Genoogle was developed to be executed as a stand alone process. This process has the Genoogle Similar Sequences Searching Engine, the Console interface, and the Web Server, with the Web Page and WebServices interface. However, it is possible, but not recommended, to execute Genoogle as a J2EE Container at Apache Tomcat or Jetty.

To execute Genoogle as a container at Apache Tomcat, the following instructions should be followed:

1) Copy the genoogle/webapps/genoogle-webservices directory to the apache-tomcat/webapps.

2) Copy or create a link of the following jars (and ONLY of them) into apache-tomcat/webapps/genoogle-webservices/WEB-INF/lib/:

activation.jar   google-collect-snapshot-20080820.jar  jaxb-impl.jar  jaxws-rt.jar     jsr181-api.jar    mimepull.jar             saaj-api.jar   streambuffer.jar
FastInfoset.jar  http.jar                              jaxb-xjc.jar   jaxws-tools.jar  jsr250-api.jar    protobuf-java-2.0.2.jar  saaj-impl.jar  woodstox.jar
genoogle.jar     jaxb-api.jar                          jaxws-api.jar  jsr173_api.jar   log4j-1.2.15.jar  resolver.jar             stax-ex.jar
dom4j-1.6.1.jar

3) Set the environment variable $GENOOGLE_HOME to Genoogle directory, which it should contains the conf/ and files/.

4) Start tomcat at the apache-tomcat/bin: ./startup.sh

Ps: the data bank files should already be formatted by format_db.sh .