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/usr/share/EMBOSS/jemboss/utils/README is in jemboss 6.6.0-1.

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install-jemboss-server.sh - install a Jemboss server (uses Apache
                            Tomcat, SOAP)
keys.sh                   - create SSL client and server certificate
                            and keystore
makeJNLP.sh               - create jnlp and web launch files for Jemboss
makeFileManagerJNLP.sh    - create jnlp and web launch files for the 
                            file manager
makeJar.csh               - create a Jemboss.jar
makeSourceJar.csh         - create a Jemboss.jar include the source code