I really hope someone can help. I have a local instance of Galaxy. I have genomes that appear in my dropdown box for Bowtie2 that I never added. These genomes are not in the Bowtie2.indices.loc file, so where are they coming from? This is driving me crazy, I have looked everywhere but can't seem to find how these are showing up. Thanks for the help.
I wanted to add that I have since figured this out. It turns out that when I utilized the data managers in an attempt to upload reference genomes they were adding information to .loc files in a different location than specified in the instructions for manually adding genomes. Once I found these and removed them they were removed from the drop down menu. For the record I find it much eaiser to add genomes manually to each tool rather than relying on Data Managers.