OK, never mind I found the answer

https://vaemendis.github.io/ubooquity-doc/pages/manual.html#using-the-command-line

--workdir

I used a script to set it to run at startup

#!/bin/sh

exec 2> /tmp/rc.local.log
exec 1>&2
set -x

nohup /usr/local/openjdk8/bin/java -jar /mnt/Ubooquity.jar --libraryport 2202 --adminport 2203 --remoteadmin

exit 0