Add STAR indexing.

Small refactor to change the order of things. Download
the transcripts first and then create the indexes after.
This lets indexers that need a GTF file to be created.
Provide consistent resolution of the GATK download file and home directory to help with debugging
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Avoid installing genomes as part of standard snpEff install. Instead prefer post-install additional of genome data.
Update to latest variant effects predictor with batch download. Only install API files and not cache files. Fixes #138. Fixes #116
Update biobambam to 0.0.116.
fix confict