Step 5: Run the Installation Script - pb-dyim/SMRT-Analysis GitHub Wiki

Run the installation script:

cd $SEYMOUR_HOME/etc/scripts/postinstall
./configure_smrtanalysis.sh

The installation script requires the following input:

  • The system name. (Default: hostname -a)
  • The port number that the services will run under. (Default: 8080)
  • The Tomcat shutdown port. (Default: 8005)
  • The user/group to run the services and set permissions for the files. (Default: smrtanalysis:smrtanalysis)
  • The mysql user name and password to install the database. (Default: root:no password)

The installation script performs the following:

  • Creates the SMRT Portal database. Note: The mysql user performing the install must have permissions to alter or create databases. Otherwise, the installer will reject the user and prompt for another.
  • Sets the host and port names for various configuration files.
  • Sets the Tomcat/kodos user. The services will run as the specified user.
  • Sets the user and group permissions and ownership of the application to the Tomcat user.
  • Adds links in /etc/init.d to the Tomcat and kodos services. (The defaults are: /etc/init.d/kodosd and /etc/init.d/tomcatd.) These are soft links to the actual service files within the application. If a file is already present (for example, tomcatd is already installed), the link can be created with a different name. The permissions of the underlying scripts are limited to the user running the services.
  • Installs the services. The services will automatically restart if the system restarts. (On CentOS, the installer will run chkconfig to install the services, rather than update-rc.d.)

Note: The installer will attempt to run without sudo access first. If this fails, the installer will prompt the user for a sudo password and retry.