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~/.emulationstation/es_input.cfg: When you first start EmulationStation, you will be prompted to configure any input devices you wish to use. The process is thus:

Press a button on any device you wish to use. This includes the keyboard. If you are unable to configure a device, hold a button on the first device to continue to step 2.

Press the displayed input for each device in sequence. You will be prompted for Up, Down, Left, Right, A (Select), B (Back), Menu, Select (fast select), PageUp, and PageDown. If your controller doesn’t have enough buttons to map PageUp/PageDown, it will be skipped.

Your config will be saved to ~/.emulationstation/es_input.cfg. If you wish to reconfigure, just delete this file.

NOTE: If ~/.emulationstation/es_input.cfg is present but does not contain any available joysticks or a keyboard, an emergency default keyboard mapping will be provided.

As long as ES hasn’t frozen, you can always press F4 to close the application.

Let me know if you need any more help. I’m rather new to retropie and Linux, but I know a bit.