We are currently using this stack https://bitnami.com/stack/youtrack
It comes with Youtrack 2017.2 including a guide how to upgrade Youtrack to newer versions. However, after YouTrack 2018.1 that guide does not work anymore cause the internal Youtrack App changed. Here you can find a ticket on the Jetbrains Youtrack: https://youtrack.jetbrains.com/issue/JT-49551
We would be happy, if there was a manual way to Upgrade Youtrack, but Jetbrains suggested to raise a ticket here and fix the Bitnami installer (see details in the ticket mentioned above).