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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 Tool Panel Administration 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 Cluster documentation 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 Bug Reports documentation 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.

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 uWSGI YAML configuration file and should contain two sections, one named uwsgi for uWSGI and one named galaxy for Galaxy.

  • The default port for the Galaxy web server is 8080, and it only binds to localhost by default. To configure uWSGI to listen on all available network addresses, set http to 0.0.0.0:<port> (e.g. http: 0.0.0.0:8080).

  • Some uWSGI options are required for uWSGI to run Galaxy properly and will be added to the uwsgi command line by run.sh if not specified in galaxy.yml.

  • uWSGI has a large number of options. The Galaxy documentation refers to some of them, but many additional advanced deployment scenarios are available.

• 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/)

Configuration Options

config_dir

Description

The directory that will be prepended to relative paths in options specifying other Galaxy config files (e.g. datatypes_config_file). Defaults to the directory in which galaxy.yml is located.

Default

None

Type

str

managed_config_dir

Description

The directory that will be prepended to relative paths in options specifying config files controlled by Galaxy (such as shed_tool_config_file, etc.). Must be writable by the user running Galaxy. Defaults to <config_dir>/ if running Galaxy from source or <data_dir>/config otherwise.

Default

None

Type

str

data_dir

Description

The directory that will be prepended to relative paths in options specifying Galaxy data/cache directories and files (such as the default SQLite database, file_path, etc.). Defaults to database/ if running Galaxy from source or <config_dir>/data otherwise.

Default

None

Type

str

cache_dir

Description

Top level cache directory. Any other cache directories (tool_cache_data_dir, template_cache_path, etc.) should be subdirectories. The value of this option will be resolved with respect to <data_dir>.

Default

cache

Type

str

database_connection

Description

By default, Galaxy uses a SQLite database at ‘<data_dir>/universe.sqlite’. You may use a SQLAlchemy connection string to specify an external database instead. Sample default ‘sqlite:///<data_dir>/universe.sqlite?isolation_level=IMMEDIATE’

Default

None

Type

str

database_engine_option_pool_size

Description

If the server logs errors about not having enough database pool connections, you will want to increase these values, or consider running more Galaxy processes.

Default

5

Type

int

database_engine_option_max_overflow

Description

If the server logs errors about not having enough database pool connections, you will want to increase these values, or consider running more Galaxy processes.

Default

10

Type

int

database_engine_option_pool_recycle

Description

If using MySQL and the server logs the error “MySQL server has gone away”, you will want to set this to some positive value (7200 should work).

Default

-1

Type

int

database_engine_option_server_side_cursors

Description

If large database query results are causing memory or response time issues in the Galaxy process, leave the result on the server instead. This option is only available for PostgreSQL and is highly recommended.

Default

false

Type

bool

database_query_profiling_proxy

Description

Log all database transactions, can be useful for debugging and performance profiling. Logging is done via Python’s ‘logging’ module under the qualname ‘galaxy.model.orm.logging_connection_proxy’

Default

false

Type

bool

database_template

Description

If auto-creating a postgres database on startup - it can be based on an existing template database. This will set that. This is probably only useful for testing but documentation is included here for completeness.

Default

None

Type

str

database_log_query_counts

Description

Log number of SQL queries executed and total time spent dispatching SQL statements for each web request. If statsd is also enabled this information will be logged there as well. This should be considered somewhat experimental, we are unsure of the performance costs of running this in production. This is useful information for optimizing database interaction performance. Similar information can be obtained on a per-request basis by enabling the sql_debug middleware and adding sql_debug=1 to a request string.

Default

false

Type

bool

slow_query_log_threshold

Description

Slow query logging. Queries slower than the threshold indicated below will be logged to debug. A value of ‘0’ is disabled. For example, you would set this to .005 to log all queries taking longer than 5 milliseconds.

Default

0.0

Type

float

enable_per_request_sql_debugging

Description

Enables a per request sql debugging option. If this is set to true, append ?sql_debug=1 to web request URLs to enable detailed logging on the backend of SQL queries generated during that request. This is useful for debugging slow endpoints during development.

Default

false

Type

bool

install_database_connection

Description

By default, Galaxy will use the same database to track user data and tool shed install data. There are many situations in which it is valuable to separate these - for instance bootstrapping fresh Galaxy instances with pretested installs. The following option can be used to separate the tool shed install database (all other options listed above but prefixed with install_ are also available). Defaults to the value of the ‘database_connection’ option.

Default

None

Type

str

database_auto_migrate

Description

Setting the following option to true will cause Galaxy to automatically migrate the database forward after updates. This is not recommended for production use.

Default

false

Type

bool

database_wait

Description

Wait for database to become available instead of failing immediately.

Default

false

Type

bool

database_wait_attempts

Description

Number of attempts before failing if database_wait is enabled.

Default

60

Type

int

database_wait_sleep

Description

Time to sleep between attempts if database_wait is enabled (in seconds).

Default

1.0

Type

float

history_audit_table_prune_interval

Description

Time (in seconds) between attempts to remove old rows from the history_audit database table. Set to 0 to disable pruning.

Default

3600

Type

int

file_path

Description

Where dataset files are stored. It must be accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar. The default value has been changed from ‘files’ to ‘objects’ as of 20.05; however, Galaxy will first check if the ‘files’ directory exists before using ‘objects’ as the default. The value of this option will be resolved with respect to <data_dir>.

Default

objects

Type

str

new_file_path

Description

Where temporary files are stored. It must be accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar. The value of this option will be resolved with respect to <data_dir>.

Default

tmp

Type

str

tool_config_file

Description

Tool config files, defines what tools are available in Galaxy. Tools can be locally developed or installed from Galaxy tool sheds. (config/tool_conf.xml.sample will be used if left unset and config/tool_conf.xml does not exist). Can be a single file, a list of files, or (for backwards compatibility) a comma-separated list of files. The value of this option will be resolved with respect to <config_dir>.

Default

tool_conf.xml

Type

any

shed_tool_config_file

Description

Tool config file for tools installed from the Galaxy Tool Shed. Must be writable by Galaxy and generally should not be edited by hand. In older Galaxy releases, this file was part of the tool_config_file option. It is still possible to specify this file (and other shed-enabled tool config files) in tool_config_file, but in the standard case of a single shed-enabled tool config, this option is preferable. This file will be created automatically upon tool installation, whereas Galaxy will fail to start if any files in tool_config_file cannot be read. The value of this option will be resolved with respect to <managed_config_dir>.

Default

shed_tool_conf.xml

Type

str

check_migrate_tools

Description

Enable / disable checking if any tools defined in the above non-shed tool_config_files (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool Shed. This functionality is largely untested in modern Galaxy releases and has serious issues such as #7273 and the possibility of slowing down Galaxy startup, so the default and recommended value is false.

Default

false

Type

bool

migrated_tools_config

Description

Tool config maintained by tool migration scripts. If you use the migration scripts to install tools that have been migrated to the tool shed upon a new release, they will be added to this tool config file. The value of this option will be resolved with respect to <managed_config_dir>.

Default

migrated_tools_conf.xml

Type

str

integrated_tool_panel_config

Description

File that contains the XML section and tool tags from all tool panel config files integrated into a single file that defines the tool panel layout. This file can be changed by the Galaxy administrator to alter the layout of the tool panel. If not present, Galaxy will create it. The value of this option will be resolved with respect to <managed_config_dir>.

Default

integrated_tool_panel.xml

Type

str

tool_path

Description

Default path to the directory containing the tools defined in tool_conf.xml. Other tool config files must include the tool_path as an attribute in the <toolbox> tag.

Default

tools

Type

str

tool_dependency_dir

Description

Various dependency resolver configuration parameters will have defaults set relative to this path, such as the default conda prefix, default Galaxy packages path, legacy tool shed dependencies path, and the dependency cache directory. Set the string to null to explicitly disable tool dependency handling. If this option is set to none or an invalid path, installing tools with dependencies from the Tool Shed or in Conda will fail. The value of this option will be resolved with respect to <data_dir>.

Default

dependencies

Type

str

dependency_resolvers_config_file

Description

Specifies the path to the standalone dependency resolvers configuration file. This configuration can now be specified directly in the Galaxy configuration, see the description of the ‘dependency_resolvers’ option for details. The value of this option will be resolved with respect to <config_dir>.

Default

dependency_resolvers_conf.xml

Type

str

conda_prefix

Description

conda_prefix is the location on the filesystem where Conda packages and environments are installed. Sample default ‘<tool_dependency_dir>/_conda’

Default

None

Type

str

conda_exec

Description

Override the Conda executable to use, it will default to the one on the PATH (if available) and then to <conda_prefix>/bin/conda

Default

None

Type

str

conda_debug

Description

Pass debug flag to conda commands.

Default

false

Type

bool

conda_ensure_channels

Description

conda channels to enable by default (https://conda.io/docs/user-guide/tasks/manage-channels.html)

Default

conda-forge,bioconda,defaults

Type

str

conda_use_local

Description

Use locally-built conda packages.

Default

false

Type

bool

conda_auto_install

Description

Set to true to instruct Galaxy to look for and install missing tool dependencies before each job runs.

Default

false

Type

bool

conda_auto_init

Description

Set to true to instruct Galaxy to install Conda from the web automatically if it cannot find a local copy and conda_exec is not configured.

Default

true

Type

bool

conda_copy_dependencies

Description

You must set this to true if conda_prefix and job_working_directory are not on the same volume, or some conda dependencies will fail to execute at job runtime. Conda will copy packages content instead of creating hardlinks or symlinks. This will prevent problems with some specific packages (perl, R), at the cost of extra disk space usage and extra time spent copying packages.

Default

false

Type

bool

local_conda_mapping_file

Description

Path to a file that provides a mapping from abstract packages to concrete conda packages. See config/local_conda_mapping.yml.sample for examples. The value of this option will be resolved with respect to <config_dir>.

Default

local_conda_mapping.yml

Type

str

modules_mapping_files

Description

Path to a file that provides a mapping from abstract packages to locally installed modules. See config/environment_modules_mapping.yml.sample for examples. The value of this option will be resolved with respect to <config_dir>.

Default

environment_modules_mapping.yml

Type

str

use_cached_dependency_manager

Description

Certain dependency resolvers (namely Conda) take a considerable amount of time to build an isolated job environment in the job_working_directory if the job working directory is on a network share. Set this option to true to cache the dependencies in a folder. This option is beta and should only be used if you experience long waiting times before a job is actually submitted to your cluster. This only affects tools where some requirements can be resolved but not others, most modern best practice tools can use prebuilt environments in the Conda directory.

Default

false

Type

bool

tool_dependency_cache_dir

Description

By default the tool_dependency_cache_dir is the _cache directory of the tool dependency directory. Sample default ‘<tool_dependency_dir>/_cache’

Default

None

Type

str

precache_dependencies

Description

By default, when using a cached dependency manager, the dependencies are cached when installing new tools and when using tools for the first time. Set this to false if you prefer dependencies to be cached only when installing new tools.

Default

true

Type

bool

tool_sheds_config_file

Description

File containing the Galaxy Tool Sheds that should be made available to install from in the admin interface (.sample used if default does not exist). The value of this option will be resolved with respect to <config_dir>.

Default

tool_sheds_conf.xml

Type

str

watch_tools

Description

Monitor the tools and tool directories listed in any tool config file specified in tool_config_file option. If changes are found, tools are automatically reloaded. Watchdog ( https://pypi.org/project/watchdog/ ) must be installed and available to Galaxy to use this option. Other options include ‘auto’ which will attempt to watch tools if the watchdog library is available but won’t fail to load Galaxy if it is not and ‘polling’ which will use a less efficient monitoring scheme that may work in wider range of scenarios than the watchdog default.

Default

false

Type

str

watch_job_rules

Description

Monitor dynamic job rules. If changes are found, rules are automatically reloaded. Takes the same values as the ‘watch_tools’ option.

Default

false

Type

str

watch_core_config

Description

Monitor a subset of options in the core configuration file (See RELOADABLE_CONFIG_OPTIONS in lib/galaxy/config/__init__.py). If changes are found, modified options are automatically reloaded. Takes the same values as the ‘watch_tools’ option.

Default

false

Type

str

watch_tours

Description

Monitor the interactive tours directory specified in the ‘tour_config_dir’ option. If changes are found, modified tours are automatically reloaded. Takes the same values as the ‘watch_tools’ option.

Default

false

Type

str

file_sources_config_file

Description

Configured FileSource plugins. The value of this option will be resolved with respect to <config_dir>.

Default

file_sources_conf.yml

Type

str

enable_mulled_containers

Description

Enable Galaxy to fetch containers registered with quay.io generated from tool requirements resolved through Conda. These containers (when available) have been generated using mulled - https://github.com/mulled. Container availability will vary by tool, this option will only be used for job destinations with Docker or Singularity enabled.

Default

true

Type

bool

container_resolvers_config_file

Description

Container resolvers configuration (beta). Set up a file describing container resolvers to use when discovering containers for Galaxy. If this is set to None, the default container resolvers loaded is determined by enable_mulled_containers.

Default

None

Type

str

container_resolvers

Description

Rather than specifying a container_resolvers_config_file, the definition of the resolvers to enable can be embedded into Galaxy’s config with this option. This has no effect if a container_resolvers_config_file is used. The syntax, available resolvers, and documentation of their options is explained in detail in the documentation: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Default

None

Type

seq

involucro_path

Description

involucro is a tool used to build Docker or Singularity containers for tools from Conda dependencies referenced in tools as requirement s. The following path is the location of involucro on the Galaxy host. This is ignored if the relevant container resolver isn’t enabled, and will install on demand unless involucro_auto_init is set to false. The value of this option will be resolved with respect to <tool_dependency_dir>.

Default

involucro

Type

str

involucro_auto_init

Description

Install involucro as needed to build Docker or Singularity containers for tools. Ignored if relevant container resolver is not used.

Default

true

Type

bool

mulled_channels

Description

Conda channels to use when building Docker or Singularity containers using involucro.

Default

conda-forge,bioconda

Type

str

enable_tool_shed_check

Description

Enable automatic polling of relative tool sheds to see if any updates are available for installed repositories. Ideally only one Galaxy server process should be able to check for repository updates. The setting for hours_between_check should be an integer between 1 and 24.

Default

false

Type

bool

hours_between_check

Description

Enable automatic polling of relative tool sheds to see if any updates are available for installed repositories. Ideally only one Galaxy server process should be able to check for repository updates. The setting for hours_between_check should be an integer between 1 and 24.

Default

12

Type

int

tool_data_table_config_path

Description

XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator (.sample used if default does not exist). The value of this option will be resolved with respect to <config_dir>.

Default

tool_data_table_conf.xml

Type

str

shed_tool_data_table_config

Description

XML config file that contains additional data table entries for the ToolDataTableManager. This file is automatically generated based on the current installed tool shed repositories that contain valid tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. The value of this option will be resolved with respect to <managed_config_dir>.

Default

shed_tool_data_table_conf.xml

Type

str

tool_data_path

Description

Directory where data used by tools is located. See the samples in that directory and the Galaxy Community Hub for help: https://galaxyproject.org/admin/data-integration

Default

tool-data

Type

str

shed_tool_data_path

Description

Directory where Tool Data Table related files will be placed when installed from a ToolShed. Defaults to the value of the ‘tool_data_path’ option.

Default

None

Type

str

watch_tool_data_dir

Description

Monitor the tool_data and shed_tool_data_path directories. If changes in tool data table files are found, the tool data tables for that data manager are automatically reloaded. Watchdog ( https://pypi.org/project/watchdog/ ) must be installed and available to Galaxy to use this option. Other options include ‘auto’ which will attempt to use the watchdog library if it is available but won’t fail to load Galaxy if it is not and ‘polling’ which will use a less efficient monitoring scheme that may work in wider range of scenarios than the watchdog default.

Default

false

Type

str

refgenie_config_file

Description

File containing refgenie configuration, e.g. /path/to/genome_config.yaml. Can be used by refgenie backed tool data tables.

Default

None

Type

str

build_sites_config_file

Description

File that defines the builds (dbkeys) available at sites used by display applications and the URL to those sites. The value of this option will be resolved with respect to <config_dir>.

Default

build_sites.yml

Type

str

builds_file_path

Description

File containing old-style genome builds. The value of this option will be resolved with respect to <tool_data_path>.

Default

shared/ucsc/builds.txt

Type

str

len_file_path

Description

Directory where chrom len files are kept, currently mainly used by trackster. The value of this option will be resolved with respect to <tool_data_path>.

Default

shared/ucsc/chrom

Type

str

datatypes_config_file

Description

Datatypes config file(s), defines what data (file) types are available in Galaxy (.sample is used if default does not exist). If a datatype appears in multiple files, the last definition is used (though the first sniffer is used so limit sniffer definitions to one file). The value of this option will be resolved with respect to <config_dir>.

Default

datatypes_conf.xml

Type

str

sniff_compressed_dynamic_datatypes_default

Description

Enable sniffing of compressed datatypes. This can be configured/overridden on a per-datatype basis in the datatypes_conf.xml file. With this option set to false the compressed datatypes will be unpacked before sniffing.

Default

true

Type

bool

datatypes_disable_auto

Description

Disable the ‘Auto-detect’ option for file uploads

Default

false

Type

bool

visualization_plugins_directory

Description

Visualizations config directory: where to look for individual visualization plugins. The path is relative to the Galaxy root dir. To use an absolute path begin the path with ‘/’. This is a comma-separated list.

Default

config/plugins/visualizations

Type

str

interactive_environment_plugins_directory

Description

Interactive environment plugins root directory: where to look for interactive environment plugins. By default none will be loaded. Set to config/plugins/interactive_environments to load Galaxy’s stock plugins. These will require Docker to be configured and have security considerations, so proceed with caution. The path is relative to the Galaxy root dir. To use an absolute path begin the path with ‘/’. This is a comma-separated list.

Default

None

Type

str

tour_config_dir

Description

Interactive tour directory: where to store interactive tour definition files. Galaxy ships with several basic interface tours enabled, though a different directory with custom tours can be specified here. The path is relative to the Galaxy root dir. To use an absolute path begin the path with ‘/’. This is a comma-separated list.

Default

config/plugins/tours

Type

str

webhooks_dir

Description

Webhooks directory: where to store webhooks - plugins to extend the Galaxy UI. By default none will be loaded. Set to config/plugins/webhooks/demo to load Galaxy’s demo webhooks. To use an absolute path begin the path with ‘/’. This is a comma-separated list. Add test/functional/webhooks to this list to include the demo webhooks used to test the webhook framework.

Default

config/plugins/webhooks

Type

str

job_working_directory

Description

Each job is given a unique empty directory as its current working directory. This option defines in what parent directory those directories will be created. The value of this option will be resolved with respect to <data_dir>.

Default

jobs_directory

Type

str

cluster_files_directory

Description

If using a cluster, Galaxy will write job scripts and stdout/stderr to this directory. The value of this option will be resolved with respect to <data_dir>.

Default

pbs

Type

str

template_cache_path

Description

Mako templates are compiled as needed and cached for reuse, this directory is used for the cache The value of this option will be resolved with respect to <cache_dir>.

Default

compiled_templates

Type

str

check_job_script_integrity

Description

Set to false to disable various checks Galaxy will do to ensure it can run job scripts before attempting to execute or submit them.

Default

true

Type

bool

check_job_script_integrity_count

Description

Number of checks to execute if check_job_script_integrity is enabled.

Default

35

Type

int

check_job_script_integrity_sleep

Description

Time to sleep between checks if check_job_script_integrity is enabled (in seconds).

Default

0.25

Type

float

default_job_shell

Description

Set the default shell used by non-containerized jobs Galaxy-wide. This defaults to bash for all jobs and can be overridden at the destination level for heterogeneous clusters. conda job resolution requires bash or zsh so if this is switched to /bin/sh for instance - conda resolution should be disabled. Containerized jobs always use /bin/sh - so more maximum portability tool authors should assume generated commands run in sh.

Default

/bin/bash

Type

str

enable_tool_document_cache

Description

Whether to enable the tool document cache. This cache stores expanded XML strings. Enabling the tool cache results in slightly faster startup times. The tool cache is backed by a SQLite database, which cannot be stored on certain network disks. The cache location is configurable using the tool_cache_data_dir setting, but can be disabled completely here.

Default

false

Type

bool

tool_cache_data_dir

Description

Tool related caching. Fully expanded tools and metadata will be stored at this path. Per tool_conf cache locations can be configured in (shed_)tool_conf.xml files using the tool_cache_data_dir attribute. The value of this option will be resolved with respect to <cache_dir>.

Default

tool_cache

Type

str

tool_search_index_dir

Description

Directory in which the toolbox search index is stored. The value of this option will be resolved with respect to <data_dir>.

Default

tool_search_index

Type

str

delay_tool_initialization

Description

Set this to true to delay parsing of tool inputs and outputs until they are needed. This results in faster startup times but uses more memory when using forked Galaxy processes.

Default

false

Type

bool

biotools_content_directory

Description

Point Galaxy at a repository consisting of a copy of the bio.tools database (e.g. https://github.com/bio-tools/content/) to resolve bio.tools data for tool metadata.

Default

None

Type

str

biotools_use_api

Description

Set this to true to attempt to resolve bio.tools metadata for tools for tool not resovled via biotools_content_directory.

Default

false

Type

bool

biotools_service_cache_type

Description

bio.tools web service request related caching. The type of beaker cache used.

Default

file

Type

str

biotools_service_cache_data_dir

Description

bio.tools web service request related caching. The data directory to point beaker cache at. The value of this option will be resolved with respect to <cache_dir>.

Default

biotools/data

Type

str

biotools_service_cache_lock_dir

Description

bio.tools web service request related caching. The lock directory to point beaker cache at. The value of this option will be resolved with respect to <cache_dir>.

Default

biotools/locks

Type

str

citation_cache_type

Description

Citation related caching. Tool citations information maybe fetched from external sources such as https://doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information.

Default

file

Type

str

citation_cache_data_dir

Description

Citation related caching. Tool citations information maybe fetched from external sources such as https://doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. The value of this option will be resolved with respect to <cache_dir>.

Default

citations/data

Type

str

citation_cache_lock_dir

Description

Citation related caching. Tool citations information maybe fetched from external sources such as https://doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. The value of this option will be resolved with respect to <cache_dir>.

Default

citations/locks

Type

str

mulled_resolution_cache_type

Description

Mulled resolution caching. Mulled resolution uses external APIs of quay.io, these requests are caching using this and the following parameters

Default

file

Type

str

mulled_resolution_cache_data_dir

Description

Data directory used by beaker for caching mulled resolution requests. The value of this option will be resolved with respect to <cache_dir>.

Default

mulled/data

Type

str

mulled_resolution_cache_lock_dir

Description

Lock directory used by beaker for caching mulled resolution requests. The value of this option will be resolved with respect to <cache_dir>.

Default

mulled/locks

Type

str

object_store_config_file

Description

Configuration file for the object store If this is set and exists, it overrides any other objectstore settings. The value of this option will be resolved with respect to <config_dir>.

Default

object_store_conf.xml

Type

str

object_store_store_by

Description

What Dataset attribute is used to reference files in an ObjectStore implementation, this can be ‘uuid’ or ‘id’. The default will depend on how the object store is configured, starting with 20.05 Galaxy will try to default to ‘uuid’ if it can be sure this is a new Galaxy instance - but the default will be ‘id’ in many cases. In particular, if the name of the directory set in <file_path> is objects, the default will be set to ‘uuid’, otherwise it will be ‘id’.

Default

None

Type

str

smtp_server

Description

Galaxy sends mail for various things: subscribing users to the mailing list if they request it, password resets, reporting dataset errors, and sending activation emails. To do this, it needs to send mail through an SMTP server, which you may define here (host:port). Galaxy will automatically try STARTTLS but will continue upon failure.

Default

None

Type

str

smtp_username

Description

If your SMTP server requires a username and password, you can provide them here (password in cleartext here, but if your server supports STARTTLS it will be sent over the network encrypted).

Default

None

Type

str

smtp_password

Description

If your SMTP server requires a username and password, you can provide them here (password in cleartext here, but if your server supports STARTTLS it will be sent over the network encrypted).

Default

None

Type

str

smtp_ssl

Description

If your SMTP server requires SSL from the beginning of the connection

Default

false

Type

bool

mailing_join_addr

Description

On the user registration form, users may choose to join a mailing list. This is the address used to subscribe to the list. Uncomment and leave empty if you want to remove this option from the user registration form. Example value ‘galaxy-announce-join@lists.galaxyproject.org’

Default

None

Type

str

mailing_join_subject

Description

The subject of the email sent to the mailing list join address. See the mailing_join_addr option for more information.

Default

Join Mailing List

Type

str

mailing_join_body

Description

The body of the email sent to the mailing list join address. See the mailing_join_addr option for more information.

Default

Join Mailing List

Type

str

error_email_to

Description

Datasets in an error state include a link to report the error. Those reports will be sent to this address. Error reports are disabled if no address is set. Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter.

Default

None

Type

str

email_from

Description

Email address to use in the ‘From’ field when sending emails for account activations, workflow step notifications, password resets, and tool error reports. We recommend using a string in the following format: Galaxy Project <galaxy-no-reply@example.com>. If not configured, ‘<galaxy-no-reply@HOSTNAME>’ will be used.

Default

None

Type

str

custom_activation_email_message

Description

This text will be inserted at the end of the activation email’s message, before the ‘Your Galaxy Team’ signature.

Default

None

Type

str

instance_resource_url

Description

URL of the support resource for the galaxy instance. Used in activation emails. Example value ‘https://galaxyproject.org/’

Default

None

Type

str

email_domain_blocklist_file

Description

E-mail domains blocklist is used for filtering out users that are using disposable email addresses at registration. If their address’s base domain matches any domain on the list, they are refused registration. Address subdomains are ignored (both ‘name@spam.com’ and ‘name@foo.spam.com’ will match ‘spam.com’). Example value ‘email_blocklist.conf’ The value of this option will be resolved with respect to <config_dir>.

Default

None

Type

str

email_domain_allowlist_file

Description

E-mail domains allowlist is used to specify allowed email address domains. If the list is non-empty and a user attempts registration using an email address belonging to a domain that is not on the list, registration will be denied. Unlike <email_domain_allowlist_file> which matches the address’s base domain, here email addresses are matched against the full domain (base + subdomain). This is a more restrictive option than <email_domain_blocklist_file>, and therefore, in case <email_domain_allowlist_file> is set and is not empty, <email_domain_blocklist_file> will be ignored. Example value ‘email_allowlist.conf’ The value of this option will be resolved with respect to <config_dir>.

Default

None

Type

str

registration_warning_message

Description

Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. If no message specified the warning box will not be shown.

Default

Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.

Type

str

user_activation_on

Description

User account activation feature global flag. If set to false, the rest of the Account activation configuration is ignored and user activation is disabled (i.e. accounts are active since registration). The activation is also not working in case the SMTP server is not defined.

Default

false

Type

bool

activation_grace_period

Description

Activation grace period (in hours). Activation is not forced (login is not disabled) until grace period has passed. Users under grace period can’t run jobs. Enter 0 to disable grace period.

Default

3

Type

int

inactivity_box_content

Description

Shown in warning box to users that were not activated yet. In use only if activation_grace_period is set.

Default

Your account has not been activated yet.  Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.

Type

str

password_expiration_period

Description

Password expiration period (in days). Users are required to change their password every x days. Users will be redirected to the change password screen when they log in after their password expires. Enter 0 to disable password expiration.

Default

0

Type

int

enable_account_interface

Description

Allow users to manage their account data, change passwords or delete their accounts.

Default

true

Type

bool

session_duration

Description

Galaxy Session Timeout This provides a timeout (in minutes) after which a user will have to log back in. A duration of 0 disables this feature.

Default

0

Type

int

ga_code

Description

You can enter tracking code here to track visitor’s behavior through your Google Analytics account. Example: UA-XXXXXXXX-Y

Default

None

Type

str

plausible_server

Description

Please enter the URL for the Plausible server (including https) so this can be used for tracking with Plausible (https://plausible.io/).

Default

None

Type

str

plausible_domain

Description

Please enter the URL for the Galaxy server so this can be used for tracking with Plausible (https://plausible.io/).

Default

None

Type

str

matomo_server

Description

Please enter the URL for the Matomo server (including https) so this can be used for tracking with Matomo (https://matomo.org/).

Default

None

Type

str

matomo_site_id

Description

Please enter the site ID for the Matomo server so this can be used for tracking with Matomo (https://matomo.org/).

Default

None

Type

str

display_servers

Description

Galaxy can display data at various external browsers. These options specify which browsers should be available. URLs and builds available at these browsers are defined in the specified files. If use_remote_user is set to true, display application servers will be denied access to Galaxy and so displaying datasets in these sites will fail. display_servers contains a list of hostnames which should be allowed to bypass security to display datasets. Please be aware that there are security implications if this is allowed. More details (including required changes to the proxy server config) are available in the Apache proxy documentation on the Galaxy Community Hub. The list of servers in this sample config are for the UCSC Main, Test and Archaea browsers, but the default if left commented is to not allow any display sites to bypass security (you must uncomment the line below to allow them).

Default

hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu

Type

str

enable_old_display_applications

Description

Set this to false to disable the old-style display applications that are hardcoded into datatype classes. This may be desirable due to using the new-style, XML-defined, display applications that have been defined for many of the datatypes that have the old-style. There is also a potential security concern with the old-style applications, where a malicious party could provide a link that appears to reference the Galaxy server, but contains a redirect to a third-party server, tricking a Galaxy user to access said site.

Default

true

Type

bool

aws_estimate

Description

This flag enables an AWS cost estimate for every job based on their runtime matrices. CPU, RAM and runtime usage is mapped against AWS pricing table. Please note, that those numbers are only estimates.

Default

false

Type

bool

interactivetools_enable

Description

Enable InteractiveTools.

Default

false

Type

bool

interactivetools_proxy_host

Description

Proxy host - assumed to just be hosted on the same hostname and port as Galaxy by default.

Default

None

Type

str

interactivetools_base_path

Description

Base path for interactive tools running at a subpath without a subdomain. Defaults to “/”.

Default

/

Type

str

interactivetools_map

Description

Map for interactivetool proxy. The value of this option will be resolved with respect to <data_dir>.

Default

interactivetools_map.sqlite

Type

str

interactivetools_prefix

Description

Prefix to use in the formation of the subdomain or path for interactive tools

Default

interactivetool

Type

str

interactivetools_shorten_url

Description

Shorten the uuid portion of the subdomain or path for interactive tools. Especially useful for avoiding the need for wildcard certificates by keeping subdomain under 63 chars

Default

false

Type

bool

retry_interactivetool_metadata_internally

Description

Galaxy Interactive Tools (GxITs) can be stopped from within the Galaxy interface, killing the GxIT job without completing its metadata setting post-job steps. In such a case it may be desirable to set metadata on job outputs internally (in the Galaxy job handler process). The default is is the value of retry_metadata_internally, which defaults to true.

Default

true

Type

bool

visualizations_visible

Description

Show visualization tab and list in masthead.

Default

true

Type

bool

message_box_visible

Description

Show a message box under the masthead.

Default

false

Type

bool

message_box_content

Description

Show a message box under the masthead.

Default

None

Type

str

message_box_class

Description

Class of the message box under the masthead. Possible values are: ‘info’ (the default), ‘warning’, ‘error’, ‘done’.

Default

info

Type

str

brand

Description

Append “{brand}” text to the masthead.

Default

None

Type

str

display_galaxy_brand

Description

Display the “Galaxy” text in the masthead.

Default

true

Type

bool

pretty_datetime_format

Description

Format string used when showing date and time information. The string may contain: - the directives used by Python time.strftime() function (see https://docs.python.org/library/time.html#time.strftime), - $locale (complete format string for the server locale), - $iso8601 (complete format string as specified by ISO 8601 international standard).

Default

$locale (UTC)

Type

str

trs_servers_config_file

Description

Allow import of workflows from the TRS servers configured in the specified YAML or JSON file. The file should be a list with ‘id’, ‘label’, and ‘api_url’ for each entry. Optionally, ‘link_url’ and ‘doc’ may be be specified as well for each entry. If this is null (the default), a simple configuration containing just Dockstore will be used. The value of this option will be resolved with respect to <config_dir>.

Default

trs_servers_conf.yml

Type

str

user_preferences_extra_conf_path

Description

Location of the configuration file containing extra user preferences. The value of this option will be resolved with respect to <config_dir>.

Default

user_preferences_extra_conf.yml

Type

str

default_locale

Description

Default localization for Galaxy UI. Allowed values are listed at the end of client/src/nls/locale.js. With the default value (auto), the locale will be automatically adjusted to the user’s navigator language. Users can override this settings in their user preferences if the localization settings are enabled in user_preferences_extra_conf.yml

Default

auto

Type

str

galaxy_infrastructure_url

Description

URL (with schema http/https) of the Galaxy instance as accessible within your local network - if specified used as a default by pulsar file staging and Jupyter Docker container for communicating back with Galaxy via the API. If you are attempting to set up GIEs on Mac OS X with Docker Desktop for Mac and your Galaxy instance runs on port 8080 this should be ‘http://host.docker.internal:8080’. For more details see https://docs.docker.com/docker-for-mac/networking/

Default

http://localhost:8080

Type

str

galaxy_infrastructure_web_port

Description

If the above URL cannot be determined ahead of time in dynamic environments but the port which should be used to access Galaxy can be - this should be set to prevent Galaxy from having to guess. For example if Galaxy is sitting behind a proxy with REMOTE_USER enabled - infrastructure shouldn’t talk to Python processes directly and this should be set to 80 or 443, etc… If unset this file will be read for a server block defining a port corresponding to the webapp.

Default

8080

Type

int

welcome_url

Description

The URL of the page to display in Galaxy’s middle pane when loaded. This can be an absolute or relative URL.

Default

/static/welcome.html

Type

str

logo_url

Description

The URL linked by the “Galaxy/brand” text.

Default

/

Type

str

logo_src

Description

The brand image source.

Default

/static/favicon.png

Type

str

logo_src_secondary

Description

The custom brand image source.

Default

None

Type

str

helpsite_url

Description

The URL linked by the “Galaxy Help” link in the “Help” menu.

Default

None

Type

str

wiki_url

Description

The URL linked by the “Wiki” link in the “Help” menu.

Default

https://galaxyproject.org/

Type

str

quota_url

Description

The URL linked for quota information in the UI.

Default

https://galaxyproject.org/support/account-quotas/

Type

str

support_url

Description

The URL linked by the “Support” link in the “Help” menu.

Default

https://galaxyproject.org/support/

Type

str

citation_url

Description

The URL linked by the “How to Cite Galaxy” link in the “Help” menu.

Default

https://galaxyproject.org/citing-galaxy

Type

str

release_doc_base_url

Description

The URL linked by the “Galaxy Version” link in the “Help” menu.

Default

https://docs.galaxyproject.org/en/release_

Type

str

search_url

Description

The URL linked by the “Search” link in the “Help” menu.

Default

https://galaxyproject.org/search/

Type

str

mailing_lists_url

Description

The URL linked by the “Mailing Lists” link in the “Help” menu.

Default

https://galaxyproject.org/mailing-lists/

Type

str

screencasts_url

Description

The URL linked by the “Videos” link in the “Help” menu.

Default

https://vimeo.com/galaxyproject

Type

str

terms_url

Description

The URL linked by the “Terms and Conditions” link in the “Help” menu, as well as on the user registration and login forms and in the activation emails.

Default

None

Type

str

qa_url

Description

The URL linked by the “Galaxy Q&A” link in the “Help” menu The Galaxy Q&A site is under development; when the site is done, this URL will be set and uncommented.

Default

None

Type

str

static_enabled

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

true

Type

bool

static_cache_time

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

360

Type

int

static_dir

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

static/

Type

str

static_images_dir

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

static/images

Type

str

static_favicon_dir

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

static/favicon.ico

Type

str

static_scripts_dir

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

static/scripts/

Type

str

static_style_dir

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

static/style

Type

str

static_robots_txt

Description

Serve static content, which must be enabled if you’re not serving it via a proxy server. These options should be self explanatory and so are not documented individually. You can use these paths (or ones in the proxy server) to point to your own styles.

Default

static/robots.txt

Type

str

display_chunk_size

Description

Incremental Display Options

Default

65536

Type

int

apache_xsendfile

Description

For help on configuring the Advanced proxy features, see: https://docs.galaxyproject.org/en/master/admin/production.html Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set this to true to inform Galaxy that mod_xsendfile is enabled upstream.

Default

false

Type

bool

nginx_x_accel_redirect_base

Description

The same download handling can be done by nginx using X-Accel-Redirect. This should be set to the path defined in the nginx config as an internal redirect with access to Galaxy’s data files (see documentation linked above).

Default

None

Type

str

upstream_gzip

Description

If using compression in the upstream proxy server, use this option to disable gzipping of dataset collection and library archives, since the upstream server will do it faster on the fly. To enable compression add application/zip to the proxy’s compressable mimetypes.

Default

false

Type

bool

upstream_mod_zip

Description

If using the mod-zip module in nginx, use this option to assemble zip archives in nginx. This is preferable over the upstream_gzip option as Galaxy does not need to serve the archive. Requires setting up internal nginx locations to all paths that can be archived. See https://docs.galaxyproject.org/en/master/admin/nginx.html#creating-archives-with-mod-zip for details.

Default

false

Type

bool

x_frame_options

Description

The following default adds a header to web request responses that will cause modern web browsers to not allow Galaxy to be embedded in the frames of web applications hosted at other hosts - this can help prevent a class of attack called clickjacking (https://www.owasp.org/index.php/Clickjacking). If you configure a proxy in front of Galaxy - please ensure this header remains intact to protect your users. Uncomment and leave empty to not set the X-Frame-Options header.

Default

SAMEORIGIN

Type

str

nginx_upload_store

Description

nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. Configuration for this is complex and explained in detail in the documentation linked above. The upload store is a temporary directory in which files uploaded by the upload module will be placed.

Default

None

Type

str

nginx_upload_path

Description

This value overrides the action set on the file upload form, e.g. the web path where the nginx_upload_module has been configured to intercept upload requests.

Default

None

Type

str

nginx_upload_job_files_store

Description

Galaxy can also use nginx_upload_module to receive files staged out upon job completion by remote job runners (i.e. Pulsar) that initiate staging operations on the remote end. See the Galaxy nginx documentation for the corresponding nginx configuration.

Default

None

Type

str

nginx_upload_job_files_path

Description

Galaxy can also use nginx_upload_module to receive files staged out upon job completion by remote job runners (i.e. Pulsar) that initiate staging operations on the remote end. See the Galaxy nginx documentation for the corresponding nginx configuration.

Default

None

Type

str

chunk_upload_size

Description

Galaxy can upload user files in chunks without using nginx. Enable the chunk uploader by specifying a chunk size larger than 0. The chunk size is specified in bytes (default: 100MB).

Default

104857600

Type

int

dynamic_proxy_manage

Description

Have Galaxy manage dynamic proxy component for routing requests to other services based on Galaxy’s session cookie. It will attempt to do this by default though you do need to install node+npm and do an npm install from lib/galaxy/web/proxy/js. It is generally more robust to configure this externally, managing it in the same way Galaxy itself is managed. If true, Galaxy will only launch the proxy if it is actually going to be used (e.g. for Jupyter).

Default

true

Type

bool

dynamic_proxy

Description

As of 16.04 Galaxy supports multiple proxy types. The original NodeJS implementation, alongside a new Golang single-binary-no-dependencies version. Valid values are (node, golang)

Default

node

Type

str

dynamic_proxy_session_map

Description

The NodeJS dynamic proxy can use an SQLite database or a JSON file for IPC, set that here. The value of this option will be resolved with respect to <data_dir>.

Default

session_map.sqlite

Type

str

dynamic_proxy_bind_port

Description

Set the port and IP for the dynamic proxy to bind to, this must match the external configuration if dynamic_proxy_manage is set to false.

Default

8800

Type

int

dynamic_proxy_bind_ip

Description

Set the port and IP for the dynamic proxy to bind to, this must match the external configuration if dynamic_proxy_manage is set to false.

Default

0.0.0.0

Type

str

dynamic_proxy_debug

Description

Enable verbose debugging of Galaxy-managed dynamic proxy.

Default

false

Type

bool

dynamic_proxy_external_proxy

Description

The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL).

Default

false

Type

bool

dynamic_proxy_prefix

Description

Additionally, when the dynamic proxy is proxied by an upstream server, you’ll want to specify a prefixed URL so both Galaxy and the proxy reside under the same path that your cookies are under. This will result in a url like https://FQDN/galaxy-prefix/gie_proxy for proxying

Default

gie_proxy

Type

str

dynamic_proxy_golang_noaccess

Description

This attribute governs the minimum length of time between consecutive HTTP/WS requests through the proxy, before the proxy considers a container as being inactive and kills it.

Default

60

Type

int

dynamic_proxy_golang_clean_interval

Description

In order to kill containers, the golang proxy has to check at some interval for possibly dead containers. This is exposed as a configurable parameter, but the default value is probably fine.

Default

10

Type

int

dynamic_proxy_golang_docker_address

Description

The golang proxy needs to know how to talk to your docker daemon. Currently TLS is not supported, that will come in an update.

Default

unix:///var/run/docker.sock

Type

str

dynamic_proxy_golang_api_key

Description

The golang proxy uses a RESTful HTTP API for communication with Galaxy instead of a JSON or SQLite file for IPC. If you do not specify this, it will be set randomly for you. You should set this if you are managing the proxy manually.

Default

None

Type

str

auto_configure_logging

Description

If true, Galaxy will attempt to configure a simple root logger if a “loggers” section does not appear in this configuration file.

Default

true

Type

bool

log_level

Description

Verbosity of console log messages. Acceptable values can be found here: https://docs.python.org/library/logging.html#logging-levels A custom debug level of “TRACE” is available for even more verbosity.

Default

DEBUG

Type

str

logging

Description

Controls where and how the server logs messages. If unset, the default is to log all messages to standard output at the level defined by the log_level configuration option. Configuration is described in the documentation at: https://docs.galaxyproject.org/en/master/admin/config_logging.html

Default

None

Type

map

database_engine_option_echo

Description

Print database operations to the server log (warning, quite verbose!).

Default

false

Type

bool

database_engine_option_echo_pool

Description

Print database pool operations to the server log (warning, quite verbose!).

Default

false

Type

bool

log_events

Description

Turn on logging of application events and some user events to the database.

Default

false

Type

bool

log_actions

Description

Turn on logging of user actions to the database. Actions currently logged are grid views, tool searches, and use of “recently” used tools menu. The log_events and log_actions functionality will eventually be merged.

Default

false

Type

bool

fluent_log

Description

Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log.

Default

false

Type

bool

fluent_host

Description

Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log.

Default

localhost

Type

str

fluent_port

Description

Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log.

Default

24224

Type

int

sanitize_all_html

Description

Sanitize all HTML tool output. By default, all tool output served as ‘text/html’ will be sanitized thoroughly. This can be disabled if you have special tools that require unaltered output. WARNING: disabling this does make the Galaxy instance susceptible to XSS attacks initiated by your users.

Default

true

Type

bool

sanitize_allowlist_file

Description

Datasets created by tools listed in this file are trusted and will not have their HTML sanitized on display. This can be manually edited or manipulated through the Admin control panel – see “Manage Allowlist” The value of this option will be resolved with respect to <mutable_config_dir>.

Default

sanitize_allowlist.txt

Type

str

serve_xss_vulnerable_mimetypes

Description

By default Galaxy will serve non-HTML tool output that may potentially contain browser executable JavaScript content as plain text. This will for instance cause SVG datasets to not render properly and so may be disabled by setting this option to true.

Default

false

Type

bool

allowed_origin_hostnames

Description

Return a Access-Control-Allow-Origin response header that matches the Origin header of the request if that Origin hostname matches one of the strings or regular expressions listed here. This is a comma-separated list of hostname strings or regular expressions beginning and ending with /. E.g. mysite.com,google.com,usegalaxy.org,/^[w.]*example.com/ See: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS

Default

None

Type

str

trust_jupyter_notebook_conversion

Description

Set to true to use Jupyter nbconvert to build HTML from Jupyter notebooks in Galaxy histories. This process may allow users to execute arbitrary code or serve arbitrary HTML. If enabled, Jupyter must be available and on Galaxy’s PATH, to do this run pip install jinja2 pygments jupyter in Galaxy’s virtualenv.

Default

false

Type

bool

debug

Description

Debug enables access to various config options useful for development and debugging: use_lint, use_profile, and use_printdebug. It also causes the files used by PBS/SGE (submission script, output, and error) to remain on disk after the job is complete. In addition, this will set uWSGI’s honour-stdin option to true; thus, preventing uWSGI from remapping stdin to /dev/null and enabling debugging with tools like pdb. To keep uWSGI’s default setting, set honor-stdin to false in the uwsgi section of this configuration file.

Default

false

Type

bool

use_lint

Description

Check for WSGI compliance.

Default

false

Type

bool

use_profile

Description

Run the Python profiler on each request.

Default

false

Type

bool

use_printdebug

Description

Intercept print statements and show them on the returned page.

Default

true

Type

bool

monitor_thread_join_timeout

Description

When stopping Galaxy cleanly, how much time to give various monitoring/polling threads to finish before giving up on joining them. Set to 0 to disable this and terminate without waiting. Among others, these threads include the job handler workers, which are responsible for preparing/submitting and collecting/finishing jobs, and which can cause job errors if not shut down cleanly. If using supervisord, consider also increasing the value of stopwaitsecs. If using job handler mules, consider also setting the mule-reload-mercy uWSGI option. See the Galaxy Admin Documentation for more.

Default

30

Type

int

use_heartbeat

Description

Write thread status periodically to ‘heartbeat.log’, (careful, uses disk space rapidly!). Useful to determine why your processes may be consuming a lot of CPU.

Default

false

Type

bool

heartbeat_interval

Description

Control the period (in seconds) between dumps. Use -1 to disable. Regardless of this setting, if use_heartbeat is enabled, you can send a Galaxy process (unless running with uWSGI) SIGUSR1 (kill -USR1) to force a dump.

Default

20

Type

int

heartbeat_log

Description

Heartbeat log filename. Can accept the template variables {server_name} and {pid}

Default

heartbeat_{server_name}.log

Type

str

sentry_dsn

Description

Log to Sentry Sentry is an open source logging and error aggregation platform. Setting sentry_dsn will enable the Sentry middleware and errors will be sent to the indicated sentry instance. This connection string is available in your sentry instance under <project_name> -> Settings -> API Keys.

Default

None

Type

str

sentry_event_level

Description

Determines the minimum log level that will be sent as an event to Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.

Default

ERROR

Type

str

statsd_host

Description

Log to statsd Statsd is an external statistics aggregator (https://github.com/etsy/statsd) Enabling the following options will cause galaxy to log request timing and other statistics to the configured statsd instance. The statsd_prefix is useful if you are running multiple Galaxy instances and want to segment statistics between them within the same aggregator.

Default

None

Type

str

statsd_port

Description

Log to statsd Statsd is an external statistics aggregator (https://github.com/etsy/statsd) Enabling the following options will cause galaxy to log request timing and other statistics to the configured statsd instance. The statsd_prefix is useful if you are running multiple Galaxy instances and want to segment statistics between them within the same aggregator.

Default

8125

Type

int

statsd_prefix

Description

Log to statsd Statsd is an external statistics aggregator (https://github.com/etsy/statsd) Enabling the following options will cause galaxy to log request timing and other statistics to the configured statsd instance. The statsd_prefix is useful if you are running multiple Galaxy instances and want to segment statistics between them within the same aggregator.

Default

galaxy

Type

str

statsd_influxdb

Description

If you are using telegraf to collect these metrics and then sending them to InfluxDB, Galaxy can provide more nicely tagged metrics. Instead of sending prefix + dot-separated-path, Galaxy will send prefix with a tag path set to the page url

Default

false

Type

bool

statsd_mock_calls

Description

Mock out statsd client calls - only used by testing infrastructure really. Do not set this in production environments.

Default

false

Type

bool

library_import_dir

Description

Add an option to the library upload form which allows administrators to upload a directory of files.

Default

None

Type

str

user_library_import_dir

Description

Add an option to the library upload form which allows authorized non-administrators to upload a directory of files. The configured directory must contain sub-directories named the same as the non-admin user’s Galaxy login ( email ). The non-admin user is restricted to uploading files or sub-directories of files contained in their directory.

Default

None

Type

str

user_library_import_dir_auto_creation

Description

If user_library_import_dir is set, this option will auto create a library import directory for every user (based on their email) upon login.

Default

false

Type

bool

user_library_import_symlink_allowlist

Description

For security reasons, users may not import any files that actually lie outside of their user_library_import_dir (e.g. using symbolic links). A list of directories can be allowed by setting the following option (the list is comma-separated). Be aware that any user with library import permissions can import from anywhere in these directories (assuming they are able to create symlinks to them).

Default

None

Type

str

user_library_import_check_permissions

Description

In conjunction or alternatively, Galaxy can restrict user library imports to those files that the user can read (by checking basic unix permissions). For this to work, the username has to match the username on the filesystem.

Default

false

Type

bool

allow_path_paste

Description

Allow admins to paste filesystem paths during upload. For libraries this adds an option to the admin library upload tool allowing admins to paste filesystem paths to files and directories in a box, and these paths will be added to a library. For history uploads, this allows pasting in paths as URIs. (i.e. prefixed with file://). Set to true to enable. Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to.

Default

false

Type

bool

disable_library_comptypes

Description

Users may choose to download multiple files from a library in an archive. By default, Galaxy allows users to select from a few different archive formats if testing shows that Galaxy is able to create files using these formats. Specific formats can be disabled with this option, separate more than one format with commas. Available formats are currently ‘zip’, ‘gz’, and ‘bz2’.

Default

None

Type

str

tool_name_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

9.0

Type

float

tool_id_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

9.0

Type

float

tool_section_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

3.0

Type

float

tool_description_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

2.0

Type

float

tool_label_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

1.0

Type

float

tool_stub_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

5.0

Type

float

tool_help_boost

Description

Boosts are used to customize this instance’s toolbox search. The higher the boost, the more importance the scoring algorithm gives to the given field. Section refers to the tool group in the tool panel. Rest of the fields are tool’s attributes.

Default

0.5

Type

float

tool_search_limit

Description

Limits the number of results in toolbox search. Can be used to tweak how many results will appear.

Default

20

Type

int

tool_enable_ngram_search

Description

Enable/ disable Ngram-search for tools. It makes tool search results tolerant for spelling mistakes in the query by dividing the query into multiple ngrams and search for each ngram

Default

true

Type

bool

tool_ngram_minsize

Description

Set minimum size of ngrams

Default

3

Type

int

tool_ngram_maxsize

Description

Set maximum size of ngrams

Default

4

Type

int

tool_test_data_directories

Description

Set tool test data directory. The test framework sets this value to ‘test-data,https://github.com/galaxyproject/galaxy-test-data.git’ which will cause Galaxy to clone down extra test data on the fly for certain tools distributed with Galaxy but this is likely not appropriate for production systems. Instead one can simply clone that repository directly and specify a path here instead of a Git HTTP repository.

Default

test-data

Type

str

id_secret

Description

Galaxy encodes various internal values when these values will be output in some format (for example, in a URL or cookie). You should set a key to be used by the algorithm that encodes and decodes these values. It can be any string with a length between 5 and 56 bytes. One simple way to generate a value for this is with the shell command: python -c ‘from __future__ import print_function; import time; print(time.time())’ | md5sum | cut -f 1 -d ‘ ‘

Default

USING THE DEFAULT IS NOT SECURE!

Type

str

use_remote_user

Description

User authentication can be delegated to an upstream proxy server (usually Apache). The upstream proxy should set a REMOTE_USER header in the request. Enabling remote user disables regular logins. For more information, see: https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html

Default

false

Type

bool

remote_user_maildomain

Description

If use_remote_user is enabled and your external authentication method just returns bare usernames, set a default mail domain to be appended to usernames, to become your Galaxy usernames (email addresses).

Default

None

Type

str

remote_user_header

Description

If use_remote_user is enabled, the header that the upstream proxy provides the remote username in defaults to HTTP_REMOTE_USER (the HTTP_ is prepended by WSGI). This option allows you to change the header. Note, you still need to prepend HTTP_ to the header in this option, but your proxy server should not include HTTP_ at the beginning of the header name.

Default

HTTP_REMOTE_USER

Type

str

remote_user_secret

Description

If use_remote_user is enabled, anyone who can log in to the Galaxy host may impersonate any other user by simply sending the appropriate header. Thus a secret shared between the upstream proxy server, and Galaxy is required. If anyone other than the Galaxy user is using the server, then apache/nginx should pass a value in the header ‘GX_SECRET’ that is identical to the one below.

Default

USING THE DEFAULT IS NOT SECURE!

Type

str

remote_user_logout_href

Description

If use_remote_user is enabled, you can set this to a URL that will log your users out.

Default

None

Type

str

normalize_remote_user_email

Description

If your proxy and/or authentication source does not normalize e-mail addresses or user names being passed to Galaxy - set this option to true to force these to lower case.

Default

false

Type

bool

single_user

Description

If an e-mail address is specified here, it will hijack remote user mechanics (use_remote_user) and have the webapp inject a single fixed user. This has the effect of turning Galaxy into a single user application with no login or external proxy required. Such applications should not be exposed to the world.

Default

None

Type

str

admin_users

Description

Administrative users - set this to a comma-separated list of valid Galaxy users (email addresses). These users will have access to the Admin section of the server, and will have access to create users, groups, roles, libraries, and more. For more information, see: https://galaxyproject.org/admin/

Default

None

Type

str

require_login

Description

Force everyone to log in (disable anonymous access).

Default

false

Type

bool

show_welcome_with_login

Description

Show the site’s welcome page (see welcome_url) alongside the login page (even if require_login is true).

Default

false

Type

bool

allow_user_creation

Description

Allow unregistered users to create new accounts (otherwise, they will have to be created by an admin).

Default

true

Type

bool

allow_user_deletion

Description

Allow administrators to delete accounts.

Default

false

Type

bool

allow_user_impersonation

Description

Allow administrators to log in as other users (useful for debugging).

Default

false

Type

bool

show_user_prepopulate_form

Description

When using LDAP for authentication, allow administrators to pre-populate users using an additional form on ‘Create new user’

Default

false

Type

bool

upload_from_form_button

Description

If ‘always-on’, add another button to tool form data inputs that allow uploading data from the tool form in fewer clicks (at the expense of making the form more complicated). This applies to workflows as well. Avoiding making this a boolean because we may add options such as ‘in-single-form-view’ or ‘in-simplified-workflow-views’. https://github.com/galaxyproject/galaxy/pull/9809/files#r461889109

Default

always-off

Type

str

allow_user_dataset_purge

Description

Allow users to remove their datasets from disk immediately (otherwise, datasets will be removed after a time period specified by an administrator in the cleanup scripts run via cron)

Default

true

Type

bool

new_user_dataset_access_role_default_private

Description

By default, users’ data will be public, but setting this to true will cause it to be private. Does not affect existing users and data, only ones created after this option is set. Users may still change their default back to public.

Default

false

Type

bool

expose_user_name

Description

Expose user list. Setting this to true will expose the user list to authenticated users. This makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and have the correct user show up. This makes less sense on large public Galaxy instances where that data shouldn’t be exposed. For semi-public Galaxies, it may make sense to expose just the username and not email, or vice versa. If enable_beta_gdpr is set to true, then this option will be overridden and set to false.

Default

false

Type

bool

expose_user_email

Description

Expose user list. Setting this to true will expose the user list to authenticated users. This makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and have the correct user show up. This makes less sense on large public Galaxy instances where that data shouldn’t be exposed. For semi-public Galaxies, it may make sense to expose just the username and not email, or vice versa. If enable_beta_gdpr is set to true, then this option will be overridden and set to false.

Default

false

Type

bool

fetch_url_allowlist

Description

List of allowed local network addresses for “Upload from URL” dialog. By default, Galaxy will deny access to the local network address space, to prevent users making requests to services which the administrator did not intend to expose. Previously, you could request any network service that Galaxy might have had access to, even if the user could not normally access it. It should be a comma-separated list of IP addresses or IP address/mask, e.g. 10.10.10.10,10.0.1.0/24,fd00::/8

Default

None

Type

str

enable_beta_gdpr

Description

Enables GDPR Compliance mode. This makes several changes to the way Galaxy logs and exposes data externally such as removing emails and usernames from logs and bug reports. It also causes the delete user admin action to permanently redact their username and password, but not to delete data associated with the account as this is not currently easily implementable. You are responsible for removing personal data from backups. This forces expose_user_email and expose_user_name to be false, and forces user_deletion to be true to support the right to erasure. Please read the GDPR section under the special topics area of the admin documentation.

Default

false

Type

bool

enable_beta_containers_interface

Description

Enable the new container interface for Interactive Environments

Default

false

Type

bool

enable_beta_workflow_modules

Description

Enable beta workflow modules that should not yet be considered part of Galaxy’s stable API. (The module state definitions may change and workflows built using these modules may not function in the future.)

Default

false

Type

bool

edam_panel_views

Description

Comma-separated list of the EDAM panel views to load - choose from merged, operations, topics. Set to empty string to disable EDAM all together. Set default_panel_view to ‘ontology:edam_topics’ to override default tool panel to use an EDAM view.

Default

operations,topics

Type

str

edam_toolbox_ontology_path

Description

Sets the path to EDAM ontology file - if the path doesn’t exist PyPI package data will be loaded. The value of this option will be resolved with respect to <data_dir>.

Default

EDAM.tsv

Type

str

panel_views_dir

Description

Directory to check out for toolbox tool panel views. The path is relative to the Galaxy root dir. To use an absolute path begin the path with ‘/’. This is a comma-separated list.

Default

config/plugins/activities

Type

str

panel_views

Description

Definitions of static toolbox panel views embedded directly in the config instead of reading YAML from directory with panel_views_dir.

Default

None

Type

seq

default_panel_view

Description

Default tool panel view for the current Galaxy configuration. This should refer to an id of a panel view defined using the panel_views or panel_views_dir configuration options or an EDAM panel view. The default panel view is simply called default and refers to the tool panel state defined by the integrated tool panel.

Default

default

Type

str

default_workflow_export_format

Description

Default format for the export of workflows. Possible values are ‘ga’ or ‘format2’.

Default

ga

Type

str

force_beta_workflow_scheduled_min_steps

Description

Following options only apply to workflows scheduled using the legacy workflow run API (running workflows via a POST to /api/workflows). Force usage of Galaxy’s beta workflow scheduler under certain circumstances - this workflow scheduling forces Galaxy to schedule workflows in the background so initial submission of the workflows is significantly sped up. This does however force the user to refresh their history manually to see newly scheduled steps (for “normal” workflows - steps are still scheduled far in advance of them being queued and scheduling here doesn’t refer to actual cluster job scheduling). Workflows containing more than the specified number of steps will always use the Galaxy’s beta workflow scheduling.

Default

250

Type

int

force_beta_workflow_scheduled_for_collections

Description

Following options only apply to workflows scheduled using the legacy workflow run API (running workflows via a POST to /api/workflows). Force usage of Galaxy’s beta workflow scheduler under certain circumstances - this workflow scheduling forces Galaxy to schedule workflows in the background so initial submission of the workflows is significantly sped up. This does however force the user to refresh their history manually to see newly scheduled steps (for “normal” workflows - steps are still scheduled far in advance of them being queued and scheduling here doesn’t refer to actual cluster job scheduling). Workflows containing more than the specified number of steps will always use the Galaxy’s beta workflow scheduling. Switch to using Galaxy’s beta workflow scheduling for all workflows involving collections.

Default

false

Type

bool

parallelize_workflow_scheduling_within_histories

Description

If multiple job handlers are enabled, allow Galaxy to schedule workflow invocations in multiple handlers simultaneously. This is discouraged because it results in a less predictable order of workflow datasets within in histories.

Default

false

Type

bool

maximum_workflow_invocation_duration

Description

This is the maximum amount of time a workflow invocation may stay in an active scheduling state in seconds. Set to -1 to disable this maximum and allow any workflow invocation to schedule indefinitely. The default corresponds to 1 month.

Default

2678400

Type

int

maximum_workflow_jobs_per_scheduling_iteration

Description

Specify a maximum number of jobs that any given workflow scheduling iteration can create. Set this to a positive integer to prevent large collection jobs in a workflow from preventing other jobs from executing. This may also mitigate memory issues associated with scheduling workflows at the expense of increased total DB traffic because model objects are expunged from the SQL alchemy session between workflow invocation scheduling iterations. Set to -1 to disable any such maximum.

Default

1000

Type

int

flush_per_n_datasets

Description

Maximum number of datasets to create before flushing created datasets to database. This affects tools that create many output datasets. Higher values will lead to fewer database flushes and faster execution, but require more memory. Set to -1 to disable creating datasets in batches.

Default

1000

Type

int

history_local_serial_workflow_scheduling

Description

Force serial scheduling of workflows within the context of a particular history

Default

false

Type

bool

enable_oidc

Description

Enables and disables OpenID Connect (OIDC) support.

Default

false

Type

bool

oidc_config_file

Description

Sets the path to OIDC configuration file. The value of this option will be resolved with respect to <config_dir>.

Default

oidc_config.xml

Type

str

oidc_backends_config_file

Description

Sets the path to OIDC backends configuration file. The value of this option will be resolved with respect to <config_dir>.

Default

oidc_backends_config.xml

Type

str

auth_config_file

Description

XML config file that allows the use of different authentication providers (e.g. LDAP) instead or in addition to local authentication (.sample is used if default does not exist). The value of this option will be resolved with respect to <config_dir>.

Default

auth_conf.xml

Type

str

api_allow_run_as

Description

Optional list of email addresses of API users who can make calls on behalf of other users.

Default

None

Type

str

master_api_key

Description

API key that allows performing some admin actions without actually having a real admin user in the database and config. Only set this if you need to bootstrap Galaxy, in particular to create a real admin user account via API. You should probably not set this on a production server.

Default

None

Type

str

enable_openid

Description

Enable access to post-authentication options via OpenID.

Default

false

Type

bool

openid_consumer_cache_path

Description

If OpenID is enabled, consumer cache directory to use. The value of this option will be resolved with respect to <cache_dir>.

Default

openid_consumer_cache

Type

str

enable_tool_tags

Description

Enable tool tags (associating tools with tags). This has its own option since its implementation has a few performance implications on startup for large servers.

Default

false

Type

bool

enable_unique_workflow_defaults

Description

Enable a feature when running workflows. When enabled, default datasets are selected for “Set at Runtime” inputs from the history such that the same input will not be selected twice, unless there are more inputs than compatible datasets in the history. When false, the most recently added compatible item in the history will be used for each “Set at Runtime” input, independent of others in the workflow.

Default

false

Type

bool

simplified_workflow_run_ui

Description

If set to ‘off’ by default, always use the traditional workflow form that renders all steps in the GUI and serializes the tool state of all steps during invocation. Set to ‘prefer’ to default to a simplified workflow UI that only renders the inputs if possible (the workflow must have no disconnected runtime inputs and not replacement parameters within tool steps). In the future ‘force’ may be added an option for Galaskio-style servers that should only render simplified workflows.

Default

prefer

Type

str

simplified_workflow_run_ui_target_history

Description

When the simplified workflow run form is rendered, should the invocation outputs be sent to the ‘current’ history or a ‘new’ history.

Default

current

Type

str

simplified_workflow_run_ui_job_cache

Description

When the simplified workflow run form is rendered, should the invocation use job caching. This isn’t a boolean so an option for ‘show-selection’ can be added later.

Default

off

Type

str

myexperiment_target_url

Description

The URL to the myExperiment instance being used (omit scheme but include port).

Default

www.myexperiment.org:80

Type

str

ftp_upload_site

Description

Enable Galaxy’s “Upload via FTP” interface. You’ll need to install and configure an FTP server (we’ve used ProFTPd since it can use Galaxy’s database for authentication) and set the following two options. This will be provided to users in the help text as ‘log in to the FTP server at ‘. Thus, it should be the hostname of your FTP server.

Default

None

Type

str

ftp_upload_dir

Description

This should point to a directory containing subdirectories matching users’ identifier (defaults to e-mail), where Galaxy will look for files.

Default

None

Type

str

ftp_upload_dir_identifier

Description

User attribute to use as subdirectory in calculating default ftp_upload_dir pattern. By default this will be email so a user’s FTP upload directory will be ${ftp_upload_dir}/${user.email}. Can set this to other attributes such as id or username though.

Default

email

Type

str

ftp_upload_dir_template

Description

Python string template used to determine an FTP upload directory for a particular user. Defaults to ‘${ftp_upload_dir}/${ftp_upload_dir_identifier}’.

Default

None

Type

str

ftp_upload_purge

Description

Set to false to prevent Galaxy from deleting uploaded FTP files as it imports them.

Default

true

Type

bool

enable_quotas

Description

Enable enforcement of quotas. Quotas can be set from the Admin interface.

Default

false

Type

bool

expose_dataset_path

Description

This option allows users to see the full path of datasets via the “View Details” option in the history. This option also exposes the command line to non-administrative users. Administrators can always see dataset paths.

Default

false

Type

bool

job_metrics_config_file

Description

XML config file that contains the job metric collection configuration. The value of this option will be resolved with respect to <config_dir>.

Default

job_metrics_conf.xml

Type

str

expose_potentially_sensitive_job_metrics

Description

This option allows users to see the job metrics (except for environment variables).

Default

false

Type

bool

enable_legacy_sample_tracking_api

Description

Enable the API for sample tracking

Default

false

Type

bool

enable_data_manager_user_view

Description

Allow non-admin users to view available Data Manager options.

Default

false

Type

bool

data_manager_config_file

Description

File where Data Managers are configured (.sample used if default does not exist). The value of this option will be resolved with respect to <config_dir>.

Default

data_manager_conf.xml

Type

str

shed_data_manager_config_file

Description

File where Tool Shed based Data Managers are configured. This file will be created automatically upon data manager installation. The value of this option will be resolved with respect to <managed_config_dir>.

Default

shed_data_manager_conf.xml

Type

str

galaxy_data_manager_data_path

Description

Directory to store Data Manager based tool-data. Defaults to the value of the <tool_data_path> option.

Default

None

Type

str

job_config_file

Description

To increase performance of job execution and the web interface, you can separate Galaxy into multiple processes. There are more than one way to do this, and they are explained in detail in the documentation: https://docs.galaxyproject.org/en/master/admin/scaling.html By default, Galaxy manages and executes jobs from within a single process and notifies itself of new jobs via in-memory queues. Jobs are run locally on the system on which Galaxy is started. Advanced job running capabilities can be configured through the job configuration file. The value of this option will be resolved with respect to <config_dir>.

Default

job_conf.xml

Type

str

job_config

Description

Description of job running configuration, can be embedded into Galaxy configuration or loaded from an additional file with the job_config_file option.

Default

None

Type

map

dependency_resolvers

Description

Rather than specifying a dependency_resolvers_config_file, the definition of the resolvers to enable can be embedded into Galaxy’s config with this option. This has no effect if a dependency_resolvers_config_file is used. The syntax, available resolvers, and documentation of their options is explained in detail in the documentation: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Default

None

Type

seq

dependency_resolution

Description

Alternative representation of various dependency resolution parameters. Takes the dictified version of a DependencyManager object - so this is ideal for automating the configuration of dependency resolution from one application that uses a DependencyManager to another.

Default

None

Type

map

default_job_resubmission_condition

Description

When jobs fail due to job runner problems, Galaxy can be configured to retry these or reroute the jobs to new destinations. Very fine control of this is available with resubmit declarations in job_conf.xml. For simple deployments of Galaxy though, the following attribute can define resubmission conditions for all job destinations. If any job destination defines even one resubmission condition explicitly in job_conf.xml - the condition described by this option will not apply to that destination. For instance, the condition: ‘attempt < 3 and unknown_error and (time_running < 300 or time_since_queued < 300)’ would retry up to two times jobs that didn’t fail due to detected memory or walltime limits but did fail quickly (either while queueing or running). The commented out default below results in no default job resubmission condition, failing jobs are just failed outright.

Default

None

Type

str

track_jobs_in_database

Description

This option is deprecated, use the mem-self handler assignment option in the job configuration instead.

Default

true

Type

bool

use_tasked_jobs

Description

This enables splitting of jobs into tasks, if specified by the particular tool config. This is a new feature and not recommended for production servers yet.

Default

false

Type

bool

local_task_queue_workers

Description

This enables splitting of jobs into tasks, if specified by the particular tool config. This is a new feature and not recommended for production servers yet.

Default

2

Type

int

job_handler_monitor_sleep

Description

Each Galaxy job handler process runs one thread responsible for discovering jobs and dispatching them to runners. This thread operates in a loop and sleeps for the given number of seconds at the end of each iteration. This can be decreased if extremely high job throughput is necessary, but doing so can increase CPU usage of handler processes. Float values are allowed.

Default

1.0

Type

float

job_runner_monitor_sleep

Description

Each Galaxy job handler process runs one thread per job runner plugin responsible for checking the state of queued and running jobs. This thread operates in a loop and sleeps for the given number of seconds at the end of each iteration. This can be decreased if extremely high job throughput is necessary, but doing so can increase CPU usage of handler processes. Float values are allowed.

Default

1.0

Type

float

metadata_strategy

Description

Determines how metadata will be set. Valid values are directory and extended. In extended mode jobs will decide if a tool run failed, the object stores configuration is serialized and made available to the job and is used for writing output datasets to the object store as part of the job and dynamic output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections, etc) happens as part of the job.

Default

directory

Type

str

retry_metadata_internally

Description

Although it is fairly reliable, setting metadata can occasionally fail. In these instances, you can choose to retry setting it internally or leave it in a failed state (since retrying internally may cause the Galaxy process to be unresponsive). If this option is set to false, the user will be given the option to retry externally, or set metadata manually (when possible).

Default

true

Type

bool

max_metadata_value_size

Description

Very large metadata values can cause Galaxy crashes. This will allow limiting the maximum metadata key size (in bytes used in memory, not the end result database value size) Galaxy will attempt to save with a dataset. Use 0 to disable this feature. The default is 5MB, but as low as 1MB seems to be a reasonable size.

Default

5242880

Type

int

outputs_to_working_directory

Description

This option will override tool output paths to write outputs to the job working directory (instead of to the file_path) and the job manager will move the outputs to their proper place in the dataset directory on the Galaxy server after the job completes. This is necessary (for example) if jobs run on a cluster and datasets can not be created by the user running the jobs (e.g. if the filesystem is mounted read-only or the jobs are run by a different user than the galaxy user).

Default

false

Type

bool

retry_job_output_collection

Description

If your network filesystem’s caching prevents the Galaxy server from seeing the job’s stdout and stderr files when it completes, you can retry reading these files. The job runner will retry the number of times specified below, waiting 1 second between tries. For NFS, you may want to try the -noac mount option (Linux) or -actimeo=0 (Solaris).

Default

0

Type

int

preserve_python_environment

Description

In the past Galaxy would preserve its Python environment when running jobs ( and still does for internal tools packaged with Galaxy). This behavior exposes Galaxy internals to tools and could result in problems when activating Python environments for tools (such as with Conda packaging). The default legacy_only will restrict this behavior to tools identified by the Galaxy team as requiring this environment. Set this to “always” to restore the previous behavior (and potentially break Conda dependency resolution for many tools). Set this to legacy_and_local to preserve the environment for legacy tools and locally managed tools (this might be useful for instance if you are installing software into Galaxy’s virtualenv for tool development).

Default

legacy_only

Type

str

cleanup_job

Description

Clean up various bits of jobs left on the filesystem after completion. These bits include the job working directory, external metadata temporary files, and DRM stdout and stderr files (if using a DRM). Possible values are: always, onsuccess, never

Default

always

Type

str

drmaa_external_runjob_script

Description

When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used to run the job script Galaxy generates for a tool execution. Example value ‘sudo -E scripts/drmaa_external_runner.py –assign_all_groups’

Default

None

Type

str

drmaa_external_killjob_script

Description

When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used to kill such jobs by Galaxy (e.g. if the user cancels the job). Example value ‘sudo -E scripts/drmaa_external_killer.py’

Default

None

Type

str

external_chown_script

Description

When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used transfer permissions back and forth between the Galaxy user and the user that is running the job. Example value ‘sudo -E scripts/external_chown_script.py’

Default

None

Type

str

real_system_username

Description

When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) Galaxy can extract the user name from the email address (actually the local-part before the @) or the username which are both stored in the Galaxy data base. The latter option is particularly useful for installations that get the authentication from LDAP. Also, Galaxy can accept the name of a common system user (eg. galaxy_worker) who can run every job being submitted. This user should not be the same user running the galaxy system. Possible values are user_email (default), username or <common_system_user>

Default

user_email

Type

str

environment_setup_file

Description

File to source to set up the environment when running jobs. By default, the environment in which the Galaxy server starts is used when running jobs locally, and the environment set up per the DRM’s submission method and policy is used when running jobs on a cluster (try testing with qsub on the command line). environment_setup_file can be set to the path of a file on the cluster that should be sourced by the user to set up the environment prior to running tools. This can be especially useful for running jobs as the actual user, to remove the need to configure each user’s environment individually.

Default

None

Type

str

enable_beta_markdown_export

Description

Enable export of Galaxy Markdown documents (pages and workflow reports) to PDF. Requires manual installation and setup of weasyprint (latest version available for Python 2.7 is 0.42).

Default

false

Type

bool

markdown_export_css

Description

CSS file to apply to all Markdown exports to PDF - currently used by WeasyPrint during rendering an HTML export of the document to PDF. The value of this option will be resolved with respect to <config_dir>.

Default

markdown_export.css

Type

str

markdown_export_css_pages

Description

CSS file to apply to “Galaxy Page” exports to PDF. Generally prefer markdown_export_css, but this is here for deployments that would like to tailor different kinds of exports. The value of this option will be resolved with respect to <config_dir>.

Default

markdown_export_pages.css

Type

str

markdown_export_css_invocation_reports

Description

CSS file to apply to invocation report exports to PDF. Generally prefer markdown_export_css, but this is here for deployments that would like to tailor different kinds of exports. The value of this option will be resolved with respect to <config_dir>.

Default

markdown_export_invocation_reports.css

Type

str

markdown_export_prologue

Description

Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing branded headers.

Default

""

Type

str

markdown_export_epilogue

Description

Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing branded footers.

Default

""

Type

str

markdown_export_prologue_pages

Description

Alternative to markdown_export_prologue that applies just to page exports.

Default

""

Type

str

markdown_export_prologue_invocation_reports

Description

Alternative to markdown_export_prologue that applies just to invocation report exports.

Default

""

Type

str

markdown_export_epilogue_pages

Description

Alternative to markdown_export_epilogue that applies just to page exports.

Default

""

Type

str

markdown_export_epilogue_invocation_reports

Description

Alternative to markdown_export_epilogue that applies just to invocation report exports.

Default

""

Type

str

job_resource_params_file

Description

Optional file containing job resource data entry fields definition. These fields will be presented to users in the tool forms and allow them to overwrite default job resources such as number of processors, memory and walltime. The value of this option will be resolved with respect to <config_dir>.

Default

job_resource_params_conf.xml

Type

str

workflow_resource_params_file

Description

Similar to the above parameter, workflows can describe parameters used to influence scheduling of jobs within the workflow. This requires both a description of the fields available (which defaults to the definitions in job_resource_params_file if not set). The value of this option will be resolved with respect to <config_dir>.

Default

workflow_resource_params_conf.xml

Type

str

workflow_resource_params_mapper

Description

This parameter describes how to map users and workflows to a set of workflow resource parameter to present (typically input IDs from workflow_resource_params_file). If this this is a function reference it will be passed various inputs (workflow model object and user) and it should produce a list of input IDs. If it is a path it is expected to be an XML or YAML file describing how to map group names to parameter descriptions (additional types of mappings via these files could be implemented but haven’t yet - for instance using workflow tags to do the mapping). Sample default path ‘config/workflow_resource_mapper_conf.yml.sample’

Default

None

Type

str

workflow_schedulers_config_file

Description

Optional configuration file similar to job_config_file to specify which Galaxy processes should schedule workflows. The value of this option will be resolved with respect to <config_dir>.

Default

workflow_schedulers_conf.xml

Type

str

cache_user_job_count

Description

If using job concurrency limits (configured in job_config_file), several extra database queries must be performed to determine the number of jobs a user has dispatched to a given destination. By default, these queries will happen for every job that is waiting to run, but if cache_user_job_count is set to true, it will only happen once per iteration of the handler queue. Although better for performance due to reduced queries, the trade-off is a greater possibility that jobs will be dispatched past the configured limits if running many handlers.

Default

false

Type

bool

tool_filters

Description

Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tools to display.

Default

None

Type

str

tool_label_filters

Description

Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tool labels to display.

Default

None

Type

str

tool_section_filters

Description

Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tool sections to display.

Default

None

Type

str

user_tool_filters

Description

Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tools to display.

Default

examples:restrict_upload_to_admins, examples:restrict_encode

Type

str

user_tool_section_filters

Description

Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tool sections to display.

Default

examples:restrict_text

Type

str

user_tool_label_filters

Description

Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tool labels to display.

Default

examples:restrict_upload_to_admins, examples:restrict_encode

Type

str

toolbox_filter_base_modules

Description

The base module(s) that are searched for modules for toolbox filtering (https://galaxyproject.org/user-defined-toolbox-filters/) functions.

Default

galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters

Type

str

amqp_internal_connection

Description

Galaxy uses AMQP internally for communicating between processes. For example, when reloading the toolbox or locking job execution, the process that handled that particular request will tell all others to also reload, lock jobs, etc. For connection examples, see http://docs.celeryproject.org/projects/kombu/en/latest/userguide/connections.html Without specifying anything here, galaxy will first attempt to use your specified database_connection above. If that’s not specified either, Galaxy will automatically create and use a separate sqlite database located in your <galaxy>/database folder (indicated in the commented out line below).

Default

sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE

Type

str

enable_celery_tasks

Description

Offload long-running tasks to a Celery task queue. Activate this only if you have setup a Celery worker for Galaxy. For details, see https://docs.galaxyproject.org/en/master/admin/production.html

Default

false

Type

bool

use_pbkdf2

Description

Allow disabling pbkdf2 hashing of passwords for legacy situations. This should normally be left enabled unless there is a specific reason to disable it.

Default

true

Type

bool

cookie_domain

Description

Tell Galaxy that multiple domains sharing the same root are associated to this instance and wants to share the same session cookie. This allow a user to stay logged in when passing from one subdomain to the other. This root domain will be written in the unique session cookie shared by all subdomains.

Default

None

Type

str

select_type_workflow_threshold

Description

Due to performance considerations (select2 fields are pretty ‘expensive’ in terms of memory usage) Galaxy uses the regular select fields for non-dataset selectors in the workflow run form. use 0 in order to always use select2 fields, use -1 (default) in order to always use the regular select fields, use any other positive number as threshold (above threshold: regular select fields will be used)

Default

-1

Type

int

enable_tool_recommendations

Description

Allow the display of tool recommendations in workflow editor and after tool execution. If it is enabled and set to true, please enable ‘tool_recommendation_model_path’ as well

Default

false

Type

bool

tool_recommendation_model_path

Description

Set remote path of the trained model (HDF5 file) for tool recommendation.

Default

https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5

Type

str

topk_recommendations

Description

Set the number of predictions/recommendations to be made by the model

Default

10

Type

int

admin_tool_recommendations_path

Description

Set path to the additional tool preferences from Galaxy admins. It has two blocks. One for listing deprecated tools which will be removed from the recommendations and another is for adding additional tools to be recommended along side those from the deep learning model. The value of this option will be resolved with respect to <config_dir>.

Default

tool_recommendations_overwrite.yml

Type

str

overwrite_model_recommendations

Description

Overwrite or append to the tool recommendations by the deep learning model. When set to true, all the recommendations by the deep learning model are overwritten by the recommendations set by an admin in a config file ‘tool_recommendations_overwrite.yml’. When set to false, the recommended tools by admins and predicted by the deep learning model are shown.

Default

false

Type

bool

error_report_file

Description

Path to error reports configuration file. The value of this option will be resolved with respect to <config_dir>.

Default

error_report.yml

Type

str

containers_config_file

Description

Path to container interface configuration file. The containers interface is only used if enable_beta_containers_interface config option is set. The value of this option will be resolved with respect to <config_dir>.

Default

containers_conf.yml

Type

str

tool_destinations_config_file

Description

Path to dynamic tool destinations configuration file. The value of this option will be resolved with respect to <config_dir>.

Default

tool_destinations.yml

Type

str

welcome_directory

Description

Location of New User Welcome data, a single directory containing the images and JSON of Topics/Subtopics/Slides as export. This location is relative to galaxy/static

Default

plugins/welcome_page/new_user/static/topics/

Type

str