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Fix Example links #10771

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Nov 19, 2020
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Fix Example links #10771

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f497fd6
Fix Example links
RichardJActon Nov 19, 2020
f09d0a7
Remove extra `/` and galaxy-dist
nsoranzo Nov 19, 2020
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8 changes: 4 additions & 4 deletions doc/source/admin/jobs.md
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Expand Up @@ -4,9 +4,9 @@ By default, jobs in Galaxy are run locally on the server on which the Galaxy app

This document is a reference for the job configuration file. [Detailed documentation](cluster.md) is provided for configuring Galaxy to work with a variety of Distributed Resource Managers (DRMs) such as TORQUE, Grid Engine, LSF, and HTCondor. Additionally, a wide range of infrastructure decisions and configuration changes should be made when running Galaxy as a production service, as one is likely doing if using a cluster. It is highly recommended that the [production server documentation](production.md) and [cluster configuration documentation](cluster.md) be read before making changes to the job configuration.

**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.**
**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/lib/galaxy/config/sample/job_conf.xml.sample_advanced) found in the Galaxy distribution.**

Configuration of where to run jobs is performed in the `job_conf.xml` file in `$GALAXY_ROOT/config/`. The path to the config file can be overridden by setting the value of `job_config_file` in `config/galaxy.yml`. Sample configurations are provided at `galaxy-dist/config/job_conf.xml.sample_basic` and `galaxy-dist/config/job_conf.xml.sample_advanced`. The job configuration file is not required - if it does not exist, a default configuration that runs jobs on the local system (with a maximum of 4 concurrent jobs) will be used. `job_conf.xml.sample_basic` provides a configuration identical to the default configuration if no `job_conf.xml` exists.
Configuration of where to run jobs is performed in the `job_conf.xml` file in `$GALAXY_ROOT/config/`. The path to the config file can be overridden by setting the value of `job_config_file` in `config/galaxy.yml`. Sample configurations are provided at `config/job_conf.xml.sample_basic` and `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

Expand Down Expand Up @@ -131,7 +131,7 @@ tool using a ``<container>`` tag in the ``<requirements>`` section.
The job configuration XML file may contain any number of macro definitions using the same
XML macro syntax used by [Galaxy tools](https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements).

See [Pull Request #362](https://github.com/galaxyproject/galaxy/pull/362) for implementation details and the [advanced sample job_conf.xml](https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced) for examples.
See [Pull Request #362](https://github.com/galaxyproject/galaxy/pull/362) for implementation details and the [advanced sample job_conf.xml](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/job_conf.xml.sample_advanced) for examples.

## Mapping Tools To Destinations

Expand Down Expand Up @@ -174,7 +174,7 @@ The two most generic and useful dynamic destination types are `python` and `dtd`

#### Dynamic Destination Mapping (DTD method)

DTD is a special dynamic job destination type that builds up rules given a YAML-based DSL - see `config/tool_destinations.yml.sample` (on [Github](https://github.com/galaxyproject/galaxy/blob/dev/config/tool_destinations.yml.sample)) for a syntax description, examples, and a description of how to validate and debug this file.
DTD is a special dynamic job destination type that builds up rules given a YAML-based DSL - see `config/tool_destinations.yml.sample` (on [Github](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/tool_destinations.yml.sample)) for a syntax description, examples, and a description of how to validate and debug this file.

To define and use rules, copy this sample file to `config/tool_destinations.yml` and add your rules. Anything routed with a `dynamic` runner of type `dtd` will then use this file (such as the destination defined with the following XML block in `job_conf.xml`).

Expand Down