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Add docs about running jobs in containers
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Explain how jobs can be run in containers (something currently documented in the `job_conf.xml.sample_advanced` file)
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pvanheus committed Oct 5, 2018
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**Note:** Currently, failure conditions for memory limits and walltime are only implemented for the [Slurm](cluster.html) job runner plugin. Contributions for other implementations would be greatly appreciated! An example job configuration and an always-fail job runner plugin for development [can be found in this gist](https://gist.github.com/natefoo/361414fbca3c0ea63aa5).


### Running jobs in containers

Galaxy can be configured to run jobs in container runtimes. Currently the two supported runtimes are [Docker](https://www.docker.com) and [Singularity](https://www.sylabs.io/). Each ``<destination>`` can enable container support
with ``<param id="docker_enabled">true</param>`` and/or ``<param id="singularity_enabled">true</param>``, as documented
in the [advanced sample job_conf.xml](https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced).
In the case of Docker, containers are run using **sudo** unless ``<param id="docker_sudo">false</param>`` is specified, thus
the user that Galaxy runs as should be able to run ``sudo docker`` without a password prompt for Docker containers to
work.

The images used for containers can either be specified explicitely in the ``<destination>`` using the *docker_default_container_id*, *docker_container_id_override*, *singularity_default_container_id* and
*singularity_container_id_override* parameters, but (perhaps more commonly) the image to use can be derived from the
tool requirements of the Galaxy tool being executed. In this latter case the image is specified by the
tool using a ``<container>`` tag in the ``<requirements>`` section.

### Macros

The job configuration XML file may contain any number of macro definitions using the same
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