Provide install target for GATK gsalib R library
Replace references to outdated env.galaxy_base with env.galaxy_home
Fix typo
Simplify Galaxy cloning method
Remove mdadm package from CloudMan's dependency list
Add a bunch of existing configuration options and documentation about each in the main fabricrc.txt
Fix typos
Log which config file is being loaded/used
Make sure env.galaxy_user owns env.galaxy_home before customizing Galaxy dir
Add VarScan variant caller; update GATK to latest point release
Add an option to automatically setup a database for Galaxy
Add files required by CloudMan to setup Hadoop atop SGE
Add files required by CloudMan to setup HTCondor
Export /opt/condor ovre NFS by default
Cleanup after installing cloud-init
Add s3fs install
Move s3fs installation to be done as part of cloudman config so it gets installed automatically vs. via custom_install method only
Streamline the Galaxy installation process a bit
Eliminate unneeded samtools 0.1.18 dependency.