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:

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 Galaxy.

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

Thanks,

J.