Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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:false
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:false
Type:str

database_connection

Description:By default, Galaxy uses a SQLite database at ‘database/universe.sqlite’. You may use a SQLAlchemy connection string to specify an external database instead. This string takes many options which are explained in detail in the config file documentation.
Default:sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
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:
Type:str

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
Type:int

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).
Default:sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
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

file_path

Description:Where dataset files are stored. It must accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar.
Default:database/files
Type:str

new_file_path

Description:Where temporary files are stored. It must accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar.
Default:database/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.
Default:config/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.
Default:config/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 <mutable_config_dir>.
Default:config/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 <mutable_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.
Default:database/dependencies
Type:str

dependency_resolvers_config_file

Description:The dependency resolvers config file specifies an ordering and options for how Galaxy resolves tool dependencies (requirement tags in Tool XML). The default ordering is to the use the Tool Shed for tools installed that way, use local Galaxy packages, and then use Conda if available. See https://github.com/galaxyproject/ galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst for more information on these options.
Default:config/dependency_resolvers_conf.xml
Type:str

conda_prefix

Description:conda_prefix is the location on the filesystem where Conda packages and environments are installed IMPORTANT: Due to a current limitation in conda, the total length of the conda_prefix and the job_working_directory path should be less than 50 characters!
Default:<tool_dependency_dir>/_conda
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:iuc,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

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
Default:<tool_dependency_dir>/_cache
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).
Default:config/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

legacy_eager_objectstore_initialization

Description:As of 18.09, Galaxy defaults to setting up the object store configuration for output datasets during the job queue step in job handlers. This should generally provide for more robust job submission, more configurability, and a better user experience but may in some cases slightly slow down the job handler job setup process. On the off chance that an admin would like to or need to optimize job handlers at the expense of user experience and web handling this option will remain for some time by setting this option to true. This behavior however should be considered deprecated and this option will likely be removed in future versions of Galaxy. For more information see https://github.com/galaxyproject/galaxy/issues/6513.
Default:false
Type:bool

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

containers_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 containers loaded is determined by enable_mulled_containers.
Default:
Type:str

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.
Default:database/dependencies/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

manage_dependency_relationships

Description:Enable use of an in-memory registry with bi-directional relationships between repositories (i.e., in addition to lists of dependencies for a repository, keep an in-memory registry of dependent items for each repository.
Default:false
Type:bool

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).
Default:config/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.
Default:config/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 tool_data_path.
Default:tool-data
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

build_sites_config_file

Description:File that defines the builds (dbkeys) available at sites used by display applications and the URL to those sites.
Default:config/build_sites.yml.sample
Type:str

builds_file_path

Description:File containing old-style genome builds
Default:tool-data/shared/ucsc/builds.txt
Type:str

len_file_path

Description:Directory where chrom len files are kept, currently mainly used by trackster
Default:tool-data/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).
Default:config/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. Defaults to “config/plugins/visualizations”.
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

interactive_environment_swarm_mode

Description:To run interactive environment containers in Docker Swarm mode (on an existing swarm), set this option to true and set docker_connect_port in the IE plugin config (ini) file(s) of any IE plugins you have enabled and ensure that you are not using any docker run-specific options in your plugins’ command_inject options (swarm mode services run using docker service create, which has a different and more limited set of options). This option can be overridden on a per-plugin basis by using the swarm_mode option in the plugin’s ini config file.
Default:false
Type:bool

swarm_manager_config_file

Description:Galaxy can run a “swarm manager” service that will monitor utilization of the swarm and provision/deprovision worker nodes as necessary. The service has its own configuration file.
Default:config/swarm_manager_conf.yml
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.
Default:database/jobs_directory
Type:str

cluster_files_directory

Description:If using a cluster, Galaxy will write job scripts and stdout/stderr to this directory.
Default:database/pbs
Type:str

template_cache_path

Description:Mako templates are compiled as needed and cached for reuse, this directory is used for the cache
Default:database/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

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.
Default:database/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.
Default:database/citations/lock
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.
Default:config/object_store_conf.xml
Type:str

object_store_store_by

Description:What Dataset attribute is used to reference files in an ObjectStore implementation, default is ‘id’ but can also be set to ‘uuid’ for more de-centralized usage.
Default:id
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:
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:
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:
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.
Default:galaxy-announce-join@bx.psu.edu
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:
Type:str

email_from

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

instance_resource_url

Description:URL of the support resource for the galaxy instance. Used in activation emails.
Default:https://galaxyproject.org/
Type:str

blacklist_file

Description:E-mail domains blacklist is used for filtering out users that are using disposable email address during the registration. If their address domain matches any domain in the blacklist, they are refused the registration.
Default:config/disposable_email_blacklist.conf
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

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:
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

interactivetools_enable

Description:Enable InteractiveTools.
Default:false
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:
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}” to the “Galaxy” text in the masthead.
Default:
Type:str

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

user_preferences_extra_conf_path

Description:Location of the configuration file containing extra user preferences.
Default:config/user_preferences_extra_conf.yml
Type:str

default_locale

Description:Default localization for Galaxy UI. Allowed values are listed at the end of client/galaxy/scripts/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

helpsite_url

Description:The URL linked by the “Galaxy Help” link in the “Help” menu.
Default:
Type:str

wiki_url

Description:The URL linked by the “Wiki” link in the “Help” menu.
Default:https://galaxyproject.org/
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

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

genomespace_ui_url

Description:Points to the GenomeSpace UI service which will be used by the GenomeSpace importer and exporter tools
Default:https://gsui.genomespace.org/jsui/
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:
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/june_2007_style/blue
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:
Type:str

upstream_gzip

Description:If using compression in the upstream proxy server, use this option to disable gzipping of library .tar.gz and .zip archives, since the proxy server will do it faster on the fly.
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:
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:
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:
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:
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.
Default:database/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:
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:true
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:true
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_whitelist_file

Description:Whitelist sanitization file. 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 Display Whitelist”
Default:config/sanitize_whitelist.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:
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, use_printdebug and use_interactive. It also causes the files used by PBS/SGE (submission script, output, and error) to remain on disk after the job is complete.
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

use_interactive

Description:Enable live debugging in your browser. This should NEVER be enabled on a public site.
Default:false
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:
Type:str

sentry_sloreq_threshold

Description:Sentry slow request logging. Requests slower than the threshold indicated below will be sent as events to the configured Sentry server (above, sentry_dsn). 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

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

library_import_dir

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

transfer_manager_port

Description:Some sequencer integration features in beta allow you to automatically transfer datasets. This is done using a lightweight transfer manager which runs outside of Galaxy (but is spawned by it automatically). Galaxy will communicate with this manager over the port specified here.
Default:8163
Type:int

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_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_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:
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:
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:
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

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_whitelist

Description:Whitelist for 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.
Default:false
Type:bool

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 (the default).
Default:-1
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.
Default:config/oidc_config.xml
Type:str

oidc_backends_config_file

Description:Sets the path to OIDC backends configuration file.
Default:config/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).
Default:config/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:
Type:str

master_api_key

Description:Master key that allows many API admin actions to be used without actually having a defined admin user in the database/config. Only set this if you need to bootstrap Galaxy, you probably do not want to set this on public servers.
Default:changethis
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.
Default:database/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

myexperiment_url

Description:The URL to the myExperiment instance being used (omit scheme but include port).
Default:www.myexperiment.org:80
Type:str

ftp_upload_dir

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

ftp_upload_site

Description:This should be the hostname of your FTP server, which will be provided to users in the help text.
Default:
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.
Default:${ftp_upload_dir}/${ftp_upload_dir_identifier}
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

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).
Default:config/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.
Default:config/shed_data_manager_conf.xml
Type:str

galaxy_data_manager_data_path

Description:Directory to store Data Manager based tool-data; defaults to tool_data_path.
Default:tool-data
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.
Default:config/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.
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

enable_job_recovery

Description:Enable job recovery (if Galaxy is restarted while cluster jobs are running, it can “recover” them when it starts). This is not safe to use if you are running more than one Galaxy server using the same database.
Default:true
Type:bool

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.
Default:sudo -E scripts/drmaa_external_runner.py --assign_all_groups
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).
Default:sudo -E scripts/drmaa_external_killer.py
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.
Default:sudo -E scripts/external_chown_script.py
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:
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.
Default:config/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).
Default:config/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 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).
Default:config/workflow_resource_mapper_conf.yml
Type:str

workflow_schedulers_config_file

Description:Optional configuration file similar to job_config_file to specify which Galaxy processes should schedule workflows.
Default:config/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.toolbox.filters,galaxy.tools.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/usergui de/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_communication_server

Description:Galaxy real time communication server settings
Default:false
Type:bool

communication_server_host

Description:Galaxy real time communication server settings
Default:http://localhost
Type:str

communication_server_port

Description:Galaxy real time communication server settings
Default:7070
Type:int

persistent_communication_rooms

Description:persistent_communication_rooms is a comma-separated list of rooms that should be always available.
Default:None
Type:str

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