GR-49 GR-50 - added gem_index and gem_t_index tools
GR-51 - added new pipeline to produce gem indices
Fixed bug in index listener and added get_genome to Dataset class
Changed genome and annotation checks
Return None in Config.get if the key is not present
Fixed index listener to create project object at call
GR-52 - added grape setup command to run the pre-processing pipeline
Fixed config test to check for None value when a key is not present