I have EAR with my web-service. No war module in my application.
I mean
http://[host]:[port]/[context-path]/MyWebService?wsdl
For JBoss I am using jboss.xml
For WebLogic I am using weblogic-webservices.xml
What about GlassFish?
It looks like this document says to use the endpoint-address-uri to set the context-root for your web service on GlassFish... That element would go into the glassfish-ejb-jar.xml file.