Download and extract:

wget http://www.atlassian.com/software/jira/downloads/binary/atlassian-jira-6.2.tar.gz
tar xzvf atlassian-jira-6.2.tar.gz
cd atlassian-jira-6.2-standalone
cp bin/*.jar atlassian-jira/WEB-INF/lib/
mkdir -p /usr/local/www/jira.freebus.org/home
chown www /usr/local/www/jira.freebus.org/home

Edit the file atlassian-jira/WEB-INF/classes/jira-application.properties

jira.home = /usr/local/www/jira.freebus.org/home

Copy the jira application to the jetty directory:

cp -a atlassian-jira /usr/local/jetty/webapps/atlassian-jira-freebus

You have to replace the path atlassian-jira-6.2-war/ with the correct full path.

Download Jira:

wget http://www.atlassian.com/software/jira/downloads/binary/atlassian-jira-6.2-war.tar.gz

Extract it:

tar xzvf atlassian-jira-6.2-war.tar.gz

Edit atlassian-jira-6.2-war/edit-webapp/WEB-INF/classes/jira-application.properties

jira.home = /usr/local/www/jira.freebus.org/home

Create the directory and adapt permissions:

mkdir -p /usr/local/www/jira.freebus.org/home
chown www !$

Create the war file:

cd atlassian-jira-6.2-war
./build.sh

Install required mysql java library:

cd /usr/ports/databases/mysql-connector-java
make install

Load the war file with jetty:

ln -s atlassian-jira-6.2-war/dist-generic/atlassian-jira-6.2.war /usr/local/jetty/webapps/atlassian-jira-freebus.war
/usr/local/etc/rc.d/jetty restart