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The sparqler has a synchronization program,  synchronize-sparqler.sh (found in folder ${REPO_HOME}/etc), that should be run (as the same user as that runs tomcat) every night.  On a Unix-like system (this would include including OS X and later above on a Mac), the system administrator should set a line in a crontab file to accomplish this (something like the following):

13 2 * * *    tomcat   cd /opt/eaglei && bash repo/etc/synchronize-sparqler.sh

(the first 6 fields are "min", "hr", "day-of-month", "day-of-week", "user";  "*" is a wild-card - so this would run daily at 02:13am as the user "tomcat").  

If you run on Windows (warning: this is at your own risk - we have not tested the system on Windows), you should set up a Unix-like environment (e.g. Cygwin) in which to perform the installation and run the shell-scripts.