Is there a kind soul that could take me through a step-by-step of fetching and indexing the mouse mm10 genome from UCSC (or wherever) on a local galaxy install, with a data manager? I have the indexers installed as well as create db key, rsync, and fetch reference genome. I just can't seem to make this work. I've also tried indexing a locally cached mm10 reference genome with the hisat indexer, but hisat2 can't seem to use it (see error description in my other post).
I totally realize this is a lot to ask, but maybe somebody is particularly kind and would take pity on me?