Ensure directory outputs exist when moving from global transaction directories. Thanks to @mjafin and @roryk. Adjust Platypus parameters to match best sensitivity/specificity with NA12878 comparions
Move supported genomes and indexes to be importable.
Update setting up a custom genome from user-provided sequences.

This picks up the installation location of tools and genomes
from the bcbio_system.yaml file. It also removes the dependency of
having cloudbiolinux installed.