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I am in as root in the terminal and have typed yast2.

Under System there is no System Service (run levels) as there was in Opensuse version 11.

Where is the proper tool to make eg mysql autostart?

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This menu entry is still there in openSUSE 12.2. Is the respective module installed?

rpm -q yast2-runlevel

Other ways for activating a service:

chkconfig --set mysql on

or the new way:

systemctl enable mysql.service

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