diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index bfb0ab9d001..ecb4a386478 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -4,19 +4,19 @@ desc: | Galaxy is configured by default to be usable in a single-user development environment. To tune the application for a multi-user production environment, see the documentation at: - + http://usegalaxy.org/production - + Throughout this sample configuration file, except where stated otherwise, uncommented values override the default if left unset, whereas commented values are set to the default value. Relative paths are relative to the root Galaxy directory. - + Examples of many of these options are explained in more detail in the Galaxy Community Hub. - + https://galaxyproject.org/admin/config - + Config hackers are encouraged to check there before asking for help. mapping: uwsgi: !include uwsgi_schema.yml @@ -33,7 +33,7 @@ mapping: If not running behind a proxy server, you may want to enable gzip compression to decrease the size of data transferred over the network. If using a proxy server, please enable gzip compression there instead. - + filter-with: type: str default: proxy-prefix @@ -42,7 +42,7 @@ mapping: If running behind a proxy server and Galaxy is served from a subdirectory, enable the proxy-prefix filter and set the prefix in the [filter:proxy-prefix] section above. - + cookie_path: type: str default: null @@ -52,7 +52,7 @@ mapping: behind one hostname, you will want to set this to the same path as the prefix in the filter above. This value becomes the "path" attribute set in the cookie so the cookies from each instance will not clobber each other. - + database_connection: type: str default: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE @@ -62,7 +62,7 @@ mapping: 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. - + database_engine_option_pool_size: type: int default: 5 @@ -71,7 +71,7 @@ mapping: 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. - + database_engine_option_max_overflow: type: int default: 10 @@ -80,7 +80,7 @@ mapping: 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. - + database_engine_option_pool_recycle: type: str default: -1 @@ -88,7 +88,7 @@ mapping: desc: | 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). - + database_engine_option_server_side_cursors: type: bool default: false @@ -97,7 +97,7 @@ mapping: 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. - + database_query_profiling_proxy: type: bool default: false @@ -106,7 +106,7 @@ mapping: 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' - + database_template: type: str default: null @@ -115,7 +115,7 @@ mapping: 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. - + slow_query_log_threshold: type: int default: 0 @@ -124,7 +124,7 @@ mapping: 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. - + install_database_connection: type: str default: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE @@ -136,7 +136,7 @@ mapping: 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). - + database_auto_migrate: type: bool default: false @@ -145,21 +145,21 @@ mapping: Setting the following option to true will cause Galaxy to automatically migrate the database forward after updates. This is not recommended for production use. - + file_path: type: str default: database/files required: false desc: | Dataset files are stored in this directory. - + new_file_path: type: str default: database/tmp required: false desc: | Temporary files are stored in this directory. - + tool_config_file: type: str default: config/tool_conf.xml,config/shed_tool_conf.xml @@ -169,7 +169,7 @@ mapping: 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). - + check_migrate_tools: type: bool default: true @@ -182,7 +182,7 @@ mapping: scratch where migrated tools do not need to be available in the Galaxy tool panel. If the following setting remains commented, the default setting will be True. - + migrated_tools_config: type: str default: config/migrated_tools_conf.xml @@ -191,7 +191,7 @@ mapping: 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. - + integrated_tool_panel_config: type: str default: integrated_tool_panel.xml @@ -201,7 +201,7 @@ mapping: 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. - + tool_path: type: str default: tools @@ -210,7 +210,7 @@ mapping: 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 tag. - + tool_dependency_dir: type: str default: database/dependencies @@ -223,7 +223,7 @@ mapping: Set the string to None 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 will fail. - + dependency_resolvers_config_file: type: str default: config/dependency_resolvers_conf.xml @@ -235,7 +235,7 @@ mapping: 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. - + conda_prefix: type: str default: /_conda @@ -244,28 +244,28 @@ mapping: 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! - + conda_exec: type: str required: false desc: | Override the Conda executable to use, it will default to the one on the PATH (if available) and then to /bin/conda - + conda_debug: type: bool default: false required: false desc: | Pass debug flag to conda commands. - + conda_ensure_channels: type: str default: iuc,bioconda,conda-forge,defaults,r required: false desc: | conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html) - + conda_auto_install: type: bool default: false @@ -273,7 +273,7 @@ mapping: desc: | Set to True to instruct Galaxy to look for and install missing tool dependencies before each job runs. - + conda_auto_init: type: bool default: true @@ -281,7 +281,7 @@ mapping: desc: | 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. - + conda_copy_dependencies: type: bool default: false @@ -292,7 +292,7 @@ mapping: 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. - + use_cached_dependency_manager: type: bool default: false @@ -304,7 +304,7 @@ mapping: 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. - + tool_dependency_cache_dir: type: str default: /_cache @@ -312,7 +312,7 @@ mapping: desc: | By default the tool_dependency_cache_dir is the _cache directory of the tool dependency directory - + precache_dependencies: type: bool default: true @@ -321,7 +321,7 @@ mapping: 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. - + tool_sheds_config_file: type: str default: config/tool_sheds_conf.xml @@ -329,7 +329,7 @@ mapping: desc: | 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). - + watch_tools: type: bool default: false @@ -344,7 +344,7 @@ mapping: 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. - + enable_beta_mulled_containers: type: bool default: false @@ -356,7 +356,7 @@ mapping: These containers are highly beta and availability will vary by tool. This option will additionally only be used for job destinations with Docker enabled. - + containers_resolvers_config_file: type: str default: null @@ -366,7 +366,7 @@ mapping: resolvers to use when discovering containers for Galaxy. If this is set to None, the default containers loaded is determined by enable_beta_mulled_containers. - + involucro_path: type: str default: database/dependencies/involucro @@ -377,7 +377,7 @@ mapping: 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. - + involucro_auto_init: type: bool default: true @@ -385,7 +385,7 @@ mapping: desc: | Install involucro as needed to build Docker containers for tools. Ignored if relevant container resolver is not used. - + enable_tool_shed_check: type: bool default: false @@ -395,7 +395,7 @@ mapping: 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. - + hours_between_check: type: int default: 12 @@ -405,7 +405,7 @@ mapping: 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. - + manage_dependency_relationships: type: bool default: false @@ -414,7 +414,7 @@ mapping: 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. - + tool_data_table_config_path: type: str default: config/tool_data_table_conf.xml @@ -423,7 +423,7 @@ mapping: 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). - + shed_tool_data_table_config: type: str default: config/shed_tool_data_table_conf.xml @@ -435,7 +435,7 @@ mapping: 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. - + tool_data_path: type: str default: tool-data @@ -444,7 +444,7 @@ mapping: 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 - + shed_tool_data_path: type: str default: tool-data @@ -452,7 +452,7 @@ mapping: desc: | Directory where Tool Data Table related files will be placed when installed from a ToolShed. Defaults to tool_data_path. - + watch_tool_data_dir: type: bool default: false @@ -467,21 +467,21 @@ mapping: 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. - + builds_file_path: type: str default: tool-data/shared/ucsc/builds.txt required: false desc: | File containing old-style genome builds - + len_file_path: type: str default: tool-data/shared/ucsc/chrom required: false desc: | Directory where chrom len files are kept, currently mainly used by trackster - + datatypes_config_file: type: str default: config/datatypes_conf.xml @@ -491,14 +491,14 @@ mapping: 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). - + datatypes_disable_auto: type: bool default: false required: false desc: | Disable the 'Auto-detect' option for file uploads - + visualization_plugins_directory: type: str default: config/plugins/visualizations @@ -508,7 +508,7 @@ mapping: 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". - + interactive_environment_plugins_directory: type: str required: false @@ -520,7 +520,7 @@ mapping: 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. - + interactive_environment_swarm_mode: type: bool default: false @@ -534,7 +534,7 @@ mapping: 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. - + swarm_manager_config_file: type: str default: config/swarm_manager_conf.yml @@ -543,7 +543,7 @@ mapping: 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. - + tour_config_dir: type: str default: config/plugins/tours @@ -554,7 +554,7 @@ mapping: 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. - + webhooks_dir: type: str default: config/plugins/webhooks @@ -565,7 +565,7 @@ mapping: 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. - + job_working_directory: type: str default: database/jobs_directory @@ -574,7 +574,7 @@ mapping: 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. - + cluster_files_directory: type: str default: database/pbs @@ -582,7 +582,7 @@ mapping: desc: | If using a cluster, Galaxy will write job scripts and stdout/stderr to this directory. - + template_cache_path: type: str default: database/compiled_templates @@ -590,7 +590,7 @@ mapping: desc: | Mako templates are compiled as needed and cached for reuse, this directory is used for the cache - + check_job_script_integrity: type: bool default: true @@ -598,21 +598,21 @@ mapping: desc: | Set to false to disable various checks Galaxy will do to ensure it can run job scripts before attempting to execute or submit them. - + check_job_script_integrity_count: type: int default: 35 required: false desc: | Number of checks to execute if check_job_script_integrity is enabled. - + check_job_script_integrity_sleep: type: str default: .25 required: false desc: | Time to sleep between checks if check_job_script_integrity is enabled (in seconds). - + default_job_shell: type: str default: /bin/bash @@ -624,7 +624,7 @@ mapping: 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. - + citation_cache_type: type: str default: file @@ -633,7 +633,7 @@ mapping: Citation related caching. Tool citations information maybe fetched from external sources such as http://dx.doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. - + citation_cache_data_dir: type: str default: database/citations/data @@ -642,7 +642,7 @@ mapping: Citation related caching. Tool citations information maybe fetched from external sources such as http://dx.doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. - + citation_cache_lock_dir: type: str default: database/citations/lock @@ -651,7 +651,7 @@ mapping: Citation related caching. Tool citations information maybe fetched from external sources such as http://dx.doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. - + collect_outputs_from: type: str default: new_file_path,job_working_directory @@ -663,7 +663,7 @@ mapping: can cause performance problems, so using job_working_directory ('.' or cwd when a job is run) is encouraged. By default, both are checked to avoid breaking existing tools. - + object_store_config_file: type: str default: config/object_store_conf.xml @@ -671,7 +671,7 @@ mapping: desc: | Configuration file for the object store If this is set and exists, it overrides any other objectstore settings. - + smtp_server: type: str default: null @@ -682,7 +682,7 @@ mapping: 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. - + smtp_username: type: str default: null @@ -691,7 +691,7 @@ mapping: 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). - + smtp_password: type: str default: null @@ -700,14 +700,14 @@ mapping: 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). - + smtp_ssl: type: bool default: false required: false desc: | If your SMTP server requires SSL from the beginning of the connection - + mailing_join_addr: type: str default: galaxy-announce-join@bx.psu.edu @@ -716,7 +716,7 @@ mapping: 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. - + error_email_to: type: str default: null @@ -726,7 +726,7 @@ mapping: 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. - + email_from: type: str default: null @@ -737,7 +737,7 @@ mapping: We recommend using string in the following format: Galaxy Project If not configured, '' will be used. - + instance_resource_url: type: str default: https://galaxyproject.org/ @@ -745,7 +745,7 @@ mapping: desc: | URL of the support resource for the galaxy instance. Used in activation emails. - + blacklist_file: type: str default: config/disposable_email_blacklist.conf @@ -754,7 +754,7 @@ mapping: 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. - + registration_warning_message: type: str 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. @@ -763,7 +763,7 @@ mapping: 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. - + user_activation_on: type: bool default: false @@ -773,7 +773,7 @@ mapping: 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. - + activation_grace_period: type: int default: 3 @@ -783,7 +783,7 @@ mapping: disabled) until grace period has passed. Users under grace period can't run jobs. Enter 0 to disable grace period. Users with OpenID logins have grace period forever. - + inactivity_box_content: type: str 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. @@ -791,7 +791,7 @@ mapping: desc: | Shown in warning box to users that were not activated yet. In use only if activation_grace_period is set. - + password_expiration_period: type: int default: 0 @@ -801,7 +801,7 @@ mapping: 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. - + session_duration: type: int default: 0 @@ -810,7 +810,7 @@ mapping: 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. - + ga_code: type: str default: null @@ -818,7 +818,7 @@ mapping: desc: | You can enter tracking code here to track visitor's behavior through your Google Analytics account. Example: UA-XXXXXXXX-Y - + display_servers: type: str 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 @@ -827,7 +827,7 @@ mapping: 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 specifield files. - + If use_remote_user = 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 @@ -835,12 +835,12 @@ mapping: 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). - + enable_old_display_applications: type: bool default: true @@ -855,35 +855,35 @@ mapping: 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. - + message_box_visible: type: bool default: false required: false desc: | Show a message box under the masthead. - + message_box_content: type: str default: null required: false desc: | Show a message box under the masthead. - + message_box_class: type: str default: info required: false desc: | Show a message box under the masthead. - + brand: type: str default: null required: false desc: | Append "/{brand}" to the "Galaxy" text in the masthead. - + pretty_datetime_format: type: str default: $locale (UTC) @@ -896,7 +896,7 @@ mapping: - $locale (complete format string for the server locale), - $iso8601 (complete format string as specified by ISO 8601 international standard). - + galaxy_infrastructure_url: type: str default: http://localhost:8080 @@ -905,12 +905,12 @@ mapping: 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 setup GIEs on Mac OS X with Docker for Mac - this should likely be the IP address of your machine on the virtualbox network (vboxnet0) setup for the Docker host VM. This can found by running ifconfig and using the IP address of the network vboxnet0. - + galaxy_infrastructure_web_port: type: int default: 8080 @@ -923,7 +923,7 @@ mapping: 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. - + welcome_url: type: str default: /static/welcome.html @@ -931,91 +931,91 @@ mapping: desc: | The URL of the page to display in Galaxy's middle pane when loaded. This can be an absolute or relative URL. - + logo_url: type: str default: / required: false desc: | The URL linked by the "Galaxy/brand" text. - + wiki_url: type: str default: https://galaxyproject.org/ required: false desc: | The URL linked by the "Wiki" link in the "Help" menu. - + support_url: type: str default: https://galaxyproject.org/support required: false desc: | The URL linked by the "Support" link in the "Help" menu. - + biostar_url: type: str default: null required: false desc: | Enable integration with a custom Biostar instance. - + biostar_key_name: type: str default: null required: false desc: | Enable integration with a custom Biostar instance. - + biostar_key: type: str default: null required: false desc: | Enable integration with a custom Biostar instance. - + biostar_enable_bug_reports: type: bool default: true required: false desc: | Enable integration with a custom Biostar instance. - + biostar_never_authenticate: type: bool default: false required: false desc: | Enable integration with a custom Biostar instance. - + citation_url: type: str default: https://galaxyproject.org/citing-galaxy required: false desc: | The URL linked by the "How to Cite Galaxy" link in the "Help" menu. - + search_url: type: str default: https://galaxyproject.org/search/ required: false desc: | The URL linked by the "Search" link in the "Help" menu. - + mailing_lists_url: type: str default: https://galaxyproject.org/mailing-lists required: false desc: | The URL linked by the "Mailing Lists" link in the "Help" menu. - + screencasts_url: type: str default: https://vimeo.com/galaxyproject required: false desc: | The URL linked by the "Videos" link in the "Help" menu. - + genomespace_ui_url: type: str default: https://gsui.genomespace.org/jsui/ @@ -1023,7 +1023,7 @@ mapping: desc: | Points to the GenomeSpace UI service which will be used by the GenomeSpace importer and exporter tools - + terms_url: type: str default: null @@ -1031,7 +1031,7 @@ mapping: desc: | 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. - + qa_url: type: str required: false @@ -1039,7 +1039,7 @@ mapping: 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. - + static_enabled: type: bool default: true @@ -1049,7 +1049,7 @@ mapping: 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. - + static_cache_time: type: int default: 360 @@ -1059,7 +1059,7 @@ mapping: 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. - + static_dir: type: str default: static/ @@ -1069,7 +1069,7 @@ mapping: 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. - + static_images_dir: type: str default: static/images @@ -1079,7 +1079,7 @@ mapping: 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. - + static_favicon_dir: type: str default: static/favicon.ico @@ -1089,7 +1089,7 @@ mapping: 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. - + static_scripts_dir: type: str default: static/scripts/ @@ -1099,7 +1099,7 @@ mapping: 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. - + static_style_dir: type: str default: static/june_2007_style/blue @@ -1109,7 +1109,7 @@ mapping: 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. - + static_robots_txt: type: str default: static/robots.txt @@ -1119,14 +1119,14 @@ mapping: 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. - + display_chunk_size: type: int default: 65536 required: false desc: | Incremental Display Options - + apache_xsendfile: type: bool default: false @@ -1134,10 +1134,10 @@ mapping: desc: | For help on configuring the Advanced proxy features, see: http://usegalaxy.org/production - + Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set this to True to inform Galaxy that mod_xsendfile is enabled upstream. - + nginx_x_accel_redirect_base: type: bool default: false @@ -1146,7 +1146,7 @@ mapping: 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). - + nginx_x_archive_files_base: type: bool default: false @@ -1154,7 +1154,7 @@ mapping: desc: | nginx can make use of mod_zip to create zip files containing multiple library files. If using X-Accel-Redirect, this can be the same value as that option. - + upstream_gzip: type: bool default: false @@ -1163,7 +1163,7 @@ mapping: 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. - + x_frame_options: type: str default: SAMEORIGIN @@ -1177,7 +1177,7 @@ mapping: 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. - + nginx_upload_store: type: bool default: false @@ -1187,7 +1187,7 @@ mapping: 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. - + nginx_upload_path: type: bool default: false @@ -1196,7 +1196,7 @@ mapping: 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. - + nginx_upload_job_files_store: type: bool default: false @@ -1206,7 +1206,7 @@ mapping: 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. - + nginx_upload_job_files_path: type: bool default: false @@ -1216,7 +1216,7 @@ mapping: 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. - + dynamic_proxy_manage: type: bool default: true @@ -1228,7 +1228,7 @@ mapping: `lib/galaxy/web/proxy/js`. It is generally more robust to configure this externally, managing it however Galaxy is managed. If True, Galaxy will only launch the proxy if it is actually going to be used (e.g. for Jupyter). - + dynamic_proxy: type: str default: node @@ -1237,7 +1237,7 @@ mapping: 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) - + dynamic_proxy_session_map: type: str default: database/session_map.sqlite @@ -1245,7 +1245,7 @@ mapping: desc: | The NodeJS dynamic proxy can use an SQLite database or a JSON file for IPC, set that here. - + dynamic_proxy_bind_port: type: int default: 8800 @@ -1253,7 +1253,7 @@ mapping: desc: | Set the port and IP for the the dynamic proxy to bind to, this must match the external configuration if dynamic_proxy_manage is False. - + dynamic_proxy_bind_ip: type: str default: 0.0.0.0 @@ -1261,14 +1261,14 @@ mapping: desc: | Set the port and IP for the the dynamic proxy to bind to, this must match the external configuration if dynamic_proxy_manage is False. - + dynamic_proxy_debug: type: bool default: false required: false desc: | Enable verbose debugging of Galaxy-managed dynamic proxy. - + dynamic_proxy_external_proxy: type: bool default: false @@ -1276,7 +1276,7 @@ mapping: desc: | The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL). - + dynamic_proxy_prefix: type: str default: gie_proxy @@ -1286,7 +1286,7 @@ mapping: 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 - + dynamic_proxy_golang_noaccess: type: int default: 60 @@ -1295,7 +1295,7 @@ mapping: 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. - + dynamic_proxy_golang_clean_interval: type: int default: 10 @@ -1304,7 +1304,7 @@ mapping: 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. - + dynamic_proxy_golang_docker_address: type: str default: unix:///var/run/docker.sock @@ -1312,7 +1312,7 @@ mapping: desc: | The golang proxy needs to know how to talk to your docker daemon. Currently TLS is not supported, that will come in an update. - + dynamic_proxy_golang_api_key: type: str default: null @@ -1322,7 +1322,7 @@ mapping: 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. - + auto_configure_logging: type: bool default: true @@ -1330,7 +1330,7 @@ mapping: desc: | If True, Galaxy will attempt to configure a simple root logger if a "loggers" section does not appear in this configuration file. - + log_level: type: str default: DEBUG @@ -1339,7 +1339,7 @@ mapping: Verbosity of console log messages. Acceptable values can be found here: https://docs.python.org/2/library/logging.html#logging-levels A custom debug level of "TRACE" is available for even more verbosity. - + logging: type: map default: galaxy.config.LOGGING_CONFIG_DEFAULT @@ -1348,28 +1348,28 @@ mapping: 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 - + database_engine_option_echo: type: bool default: false required: false desc: | Print database operations to the server log (warning, quite verbose!). - + database_engine_option_echo_pool: type: bool default: false required: false desc: | Print database pool operations to the server log (warning, quite verbose!). - + log_events: type: bool default: true required: false desc: | Turn on logging of application events and some user events to the database. - + log_actions: type: bool default: true @@ -1378,7 +1378,7 @@ mapping: 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. - + fluent_log: type: bool default: false @@ -1386,7 +1386,7 @@ mapping: desc: | Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log. - + fluent_host: type: str default: localhost @@ -1394,7 +1394,7 @@ mapping: desc: | Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log. - + fluent_port: type: int default: 24224 @@ -1402,7 +1402,7 @@ mapping: desc: | Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log. - + sanitize_all_html: type: bool default: true @@ -1412,7 +1412,7 @@ mapping: '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. - + sanitize_whitelist_file: type: str default: config/sanitize_whitelist.txt @@ -1422,7 +1422,7 @@ mapping: 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" - + serve_xss_vulnerable_mimetypes: type: bool default: false @@ -1432,7 +1432,7 @@ mapping: 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 the following option to True. - + allowed_origin_hostnames: type: str default: null @@ -1444,7 +1444,7 @@ mapping: 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/Access_control_CORS - + trust_jupyter_notebook_conversion: type: bool default: false @@ -1455,7 +1455,7 @@ mapping: 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. - + debug: type: bool default: false @@ -1465,28 +1465,28 @@ mapping: 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. - + use_lint: type: bool default: false required: false desc: | Check for WSGI compliance. - + use_profile: type: bool default: false required: false desc: | Run the Python profiler on each request. - + use_printdebug: type: bool default: true required: false desc: | Intercept print statements and show them on the returned page. - + use_interactive: type: bool default: true @@ -1494,7 +1494,7 @@ mapping: desc: | Enable live debugging in your browser. This should NEVER be enabled on a public site. Enabled in the sample config for development. - + monitor_thread_join_timeout: type: int default: 5 @@ -1503,7 +1503,7 @@ mapping: 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 restore the pre-18.01 default behavior. - + use_heartbeat: type: bool default: false @@ -1512,7 +1512,7 @@ mapping: 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. - + heartbeat_interval: type: int default: 20 @@ -1521,7 +1521,7 @@ mapping: 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. - + heartbeat_log: type: str default: heartbeat_{server_name}.log @@ -1529,7 +1529,7 @@ mapping: desc: | Heartbeat log filename. Can accept the template variables {server_name} and {pid} - + sentry_dsn: type: str default: null @@ -1540,7 +1540,7 @@ mapping: 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 -> Settings -> API Keys. - + statsd_host: type: str required: false @@ -1551,7 +1551,7 @@ mapping: 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. - + statsd_port: type: int default: 8125 @@ -1563,7 +1563,7 @@ mapping: 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. - + statsd_prefix: type: str default: galaxy @@ -1575,7 +1575,7 @@ mapping: 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. - + graphite_host: type: str required: false @@ -1586,7 +1586,7 @@ mapping: other statistics to the configured graphite instance. The graphite_prefix is useful if you are running multiple Galaxy instances and want to segment statistics between them within the same aggregator. - + graphite_port: type: int default: 2003 @@ -1598,7 +1598,7 @@ mapping: other statistics to the configured graphite instance. The graphite_prefix is useful if you are running multiple Galaxy instances and want to segment statistics between them within the same aggregator. - + graphite_prefix: type: str default: galaxy @@ -1610,7 +1610,7 @@ mapping: other statistics to the configured graphite instance. The graphite_prefix is useful if you are running multiple Galaxy instances and want to segment statistics between them within the same aggregator. - + library_import_dir: type: str default: null @@ -1618,7 +1618,7 @@ mapping: desc: | Add an option to the library upload form which allows administrators to upload a directory of files. - + user_library_import_dir: type: str default: null @@ -1637,7 +1637,7 @@ mapping: desc: | 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. - + user_library_import_symlink_whitelist: type: str default: null @@ -1649,7 +1649,7 @@ mapping: 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). - + user_library_import_check_permissions: type: bool default: false @@ -1658,7 +1658,7 @@ mapping: 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. - + allow_path_paste: type: bool default: false @@ -1671,7 +1671,7 @@ mapping: (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. - + disable_library_comptypes: type: str required: false @@ -1681,7 +1681,7 @@ mapping: 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'. - + transfer_manager_port: type: int default: 8163 @@ -1691,7 +1691,7 @@ mapping: 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. - + tool_name_boost: type: float default: 9 @@ -1701,7 +1701,7 @@ mapping: 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. - + tool_section_boost: type: float default: 3 @@ -1711,7 +1711,7 @@ mapping: 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. - + tool_description_boost: type: float default: 2 @@ -1721,7 +1721,7 @@ mapping: 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. - + tool_label_boost: type: float default: 1 @@ -1731,7 +1731,7 @@ mapping: 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. - + tool_stub_boost: type: float default: 5 @@ -1741,7 +1741,7 @@ mapping: 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. - + tool_help_boost: type: float default: 0.5 @@ -1751,7 +1751,7 @@ mapping: 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. - + tool_search_limit: type: int default: 20 @@ -1759,7 +1759,7 @@ mapping: desc: | Limits the number of results in toolbox search. Can be used to tweak how many results will appear. - + tool_enable_ngram_search: type: bool default: false @@ -1769,21 +1769,21 @@ mapping: search results tolerant for spelling mistakes in the query by dividing the query into multiple ngrams and search for each ngram - + tool_ngram_minsize: type: int default: 3 required: false desc: | Set minimum size of ngrams - + tool_ngram_maxsize: type: int default: 4 required: false desc: | Set maximum size of ngrams - + id_secret: type: str default: USING THE DEFAULT IS NOT SECURE! @@ -1795,7 +1795,7 @@ mapping: string up to 448 bits long. One simple way to generate a value for this is with the shell command: python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' ' - + use_remote_user: type: bool default: false @@ -1805,7 +1805,7 @@ mapping: Apache). The upstream proxy should set a REMOTE_USER header in the request. Enabling remote user disables regular logins. For more information, see: https://galaxyproject.org/admin/config/apache-proxy - + remote_user_maildomain: type: str default: null @@ -1814,7 +1814,7 @@ mapping: 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). - + remote_user_header: type: str default: HTTP_REMOTE_USER @@ -1825,7 +1825,7 @@ mapping: 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. - + remote_user_secret: type: str default: USING THE DEFAULT IS NOT SECURE! @@ -1837,7 +1837,7 @@ mapping: 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. - + remote_user_logout_href: type: str default: null @@ -1845,7 +1845,7 @@ mapping: desc: | If use_remote_user is enabled, you can set this to a URL that will log your users out. - + normalize_remote_user_email: type: bool default: false @@ -1854,7 +1854,7 @@ mapping: If your proxy and/or authentication source does not normalize e-mail addresses or user names being passed to Galaxy - set the following option to True to force these to lower case. - + single_user: type: str required: false @@ -1864,7 +1864,7 @@ mapping: 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. - + admin_users: type: str default: null @@ -1875,14 +1875,14 @@ mapping: of the server, and will have access to create users, groups, roles, libraries, and more. For more information, see: https://galaxyproject.org/admin/ - + require_login: type: bool default: false required: false desc: | Force everyone to log in (disable anonymous access). - + show_welcome_with_login: type: bool default: false @@ -1890,7 +1890,7 @@ mapping: desc: | Show the site's welcome page (see welcome_url) alongside the login page (even if require_login is True) - + allow_user_creation: type: bool default: true @@ -1898,21 +1898,21 @@ mapping: desc: | Allow unregistered users to create new accounts (otherwise, they will have to be created by an admin). - + allow_user_deletion: type: bool default: false required: false desc: | Allow administrators to delete accounts. - + allow_user_impersonation: type: bool default: false required: false desc: | Allow administrators to log in as other users (useful for debugging) - + show_user_prepopulate_form: type: bool default: false @@ -1920,7 +1920,7 @@ mapping: desc: | When using LDAP for authentication, allow administrators to pre-populate users using an additional form on 'Create new user' - + allow_user_dataset_purge: type: bool default: true @@ -1929,7 +1929,7 @@ mapping: 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) - + new_user_dataset_access_role_default_private: type: bool default: false @@ -1939,7 +1939,7 @@ mapping: 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. - + expose_user_name: type: bool default: false @@ -1951,7 +1951,7 @@ mapping: 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. - + expose_user_email: type: bool default: false @@ -1963,7 +1963,7 @@ mapping: 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. - + fetch_url_whitelist: type: str required: false @@ -1975,7 +1975,7 @@ mapping: 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 - + enable_beta_ts_api_install: type: bool default: true @@ -1983,14 +1983,14 @@ mapping: desc: | Enable the new interface for installing tools from Tool Shed via the API. Admin menu will list both if enabled. - + enable_beta_containers_interface: type: bool default: false required: false desc: | Enable the new container interface for Interactive Environments - + tool_submission_burst_threads: type: int default: 1 @@ -2001,7 +2001,7 @@ mapping: through the tool form or as part of an individual workflow step across large collection). This affects workflow scheduling and web processes, not job handlers. This is a beta option and should not be used in production. - + tool_submission_burst_at: type: int default: 10 @@ -2009,7 +2009,7 @@ mapping: desc: | If tool_submission_burst_threads is set to a number greater than 1, this is the number of jobs to schedule at which the task queue will be created. - + enable_beta_workflow_modules: type: bool default: false @@ -2017,7 +2017,7 @@ mapping: desc: | Enable beta workflow modules that should not yet be considered part of Galaxy's stable API. - + force_beta_workflow_scheduled_min_steps: type: int default: 250 @@ -2034,7 +2034,7 @@ mapping: scheduling). Workflows containing more than the specified number of steps will always use the Galaxy's beta workflow scheduling. - + force_beta_workflow_scheduled_for_collections: type: bool default: false @@ -2053,7 +2053,7 @@ mapping: the Galaxy's beta workflow scheduling. Switch to using Galaxy's beta workflow scheduling for all workflows involving collections. - + parallelize_workflow_scheduling_within_histories: type: bool default: false @@ -2062,7 +2062,7 @@ mapping: 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. - + maximum_workflow_invocation_duration: type: int default: 2678400 @@ -2071,7 +2071,7 @@ mapping: 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. - + maximum_workflow_jobs_per_scheduling_iteration: type: str default: -1 @@ -2083,14 +2083,14 @@ mapping: 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). - + history_local_serial_workflow_scheduling: type: bool default: false required: false desc: | Force serial scheduling of workflows within the context of a particular history - + enable_openid: type: bool default: false @@ -2098,7 +2098,7 @@ mapping: desc: | Enable authentication via OpenID. Allows users to log in to their Galaxy account by authenticating with an OpenID provider. - + openid_config_file: type: str default: config/openid_conf.xml @@ -2106,14 +2106,14 @@ mapping: desc: | If OpenID is enabled, this configuration file specifies providers to use. Falls back to the .sample variant in config if default does not exist. - + openid_consumer_cache_path: type: str default: database/openid_consumer_cache required: false desc: | If OpenID is enabled, consumer cache directory to use. - + auth_config_file: type: str default: config/auth_conf.xml @@ -2122,7 +2122,7 @@ mapping: 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). - + api_allow_run_as: type: str default: null @@ -2130,7 +2130,7 @@ mapping: desc: | Optional list of email addresses of API users who can make calls on behalf of other users. - + master_api_key: type: str default: changethis @@ -2140,7 +2140,7 @@ mapping: 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. - + enable_tool_tags: type: bool default: false @@ -2149,7 +2149,7 @@ mapping: 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. - + enable_unique_workflow_defaults: type: bool default: false @@ -2161,14 +2161,14 @@ mapping: 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 - + myexperiment_url: type: str default: www.myexperiment.org:80 required: false desc: | The URL to the myExperiment instance being used (omit scheme but include port) - + ftp_upload_dir: type: str default: null @@ -2179,7 +2179,7 @@ mapping: 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. - + ftp_upload_site: type: str default: null @@ -2187,7 +2187,7 @@ mapping: desc: | This should be the hostname of your FTP server, which will be provided to users in the help text. - + ftp_upload_dir_identifier: type: str default: email @@ -2197,7 +2197,7 @@ mapping: 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. - + ftp_upload_dir_template: type: str default: ${ftp_upload_dir}/${ftp_upload_dir_identifier} @@ -2205,7 +2205,7 @@ mapping: desc: | Python string template used to determine an FTP upload directory for a particular user. - + ftp_upload_purge: type: bool default: true @@ -2213,14 +2213,14 @@ mapping: desc: | This should be set to False to prevent Galaxy from deleting uploaded FTP files as it imports them. - + enable_quotas: type: bool default: false required: false desc: | Enable enforcement of quotas. Quotas can be set from the Admin interface. - + expose_dataset_path: type: bool default: false @@ -2229,7 +2229,7 @@ mapping: 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. - + expose_potentially_sensitive_job_metrics: type: bool default: false @@ -2237,21 +2237,21 @@ mapping: desc: | This option allows users to see the job metrics (except for environment variables). - + enable_legacy_sample_tracking_api: type: bool default: false required: false desc: | Enable the API for sample tracking - + enable_data_manager_user_view: type: bool default: false required: false desc: | Allow non-admin users to view available Data Manager options. - + data_manager_config_file: type: str default: config/data_manager_conf.xml @@ -2259,21 +2259,21 @@ mapping: desc: | File where Data Managers are configured (.sample used if default does not exist). - + shed_data_manager_config_file: type: str default: config/shed_data_manager_conf.xml required: false desc: | File where Tool Shed based Data Managers are configured. - + galaxy_data_manager_data_path: type: str default: tool-data required: false desc: | Directory to store Data Manager based tool-data; defaults to tool_data_path. - + job_config_file: type: str default: config/job_conf.xml @@ -2282,14 +2282,14 @@ mapping: 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://galaxyproject.org/admin/config/performance/scaling - + 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_job_resubmission_condition: type: str required: false @@ -2306,7 +2306,7 @@ mapping: 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. - + track_jobs_in_database: type: bool default: true @@ -2315,7 +2315,7 @@ mapping: In multiprocess configurations, notification between processes about new jobs must be done via the database. In single process configurations, this can be done in memory, which is a bit quicker. - + use_tasked_jobs: type: bool default: false @@ -2324,7 +2324,7 @@ mapping: 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. - + local_task_queue_workers: type: int default: 2 @@ -2333,7 +2333,7 @@ mapping: 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. - + enable_job_recovery: type: bool default: true @@ -2342,7 +2342,7 @@ mapping: 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. - + retry_metadata_internally: type: bool default: true @@ -2353,7 +2353,7 @@ mapping: 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). - + max_metadata_value_size: type: int default: 5242880 @@ -2364,18 +2364,20 @@ mapping: 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. - + outputs_to_working_directory: type: bool default: false required: false desc: | - If (for example) you run on a cluster and your datasets (by default, - database/files/) are mounted read-only, this option will override tool output - paths to write outputs to the working directory instead, 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 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). + retry_job_output_collection: type: int default: 0 @@ -2386,7 +2388,7 @@ mapping: 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). - + preserve_python_environment: type: str default: legacy_only @@ -2402,7 +2404,7 @@ mapping: 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). - + cleanup_job: type: str default: always @@ -2412,43 +2414,43 @@ mapping: 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 - + drmaa_external_runjob_script: type: str default: sudo -E scripts/drmaa_external_runner.py --assign_all_groups required: false desc: | - When running DRMAA jobs as the Galaxy user - (https://galaxyproject.org/admin/config/performance/cluster/#submitting-jobs-as-the-real-user) + When running DRMAA jobs as the Galaxy user + (https://docs.galaxyproject.org/en/latest/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used to run the job script Galaxy generates for a tool execution. - + drmaa_external_killjob_script: type: str default: sudo -E scripts/drmaa_external_killer.py required: false desc: | - When running DRMAA jobs as the Galaxy user - (https://galaxyproject.org/admin/config/performance/cluster/#submitting-jobs-as-the-real-user) + When running DRMAA jobs as the Galaxy user + (https://docs.galaxyproject.org/en/latest/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). - + external_chown_script: type: str default: sudo -E scripts/external_chown_script.py required: false desc: | - When running DRMAA jobs as the Galaxy user - (https://galaxyproject.org/admin/config/performance/cluster/#submitting-jobs-as-the-real-user) + When running DRMAA jobs as the Galaxy user + (https://docs.galaxyproject.org/en/latest/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. - + real_system_username: type: str default: user_email required: false desc: | - When running DRMAA jobs as the Galaxy user - (https://galaxyproject.org/admin/config/performance/cluster/#submitting-jobs-as-the-real-user) + When running DRMAA jobs as the Galaxy user + (https://docs.galaxyproject.org/en/latest/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 @@ -2457,7 +2459,7 @@ mapping: 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 - + environment_setup_file: type: str default: null @@ -2472,7 +2474,7 @@ mapping: 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. - + job_resource_params_file: type: str default: config/job_resource_params_conf.xml @@ -2482,7 +2484,7 @@ mapping: 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. - + cache_user_job_count: type: bool default: false @@ -2496,28 +2498,28 @@ mapping: 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. - + tool_filters: type: str required: false desc: | Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tools to display. - + tool_label_filters: type: str required: false desc: | Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tool labels to display. - + tool_section_filters: type: str required: false desc: | Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tool sections to display. - + user_tool_filters: type: str default: examples:restrict_upload_to_admins, examples:restrict_encode @@ -2525,7 +2527,7 @@ mapping: desc: | Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tools to display. - + user_tool_section_filters: type: str default: examples:restrict_text @@ -2533,7 +2535,7 @@ mapping: desc: | Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tool sections to display. - + user_tool_label_filters: type: str default: examples:restrict_upload_to_admins, examples:restrict_encode @@ -2541,7 +2543,7 @@ mapping: desc: | Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tool labels to display. - + toolbox_filter_base_modules: type: str default: galaxy.tools.toolbox.filters,galaxy.tools.filters @@ -2549,7 +2551,7 @@ mapping: desc: | The base module(s) that are searched for modules for toolbox filtering (https://galaxyproject.org/user-defined-toolbox-filters/) producedures. - + amqp_internal_connection: type: str default: sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE @@ -2560,36 +2562,36 @@ mapping: 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 /database folder (indicated in the commented out line below). - + enable_communication_server: type: bool default: false required: false desc: | Galaxy real time communication server settings - + communication_server_host: type: str default: http://localhost required: false desc: | Galaxy real time communication server settings - + communication_server_port: type: int default: 7070 required: false desc: | Galaxy real time communication server settings - + persistent_communication_rooms: type: str required: false desc: | persistent_communication_rooms is a comma-separated list of rooms that should be always available. - +