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I would like to set an environment variable so that it is set when I launch a specific Flatpak application, and only set for this application. How do I go about doing this in a permanent manner?

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You can do this via the flatpak override command.

To set only one environment variable you can use this syntax:

flatpak override --env=VARIABLE_NAME=VARIABLE_VALUE full.application.Name

To set multiple environment variables you can use this syntax:

flatpak override --env="VARIABLE_NAME_ONE=VARIABLE_VALUE_ONE VARIABLE_NAME_TWO=VARIABLE_VALUE_TWO" full.application.Name

This will set it globally and therefore requires you to run the command as root. If you want to do this for your current user, you can add the --user parameter to the command, like so:

flatpak override --user --env=VARIABLE_NAME=VARIABLE_VALUE full.application.Name

Source and further reading: http://docs.flatpak.org/en/latest/flatpak-command-reference.html#flatpak-override

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