Create a couple more RNA-seq specific files.

interval file for Picard's RNASeqStats, rRNA GTF file,
mask-file of usually-maksed RNA species and a MISO index.
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
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Final transcript file generator.
Ensure beast and tracer implementations use localhost-aware run and exists functions. Fixes #119
Streamline use of ngs pipeline minimal flavor by generalizing CloudBioLinux targets. Remove problematic darcs which pulls in postfix
Add _transcriptome extension to Tophat index.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Cleanup unused data files, relocate Tophat directory.
Provide RNA-seq download information for mm10. Symlink reference genomes to avoid re-building fasta files and indexes in TopHat. Clean up genome download to not need ucsc as standard default
Provide relative symlinks for rnaseq resources and avoid noisy extraction
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Merge branch 'master' of https://github.com/heuermh/cloudbiolinux