Installation

Installing:

Install pre-requisite

$ flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
$ flatpak install flathub org.gnome.Platform//3.36 org.gnome.Sdk//3.36 --system

Clone

Do not download the ZIP file as it doesn't contain the required files from shared-modules repository.
Instead, do:

git clone --recurse-submodules https://github.com/dgcampea/desmume-flatpak.git

Build + Install

$ flatpak-builder builddir org.desmume.DeSmuME.yaml --force-clean --install --user

Notes:

By default, this flatpak only allows reading from HOME and saving to XDG-VIDEOS and XDG-MUSIC directories.
If you want to save/read from other locations:

flatpak override org.desmume.DeSmuME --filesystem=host

Where are my savefiles?

Located at ~/.var/app/org.desmume.DeSmuME/config/desmume/