This is how to deploy in the server . 
[[BR]][[BR]]locally [[BR]][[BR]]
{{{
Despoina-Antonakakis-!MacBook-Pro:-Tmp- despoina$ scp ~/Desktop/molgenis_apps_28_july.war antonakd@vm7.target.rug.nl:.   
}}}
[[BR]]======================[[BR]][[BR]](in vm7 )
{{{
[[BR]][[BR]]
antonakd@vm7 >>>>:~$ ls[[BR]][[BR]]BBMRI   create_tables.sql  deployLifelines.sh  index      Lifelines      lifelines.war  logger.out.1       molgenis_apps_28_july.war    !MySqlDumps

[[BR]][[BR]]!BbmriWars  d2r-server-0.7     gcc.war  instantclient_10_2  lifelinesData  logger.out     molgenis_apps_27_july.war  molgenis_rdf_mapping_GCC.n3[[BR]][[BR]]
antonakd@vm7 >>>>:~$ cd BBMRI/[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI$ bin/shutdown.sh [[BR]][[BR]]Using CATALINA_BASE:   /home/antonakd/BBMRI[[BR]][[BR]]Using CATALINA_HOME:   /usr/share/tomcat6[[BR]][[BR]]Using CATALINA_TMPDIR: /home/antonakd/BBMRI/temp[[BR]][[BR]]Using JRE_HOME:        /usr[[BR]][[BR]]Using CLASSPATH:       /usr/share/tomcat6/bin/bootstrap.jar[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI$ rm conf/Catalina/localhost/bbmri_gcc.xml [[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI$ cd webapps/[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ ls[[BR]][[BR]]bbmri_gcc  bbmri_gcc.war  logger.out  logger.out.1[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ rm -rf bbmri_gcc[[BR]][[BR]]rm bbmri_gcc.war
antonakd@vm7 >>>>:~/BBMRI/webapps$ rm bbmri_gcc.war[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ mv ../../molgenis_apps_28_july.war .[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ ls[[BR]][[BR]]logger.out  logger.out.1  molgenis_apps_28_july.war[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ mv molgenis_apps_28_july.war bbmri_gcc.war[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ ../bin/startup.sh [[BR]][[BR]]Using CATALINA_BASE:   /home/antonakd/BBMRI[[BR]][[BR]]Using CATALINA_HOME:   /usr/share/tomcat6[[BR]][[BR]]Using CATALINA_TMPDIR: /home/antonakd/BBMRI/temp[[BR]][[BR]]Using JRE_HOME:        /usr[[BR]][[BR]]Using CLASSPATH:       /usr/share/tomcat6/bin/bootstrap.jar[[BR]][[BR]]
antonakd@vm7 >>>>:~/BBMRI/webapps$ 
}}}
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