Add the genome to your account as a Custom Reference Genome.
Extra details for successfully using a custom genome are in this tutorial: Fasta Format, Custom Genomes, and GATK Chromosome ordering
While the tutorial focuses on a specific human genome example, the general rules about verifying sequence identifiers and the other ways to avoid data mismatch issues will apply to all genomes. That information is covered in the wiki, but sometimes reading about a specific example can be helpful.
Thanks! Jen, Galaxy team