Deploy on tomcat6 and mysql

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# SOP: Installation of tomcat6 + mysql app (any gcc member)
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# Change lines below to match your app and environment
app=animaldb
# On CentOS VM:
export CATALINA_HOME=/usr/share/tomcat6/
# on SuSE VM:
export CATALINA_HOME=/srv/tomcat6/

# Become molgenis user
sudo su - molgenis
cd /srv/molgenis

# If /srv/molgenis doesn't exist, ask 'root' user to run installation SOP

# Checkout
mkdir $app
cd $app
git clone https://github.com/molgenis/molgenis.git
git clone https://github.com/molgenis/molgenis_apps.git
cd molgenis_apps

# Optionally: check and make sure both Tomcat and MySQL are running
sudo service tomcat6 status
sudo service mysqld status

# Create mysql
mysql -u molgenis -pmolgenis -e "create database $app"; 

# Generate war
ant -f build_$app.xml clean-generate-compile-war

# Delete previous war, if updating.
rm ${CATALINA_HOME}/webapps/$app.war

# Copy new war (tomcat will automatically reload the app)
newgrp tomcat; cp dist/war/$app.war ${CATALINA_HOME}/webapps/$app.war; exit