Hi guys, I am new to galaxy and am in the process of setting it up on a cluster with some help. I am trying to install bowtie2 to my local galaxy through the toolshed. I have a few questions. - Which bowtie2 should I install? When I search for bowtie2 a bunch of results come up? - What are repository dependencies? Why would I need these if bowtie2 is already installed on my system? - I have been installing bowtie2 by unchecking the repository dependencies and tool dependencies boxes. Is this correct? - Finally when I install bowtie2 this way it creates 2 bowtie2_indices.loc files, one in galaxy/tool-data and the other in shed_tools/toolshed.g2.gx.psu.edu/dev/bowtie2, which one do I need to edit to point to my index files? No matter which one I change I can't seem to see the indices. I hope someone on here can help me out. Thanks a lot Ravi.