I was able to do it not within the RouteBuilder but before adding context to the camelMain
.
JndiRegistry registry = new JndiRegistry();
...
registry.bind("myAntFilter", filter);
DefaultCamelContext context = new DefaultCamelContext(registry);
camelMain.getCamelContexts().add(context);
It is also important to note that you need to have a jndi.properties in your /resources with the following content:
java.naming.factory.initial = org.apache.camel.util.jndi.CamelInitialContextFactory
Without this, I'm getting an exception.
Hope it helps people who stumbled on the same problem