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
Do not install cloudman by default, re-enable by hand for AWS builds. Make SGE install safe for local installation. Thanks to Venkatesh Duvvuri
Avoid standard seal/pydoop installation. Requires new dependencies and best suited for a custom flavor devoted to Cloud/Hadoop
Include 1000G high confidence SNPs in GATK bundle downloads. Used for VQSR
Make keyserver errors warn-only to avoid erroring out when down. Thanks to Biju
Merge remote-tracking branch 'upstream/master'