diff --git a/doc/source/admin/jobs.md b/doc/source/admin/jobs.md index bb6a5455da1..35dc20471ea 100644 --- a/doc/source/admin/jobs.md +++ b/doc/source/admin/jobs.md @@ -6,15 +6,13 @@ This document is a reference for the job configuration file. [Detailed document **The most up-to-date details of advanced job configuration features can be found in the [sample job_conf.xml](https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced) found in the Galaxy distribution.** -### Galaxy Configuration - Configuration of where to run jobs is performed in the `job_conf.xml` file in `$GALAXY_ROOT/config/`. The path to the config file can be overridden by setting the value of `job_config_file` in `config/galaxy.ini`. Sample configurations are provided at `galaxy-dist/config/job_conf.xml.sample_basic` and `galaxy-dist/config/job_conf.xml.sample_advanced`. The job configuration file is not required - if it does not exist, a default configuration that runs jobs on the local system (with a maximum of 4 concurrent jobs) will be used. `job_conf.xml.sample_basic` provides a configuration identical to the default configuration if no `job_conf.xml` exists. ## job_conf.xml Syntax The root element is ``. -## Job Runner Plugins +### Job Runner Plugins The `` collection defines job runner plugins that should be loaded when Galaxy starts. @@ -38,7 +36,7 @@ workers on ``plugins`` configuration). ``` -## Job Handlers +### Job Handlers The `` configuration elements defines which Galaxy server processes (when [running multiple server processes](https://galaxyproject.org/admin/config/performance/scaling/)) should be used for running jobs, and how to group those processes. @@ -55,7 +53,7 @@ tags A comma-separated set of strings that optional define tags to which this handler belongs. ``` -## Job Destinations +### Job Destinations The `` collection defines the parameters that should be used to run a job that is sent to the specified destination. This configuration element should define a ``default`` attribute that should be the ``id`` of the ``destination`` to used if no explicit destination is defined for a job. @@ -75,7 +73,7 @@ tags ``destination`` elements may contain zero or more ````s, which are passed to the destination's defined runner plugin and interpreted in a way native to that plugin. For details on the parameter specification, see the documentation on [Cluster configuration](cluster.html). -## Environment Modifications +### Environment Modifications As of the June 2014 release, destinations may contain additional `env` elements to configure the environment for jobs on that resource. These each map to shell commands that will be injected to Galaxy's job script and executed on the destination resource.