Automated refresh from external applications

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How can I automate updating from an external application like bugzilla or jira? I would like to synchronize the data in our bugzilla and scrumworks databases daily since we use scrumworks while fixing defects and estimating new work. I currently have to manually go through the desktop client UI to do this, and I would much prefer a cron job or some type of script automatically do this overnight so we are ready to go when we start work in the morning.