Using Containers
================

``Docker`` provides the easiest way of installing. We recommend this for users, who do not have access to a Linux system
or Window Subsystem for Linux (WSL) or need to transport their code onto supercomputers. Of course, the ``Docker``
service must be available on the system, where computations with ``13CFLUX`` are supposed to be executed.

The provided ``Docker`` image acts as a blueprint of a system with a ready installation and is instantiated as a
container. Containers are similar to a running virtual machine, but leverage the local hardware more efficiently.

To get the ``Docker`` image with pre-installed ``13CFLUX``, simply run

.. code:: bash

   docker pull jugit-registry.fz-juelich.de/ibg-1/modsim/fluxomics/13cflux

in a terminal or by using the URL in the ``Docker`` client GUI.

A blueprint to execute jobs with ``13CFLUX`` is given by

.. code:: bash

   docker run -v /LOCAL/PATH:/task --rm --name x3cflux-container \
               jugit-registry.fz-juelich.de/ibg-1/modsim/fluxomics/13cflux \
               /opt/python/cp313-cp313/bin/python /task/SOME_SCRIPT.py

which instantiates a container from an image, maps the external path ``/LOCAL/PATH`` to the internal path ``/task`` and
executes the script ``SOME_SCRIPT.py`` that was mounted in the container. Within the script, ``13CFLUX`` is executed,
results are stored somewhere ``/task`` and are thereby also available on the local filesystem after the container has
stopped. Omit the ``--rm`` option, if you want to use the same container multiple times.