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Funny, I had this EXACT same problem this morning myself. I did some more digging and while I don't know what step we both missed that properly adds the jar to the environment or whatever, I did find the workaround that'll get you going. You need to invoke the jar in which the weblogic.Server class is found. Assuming you've set up the WLS_HOME environment variable during the install (I followed these instructions myself - http://www.oracle-base.com/articles/12c/weblogic-development-only-installation-on-oracle-linux-5-and-6-12cr1.php) then you can set up your domain by using the following command:
*$JAVA_HOME/bin/java $JAVA_OPTIONS -jar $WLS_HOME/server/lib/weblogic.jar weblogic.Server*
You can add whatever memory conditions you want before the -jar flag. That'll start the configuration and allow you to proceed with creating the domain.