Although it is also documented in the IBM Connections wiki here it is a short summary of the commands for Linux which might be useful. Although it describes the update to IBM COnnections 188.8.131.52 CR1 it can be used for other fixes/fixpack as well:
If you are not logged in as "root" change to root access with just "su" and NOT "su -". And also be sure that you use the syntax ". ./setupCmdLine.sh". If you do not precede the command with the period and space, the Java environment will not be properly set for the active shell.