Using my local instance, I was able to run Bowtie2 using a genome in the 
history. This means the problem is likely with your local instance.

This appears to be the problem:

> Error: could not open Nagenome.fasta
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: bowtie2-build -f Nagenome.fasta /tmp/tmplBdrjc/Nagenome

It appears that bowtie2-build cannot open your genome file. I suspect that you 
entered the genome file's path wrong when creating the script command line 
manually, so correcting this likely won't solve the issue when running inside 

What is the error that you see when trying to run Bowtie2 in Galaxy (click on 
the bug icon to see the error)?

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