Cannot see the SMRT® Portal page

Cause 1: The hostname and/or port is incorrect. The hostname and port is designated when you installed smrtanalysis. For example, if your want your SMRT Portal URI to be http://server1:8080/smrtportal/, the hostname should be set as server1 and the port should be set as 8080. To reset these variables, re-run configure_smrtanalysis.sh and enter server1 and 8080 when prompted by the script.

Cause 2: Networking issues The client computer/laptop cannot see the server. SMRT Portal is a client-server application. This means that the client computer (your laptop) must know that the server computer (server1) exists somewhere in its network. Some institutions require vpn to login to their network. You must ask your network administrator for what "hostname" to assign to SMRT Portal such that client computers can recognize it.

Cause 3: Tomcat is not on Tomcat is the webserver that hosts SMRT Portal. It must be turned on for SMRT Portal to function. When it is off, the ps command will below returns only a single line. When it is on, the ps command below will return an additional line detailing the path to the tomcatd process.

user@server1$ ps -ef | grep tomcat
71063    15603 23660  0 16:43 pts/15   00:00:00 grep tomcat

user@server1$ /opt/smrtanalysis/etc/scripts/tomcatd start

user@server1$ ps -ef | grep tomcat
71063    15603 23660  0 16:43 pts/15   00:00:00 grep tomcat
71109    16203     1  0 Dec05 ?        00:55:17 /opt/smrtanalysis-1.3.3//redist/java/bin/java -Djava.util.logging.config.file=/opt/smrtanalysis-1.3.3//redist/tomcat/conf/logging.properties -d64 -server -Xmx8g -Djava.library.path=/opt/smrtanalysis-1.3.3//common/lib -Djava.security.auth.login.config=/opt/smrtanalysis-1.3.3//redist/tomcat/conf/kerb5.conf -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/opt/smrtanalysis-1.3.3//redist/tomcat/endorsed -classpath /opt/smrtanalysis-1.3.3//redist/tomcat/bin/bootstrap.jar:/opt/smrtanalysis-1.3.3//redist/tomcat/bin/tomcat-juli.jar -Dcatalina.base=/opt/smrtanalysis-1.3.3//redist/tomcat -Dcatalina.home=/opt/smrtanalysis-1.3.3//redist/tomcat -Djava.io.tmpdir=/opt/smrtanalysis-1.3.3//redist/tomcat/temp org.apache.catalina.startup.Bootstrap start