Documentation for JIRA 5.2. Documentation for other versions of JIRA is available too. 

*nix-based operating system administration is outside the scope of Atlassian support. This document is provided for information-purposes only.
On *nix-based BSD operating systems, the best practice is to install, configure and run each service (including JIRA) as a dedicated user with only the permissions they require.
To run JIRA automatically on FreeBSD:
As root, create the file /usr/local/etc/rc.d/jira.sh (code shown below), which will be responsible for starting up JIRA after a reboot (or when manually invoked). If you are not using postgresql for your database, change the REQUIRE line to whatever is in the PROVIDE line in your database init script. 
#!/bin/sh
#
# Startup script for JIRA on FreeBSD
#
# This goes in /usr/local/etc/rc.d and gets run at boot-time.
# PROVIDE: jira
# REQUIRE: postgresql
# KEYWORD: shutdown
#
# Add the following lines to /etc/rc.conf to enable jira:
#
#jira_enable="YES"
#
jira_enable="${jira_enable-NO}"
. /etc/rc.subr
name="jira"
rcvar=`set_rcvar`
start_cmd="${name}_start"
stop_cmd="${name}_stop"
jira_start()
{
    echo -n " Starting JIRA"
    su - atlassian -c '/home/atlassian/jira/bin/startup.sh'
}
jira_stop()
{
    echo -n " Stopping JIRA"
    su - atlassian -c '/home/atlassian/jira/bin/shutdown.sh'
}
load_rc_config $name
run_rc_command "$1"
Make the init script executable:
chmod \+x /usr/local/etc/rc.d/jira.sh
Make the init script readonly:
chmod \-w /usr/local/etc/rc.d/jira.sh
Add the following line to /etc/rc.conf 
jira_enable="YES"
More information can be found in this article.