Thanks for reporting this error. I noticed we have a small bug here, the value is always set to true at the moment, so it does not make a difference if you actively set it or not, it is always active. To bypass this error, just uncheck it and it should be fine. Only in the case you want to keep self ligations, you need to wait for the upcoming 3.7 release of HiCExplorer.
Reference genome: That’s an issue for the Galaxy admin of your server. If you use usegalaxy.eu, please inform me and I will forward it to our admins.
Homer: If Galaxy wrappers are existing, that’s also an issue for the galaxy admins of your server to install it. If no wrappers are existing, maybe you can ask the developers of Homer to write any.