In the server installation directory you will find a file called CLCServer.vmoptions, where CLCServer will be the name of your particular CLC server: CLCGenomicsServer
Open the file in a text editor and add a new line like this:
-Djava.io.tmpdir=/path/to/tmp with the path to the new tmp directory. Restart the server for the change to take effect (see how to restart the server in Starting and stopping the server).
We highly recommend that the tmp area is set to a file system local to the server machine. Having tmp set to a file system on a network mounted drive can substantially affect the speed of performance.