Tomcat issue with cBioPortal on docker container

[Muralidharan, Aditya Trilok]

Hi,

 

I stopped the Tomcat container while trying to debug and as a result, it crashed the container.  So I stopped the container and then removed it. Then, I did the following to resurrect the setup, but I see that the cbioportal app is not getting deployed in the tomcat webapps folder on the cbioportal docker container.

 

1)      Ran the cbiodocker.sh file in  /home/cbioportal/cbio/bin/

2)      docker exec –it cbioportal bash

3)      Navigated to tomcat folder and ran the startup.sh file (even though we do not have to explicitly start Tomcat and it is expected to run with the docker run command)

4)      Now when I try to hit http://cbioportal:8080/cbioportal, I get a 404, because the cbioportal war file is not in the webapps folder.

 

Here are the contents of the cbiodocker.sh file:

docker run -d --name cbioportal \

    --restart=always \

    --net=cbio-net \

    -p 8080:8080 \

    -v /home/cbioportal/cbio/conf/portal.properties:/cbioportal/src/main/resources/portal.properties:ro \

    -v /home/cbioportal/cbio/conf/log4j.properties:/cbioportal/src/main/resources/log4j.properties:ro \

    -v /home/cbioportal/cbio/cbioportal/.travis/settings.xml:/root/.m2/settings.xml:ro \

    -v /home/cbioportal/cbio/conf/context.xml:/usr/local/tomcat/conf/context.xml:ro \

    -v /home/cbioportal/cbio/logs:/cbioportal_logs/ \

    -v /home/cbioportal/cbio/logs/tomcat:/usr/local/tomcat/logs/ \

    -v /home/cbioportal/cbio/studies:/cbioportal_studies/:ro \

    cbioportal/cbioportal:latest

 

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[Pieter Lukasse]

HI ,

if you are getting 404 you can try to find the error in the log file using the following:

- docker logs <container_name>   (this is the catalina log)

- docker cp <container_name>:/tmp/cbioportal.log cbioportal.log  (this gives you the log file configured in log4j.properties - check your config first to make sure this is the right log file name)

Alternatively, you can always try The Hyve's docker setup documented here: https://github.com/cBioPortal/cbioportal-docker

Best regards,

Pieter

[JJ Gao]

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