.. _`cistem-dockerimage`:

==================
cisTEM Dockerimage
==================

.. 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>`


.. _`cistem-dockerimage-software`:

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

- cisTem (https://cistem.org/software)


.. _`cistem-dockerimage-development`:

Development Notes
-----------------

- The official cisTEM documentation can be `found here. <https://cistem.org/system/tdf/uploads/cisTEM_tutorial.pdf?file=1&type=cistem_details&id=7&force=>`__


.. _`cistem-dockerimage-dockerfile`:

Dockerfile
----------

- The cisTEM image is hosted at the following location.

.. code::

    gcr.io/ris-registry-shared/cistem


.. _`cistem-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/cistem

.. _`rstudio-docker-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 cisTEM session using the following command:

.. code::

    cisTEM

.. image:: ./images/cistem.start.png

.. image:: ./images/cistem.software.png