[brlug-general] question about installing stuff

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I'm attempting to install FlowScan on a Debian box at work.
I am creating a "user" that will run the software.
Should I install everything as root then give my flowscan user the rights to 
the relevant directories? 
Should I login as the flowscan user and just "su" to do the installation?  
Opinions?
TIA,
Cleve