This will eventually be published here: flurdy.com/docs/jira/.
Below is my initial draft howto, but a much more up to date version is on my site.
sudo aptitude install sun-java6-jdk;sudo update-alternatives --config java;sudo echo JAVA_HOME=/usr/lib/jvm/java-6-sun > /etc/profile.d/java.sh;sudo echo EXPORT JAVA_HOME >> /etc/profile.d/java.sh;sudo chmod +x /etc/profile.d/java.shtar xzf atlassian-jira-enterprise-4.0.1-standalone.tar.gz;sudo mkdir /opt/atlassian;sudo mv atlassian-jira*-standalone /opt/atlassian/jira-4.0.1sudo /usr/sbin/useradd --create-home --home-dir /usr/local/jira --shell /bin/bash jira;sudo chown -R jira:jira /opt/atlassian/jira-4.0.1sudo /opt/atlassian/jira-4.0.1/bin/startup.shsudo mkdir /etc/opt/atlassian /etc/opt/atlassian/jira;sudo mkdir /var/opt/atlassian /var/opt/atlassian/jira;sudo chown jira:jira /etc/opt/atlassian/jira /var/opt/atlassian/jirasudo mv /opt/atlassian/jira-4.0.1/logs /var/log/jira;sudo touch /var/log/jira/atlassian-jira.log;sudo chown jira:jira /var/log/jira/atlassian-jira.log;sudo ln -s /var/log/jira/atlassian-jira.log /opt/atlassian/jira-4.0.1/atlassian-jira.log;sudo ln -s /opt/atlassian/jira-4.0.1/atlassian-jira/WEB-INF/classes/jira-application.properties\
/etc/opt/atlassian/jira/;sudo ln -s /opt/atlassian/jira-4.0.1/atlassian-jira/WEB-INF/classes/log4j.properties\
/etc/opt/atlassian/jira/;sudo mv /opt/atlassian/jira-4.0.1/conf\
/etc/opt/atlassian/jira/tomcat;sudo ln -s /etc/opt/atlasiian/jira/tomcat\
/opt/atlassian/jira-4.0.1/confsudo vi /etc/opt/atlassian/jira/jira-application.properties;jira.home=/var/opt/atlassian/jirasudo mkdir /var/lib/hsqldb;sudo mkdir /var/lib/hsqldb/jira;sudo chown jira:jira /var/lib/hsqldb/jira;sudo ln -s /var/lib/hsqldb/jira\
/opt/atlassian/jira-4.0.1/databasesudo mkdir /var/opt/atlassian/jira-tomcat;sudo mv /opt/atlassian/jira-4.0.1/work\
/var/opt/atlassian/jira-tomcat/;sudo mv /opt/atlassian/jira-4.0.1/temp\
/var/opt/atlassian/jira-tomcat/;sudo ln -s /var/opt/atlassian/jira-tomcat/work\
/opt/atlassian/jira-4.0.1/;sudo ln -s /var/opt/atlassian/jira-tomcat/temp\
/opt/atlassian/jira-4.0.1/