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Thanks to @kbarni, I was able to make it work :

With Ubuntu MATE on Le Maker Guitar (so, specific hardware + distro), putting my application in "Startup Applications" seems to not work at all. I gave a try at Upstart, rc.local and runlevels init, without success. However, I was able to make my own systemd user service to start my application.

This link helped me to build my service step by step : (take a look at the whole help page to use the full potential of systemd)

You should be able to make your service work for a specific user by taking a look at this link :

(Don't know why, hyperlink doesn't work on the forum right now)