The epiVIA tool hasn’t been wrapped for Galaxy yet, but I don’t see why it couldn’t (or did I miss a licensing restriction?).
Below is how to make the request. I’m sure the UPenn researchers are aware of Galaxy, so reaching out to both them and the IUC and cross-linking the tickets seems like a good way to gather more support and coordination around this project.
The remainder of the bioinformatics tools/manipulations are already available in Galaxy from what I can tell – so creating a workflow shouldn’t be a trouble. You will just need this new part added which performs the BWA alignment sorting.
Hope this helps! If there is another tool that someone knows about that is already in Galaxy, please feel free to correct me and offer other pointers
