AGTHC (AGTH 1) Companion) is a unified frontend for various Japanese translators, transliterators, dictionaries and part-of-speech taggers. Since AGTH has no problems running under GNU/Linux with Wine, this script can be considered as a free alternative to ATLAS. You don't really need AGTH to use this program, it's just AGTHC can work together with it.
You can grab the latest release here.
Ordinarily, once you get tor running, these proxy settings should do the job
Host: localhost Port: 8118 Connection: HTTP