See EMBOSS administration documents.
To add embassy packages to Jemboss, after running the installation script and then installing embassy packages, wossname.jar needs to be updated for them to appear in the menus. This can be done as follows:
mv wossname.jar wossname.jar_old
$EMBOSS_INSTALL/bin/wossname -colon -gui -outf wossname.out -auto
jar cvf wossname.jar wossname.out
Now try running the client:
the installed EMBASSY packages should now appear in the Jemboss
If you have a web launch page, you will need to re-run makeJNLP.sh.