Depends on your environment, number of hosts, etc. really. You probably don't want to stick it into the same install script because:

- your app user doesn't need rights to modify the schema

- you need to handle concurrency of schema upgrades (what if two hosts upgrade at the same time?)

- if your migration fails it may leave you in the weird installation state and not restart the service

Ideal solution: deploy code which can cope with both pre-migration and post-migration schema -> upgrade schema -> deploy code with new features.