cisTEM Dockerimage

Owned by Former user (Deleted)
Last updated: Jun 06, 2023 by RIS-SVC-conf-publish
2 min read

Compute Resources

Docker Usage

Software Included

Development Notes

Dockerfile

  • The cisTEM image is hosted at the following location.

gcr.io/ris-registry-shared/cistem

Requirements for Usage in RIS

  • The following LSF variables are necessary for the image to run.

export LSF_DOCKER_PORTS='8080:8080'
export PASSWORD=PASSWORD

  • Please see our documentation for more information on selecting a port.

The password cannot be left blank.

  • Once your LSF variables are set you can start up the docker image with the following command.

bsub -Is -G group-name -R 'rusage[mem=64000] select[port8080=1]' -q general-interactive -a 'docker(gcr.io/ris-registry-shared/cistem)' supervisord -c /app/supervisord.conf

If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with -G group_name or by setting the LSB_SUB_USER_GROUP variable.

  • Once the job is running it will output the node that the job started on.

<<Starting on compute1-exec-N.ris.wustl.edu>>

  • This then will be needed as part of the web address required to access the GUI.

https://compute1-exec-N.compute.ris.wustl.edu:8080/vnc.html

  • The password it asks for will be the one you set with the variable above.

  • To open the cisTEM application, type the following into the terminal inside the GUI and hit enter.

cisTEM

If you want to change the GUI display size in the browser, you can do so by using the following variables before running the job. The default width is 1024 and the default height is 768.

export DISPLAY_WIDTH=width
export DISPLAY_HEIGHT=height