Setting up phenotips on Ubuntu Xenial with Tomcat

phenotips_tomcat.sh

#!/bin/sh

set -exu

directory=ubuntu-xenial-robot

debootstrap --variant=minbase --include=dbus,systemd-sysv xenial "$directory" http://archive.ubuntu.com/ubuntu/

systemd-nspawn --boot --resolv-conf=copy-host --directory="$directory" &
pid=$!

sleep 10 # wait for the system to boot

machinectl shell "$directory" /bin/sh -c "
set -exu

apt update
apt install --yes tomcat8
mkdir /var/lib/phenotips
chown -R tomcat8:tomcat8 /var/lib/phenotips
"

mkdir "$directory"/var/lib/tomcat8/webapps/phenotips
if [ ! -e phenotips-war-1.3.7.war ]; then
	curl https://nexus.phenotips.org/nexus/content/repositories/releases/org/phenotips/phenotips-war/1.3.7/phenotips-war-1.3.7.war > phenotips-war-1.3.7.war
fi
echo 0f1b9e1bea6ad479e46a6fbda253ad45  phenotips-war-1.3.7.war | md5sum --check
unzip -d "$directory"/var/lib/tomcat8/webapps/phenotips phenotips-war-1.3.7.war

machinectl poweroff "$directory"

wait $pid