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You need to update the RetroPie Setup Script first. To do so, change to the directory of RetroPie Setup Script,

cd /home/pi/RetroPie-Setup/

and update the script via git,

git pull

Then, start the setup script via

sudo ./

change to source-based installation and select only the GBA emulator gpsp to be installed.

Afterwards, re-enerate the Emulation Station configuration file from the “setup” menu.

I have written this without explicit testing, please report any issues that possibly occur.

Hope that helps!