From a5d794dc4d1ee48539aa36c82ec56ac40760e0fa Mon Sep 17 00:00:00 2001 From: pvanheus Date: Fri, 5 Oct 2018 15:49:47 +0200 Subject: [PATCH] Add docs about running jobs in containers Explain how jobs can be run in containers (something currently documented in the `job_conf.xml.sample_advanced` file) --- doc/source/admin/jobs.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/doc/source/admin/jobs.md b/doc/source/admin/jobs.md index 9bb5a2ae299f..d3320f83c9ed 100644 --- a/doc/source/admin/jobs.md +++ b/doc/source/admin/jobs.md @@ -111,6 +111,21 @@ destination **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 ```` can enable container support +with ``true`` and/or ``true``, 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 ``false`` 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 ```` 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 ```` tag in the ```` section. + ### Macros The job configuration XML file may contain any number of macro definitions using the same