We’ve pre-indexed these genomes and made them available for download to get you going more quickly with Goby.

NCBI36.54, homo_sapiens, base-space, for bwa [~4.1 GB]
NCBI36.54, homo_sapiens, color-space, for bwa [~5 GB]
NCBI37.55/MM9, mus_musculus, base-space, for bwa [~3.3 GB]
NCBI37.55/MM9, mus_musculus, color-space, for bwa [~3.9 GB]

Download these files, unpack them and move the content to your database cache directory.