Quartus and ModelSim
Running Quartus on Linux
Quartus actually works surprisingly well on linux, although the old version that we're required to use may have some library issues. To install it, download the linux version of Quartus from the intel website (make sure to get the specific version required for your class) and run setup.sh. Once installed, make sure to test compilation, simulation, and board programming. You will probably find that you're missing some required libraries, so make sure you install those.
Running ModelSim on Linux
ModelSim depends on some very outdated libraries, so it can be difficult to get it to run on linux. However, ScanuRag was able to get it to run on linux in a Fedora toolbox. This gist details the installation process. You may also need to change the font size.