I use Atlassian JIRA as a tool to control my software development process, registering issues, tasks and bugs and planning development cycles.
So now that I switched to Ubuntu as development platform, I need to setup JIRA on my new Linux machine. I wrote down the steps I followed to achieve this.

1. Install Java
First of all, of course, install Java in your Ubuntu server and test the installation:

dambrosio@Sepultura:~$ java -version
java version "1.6.0_15"
Java(TM) SE Runtime Environment (build 1.6.0_15-b03)
Java HotSpot(TM) Client VM (build 14.1-b02, mixed mode, sharing)

2. Install Jira Standalone
I started with Jira Standalone version because it has a bundled HSQLDB database and an embedded Tomcat server, so it is the fastest way to start with Jira. Later on, simply changing the database to, let's say, MySQL would be a great idea for production servers. Atlassian offers a simple step-by-step guide for installing Jira Standalone in Linux.
Note: Do not forget to create a 'jira' user to be used to run the server. I used a slightly different command from the one they suggest in their guide
Another Note: I created a '/usr/local/jira' symbolic link that points to the folder with the files.
Yet Another Note: I also created the '/var/local/jira' folder to contain jira data

dambrosio@Sepultura:~$ sudo /usr/sbin/useradd --create-home --home-dir /home/jira --shell /bin/bash -U jira

3. Prepare a startup script for Jira
Now, I want Jira to be started whenever the system boots. I found this guide that offers a script based on tomcat's startup scripts. I also changed it a little bit so I copied it down here.
Simply save the script as '/etc/init.d/jira' and make it runnable:

dambrosio@Sepultura:~$ sudo chmod +x /etc/init.d/jira

Here is the slightly (path to Catalina Home) changed script:

#!/bin/sh
#
# /etc/init.d/jira -- startup script for the Jira standalone server
# Based on the startup script for Tomcat 6 servlet engine
#
# Written by Miquel van Smoorenburg .
# Modified for Debian GNU/Linux    by Ian Murdock .
# Modified for Tomcat by Stefan Gybas .
# Modified for Tomcat6 by Thierry Carrez .
# Modified for Jira standalone by MCC and dambrosio
#
### BEGIN INIT INFO
# Provides:          jira
# Required-Start:    $local_fs $remote_fs $network
# Required-Stop:     $local_fs $remote_fs $network
# Should-Start:      $named
# Should-Stop:       $named
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: Start Jira.
# Description:       Start the Jira standalone server.
### END INIT INFO

set -e

PATH=/bin:/usr/bin:/sbin:/usr/sbin
NAME=jira
DESC="Jira Server"
DAEMON=/usr/bin/jsvc
CATALINA_HOME=/usr/local/$NAME
DEFAULT=/etc/default/$NAME
JVM_TMP=/tmp/jira-temp

if [ `id -u` -ne 0 ]; then
 echo "You need root privileges to run this script"
 exit 1
fi

# Make sure jira is started with system locale
if [ -r /etc/default/locale ]; then
 . /etc/default/locale
 export LANG
fi

. /lib/lsb/init-functions
. /etc/default/rcS

# The following variables can be overwritten in $DEFAULT

# Run Jira as this user ID
JIRA_USER=jira

# The first existing directory is used for JAVA_HOME (if JAVA_HOME is not
# defined in $DEFAULT)
JDK_DIRS="/usr/lib/jvm/java-6-sun /usr/lib/jvm/java-6-openjdk /usr/lib/jvm/java-1.5.0-sun /usr/lib/j2sdk1.5-sun /usr/lib/j2sdk1.5-ibm"

# Look for the right JVM to use
for jdir in $JDK_DIRS; do
 if [ -r "$jdir/bin/java" -a -z "${JAVA_HOME}" ]; then
 JAVA_HOME="$jdir"
 fi
done
export JAVA_HOME

# Directory for per-instance configuration files and webapps
CATALINA_BASE=$CATALINA_HOME

# Use the Java security manager? (yes/no)
JIRA_SECURITY=no

# Default Java options
# Set java.awt.headless=true if JAVA_OPTS is not set so the
# Xalan XSL transformer can work without X11 display on JDK 1.4+
# It also looks like the default heap size of 64M is not enough for most cases
# so the maximum heap size is set to 128M
if [ -z "$JAVA_OPTS" ]; then
 JAVA_OPTS="-Djava.awt.headless=true -Xmx128M"
fi

# End of variables that can be overwritten in $DEFAULT

# overwrite settings from default file
if [ -f "$DEFAULT" ]; then
 . "$DEFAULT"
fi

if [ ! -f "$CATALINA_HOME/bin/bootstrap.jar" ]; then
 log_failure_msg "$NAME is not installed"
 exit 1
fi

if [ ! -f "$DAEMON" ]; then
 log_failure_msg "missing $DAEMON"
 exit 1
fi

POLICY_CACHE="$CATALINA_BASE/work/catalina.policy"

JAVA_OPTS="$JAVA_OPTS -Djava.endorsed.dirs=$CATALINA_HOME/endorsed -Dcatalina.base=$CATALINA_BASE -Dcatalina.home=$CATALINA_HOME -Djava.io.tmpdir=$JVM_TMP"

# Set the JSP compiler if set in the tomcat6.default file
if [ -n "$JSP_COMPILER" ]; then
 JAVA_OPTS="$JAVA_OPTS -Dbuild.compiler=$JSP_COMPILER"
fi

if [ "$JIRA_SECURITY" = "yes" ]; then
 JAVA_OPTS="$JAVA_OPTS -Djava.security.manager -Djava.security.policy=$POLICY_CACHE"
fi

# Set juli LogManager if logging.properties is provided
if [ -r "$CATALINA_BASE"/conf/logging.properties ]; then
 JAVA_OPTS="$JAVA_OPTS "-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager" "-Djava.util.logging.config.file="$CATALINA_BASE/conf/logging.properties"
fi

# Define other required variables
CATALINA_PID="/var/run/$NAME.pid"
BOOTSTRAP_CLASS=org.apache.catalina.startup.Bootstrap
JSVC_CLASSPATH="/usr/share/java/commons-daemon.jar:$CATALINA_HOME/bin/bootstrap.jar"

# Look for Java Secure Sockets Extension (JSSE) JARs
if [ -z "${JSSE_HOME}" -a -r "${JAVA_HOME}/jre/lib/jsse.jar" ]; then
 JSSE_HOME="${JAVA_HOME}/jre/"
fi
export JSSE_HOME

case "$1" in
 start)
 if [ -z "$JAVA_HOME" ]; then
 log_failure_msg "no JDK found - please set JAVA_HOME"
 exit 1
 fi

 if [ ! -d "$CATALINA_BASE/conf" ]; then
 log_failure_msg "invalid CATALINA_BASE: $CATALINA_BASE"
 exit 1
 fi

 log_daemon_msg "Starting $DESC" "$NAME"
 if start-stop-daemon --test --start --pidfile "$CATALINA_PID" \
 --user $JIRA_USER --startas "$JAVA_HOME/bin/java" \
 >/dev/null; then

 # Regenerate POLICY_CACHE file
 #umask 022
 #echo "// AUTO-GENERATED FILE from /etc/tomcat6/policy.d/" \
 #    > "$POLICY_CACHE"
 #echo ""  >> "$POLICY_CACHE"
 #cat $CATALINA_BASE/conf/policy.d/*.policy \
 #    >> "$POLICY_CACHE"

 # Remove / recreate JVM_TMP directory
 rm -rf "$JVM_TMP"
 mkdir "$JVM_TMP" || {
 log_failure_msg "could not create JVM temporary directory"
 exit 1
 }
 chown $JIRA_USER "$JVM_TMP"
 cd "$JVM_TMP"

 $DAEMON -user "$JIRA_USER" -cp "$JSVC_CLASSPATH" \
 -outfile SYSLOG -errfile SYSLOG \
 -pidfile "$CATALINA_PID" $JAVA_OPTS "$BOOTSTRAP_CLASS"

 sleep 5
 if start-stop-daemon --test --start --pidfile "$CATALINA_PID" \
 --user $JIRA_USER --startas "$JAVA_HOME/bin/java" \
 >/dev/null; then
 log_end_msg 1
 else
 log_end_msg 0
 fi
 else
 log_progress_msg "(already running)"
 log_end_msg 0
 fi
 ;;
 stop)
 log_daemon_msg "Stopping $DESC" "$NAME"
 if start-stop-daemon --test --start --pidfile "$CATALINA_PID" \
 --user "$JIRA_USER" --startas "$JAVA_HOME/bin/java" \
 >/dev/null; then
 log_progress_msg "(not running)"
 else
 $DAEMON -cp "$JSVC_CLASSPATH" -pidfile "$CATALINA_PID" \
 -stop "$BOOTSTRAP_CLASS"
 fi
 rm -rf "$JVM_TMP"
 log_end_msg 0
 ;;
 status)
 if start-stop-daemon --test --start --pidfile "$CATALINA_PID" \
 --user $JIRA_USER --startas "$JAVA_HOME/bin/java" \
 >/dev/null; then

 if [ -f "$CATALINA_PID" ]; then
 log_success_msg "$DESC is not running, but pid file exists."
 exit 1
 else
 log_success_msg "$DESC is not running."
 exit 3
 fi
 else
 log_success_msg "$DESC is running with pid `cat $CATALINA_PID`"
 fi
 ;;
 restart|force-reload)
 if start-stop-daemon --test --stop --pidfile "$CATALINA_PID" \
 --user $JIRA_USER --startas "$JAVA_HOME/bin/java" \
 >/dev/null; then
 $0 stop
 sleep 1
 fi
 $0 start
 ;;
 try-restart)
 if start-stop-daemon --test --start --pidfile "$CATALINA_PID" \
 --user $JIRA_USER --startas "$JAVA_HOME/bin/java" \
 >/dev/null; then
 $0 start
 fi
 ;;
 *)
 log_success_msg "Usage: $0 {start|stop|restart|try-restart|force-reload|status}"
 exit 1
 ;;
esac

exit 0

4. Make Sure you have the JSVC package
JSVC is a wrapper to launch Java Applications as daemons and it is not installed by default with Java but our script will need it. You will be sure that you need it if you get this (pretty obvious) error message when running the startup script: 'missing /usr/bin/jsvc'. So go ahead and install it.

dambrosio@Sepultura:~$ sudo apt-get install jsvc

5. Ensure Jira is started successfully
Run the command below and acess 'http://localhost:8080' and you should see your Jira page.
As a last test, reboot your system and check that Jira is started up too.

dambrosio@Sepultura:~$ sudo /etc/init.d/jira start
 * Starting Jira Server jira                                             [ OK ]