The best solution is to use the fasta version of the reference genome
when running the Galaxy analysis tools and then link back in the
annotation as needed using the tool "Join, Subtract and Group ->
This would require you to covert/load the genbank .gb data in tabular
format and possibly to use some of the tools in "Text Manipulation".
Galaxy currently does not have a genbank .gb file converter, but a
web search brings up several options for you to choose from.
We hope this helps to get you started,