Vagrant example VM script pulls pre-built jars and war file from dropbox. The version is 3.2.10
Modify and test with a new version of Rya, as of this writing, about to release: 3.2.11
Also, if possible use prebuild binaries from the Nexus repository. The current prebuilt WAR file probably includes some configuration that would be needed to be added to the Vagrant script. Also there might be some special things done to make it work with the OpenRDF/Seaseme/ Rdf4J Workbench. Aaron did a nice job with that integration.