.. _`relion-dockerimage`:

======
RELION
======

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

.. _`relion-dockerimage-details`:

Image Details
-------------

- Docker image hosted at `gcr.io/ris-registry-shared/relion`.

- Versions Available <tags>:
    - 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)

.. _`relion-dockerimage-requirements`:

Requirements for Usage in RIS
-----------------------------

- Interactions GUI sessions are done via the ``Custom noVNC Image`` application in Open On Demand (OOD).
- You can find out more about OOD here: :ref:`Compute Quick Start <compute-quick-start>`.
- There are two fields beyond the basics that will need information specific to this image.
    - Environment Variables
    - Docker Image

Environment Variables
~~~~~~~~~~~~~~~~~~~~~

- This information should be space separated in the field.

.. code::

    PASSWORD=password

- Optional variables
    - GUI display size. This can be changed with the following variables.
        - Width default: 1024
        - Height default: 768

    .. code::

        DISPLAY_WIDTH=<width> DISPLAY_HEIGHT=<height>

Docker Image
~~~~~~~~~~~~

.. code::

    gcr.io/ris-registry-shared/relion:<tag>

- Fill out the rest of the fields with the appropriate information (explained in the quick start).
- Launch the job through the methods described in the quick start.
- Once in an interactive relion session using the following command:

.. code::

    relion