We are currently planning on using Environment Variables to set the output location for Workspaces put through the Job Submitter Service on the server. I was wondering if there is a better way where we can set a parameter within FME Server for the same purpose?
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There's a number of FME Server specific user parameters available in Workbench for you to use:
In your case the FME_SHAREDRESOURCE_DATA is probably the one to look in to.
I agree about using the FME Server shared resources, see the documentation: http://docs.safe.com/fme/html/FME_Server_Documentation/Content/WebUI/Resources.htm
It is also possible to add your own resources, e.g. referencing a network directory or other shared folder: http://docs.safe.com/fme/html/FME_Server_Documentation/Content/AdminGuide/Adding-Modifying-Resources-Directories.htm