setup and run_gui: fix conda init and activation

[ianohara]

See title.

Tested by:

1. Blasting all conda init from my .bashrc and .zshrc including any PATH. ag conda returns nothing on both.
2. Open a new shell to make sure my env is clean
3. run the setup script
4. Follow the instructions the setup script prints to run the gui
5. Open a new shell
6. Run the gui

Both 4 and 6 result in successfully running the gui. The setup script instructions are still needed if the user wants to run in the same terminal since we can't affect the caller's env.