Integrative Genomics Viewer (IGV)

• Software Included

• Build IGV Docker Image

• Submitting the IGV job

Software Included

• noVNC (https://novnc.com/info.html)

• IGV for Linux (https://www.igv.org/)

Build IGV Docker Image

1. Log onto compute1

> ssh wustlkey@compute1-client-1.ris.wustl.edu

1. Create IGV-specific noVNC Dockerfile by entering the following command in its entirety:

> cat <<'EOF' > $HOME/noVNC/Dockerfile

FROM gcr.io/ris-registry-shared/novnc:ubuntu20.04
# Install IGV
ENV IGV_URL="https://data.broadinstitute.org/igv/projects/downloads/2.9/IGV_Linux_2.9.4_WithJava.zip"
RUN wget ${IGV_URL} -O IGV.zip \
    && IGV_DIR=`zipinfo -1 IGV.zip | cut -f 1 -d '/' | sort | uniq` \
    && unzip IGV.zip \
    && mv $IGV_DIR IGV \
    && rm IGV.zip \
    && chmod -R 777 IGV \
    && cd IGV \
    && chmod a+x igv.sh
ENV PATH=/app/IGV:$PATH
EOF

1. Build and push your Docker container to Docker Hub. Documentation on how to do this can be found here.

Submitting the IGV job

1. Set the noVNC password

> export PASSWORD=

1. Submit the IGV job to compute1

> PATH="/app/IGV:$PATH" LSF_DOCKER_PORTS='8080:8080' bsub -Is -R 'select[port8080=1]' -q general-interactive -a 'docker(location-of-docker-image)' supervisord -c /app/supervisord.conf

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

• Since LSF is running interactively, it will output the name of the host it’s running on in the terminal.

• The host will be the IP address needed to access the VNC.

• For example: <<Starting on compute1-exec-187.ris.wustl.edu>> translates to the IP being https://compute1-exec-187.compute.ris.wustl.edu:8080/vnc.html

• The password will be what was set above with the export PASSWORD= command.

1. Once connected, you can open IGV by entering igv.sh into the GUI terminal.

> igv.sh