Honestly tired of Galaxy not having GATK4 tools, so I am trying to build a docker integration that will allow it to work. Please be warned. This script is not working. More options will be added to the tool once I get the basics working. I greatly appreciate if anyone wants to help get this working.
I am able to successfully launch the GATK4 docker container from Galaxy and pass commands and files to it!!!! Finally!!! this was the most confusing part, I think. Setting the right directory was difficult, especially since I am quite inexperienced with building tools with Galaxy. But now the rest should be more straight forward.
