Only download chromosomes or scaffolds from VectorBase, not both.
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
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
If passed as number mode gets converted to decimal, should be string
Ensure CloudMan and Galaxy packages are only added when building CloudBioLinux AMIs. Thanks to  Venkatesh Duvvuri
Merge pull request #157 from nuada/upstream

If passed as number mode gets converted to decimal, should be string
Move Homebrew installation after loading of brew packages. Enables skipping Homebrew install steps if no packages needed. Fixes #156
Handle finding flavor module if not suffixed with 'flavor'. Fixes #158
Don't reconfigure fabric env in fabfile.install_brew() if automated
install.

Without this fix, the env flavor is getting reset inside of
install_brew().
Merge pull request #159 from glebkuznetsov/master

Don't reconfigure fabric env in fabfile.install_brew() if automated install.
For remote env.safe_run_output disable shell by default