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JIRA comes with Tomcat by default and offers support for those using Tomcat, however I am already running apache2 (on debian) hosting a subversion source control server and would like to use apache for this as well. Or should I/can I install Tomcat and run JIRA over that? Thoughts?

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Sure, there are many ways you can do that. You can just run your tomcat instance on the same IP but a different port, 8080 or 8443 or 12345 or whatever, or run it on a different IP after bringing up an alias. You may also be able make it appear to be in the same web root as your existing server by using apache's built in proxy support but that would require JIRA to be configurable to not need to be at the top of the web root.

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yea it looks like JIRA is configurable in the way you suggest. confluence.atlassian.com/display/JIRA/… so i'm thinking that may be the best way to go. –  Tone Jul 22 '10 at 3:09
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