mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Sergey GolitsynskiyandNicola Soranzo
4814ef709e
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
113 lines
7.2 KiB
ReStructuredText
113 lines
7.2 KiB
ReStructuredText
Galaxy Configuration
|
|
========================================
|
|
|
|
Overview
|
|
----------------------------
|
|
|
|
Galaxy has a large number of configuration files in an array of formats. Although it is not required to modify *any*
|
|
Galaxy configuration files to run the server, most Galaxy servers will modify at least the core configuration file.
|
|
These have grown organically over time as new features with the needs for advanced syntaxes and config isolation have
|
|
been added. An effort is under way to `standardize and unify configuration formats`_.
|
|
|
|
Configuration files can be found underneath the ``config/`` subdirectory, wherein you can find ``<name>.sample`` files
|
|
corresponding to configuration files that you can modify by copying the ``<name>.sample`` to ``<name>``. In many cases,
|
|
you will find that the sample configuration provides the most up-to-date and detailed documentation about the features
|
|
configured therein.
|
|
|
|
Most config files are administered by hand, although a few (ones which begin with ``shed_*``) are modified by Galaxy
|
|
when installing from the Galaxy Tool Shed. When starting Galaxy for the first time, these files are copied from their
|
|
sample files automatically. You should not need to modify these unless you want to change the directory in to which Tool
|
|
Shed tools are installed.
|
|
|
|
|
|
Configuration Files
|
|
----------------------------
|
|
|
|
The primary Galaxy configuration file is ``galaxy.yml``. You will need to use this file to modify core functionality
|
|
such as the port on which Galaxy listens, the directory in which Galaxy datasets are stored, the database connection
|
|
options, and so forth.
|
|
|
|
The most commonly modified configuration files include:
|
|
|
|
- ``galaxy.yml``: Core Galaxy configuration file.
|
|
- ``tool_conf.xml``: Describes the paths to local tool configurations that Galaxy should attempt to load. Tools that
|
|
are installed via the Tool Shed are configured to load in the ``shed_tool_conf.xml`` file. See the :doc:`Tool Panel
|
|
Administration <tool_panel>` and `Installing Tools into Galaxy`_ documentation for more.
|
|
- ``datatypes_conf.xml``: Describes the file formats that are supported in Galaxy. See the `Datatypes documentation`_
|
|
for more.
|
|
- ``job_conf.xml``: Controls how Galaxy runs tools, e.g. to run them on a compute cluster. See the :doc:`Cluster
|
|
documentation <cluster>` for more.
|
|
|
|
Some configuration files are only used when adding local components, rather than ones installed from the Tool Shed:
|
|
|
|
- ``tool_conf.xml``: As described above.
|
|
- ``tool_data_table_conf.xml``: Describes the mapping between Data Tables - the structured format that allow tools to
|
|
work with locally cached reference data - and the location files that describe the actual data that is available (e.g.
|
|
paths, genome builds, etc.). Data table configurations are also provided by tools in the Tool Shed, those are
|
|
configured in ``shed_tool_data_table_conf.xml``. See the `Data Preparation documentation`_ for more.
|
|
- ``data_manager_conf.xml``: Describes the paths to local Data Managers, special Galaxy tools that automatically fetch
|
|
or create data for Data Tables and manage the corresponding data table and location configuration files. See the `Data
|
|
Managers documentation`_ for more.
|
|
- ``local_conda_mapping.yml``: Define mappings between the names specified in the tool configuration (``<requirement>``
|
|
tags) and the conda resolver's names (conda package name).
|
|
- ``lmod_modules_mapping.yml``: Define mappings between the names specified in the tool configuration (``<requirement>``
|
|
tags) and the Lmod system.
|
|
|
|
Some configuration files are used to control the way that Galaxy resolves tool dependencies. Most Galaxy tools are only
|
|
descriptions of how to run a particular command line tool, and they do not contain the dependent command line tool. The
|
|
task of locating and making available these command line tools is performed by the Galaxy tool dependencies system,
|
|
which has configuration files of its own:
|
|
|
|
Additional configuration files and their purposes are:
|
|
|
|
- ``auth_conf.xml``: Configures the pluggable authentication service. By default, Galaxy users are created and managed
|
|
internally.
|
|
- ``build_sites.yml``: Controls which display applications are available and their configuration paths
|
|
- ``containers_conf.yml``: Configures the beta Galaxy containers interface, currently only used by Galaxy Interactive
|
|
Environments, and only neccesary for Docker Swarm support.
|
|
- ``dependency_resolvers_conf.xml``: Describes how Galaxy tools (which are typically just descriptions of how to run a
|
|
particular command line tool) should locate their dependencies (the command line tool) that are not part of the tool.
|
|
See the `Dependency Resolvers documentation <dependency_resolvers>` for more.
|
|
- ``error_report.yml``: Controls how user-initiated error reporting (e.g. due to tool failure) is performed. See the
|
|
:doc:`Bug Reports documentation <special_topics/bug_reports>` for more.
|
|
- ``job_metrics_conf.xml``: Enables reporting of certain conditions and collection of metrics when jobs run.
|
|
- ``job_resource_params_conf.xml``: Describes tool form elements that should be inserted into tool forms that can be
|
|
used by users to control runtime parameters such as memory allocations, cluster selection, and so forth.
|
|
- ``object_store_conf.xml``: Configures more advanced storage paradigms for Galaxy datasets, including layout across
|
|
multiple filesystems, or in object storage systems such as Swift or Amazon S3.
|
|
- ``swarm_manager_conf.yml``: Configures the experimental Docker Swarm manager.
|
|
- ``tool_destinations.yml``: Configures dynamic tool destinations, which allow for mapping tools to job destinations
|
|
based on certain runtime job properties, such as the user submitting it, input sizes, and so forth.
|
|
- ``tool_sheds_conf.xml``: Defines the list of Tool Shed servers that should appear in the Galaxy Administration
|
|
interface when searching for new tools.
|
|
- ``workflow_schedulers_conf.xml``: Similar to the job configuration, controls the scheduling of workflows as jobs.
|
|
|
|
.. _standardize and unify configuration formats: https://github.com/galaxyproject/galaxy/issues/5148
|
|
.. _Installing Tools into Galaxy: https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/
|
|
.. _Datatypes documentation: https://galaxyproject.org/learn/datatypes/
|
|
.. _Data Preparation documentation: https://galaxyproject.org/admin/data-preparation/
|
|
.. _Data Managers documentation: https://galaxyproject.org/admin/tools/data-managers/
|
|
|
|
|
|
Configuration Basics
|
|
----------------------------
|
|
|
|
- Edit ``config/galaxy.yml`` (copy it from ``config/galaxy.yml.sample`` if it does not exist) to make configuration
|
|
changes. This is a `YAML configuration file`_ and should contain one or two sections, one named ``gravity`` for
|
|
process management via `Gravity`_ (optional) and one named ``galaxy`` for Galaxy (required).
|
|
|
|
- The `gravity` section contain several important options about how to
|
|
launch Galaxy web workers and job handlers, which are documented in the
|
|
:doc:`Scaling and Load Balancing <scaling>` documentation.
|
|
|
|
- Run Galaxy with ``sh run.sh``
|
|
- Use a web browser and go to the address you configured in ``galaxy.yml`` (defaults to http://localhost:8080/)
|
|
|
|
.. _Gravity: https://github.com/galaxyproject/gravity
|
|
|
|
----------------------------
|
|
Configuration Options
|
|
----------------------------
|
|
|
|
.. include:: galaxy_options.rst
|