Fix skipping of GATK protected download to avoid creating an empty symlinked java directory. Instead checks up front and only creates the directory if moving forward with an installation. chapmanb/bcbio-nextgen#111
Remove gatk-protected as a standard package for ngs flavors. Add in a hook to allow specification of new custom tools (including gatk-protected) as part of deploy infrastructure. chapmanb/bcbio-nextgen#111