Set up dbNP instance on an NBX

Set up tomcat user

• Login as manager
• Create user tomcat:

  sudo adduser tomcat
  

• Switch to user tomcat and its home directory

  sudo su - tomcat
  

• Change default shell to bash:

  chsh -s /bin/bash
  

• Check out deploy scripts and virtual host configurations

  svn checkout --username=anonymous https://svn.osx.eu/gscf-misc/scripts
  svn checkout --username=anonymous https://svn.osx.eu/gscf-misc/vhost
  

• Download Tomcat (to find the newest version, go to ​http://tomcat.apache.org/, find it, click Download and look up the Core .tar.gz file)

  wget http://apache.mirrors.webazilla.nl/tomcat/tomcat-7/v7.0.16/bin/apache-tomcat-7.0.16.tar.gz
  tar -zxvf apache-tomcat-7.0.16.tar.gz
  

• Add CATALINA_OPTS parameter to default bash environment of Tomcat user (convenient when restarting Tomcat manually)

  echo "export CATALINA_OPTS=\"-Xms128m -Xmx2048m -XX:MaxPermSize=720m -XX:MaxHeapFreeRatio=70 -XX:MaxGCPauseMillis=10 -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled\"" >> ~/.bashrc
  

• Return to your own (manager) shell

  exit
  

Set up Apache virtual host configuration

• Copy the appropriate virtual host configuration from the SVN templates to the apache virtual host directory and adjust the

sudo cp /home/tomcat/vhost/dbnp.org_gscf-www.conf /etc/apache2/sites-available cd /etc/apache2/sites-enabled sudo ln -s ../sites-available/dbnp.org_gscf-www.conf sudo vi dbnp.org_gscf-www.conf }}}

• Install modproxy and restart Apache webserver

  sudo apt-get install libapache2-mod-proxy-html
  sudo ln -s /etc/apache2/mods-available/proxy* /etc/apache2/mods-enabled/
  sudo /etc/init.d/apache2 reload
  

Set up Postgres database

• As user postgres, create a new database user account

  sudo -u postgres createuser -d -R -P dbnp;
  

You will be asked for a password, it is advisable to create a secure (e.g. 20 characters) random password, for example with a password generator website

• Create a gscf database and make the newly created database account owner

  sudo -u postgres createdb -O dbnp gscf-www;
  

Set up custom GSCF configuration

You can create the configuration by running GSCF setup wizard. Alternatively, you can write it from scratch:

• As user tomcat, write the GSCF configuration:

  sudo -u tomcat nano /home/tomcat/.gscf/www.properties
  

You can copy the default configuration from ​https://trac.nbic.nl/gscf/browser/trunk/grails-app/conf/default.properties, but make sure to change the application URL, the database driver, the database user name and password (to what you just entered).