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On Debian based systems we run shepherd as a shepherd user. The service gets started up through systemd:
[Unit] Description=Launch user shepherd daemon Wants=guix-daemon.service [Service] Type=oneshot ExecStart=/var/guix/profiles/per-user/shepherd/guix-profile/bin/shepherd --socket=/home/shepherd/.config/shepherd/shepherd.sock User=shepherd Group=shepherd [Install] WantedBy=multi-user.target