Turn on download of dnSNP and RNA-seq resources for canFam3: chapmanb/bcbio-nextgen#386
When configuring the remote desktop, set nginx PAM module to allow logins for any system user
Update custom nginx package version
For the remote desktop, switch to xfce4 (vs. jwm) window manager because it's more feature-full
Update canFam3 dbSNP to remove INFO whitespace. chapmanb/bcbio-nextgen#386
Add support for latest Zebrafish genome build: Zv9
Remove separate tabix install since tabix now included in bcftools as of the latest release candidate
brew: check for vcfutils.pl samtools overlap with bcftools and reinstall samtools as needed
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