Downloading mm10 reference from usegalaxy.org

Explore all of the data/indexes available for mm10 in the second link @marten set.

/seq has the .fa. (fasta)
/samtools has a link to that same .fa plus the sam index .fai.

You’ll probably want to get them all and then set up your .loc files to match.

Downloading and using pre-built indexes is the more different way to install a genome. Using Data Managers is much better if you prefer to use the administrator web interface. To have the genomes match up, just get the fasta, then use that “from the history” when running other DMs, including Samtools.

More help is in this prior Q&A: Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting