I am using a local instance of Galaxy to call variants among six sets of reads from mouse strains that I aligned to the mm10 reference genome using Bowtie2. The alignments were done on the main Galaxy server, but I have switched to a local Galaxy instance because the files exceed the maximum space allowed on this server. The problem I am having is that the mm10 reference genome is not available in the local Galaxy instance, and so the programs I need do not recognise the database for the aligned read files.
I have tried to follow the instructions given here: https://wiki.galaxyproject.org/Admin/UseGalaxyRsync, however they seem not to have worked (I still can't see mm10 in the list of options when I try to update the database for a sample).
I would appreciate any further guidance on how to import a reference genome from the main Galaxy to my local instance.