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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