RELION

Image Details
Requirements for Usage in RIS

Compute Resources

Have questions or need help with compute, including activation or issues? Follow this link.
User Agreement

Docker Usage

The information contained on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. If you need to review that information, please see the links below.
Docker and the RIS Compute Service
Docker Basics: Building, Tagging, & Pushing A Custom Docker Image

Image Details

Docker image hosted at gcr.io/ris-registry-shared/relion.
Versions Available:
- latest, 3.1
- ood
Software Included:
- Relion (https://www3.mrc-lmb.cam.ac.uk/relion//index.php/Main_Page)
- CTFFIND (https://grigoriefflab.umassmed.edu/ctffind4)
- GCTF (hhttps://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/)
- MotionCor2 (https://emcore.ucsf.edu/ucsf-motioncor2)

Requirements for Usage in RIS

A password variable is required to use the docker image.

export PASSWORD=password

The command to run the RELION docker image in the RIS Compute environment is as follows. Replace <tag> with the appropriate available version.

LSF_DOCKER_NETWORK=host LSF_DOCKER_IPC=host bsub -gpu "num=4" -Is -R 'gpuhost rusage[mem=64GB]' -q general-interactive -a 'docker(gcr.io/ris-registry-shared/relion:<tag>)' 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.

Since the job is running interactively it will output the name of the blade it’s running on in the terminal. The blade will be the IP address needed to access the VNC.

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

translates to the IP address you enter into the web browser being

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

The password will be what you set above.
You can open the application GUI by entering relion into the terminal within the GUI accessed via the web browser.
You can change GUI display size by clicking on the settings icon on the left of the browser and selecting ‘Local Scaling’ from the Scaling Mode dropdown. Click the settings icon again to resume session.
The display height and width can also be changed by passing them as variables.

export DISPLAY_WIDTH=width (default is 1024)
export DISPLAY_HEIGHT=height (default is 768)