Custom reference genomes, bowtie fails to recognize

Hi,

I'm trying to install the `Schizosaccharomyces Pombe` reference genome for use on Galaxy. I've found various instructions on how to do so (it seems routines on using `.loc` files has changed in recent iterations of Galaxy?), and I see that for bowtie `tool-data/bowtie-indices.loc` is used for locating reference genome bowtie files. Yet after installing the genome in an accessible location and updating `.loc`-files (and restarting), the option of applying the S. Pombe genome as reference is still not available.

Specifically the tool I'm interrested in using is `Map with Bowtie for Illumina`.

What are the most up-to-date instructions on installing reference genomes?