This is how to deploy in the server .  '''locally''' 

{{{
Despoina-Antonakakis-!MacBook-Pro:-Tmp- despoina$ scp ~/Desktop/molgenis_apps_28_july.war antonakd@vm7.target.rug.nl:.   
}}}
======================'''(in vm7 )'''

{{{

antonakd@vm7 >>>>:~$ ls
BBMRI   create_tables.sql  deployLifelines.sh  index      Lifelines      lifelines.war  logger.out.1       molgenis_apps_28_july.war    !MySqlDumps
BbmriWars  d2r-server-0.7     gcc.war  instantclient_10_2  lifelinesData  logger.out     molgenis_apps_27_july.war  molgenis_rdf_mapping_GCC.n3
antonakd@vm7 >>>>:~$ cd BBMRI/
antonakd@vm7 >>>>:~/BBMRI$ bin/shutdown.sh Using CATALINA_BASE:   /home/antonakd/BBMRIUsing CATALINA_HOME:   /usr/share/tomcat6Using CATALINA_TMPDIR: /home/antonakd/BBMRI/tempUsing JRE_HOME:        /usrUsing CLASSPATH:       /usr/share/tomcat6/bin/bootstrap.jar
antonakd@vm7 >>>>:~/BBMRI$ rm conf/Catalina/localhost/bbmri_gcc.xml 
antonakd@vm7 >>>>:~/BBMRI$ cd webapps/
antonakd@vm7 >>>>:~/BBMRI/webapps$ lsbbmri_gcc  bbmri_gcc.war  logger.out  logger.out.1
antonakd@vm7 >>>>:~/BBMRI/webapps$ rm -rf bbmri_gccrm bbmri_gcc.war
antonakd@vm7 >>>>:~/BBMRI/webapps$ rm bbmri_gcc.war
antonakd@vm7 >>>>:~/BBMRI/webapps$ mv ../../molgenis_apps_28_july.war .
antonakd@vm7 >>>>:~/BBMRI/webapps$ lslogger.out  logger.out.1  molgenis_apps_28_july.war
antonakd@vm7 >>>>:~/BBMRI/webapps$ mv molgenis_apps_28_july.war bbmri_gcc.war
antonakd@vm7 >>>>:~/BBMRI/webapps$ ../bin/startup.sh Using CATALINA_BASE:   /home/antonakd/BBMRIUsing CATALINA_HOME:   /usr/share/tomcat6Using CATALINA_TMPDIR: /home/antonakd/BBMRI/tempUsing JRE_HOME:        /usrUsing CLASSPATH:       /usr/share/tomcat6/bin/bootstrap.jar
antonakd@vm7 >>>>:~/BBMRI/webapps$ 
}}}
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