What type of data are you trying to add? For NGS references, see https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup. Let us know if that isn't enough info.

Ah, thanks Kelly. I had not come across this page. Following these instructions, I was able to get a genome to show up in the drop down for "Map with Bowtie for Illumina". However, the same drop down is not showing my genome in "Map with Bowtie for SOLiD". Any idea as to why these would be different?

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