Install and set up tomcat7 server in ubuntu. Use https protocol

Tomcat Server

Tomcat installation:

    sudo apt-get install tomcat7 (Minimun installation)
    sudo apt-get install tomcat7-admin tomcat7-common tomcat7-docs tomcat7-examples
    This installation implies that tomcat is installed as a service. /usr/share/tomcat7/bin/startup.sh cannot be used to start tomcat. 

Set up environment variables. Edit .bashrc and add:

    export JAVA_HOME=/usr/lib/jvm/default-java
    export CATALINA_HOME=/usr/share/tomcat7
    export CATALINA_BASE=/usr/share/tomcat7

Other tomcat folders: 

    /etc/tomcat7 ---> config files CATALINA_HOME
    /etc/init.d/tomcat7
    /usr/share/tomcat7 ---> bin, jars
    /usr/share/tomcat7-root/default_root/ 
    /var/lib/tomcat7 ---> contains webapps CATALINA_BASE
    /var/log/tomcat7/ --> logs

Create a certificate, provide permissions. The default folder where it is stored is the home folder (/root/). To avoid the modification of this folder permissions, move the file to the conf tomcat folder:

    $JAVA_HOME/bin/keytool -genkey -alias tomcat -keyalg RSA
    CN=amiga, OU=AMIGA, O=IAA-CSIC, L=Granada, ST=Spain, C=ES
    chmod 755 /root/.keystore

    mv /root/.keystore /etc/tomcat7/

Edit server.xml in /etc/tomcat7 to modify the connector (port and secure configuration)

    Comment the connector that use 8080 port number. 
    Include a new connector for TSL connections according to the Taverna Tutorial specifications. 

server.xml
    <Connector port="8443" protocol="HTTP/1.1" SSLEnabled="true"
        maxThreads="150" scheme="https" secure="true"
        keystoreFile="/etc/tomcat7/.keystore" keystorePass="amigatserver"
        clientAuth="false" sslProtocol="TLS" />

Start and Stop the service:

    service tomcat7 start
    service tomcat7 stop

If there is any problem:

    Check the logs at /var/logs/tomcat7
    Check if the service is running in the right port: netstat -anp | grep 8443
    Check if the service is running: ps -ef | grep tomcat

Verify that default web app is working:

    https://xxx.xxx.xxx.xx:8443   You should get a web page saying "It Works!"

Modify tomcat-users and add the manager-gui role and manag user. 

See the deployed (and deploy) web applications using https://161.111.165.90:8443/manager/html  interface. The required user is "manag" the password is in /var/lib/tomcat7/conf/tomcat-users.xml