We are working to add the indexes right now for a subset of databases.
These are the initial genomes that will be added along with status.
You can wait for the deployment to Galaxy Main (http://usegalaxy.org) - OR - if your database is not included in that set of initial genomes and/or you do not wish to wait, a Custom reference genome can be used instead. Please be aware that the tool may fail for exceeding memory resources on larger custom genomes when working at http://usegalaxy.org
I am not sure what the current plans are for adding additional tools from this tool suite. A request ticket has been created for review. Progress can be followed here: https://github.com/galaxyproject/galaxy/issues/4220. Meanwhile, either tool (and all others) are available to install and use in a local or cloud Galaxy sourced from the Tool Shed.
Thanks! Jen, Galaxy team