First, Tyrus is for containers that don't have their own WebSocket implementation.
Jetty (and Tomcat) both implement JSR356 natively, use those, not Tyrus.
Jetty, unlike Tomcat, is a modular container, everything is optional (even the Server!).
When you go standalone, the modules are glued together to fit the various specs most people are comfortable with.
When you go embedded, all of that glue is now on you to piece together to suit your needs specifically.
What is likely happening, is that you are including Tyrus (don't), and have not enabled the Annotation scanning.
To enable annotations ...
org.eclipse.jetty.webapp.Configuration.ClassList classlist = org.eclipse.jetty.webapp.Configuration.ClassList.setServerDefault(server);
classlist.addAfter("org.eclipse.jetty.webapp.FragmentConfiguration",
"org.eclipse.jetty.plus.webapp.EnvConfiguration",
"org.eclipse.jetty.plus.webapp.PlusConfiguration");
classlist.addBefore("org.eclipse.jetty.webapp.JettyWebXmlConfiguration",
"org.eclipse.jetty.annotations.AnnotationConfiguration");
Try that first.
Otherwise you can look at the embedded-jetty examples below ...