Only download chromosomes or scaffolds from VectorBase, not both.
Move biobambam and libmaus build to brew packages instead of custom builds. Clean up unused custom builds
Bump to latest version of bcbio.variation with support for 0.7.8 validation
Ensure htslib and libmaus dependencies are pre-installed and linked. chapmanb/bcbio-nextgen#356
Skip build of vcftools for bcbio pipeline due to issues with default libz on ubuntu 12.04. Fixes chapmanb/bcbio-nextgen#353
Alternative approach to avoiding color output that will work with Mac ls. Fixes gemini bug: https://groups.google.com/forum/?fromgroups=#!topic/gemini-variation/aT0KmO1FM1s
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Upgrade subread to 1.4.4.
Update Cosmic to v68. Fixes chapmanb/bcbio-nextgen#365. Use bgzipped and tabix indexed files for all associated variant references including dbSNP and other GATK bundle resources
Merge branch 'master' of github.com:chapmanb/cloudbiolinux