If a file is removed with
rm -rf, it is gone. Technically the data is probably on disc somewhere if it just happened but it will be overwritten.
The good news is that you can obtain new copies from the Galaxy distribution. Restart the Galaxy server after. Disclaimer: I haven't tried this - and am not exactly sure how the
setup.cfg will reinitialize. You'll have to see how it works. https://github.com/galaxyproject/galaxy
You could also just start over if this is your own local. The old database could be backed up and migrated to the new instance (you'll need the scripts back first). https://galaxyproject.org/admin/get-galaxy/#keep-your-instance-backed-up
Hope that helps! Jen, Galaxy team