Replace sickle with scythe for default installation.
scythe -> sickle
Move Tophat and Bowtie2 to being a homebrew installation.

This moves us off of Tophat 2.0.9, since it has been fixed
to work with the newest Bowtie2.
Replace tophat with tophat-binary.

This removes the boost dependency, which causes issues.
Add delly structural variant caller with binary install. Enable passing arguments to homebrew builds to enable
Support preparation of SNAP aligner indexes. Clean up S3 download error messages to be less worrisome
Ensure spaces used as terminators when preparing SNAP indexes to avoid extra long chromosome names
Merge branch 'master' into nmdp-ngs-pipeline