From f09d0a7d0380345ea55ab78f16763fe9c53b5e76 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 19 Nov 2020 13:39:21 +0000 Subject: [PATCH] Remove extra `/` and galaxy-dist --- doc/source/admin/jobs.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/admin/jobs.md b/doc/source/admin/jobs.md index a24adc1b18e..a88b8adfe56 100644 --- a/doc/source/admin/jobs.md +++ b/doc/source/admin/jobs.md @@ -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/lib/galaxy/config/sample//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 @@ -131,7 +131,7 @@ tool using a ```` tag in the ```` 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/lib/galaxy/config/sample//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 @@ -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/lib/galaxy/config/sample//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`).