I've been trying to get genomes into my local galaxy instance to use the "Fetch Sequences - Extract Genomic DNA" tool. I've read plenty of posts about adding custom genomes but I'm just looking to download the standard genomes already included with Galaxy, ie. mm9, hg19, etc.
You'll need to download the genomes you are interested in, index them with faToTwoBit from UCSC:
and then add the locations of the index files to tool-data/alignseq.loc.
I've been working on a script to automate this process, which also deals with indexing the genomes for next gen analysis:
It's targeted for cloud instances, but you can adjust the amazon_ec2 function to deal with your local setup and customize the scripts to only download and index what you want.
Hope this helps, Brad