.. _`igv-dockerimage`:

=================================
Integrative Genomics Viewer (IGV)
=================================

.. contents::
   :depth: 1
   :local:

.. admonition:: Compute Resources

    - Have questions or need help with compute, including activation or issues? Follow `this link. <https://washu.atlassian.net/servicedesk/customer/portal/2/group/6/create/43>`__
    - :ref:`User Agreement <compute-user-agreement>`

.. admonition:: Docker Usage

    - The information 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.
    - :ref:`Docker and the RIS Compute Service <docker-on-compute>`
    - :ref:`Docker Basics: Building, Tagging, & Pushing A Custom Docker Image <ris-docker-basics>`


.. _`igv-dockerimage-software`:

Software Included
-----------------

- noVNC (https://novnc.com/info.html)
- IGV for Linux (https://www.igv.org/)

.. _`igv-dockerimage-build`:

Build IGV Docker Image
----------------------

1. Log onto compute1

::

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

2. 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

3. Build and push your Docker container to `Docker Hub <https://hub.docker.com/>`__. Documentation on how
   to do this can be found :ref:`here <ris-docker-workshop>`.

.. _`igv-dockerimage-submit`:

Submitting the IGV job
-----------------------

1. Set the noVNC password

::

    > export PASSWORD=

.. warning ::

    Complete export PASSWORD= with that of your choosing. Do not leave this blank.

2. 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 :ref:`documentation <ris-vetted-compute-port-selection>`
  for more information on selecting a port.

.. admonition:: You are a member of multiple LSF User Groups

    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 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.

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

::

    > igv.sh

.. image:: ../images/igv-success.png


.. admonition:: Using a different IGV version

    The above instructions are current for IGV v.2.9.4. If you would like to use another version of IGV,
    substitute the ``IGV_URL`` in the ``Dockerfile`` with the URL of the version of IGV for Linux you would
    like to use.