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 

I hope someone on here can help me out.
Thanks a lot
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