Catch if symlink to FASTA file is already created.
Improve checking of symbolic links, overwriting links that exist but are not correct. Prefer creation of relative symlinks. Fixes chapmanb/bcbio-nextgen#478
Use relative symlinks and correctly overwrite bad symlinks for custom java installs
Set executable and read permissions for downloaded executables.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Create STAR index in star directory.
Synchronize multiple readmes, remove older markdown in favor of ReST based we can move to readthedocs
Documentation work: emphasize and include demo flavor, add Docker usage and homebrew integration
Merge branch 'master' into nmdp-ngs-pipeline