Hey John,
I can only imagine that the ownership of some folder or file at some level down to the xnat/plugin-resources/maven-1.0.2/bin/maven script is not owned by the user running the setup.sh script. So I think the sudo/chmod operation is actually what you want to do. Basically your xnat folder and everything underneath it should be owned and accessible to the same user account you’re using when launching the setup.sh script.
You could do something like:
find ~/xnat –ls
Look and see if anything looks weird, i.e. root owns some folder or permissions are set to 000 or whatever.
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