Set jira.home in /atlassian-jira/WEB-INF/classes/jira-application.properties

eg /data/sites/jira.tgn.tv/home

Download Universal Plugin Manager 1.1.2 (not 1.3, doesn't work with Jira)

See

Upload jira-greenhopper-plugin-5.4.1.jar to home/plugins/installed-plugins/