S3.
Merge pull request #169 from kern3020/master

updating sacCer2 to sacCer3
Include download of human ancestral sequence used by VEP LOFTEE plugin to assess loss of function mutations