Setting up a local or cloud Galaxy of your own is how to use Megablast with alternate genomes.
Obtain the tool from the Tool Shed (http://getgalaxy.org/toolshed) but install the data according to these older rules (scroll down to Megablast section: https://wiki.galaxyproject.org/Admin/DataPreparation). In short, formatdb the genome, adjust the loc and builds files, then restart the server. The test is that if megablast will run line-command with given inputs/parameters/indexes, the server has the resources to run megablast within Galaxy given the same.
Best, Jen, Galaxy team