.. _`tortoise-dockerimage`:

=============
AFNI/TORTOISE
=============

.. 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>`

.. _`tortoise-image-details`:

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

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

- Versions Available:
    - latest, v3.2.0
    - v3.1.4

- Software Included
    - AFNI
    - TORTOISE, comprised of the following tools:
        - DIFFPREP
        - DRBUDDI
        - DIFFCALC - CLI version
        - DRTAMAS
    - R Packages
    - GUI is not currently included in this image

.. _`tortoise-dockerimage-requirements`:

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

Initial Setup
~~~~~~~~~~~~~

- An initial setup of dependent files and directory structure in your compute home directory is required.

.. Note::

    - Setup will create/modify the following in the compute home directory: ``.afni/``, ``.afnirc``, ``.bashrc``, ``.sumarc``.
    - In rare cases, $HOME is not /home/wustlkey. See the :ref:`RIS Compute Quick Start <compute-quick-start>` for details. If this is the case, enter echo $HOME and insert the result at the appropriate places below.

- Connect to compute and run the following, adjusting for individual compute username, home location, etc.

    .. code::

        LSF_DOCKER_VOLUMES='/home/wustlkey:/home/wustlkey' PATH=/home/wustlkey:/linux_centos_7_64:$PATH
        bsub -q general-interactive -Is -a 'docker(gcr.io/ris-registry-shared/afni-tortoise)' /bin/bash -c "cp /linux_centos_7_64/AFNI.afnirc ~/.afnirc; suma -update_env; apsearch -update_all_afni_help; /bin/bash"


.. Note::

    - 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.

- Paste the following in its entirety and run to append the .bashrc file.

.. code::

    cat <<EOF >> $HOME/.bashrc
    ahdir=`apsearch -afni_help_dir`
    if [ -f "$ahdir/all_progs.COMP.bash" ]
    then
        . $ahdir/all_progs.COMP.bash
    fi
    export R_LIBS=/usr/local/lib/R/library/’
    EOF

- Update shell.

.. code::

    . ~/.bashrc

Run on LSF
~~~~~~~~~~

- Connect to compute and run the following, adjusting for individual parameters and replacing `<tag>`
  with the appropriate version.

.. code::

    LSF_DOCKER_VOLUMES='/home/wustlkey:/home/wustlkey' PATH=/home/wustlkey:/linux_centos_7_64:$PATH
    bsub -q general-interactive -Is -a 'docker(gcr.io/ris-registry-shared/afni-tortoise:<tag>)' /bin/bash