Running SMRT View in a different tomcat instance - dyim42/SMRT-Analysis GitHub Wiki

SMRT View may be run from it's own tomcat instance by making the following configuration change to SMRT Portal:

Edit the configuration file $SMRT_ROOT/current/etc/config.xml to include the host attributes smrtview and smrtviewhttpport where the name and httpport are defined. For example:

Change this:
     <host name="172.16.13.213" httpport="8080" httpsport=""  />
to this:
     <host name="172.16.13.213" httpport="8080" httpsport="" smrtview="172.16.13.213" smrtviewhttpport="8084" />
where SMRT View is installed on the same machine as SMRT Portal with a tomcat running port 8084.

SMRT View requires access to the same paths where SMRT Portal is installed (it uses data from the references and jobs folders using the same paths that SMRT Portal sees for these files). This is something that needs to be kept in mind if installing SMRT View on a different machine than SMRT Portal.

The recommended way to install SMRT View is to follow the instructions here https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View Note that you will likely have to modify the redist/tomcat/conf/server.xml file to specify unique ports for the machine that you are running it on.

Another simple way to install SMRT View is to just do a fresh install of SMRT Analysis choosing different ports for the services when prompted. You can then launch SMRT View by using $SMRT_ROOT/admin/bin/tomcatd-initd start.