diff --git a/lib/galaxy/schema/configuration.py b/lib/galaxy/schema/configuration.py index 57c832c13e6c..476f43c40f38 100644 --- a/lib/galaxy/schema/configuration.py +++ b/lib/galaxy/schema/configuration.py @@ -40,9 +40,7 @@ class ComputedGalaxyConfig(Model): Field( deprecated=True, # TODO: This option seems to be unused in the codebase (?) title="Lims Doc Url", - description="""The URL linked by the "LIMS Documentation" link in the "Help" menu. -**Deprecated**: This is deprecated and will be removed in a future release. -Please use the `helpsite_url` option instead.""", + description="""The URL linked by the "LIMS Documentation" link in the "Help" menu. **Deprecated**: This is deprecated and will be removed in a future release. Please use the `helpsite_url` option instead.""", ), ] = "https://usegalaxy.org/u/rkchak/p/sts" @@ -51,8 +49,7 @@ class ComputedGalaxyConfig(Model): Field( deprecated=True, # TODO: This option seems to be used only in tests (?) title="Markdown To Pdf Available", - description="""Determines if the markdown to pdf conversion is available. -**Deprecated**: This is deprecated and will be removed in a future release.""", + description="""Determines if the markdown to pdf conversion is available. **Deprecated**: This is deprecated and will be removed in a future release.""", ), ] = False @@ -196,8 +193,7 @@ class AdminOnlyComputedGalaxyConfig(ComputedGalaxyConfig): List[str], Field( title="Tool Shed Urls", - description="""List of Tool Shed URLs to search for tools. This is a list of -fully qualified URLs (e.g., https://toolshed.g2.bx.psu.edu/).""", + description="""List of Tool Shed URLs to search for tools. This is a list of fully qualified URLs (e.g., https://toolshed.g2.bx.psu.edu/).""", ), ] = [] @@ -213,8 +209,7 @@ class UserOnlyComputedGalaxyConfig(ComputedGalaxyConfig): PanelViewDict = Dict[str, Any] PanelViewField = Field( title="Panel Views", - description="""Definitions of static toolbox panel views embedded directly in the config instead of reading -YAML from directory with panel_views_dir.""", + description="""Definitions of static toolbox panel views embedded directly in the config instead of reading YAML from directory with panel_views_dir.""", ) @@ -285,8 +280,7 @@ class ExposableGalaxyConfig(Model): Field( per_host=True, title="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.""", + 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.""", ), ] = None @@ -355,12 +349,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Default Locale", - description="""Default localization for Galaxy UI. -Allowed values are listed at the end of client/src/nls/locale.js. -With the default value (auto), the locale will be automatically adjusted to -the user's navigator language. -Users can override this settings in their user preferences if the localization -settings are enabled in user_preferences_extra_conf.yml""", + description="""Default localization for Galaxy UI. Allowed values are listed at the end of client/src/nls/locale.js. With the default value (auto), the locale will be automatically adjusted to the user's navigator language. Users can override this settings in their user preferences if the localization settings are enabled in user_preferences_extra_conf.yml""", ), ] = "auto" @@ -376,8 +365,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Enable Tool Recommendations", - description="""Allow the display of tool recommendations in workflow editor and after tool execution. -If it is enabled and set to true, please enable 'tool_recommendation_model_path' as well""", + description="""Allow the display of tool recommendations in workflow editor and after tool execution. If it is enabled and set to true, please enable 'tool_recommendation_model_path' as well""", ), ] = False @@ -394,9 +382,7 @@ class ExposableGalaxyConfig(Model): Field( path_resolves_to=CONFIG_DIR, title="Admin Tool Recommendations Path", - description="""Set path to the additional tool preferences from Galaxy admins. -It has two blocks. One for listing deprecated tools which will be removed from the recommendations and -another is for adding additional tools to be recommended along side those from the deep learning model.""", + description="""Set path to the additional tool preferences from Galaxy admins. It has two blocks. One for listing deprecated tools which will be removed from the recommendations and another is for adding additional tools to be recommended along side those from the deep learning model.""", ), ] = "tool_recommendations_overwrite.yml" @@ -404,9 +390,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Overwrite Model Recommendations", - description="""Overwrite or append to the tool recommendations by the deep learning model. When set to true, all the recommendations by the deep learning model -are overwritten by the recommendations set by an admin in a config file 'tool_recommendations_overwrite.yml'. When set to false, the recommended tools -by admins and predicted by the deep learning model are shown.""", + description="""Overwrite or append to the tool recommendations by the deep learning model. When set to true, all the recommendations by the deep learning model are overwritten by the recommendations set by an admin in a config file 'tool_recommendations_overwrite.yml'. When set to false, the recommended tools by admins and predicted by the deep learning model are shown.""", ), ] = False @@ -438,9 +422,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="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)""", + 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)""", ), ] = True @@ -448,10 +430,7 @@ class ExposableGalaxyConfig(Model): Optional[bool], Field( title="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""", + 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""", ), ] = False @@ -468,11 +447,7 @@ class ExposableGalaxyConfig(Model): Optional[Union[bool, str]], Field( title="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.""", + 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.""", ), ] = None @@ -530,8 +505,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Google Analytics Code", - description="""You can enter tracking code here to track visitor's behavior -through your Google Analytics account. Example: UA-XXXXXXXX-Y""", + description="""You can enter tracking code here to track visitor's behavior through your Google Analytics account. Example: UA-XXXXXXXX-Y""", ), ] = None @@ -539,8 +513,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Plausible Server", - description="""Please enter the URL for the Plausible server (including https) so this can be used for tracking -with Plausible (https://plausible.io/).""", + description="""Please enter the URL for the Plausible server (including https) so this can be used for tracking with Plausible (https://plausible.io/).""", ), ] = None @@ -548,8 +521,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Plausible Domain", - description="""Please enter the URL for the Galaxy server so this can be used for tracking -with Plausible (https://plausible.io/).""", + description="""Please enter the URL for the Galaxy server so this can be used for tracking with Plausible (https://plausible.io/).""", ), ] = None @@ -557,8 +529,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Matomo Server", - description="""Please enter the URL for the Matomo server (including https) so this can be used for tracking -with Matomo (https://matomo.org/).""", + description="""Please enter the URL for the Matomo server (including https) so this can be used for tracking with Matomo (https://matomo.org/).""", ), ] = None @@ -566,8 +537,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Matomo Site Id", - description="""Please enter the site ID for the Matomo server so this can be used for tracking -with Matomo (https://matomo.org/).""", + description="""Please enter the site ID for the Matomo server so this can be used for tracking with Matomo (https://matomo.org/).""", ), ] = None @@ -575,12 +545,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="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.""", + 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.""", ), ] = False @@ -588,9 +553,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Enable Beta Markdown Export", - description="""Enable export of Galaxy Markdown documents (pages and workflow reports) -to PDF. Requires manual installation and setup of weasyprint (latest version -available for Python 2.7 is 0.42).""", + description="""Enable export of Galaxy Markdown documents (pages and workflow reports) to PDF. Requires manual installation and setup of weasyprint (latest version available for Python 2.7 is 0.42).""", ), ] = False @@ -607,13 +570,7 @@ class ExposableGalaxyConfig(Model): Field( per_host=True, title="Simplified Workflow Run Ui", - description="""If set to 'off' by default, always use the traditional workflow form that renders -all steps in the GUI and serializes the tool state of all steps during -invocation. Set to 'prefer' to default to a simplified workflow UI that -only renders the inputs if possible (the workflow must have no disconnected -runtime inputs and not replacement parameters within tool steps). In the -future 'force' may be added an option for Galaskio-style servers that should -only render simplified workflows.""", + description="""If set to 'off' by default, always use the traditional workflow form that renders all steps in the GUI and serializes the tool state of all steps during invocation. Set to 'prefer' to default to a simplified workflow UI that only renders the inputs if possible (the workflow must have no disconnected runtime inputs and not replacement parameters within tool steps). In the future 'force' may be added an option for Galaskio-style servers that should only render simplified workflows.""", ), ] = "prefer" @@ -622,13 +579,7 @@ class ExposableGalaxyConfig(Model): Field( per_host=True, title="Simplified Workflow Run Ui Target History", - description="""When the simplified workflow run form is rendered, should the invocation outputs -be sent to the 'current' history or a 'new' history. If the user should be presented -and option between these - set this to 'prefer_current' or 'prefer_new' to display -a runtime setting with the corresponding default. The default is to provide the -user this option and default it to the current history (the traditional behavior -of Galaxy for years) - this corresponds to the setting 'prefer_current'. -""", + description="""When the simplified workflow run form is rendered, should the invocation outputs be sent to the 'current' history or a 'new' history. If the user should be presented and option between these - set this to 'prefer_current' or 'prefer_new' to display a runtime setting with the corresponding default. The default is to provide the user this option and default it to the current history (the traditional behavior of Galaxy for years) - this corresponds to the setting 'prefer_current'.""", ), ] = "prefer_current" @@ -637,8 +588,7 @@ class ExposableGalaxyConfig(Model): Field( per_host=True, title="Simplified Workflow Run Ui Job Cache", - description="""When the simplified workflow run form is rendered, should the invocation use job -caching. This isn't a boolean so an option for 'show-selection' can be added later.""", + description="""When the simplified workflow run form is rendered, should the invocation use job caching. This isn't a boolean so an option for 'show-selection' can be added later.""", ), ] = "off" @@ -646,8 +596,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="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.""", + 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.""", ), ] @@ -655,10 +604,7 @@ class ExposableGalaxyConfig(Model): int, Field( title="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: 10MB). -""", + 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: 10MB).""", ), ] = 10485760 @@ -667,11 +613,7 @@ class ExposableGalaxyConfig(Model): Field( per_host=True, title="Ftp Upload Site", - description="""Enable Galaxy's "Upload via FTP" interface. -You'll need to install and configure an FTP server (we've used ProFTPd since it can use Galaxy's -database for authentication) and set the following two options. -This will be provided to users in the help text as 'log in to the FTP server at '. -Thus, it should be the hostname of your FTP server.""", + description="""Enable Galaxy's "Upload via FTP" interface. You'll need to install and configure an FTP server (we've used ProFTPd since it can use Galaxy's database for authentication) and set the following two options. This will be provided to users in the help text as 'log in to the FTP server at '. Thus, it should be the hostname of your FTP server.""", ), ] = None @@ -687,8 +629,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Inactivity Box Content", - description="""Shown in warning box to users that were not activated yet. -In use only if activation_grace_period is set.""", + description="""Shown in warning box to users that were not activated yet. In use only if activation_grace_period is set.""", ), ] = "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." @@ -712,9 +653,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Aws Estimate", - description="""This flag enables an AWS cost estimate for every job based on their runtime matrices. -CPU, RAM and runtime usage is mapped against AWS pricing table. -Please note, that those numbers are only estimates.""", + description="""This flag enables an AWS cost estimate for every job based on their runtime matrices. CPU, RAM and runtime usage is mapped against AWS pricing table. Please note, that those numbers are only estimates.""", ), ] = False @@ -722,12 +661,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Carbon Emission Estimates", - description="""This flag enables carbon emissions estimates for every job based on its runtime metrics. -CPU and RAM usage and the total job runtime are used to determine an estimate value. -These estimates and are based off of the work of the Green Algorithms Project and -the United States Environmental Protection Agency (EPA). -Visit https://www.green-algorithms.org/ and https://www.epa.gov/energy/greenhouse-gas-equivalencies-calculator. -for more details.""", + description="""This flag enables carbon emissions estimates for every job based on its runtime metrics. CPU and RAM usage and the total job runtime are used to determine an estimate value. These estimates and are based off of the work of the Green Algorithms Project and the United States Environmental Protection Agency (EPA). Visit https://www.green-algorithms.org/ and https://www.epa.gov/energy/greenhouse-gas-equivalencies-calculator for more details.""", ), ] = True @@ -735,11 +669,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Geographical Server Location Code", - description="""The estimated geographical location of the server hosting your galaxy instance given as an ISO 3166 code. -This is used to make carbon emissions estimates more accurate as the location effects the -carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the -`geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations, -visit https://galaxyproject.org/admin/carbon_emissions""", + description="""The estimated geographical location of the server hosting your galaxy instance given as an ISO 3166 code. This is used to make carbon emissions estimates more accurate as the location effects the carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations, visit https://galaxyproject.org/admin/carbon_emissions""", ), ] = "GLOBAL" @@ -747,11 +677,7 @@ class ExposableGalaxyConfig(Model): float, Field( title="Power Usage Effectiveness", - description="""The estimated power usage effectiveness of the data centre housing the server your galaxy -instance is running on. This can make carbon emissions estimates more accurate. -For more information on how to calculate a PUE value, visit -https://en.wikipedia.org/wiki/Power_usage_effectiveness -""", + description="""The estimated power usage effectiveness of the data centre housing the server your galaxy instance is running on. This can make carbon emissions estimates more accurate. For more information on how to calculate a PUE value, visit https://en.wikipedia.org/wiki/Power_usage_effectiveness""", ), ] = 1.67 @@ -778,8 +704,7 @@ class ExposableGalaxyConfig(Model): Field( reloadable=True, title="Message Box Class", - description="""Class of the message box under the masthead. -Possible values are: 'info' (the default), 'warning', 'error', 'done'.""", + description="""Class of the message box under the masthead. Possible values are: 'info' (the default), 'warning', 'error', 'done'.""", ), ] = "info" @@ -787,11 +712,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Mailing Join Address", - description="""On the user registration form, users may choose to join a mailing list. This -is the address used to subscribe to the list. Uncomment and leave empty if you -want to remove this option from the user registration form. - -Example value 'galaxy-announce-join@lists.galaxyproject.org'""", + description="""On the user registration form, users may choose to join a mailing list. This is the address used to subscribe to the list. Uncomment and leave empty if you want to remove this option from the user registration form. Example value 'galaxy-announce-join@lists.galaxyproject.org'""", ), ] = "galaxy-announce-join@bx.psu.edu" @@ -799,9 +720,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="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.""", + 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.""", ), ] = "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." @@ -811,8 +730,7 @@ class ExposableGalaxyConfig(Model): reloadable=True, per_host=True, title="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.""", + description="""The URL of the page to display in Galaxy's middle pane when loaded. This can be an absolute or relative URL.""", ), ] = "/static/welcome.html" @@ -820,8 +738,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Show Welcome With Login", - description="""Show the site's welcome page (see welcome_url) alongside the login page -(even if require_login is true).""", + description="""Show the site's welcome page (see welcome_url) alongside the login page (even if require_login is true).""", ), ] = False @@ -829,10 +746,7 @@ class ExposableGalaxyConfig(Model): Optional[str], Field( title="Cookie Domain", - description="""Tell Galaxy that multiple domains sharing the same root are associated -to this instance and wants to share the same session cookie. -This allow a user to stay logged in when passing from one subdomain to the other. -This root domain will be written in the unique session cookie shared by all subdomains.""", + description="""Tell Galaxy that multiple domains sharing the same root are associated to this instance and wants to share the same session cookie. This allow a user to stay logged in when passing from one subdomain to the other. This root domain will be written in the unique session cookie shared by all subdomains.""", ), ] @@ -840,10 +754,7 @@ class ExposableGalaxyConfig(Model): int, Field( title="Select Type Workflow Threshold", - description="""Due to performance considerations (select2 fields are pretty 'expensive' in terms of memory usage) -Galaxy uses the regular select fields for non-dataset selectors in the workflow run form. -use 0 in order to always use select2 fields, use -1 (default) in order to always use the regular select fields, -use any other positive number as threshold (above threshold: regular select fields will be used)""", + description="""Due to performance considerations (select2 fields are pretty 'expensive' in terms of memory usage) Galaxy uses the regular select fields for non-dataset selectors in the workflow run form. Use 0 in order to always use select2 fields, use -1 (default) in order to always use the regular select fields, use any other positive number as threshold (above threshold: regular select fields will be used)""", ), ] = -1 @@ -852,10 +763,7 @@ class ExposableGalaxyConfig(Model): Field( reloadable=True, title="Toolbox Auto Sort", - description="""If true, the toolbox will be sorted by tool id when the toolbox is loaded. -This is useful for ensuring that tools are always displayed in the same -order in the UI. If false, the order of tools in the toolbox will be -preserved as they are loaded from the tool config files.""", + description="""If true, the toolbox will be sorted by tool id when the toolbox is loaded. This is useful for ensuring that tools are always displayed in the same order in the UI. If false, the order of tools in the toolbox will be preserved as they are loaded from the tool config files.""", ), ] = True @@ -863,10 +771,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Default Panel View", - description="""Default tool panel view for the current Galaxy configuration. This should refer to an id of -a panel view defined using the panel_views or panel_views_dir configuration options or an -EDAM panel view. The default panel view is simply called `default` and refers to the tool -panel state defined by the integrated tool panel.""", + description="""Default tool panel view for the current Galaxy configuration. This should refer to an id of a panel view defined using the panel_views or panel_views_dir configuration options or an EDAM panel view. The default panel view is simply called `default` and refers to the tool panel state defined by the integrated tool panel.""", ), ] = "default" @@ -874,11 +779,7 @@ class ExposableGalaxyConfig(Model): Literal["always-on", "always-off"], Field( title="Upload From Form Button", - description="""If 'always-on', add another button to tool form data inputs that allow uploading -data from the tool form in fewer clicks (at the expense of making the form more complicated). This applies to workflows as well. - -Avoiding making this a boolean because we may add options such as 'in-single-form-view' -or 'in-simplified-workflow-views'. https://github.com/galaxyproject/galaxy/pull/9809/files#r461889109""", + description="""If 'always-on', add another button to tool form data inputs that allow uploading data from the tool form in fewer clicks (at the expense of making the form more complicated). This applies to workflows as well. Avoiding making this a boolean because we may add options such as 'in-single-form-view' or 'in-simplified-workflow-views'. https://github.com/galaxyproject/galaxy/pull/9809/files#r461889109""", ), ] = "always-off" @@ -894,14 +795,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="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.""", + 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.""", ), ] = False @@ -909,11 +803,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Enable Tool Source Display", - description="""This option allows users to view the tool wrapper source code. This is -safe to enable if you have not hardcoded any secrets in any of the tool -wrappers installed on this Galaxy server. If you have only installed tool -wrappers from public tool sheds and tools shipped with Galaxy there you -can enable this option.""", + description="""This option allows users to view the tool wrapper source code. This is safe to enable if you have not hardcoded any secrets in any of the tool wrappers installed on this Galaxy server. If you have only installed tool wrappers from public tool sheds and tools shipped with Galaxy there you can enable this option.""", ), ] = False @@ -921,9 +811,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Enable Celery Tasks", - description="""Offload long-running tasks to a Celery task queue. -Activate this only if you have setup a Celery worker for Galaxy. -For details, see https://docs.galaxyproject.org/en/master/admin/production.html""", + description="""Offload long-running tasks to a Celery task queue. Activate this only if you have setup a Celery worker for Galaxy. For details, see https://docs.galaxyproject.org/en/master/admin/production.html""", ), ] = False @@ -931,9 +819,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Welcome Directory", - description="""Location of New User Welcome data, a single directory containing the -images and JSON of Topics/Subtopics/Slides as export. This location -is relative to galaxy/static""", + description="""Location of New User Welcome data, a single directory containing the images and JSON of Topics/Subtopics/Slides as export. This location is relative to galaxy/static""", ), ] = "plugins/welcome_page/new_user/static/topics/" @@ -941,11 +827,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Tool Training Recommendations", - description="""Displays a link to training material, if any includes the current tool. -When activated the following options also need to be set: - tool_training_recommendations_link, - tool_training_recommendations_api_url -""", + description="""Displays a link to training material, if any includes the current tool. When activated the following options also need to be set: tool_training_recommendations_link, tool_training_recommendations_api_url""", ), ] = True @@ -953,14 +835,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Tool Training Recommendations Link", - description="""Template URL to display all tutorials containing current tool. -Valid template inputs are: - {repository_owner} - {name} - {tool_id} - {training_tool_identifier} - {version} -""", + description="""Template URL to display all tutorials containing current tool. Valid template inputs are: {repository_owner} {name} {tool_id} {training_tool_identifier} {version}""", ), ] = "https://training.galaxyproject.org/training-material/by-tool/{training_tool_identifier}.html" @@ -968,8 +843,7 @@ class ExposableGalaxyConfig(Model): str, Field( title="Tool Training Recommendations Api Url", - description="""URL to API describing tutorials containing specific tools. -When CORS is used, make sure to add this host.""", + description="""URL to API describing tutorials containing specific tools. When CORS is used, make sure to add this host.""", ), ] = "https://training.galaxyproject.org/training-material/api/top-tools.json" @@ -977,14 +851,7 @@ class ExposableGalaxyConfig(Model): bool, Field( title="Enable Notification System", - description="""Enables the Notification System integrated in Galaxy. - -Users can receive automatic notifications when a certain resource is shared with them or when some long running operations have finished, etc. - -The system allows notification scheduling and expiration, and users can opt-out of specific notification categories or channels. - -Admins can schedule and broadcast notifications that will be visible to all users, including special server-wide announcements such as scheduled maintenance, high load warnings, and event announcements, to name a few examples. -""", + description="""Enables the Notification System integrated in Galaxy. Users can receive automatic notifications when a certain resource is shared with them or when some long running operations have finished, etc. The system allows notification scheduling and expiration, and users can opt-out of specific notification categories or channels. Admins can schedule and broadcast notifications that will be visible to all users, including special server-wide announcements such as scheduled maintenance, high load warnings, and event announcements, to name a few examples.""", ), ] = False @@ -999,8 +866,7 @@ class AdminExposableGalaxyConfig(ExposableGalaxyConfig): Optional[str], Field( title="Library Import Dir", - description="""Add an option to the library upload form which allows administrators to -upload a directory of files.""", + description="""Add an option to the library upload form which allows administrators to upload a directory of files.""", ), ] = None @@ -1008,11 +874,7 @@ class AdminExposableGalaxyConfig(ExposableGalaxyConfig): Optional[str], Field( title="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.""", + 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.""", ), ] = None @@ -1020,8 +882,7 @@ class AdminExposableGalaxyConfig(ExposableGalaxyConfig): bool, Field( title="Allow Library Path Paste", - description="""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.""", + description="""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.""", ), ] = False @@ -1044,10 +905,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -1055,11 +913,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Managed Config Dir", - description="""The directory that will be prepended to relative paths in options specifying -config files controlled by Galaxy (such as shed_tool_config_file, etc.). Must be -writable by the user running Galaxy. Defaults to `/` if running -Galaxy from source or `/config` otherwise. -""", + description="""The directory that will be prepended to relative paths in options specifying config files controlled by Galaxy (such as shed_tool_config_file, etc.). Must be writable by the user running Galaxy. Defaults to `/` if running Galaxy from source or `/config` otherwise.""", ), ] = None @@ -1067,11 +921,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 -`/data` otherwise. -""", + 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 `/data` otherwise.""", ), ] = None @@ -1089,8 +939,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=DATA_DIR, title="Cache Dir", - description="""Top level cache directory. Any other cache directories (tool_cache_data_dir, -template_cache_path, etc.) should be subdirectories.""", + description="""Top level cache directory. Any other cache directories (tool_cache_data_dir, template_cache_path, etc.) should be subdirectories.""", ), ] = "cache" @@ -1098,22 +947,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Database Connection", - description="""By default, Galaxy uses a SQLite database at '/universe.sqlite'. You -may use a SQLAlchemy connection string to specify an external database instead. - -Sample default 'sqlite:////universe.sqlite?isolation_level=IMMEDIATE' - -You may specify additional options that will be passed to the SQLAlchemy -database engine by using the prefix "database_engine_option_". For some of these -options, default values are provided (e.g. see database_engine_option_pool_size, -etc.). - -The same applies to `install_database_connection`, for which you should use the -"install_database_engine_option_" prefix. - -For more options, please check SQLAlchemy's documentation at -https://docs.sqlalchemy.org/en/14/core/engines.html?highlight=create_engine#sqlalchemy.create_engine -""", + description="""By default, Galaxy uses a SQLite database at '/universe.sqlite'. You may use a SQLAlchemy connection string to specify an external database instead. Sample default 'sqlite:////universe.sqlite?isolation_level=IMMEDIATE' You may specify additional options that will be passed to the SQLAlchemy database engine by using the prefix "database_engine_option_". For some of these options, default values are provided (e.g. see database_engine_option_pool_size, etc.). The same applies to `install_database_connection`, for which you should use the "install_database_engine_option_" prefix. For more options, please check SQLAlchemy's documentation at https://docs.sqlalchemy.org/en/14/core/engines.html?highlight=create_engine#sqlalchemy.create_engine""", ), ] = None @@ -1121,8 +955,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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.""", + 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.""", ), ] = 5 @@ -1130,8 +963,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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.""", + 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.""", ), ] = 10 @@ -1139,8 +971,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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).""", + 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).""", ), ] = -1 @@ -1148,10 +979,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -1159,10 +987,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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' -""", + 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'""", ), ] = False @@ -1170,10 +995,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -1181,13 +1003,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Database Log Query Counts", - description="""Log number of SQL queries executed and total time spent dispatching SQL statements for -each web request. If statsd is also enabled this information will be logged there as well. -This should be considered somewhat experimental, we are unsure of the performance costs of -running this in production. This is useful information for optimizing database interaction -performance. Similar information can be obtained on a per-request basis by enabling the -sql_debug middleware and adding sql_debug=1 to a request string. -""", + description="""Log number of SQL queries executed and total time spent dispatching SQL statements for each web request. If statsd is also enabled this information will be logged there as well. This should be considered somewhat experimental, we are unsure of the performance costs of running this in production. This is useful information for optimizing database interaction performance. Similar information can be obtained on a per-request basis by enabling the sql_debug middleware and adding sql_debug=1 to a request string.""", ), ] = False @@ -1195,10 +1011,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[float], Field( title="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. -""", + 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.""", ), ] = 0.0 @@ -1206,11 +1019,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -1218,15 +1027,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Install Database Connection", - description="""By default, Galaxy will use the same database to track user data and -tool shed install data. There are many situations in which it is -valuable to separate these - for instance bootstrapping fresh Galaxy -instances with pretested installs. The following option can be used to -separate the tool shed install database (all other options listed above -but prefixed with ``install_`` are also available). - -Defaults to the value of the 'database_connection' option. -""", + description="""By default, Galaxy will use the same database to track user data and tool shed install data. There are many situations in which it is valuable to separate these - for instance bootstrapping fresh Galaxy instances with pretested installs. The following option can be used to separate the tool shed install database (all other options listed above but prefixed with ``install_`` are also available). Defaults to the value of the 'database_connection' option.""", ), ] = None @@ -1234,9 +1035,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -1268,9 +1067,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="History Audit Table Prune Interval", - description="""Time (in seconds) between attempts to remove old rows from the history_audit database table. -Set to 0 to disable pruning. -""", + description="""Time (in seconds) between attempts to remove old rows from the history_audit database table. Set to 0 to disable pruning.""", ), ] = 3600 @@ -1279,11 +1076,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=DATA_DIR, title="File Path", - description="""Where dataset files are stored. It must be accessible at the same path on any cluster -nodes that will run Galaxy jobs, unless using Pulsar. The default value has been changed -from 'files' to 'objects' as of 20.05; however, Galaxy will first check if the 'files' -directory exists before using 'objects' as the default. -""", + description="""Where dataset files are stored. It must be accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar. The default value has been changed from 'files' to 'objects' as of 20.05; however, Galaxy will first check if the 'files' directory exists before using 'objects' as the default.""", ), ] = "objects" @@ -1292,9 +1085,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=DATA_DIR, title="New File Path", - description="""Where temporary files are stored. It must be accessible at the same path on any cluster -nodes that will run Galaxy jobs, unless using Pulsar. -""", + description="""Where temporary files are stored. It must be accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar.""", ), ] = "tmp" @@ -1302,9 +1093,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Maximum Upload File Size", - description="""Maximum size of uploadable files, specified in bytes (default: 100GB). -This value is ignored if an external upload server is configured. -""", + description="""Maximum size of uploadable files, specified in bytes (default: 100GB). This value is ignored if an external upload server is configured.""", ), ] = 107374182400 @@ -1313,12 +1102,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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. -""", + 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.""", ), ] = "tool_conf.xml" @@ -1327,16 +1111,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=MANAGED_CONFIG_DIR, title="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. -""", + 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.""", ), ] = "shed_tool_conf.xml" @@ -1346,11 +1121,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) path_resolves_to=MANAGED_CONFIG_DIR, deprecated=True, title="Migrated Tools Config", - description="""This option is deprecated. -In previous releases this file was maintained by tool migration scripts that are no -longer part of the code base. The option remains as a placeholder for deployments where -these scripts were previously run and such a file exists. -""", + description="""This option is deprecated. In previous releases this file was maintained by tool migration scripts that are no longer part of the code base. The option remains as a placeholder for deployments where these scripts were previously run and such a file exists.""", ), ] = "migrated_tools_conf.xml" @@ -1358,13 +1129,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 . -""", + 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 .""", ), ] = "integrated_tool_panel.xml" @@ -1372,10 +1137,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 - tag. -""", + 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 tag.""", ), ] = "tools" @@ -1384,14 +1146,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=DATA_DIR, title="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. -""", + 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.""", ), ] = "dependencies" @@ -1400,10 +1155,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Dependency Resolvers Config File", - description="""Specifies the path to the standalone dependency resolvers configuration file. This -configuration can now be specified directly in the Galaxy configuration, see the -description of the 'dependency_resolvers' option for details. -""", + description="""Specifies the path to the standalone dependency resolvers configuration file. This configuration can now be specified directly in the Galaxy configuration, see the description of the 'dependency_resolvers' option for details.""", ), ] = "dependency_resolvers_conf.xml" @@ -1411,11 +1163,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Conda Prefix", - description="""conda_prefix is the location on the filesystem where Conda packages and environments are -installed. - -Sample default '/_conda' -""", + description="""conda_prefix is the location on the filesystem where Conda packages and environments are installed. Sample default '/_conda'""", ), ] = None @@ -1423,9 +1171,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Conda Exec", - description="""Override the Conda executable to use, it will default to the one on the -PATH (if available) and then to /bin/conda -""", + description="""Override the Conda executable to use, it will default to the one on the PATH (if available) and then to /bin/conda""", ), ] = None @@ -1441,9 +1187,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Conda Ensure Channels", - description="""conda channels to enable by default -(https://conda.io/docs/user-guide/tasks/manage-channels.html) -""", + description="""conda channels to enable by default (https://conda.io/docs/user-guide/tasks/manage-channels.html)""", ), ] = "conda-forge,bioconda,defaults" @@ -1459,9 +1203,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Conda Auto Install", - description="""Set to true to instruct Galaxy to look for and install missing tool -dependencies before each job runs. -""", + description="""Set to true to instruct Galaxy to look for and install missing tool dependencies before each job runs.""", ), ] = False @@ -1469,9 +1211,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -1479,12 +1219,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -1493,9 +1228,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Local Conda Mapping File", - description="""Path to a file that provides a mapping from abstract packages to concrete conda packages. -See `config/local_conda_mapping.yml.sample` for examples. -""", + description="""Path to a file that provides a mapping from abstract packages to concrete conda packages. See `config/local_conda_mapping.yml.sample` for examples.""", ), ] = "local_conda_mapping.yml" @@ -1504,9 +1237,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Modules Mapping Files", - description="""Path to a file that provides a mapping from abstract packages to locally installed modules. -See `config/environment_modules_mapping.yml.sample` for examples. -""", + description="""Path to a file that provides a mapping from abstract packages to locally installed modules. See `config/environment_modules_mapping.yml.sample` for examples.""", ), ] = "environment_modules_mapping.yml" @@ -1514,17 +1245,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -1532,11 +1253,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Tool Dependency Cache Dir", - description="""By default the tool_dependency_cache_dir is the _cache directory -of the tool dependency directory. - -Sample default '/_cache' -""", + description="""By default the tool_dependency_cache_dir is the _cache directory of the tool dependency directory. Sample default '/_cache'""", ), ] = None @@ -1544,10 +1261,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -1556,9 +1270,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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). -""", + 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).""", ), ] = "tool_sheds_conf.xml" @@ -1566,14 +1278,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) WatchToolOptions, Field( title="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. -""", + 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.""", ), ] = "false" @@ -1581,9 +1286,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) WatchToolOptions, Field( title="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. -""", + description="""Monitor dynamic job rules. If changes are found, rules are automatically reloaded. Takes the same values as the 'watch_tools' option.""", ), ] = "false" @@ -1591,10 +1294,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) WatchToolOptions, Field( title="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. -""", + 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.""", ), ] = "false" @@ -1602,10 +1302,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) WatchToolOptions, Field( title="Watch Tours", - description="""Monitor the interactive tours directory specified in the 'tour_config_dir' option. If -changes are found, modified tours are automatically reloaded. Takes the same values as the -'watch_tools' option. -""", + description="""Monitor the interactive tours directory specified in the 'tour_config_dir' option. If changes are found, modified tours are automatically reloaded. Takes the same values as the 'watch_tools' option.""", ), ] = "false" @@ -1614,13 +1311,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CACHE_DIR, title="Short Term Storage Dir", - description="""Location of files available for a short time as downloads (short term storage). -This directory is exclusively used for serving dynamically generated downloadable -content. Galaxy may uses the new_file_path parameter as a general temporary directory -and that directory should be monitored by a tool such as tmpwatch in production -environments. short_term_storage_dir on the other hand is monitored by Galaxy's task -framework and should not require such external tooling. -""", + description="""Location of files available for a short time as downloads (short term storage). This directory is exclusively used for serving dynamically generated downloadable content. Galaxy may uses the new_file_path parameter as a general temporary directory and that directory should be monitored by a tool such as tmpwatch in production environments. short_term_storage_dir on the other hand is monitored by Galaxy's task framework and should not require such external tooling.""", ), ] = "short_term_web_storage" @@ -1628,9 +1319,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Short Term Storage Default Duration", - description="""Default duration before short term web storage files will be cleaned up by Galaxy -tasks (in seconds). The default duration is 1 day. -""", + description="""Default duration before short term web storage files will be cleaned up by Galaxy tasks (in seconds). The default duration is 1 day.""", ), ] = 86400 @@ -1638,9 +1327,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Short Term Storage Maximum Duration", - description="""The maximum duration short term storage files can hosted before they will be marked for -clean up. The default setting of 0 indicates no limit here. -""", + description="""The maximum duration short term storage files can hosted before they will be marked for clean up. The default setting of 0 indicates no limit here.""", ), ] = 0 @@ -1648,9 +1335,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Short Term Storage Cleanup Interval", - description="""How many seconds between instances of short term storage being cleaned up in default -Celery task configuration. -""", + description="""How many seconds between instances of short term storage being cleaned up in default Celery task configuration.""", ), ] = 3600 @@ -1675,12 +1360,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -1688,12 +1368,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Container Resolvers Config File", - description="""Container resolvers configuration. Set up a file describing -container resolvers to use when discovering containers for Galaxy. If -this is set to None, the default container resolvers loaded is -determined by enable_mulled_containers. -For available options see https://docs.galaxyproject.org/en/master/admin/container_resolvers.html -""", + description="""Container resolvers configuration. Set up a file describing container resolvers to use when discovering containers for Galaxy. If this is set to None, the default container resolvers loaded is determined by enable_mulled_containers. For available options see https://docs.galaxyproject.org/en/master/admin/container_resolvers.html""", ), ] = None @@ -1701,11 +1376,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[List[Any]], Field( title="Container Resolvers", - description="""Rather than specifying a container_resolvers_config_file, the definition of the -resolvers to enable can be embedded into Galaxy's config with this option. -This has no effect if a container_resolvers_config_file is used. -Takes the same options that can be set in container_resolvers_config_file. -""", + description="""Rather than specifying a container_resolvers_config_file, the definition of the resolvers to enable can be embedded into Galaxy's config with this option. This has no effect if a container_resolvers_config_file is used. Takes the same options that can be set in container_resolvers_config_file.""", ), ] = None @@ -1714,12 +1385,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=TOOL_DEPENDENCY_DIR, title="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. -""", + 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.""", ), ] = "involucro" @@ -1727,9 +1393,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Involucro Auto Init", - description="""Install involucro as needed to build Docker or Singularity containers for tools. Ignored if -relevant container resolver is not used. -""", + description="""Install involucro as needed to build Docker or Singularity containers for tools. Ignored if relevant container resolver is not used.""", ), ] = True @@ -1745,11 +1409,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -1757,11 +1417,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 12 @@ -1770,10 +1426,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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). -""", + 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).""", ), ] = "tool_data_table_conf.xml" @@ -1782,13 +1435,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=MANAGED_CONFIG_DIR, title="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. -""", + 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.""", ), ] = "shed_tool_data_table_conf.xml" @@ -1796,10 +1443,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 -""", + 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""", ), ] = "tool-data" @@ -1807,9 +1451,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Shed Tool Data Path", - description="""Directory where Tool Data Table related files will be placed when installed from a -ToolShed. Defaults to the value of the 'tool_data_path' option. -""", + description="""Directory where Tool Data Table related files will be placed when installed from a ToolShed. Defaults to the value of the 'tool_data_path' option.""", ), ] = None @@ -1817,14 +1459,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) WatchToolOptions, Field( title="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. -""", + 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.""", ), ] = "false" @@ -1841,9 +1476,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Build Sites Config File", - description="""File that defines the builds (dbkeys) available at sites used by display applications -and the URL to those sites. -""", + description="""File that defines the builds (dbkeys) available at sites used by display applications and the URL to those sites.""", ), ] = "build_sites.yml" @@ -1851,10 +1484,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Builds File Path", - description="""File containing old-style genome builds. - -The value of this option will be resolved with respect to . -""", + description="""File containing old-style genome builds. The value of this option will be resolved with respect to .""", ), ] = "shared/ucsc/builds.txt" @@ -1862,10 +1492,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Len File Path", - description="""Directory where chrom len files are kept, currently mainly used by trackster. - -The value of this option will be resolved with respect to . -""", + description="""Directory where chrom len files are kept, currently mainly used by trackster. The value of this option will be resolved with respect to .""", ), ] = "shared/ucsc/chrom" @@ -1874,11 +1501,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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). -""", + 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).""", ), ] = "datatypes_conf.xml" @@ -1886,11 +1509,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -1898,10 +1517,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "config/plugins/visualizations" @@ -1909,12 +1525,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "config/plugins/tours" @@ -1922,12 +1533,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "config/plugins/webhooks" @@ -1935,12 +1541,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Job Working Directory", - description="""Each job is given a unique empty directory as its current working directory. -This option defines in what parent directory those directories will be -created. - -The value of this option will be resolved with respect to . -""", + description="""Each job is given a unique empty directory as its current working directory. This option defines in what parent directory those directories will be created. The value of this option will be resolved with respect to .""", ), ] = "jobs_directory" @@ -1949,9 +1550,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CACHE_DIR, title="Template Cache Path", - description="""Mako templates are compiled as needed and cached for reuse, this directory is -used for the cache -""", + description="""Mako templates are compiled as needed and cached for reuse, this directory is used for the cache.""", ), ] = "compiled_templates" @@ -1959,9 +1558,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -1985,13 +1582,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "/bin/bash" @@ -1999,12 +1590,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Enable Tool Document Cache", - description="""Whether to enable the tool document cache. This cache stores -expanded XML strings. Enabling the tool cache results in slightly faster startup -times. The tool cache is backed by a SQLite database, which cannot -be stored on certain network disks. The cache location is configurable -using the ``tool_cache_data_dir`` setting, but can be disabled completely here. -""", + description="""Whether to enable the tool document cache. This cache stores expanded XML strings. Enabling the tool cache results in slightly faster startup times. The tool cache is backed by a SQLite database, which cannot be stored on certain network disks. The cache location is configurable using the ``tool_cache_data_dir`` setting, but can be disabled completely here.""", ), ] = False @@ -2012,10 +1598,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Tool Cache Data Dir", - description="""Tool related caching. Fully expanded tools and metadata will be stored at this path. -Per tool_conf cache locations can be configured in (``shed_``)tool_conf.xml files using -the tool_cache_data_dir attribute. -""", + description="""Tool related caching. Fully expanded tools and metadata will be stored at this path. Per tool_conf cache locations can be configured in (``shed_``)tool_conf.xml files using the tool_cache_data_dir attribute.""", ), ] = "tool_cache" @@ -2032,9 +1615,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Biotools Content Directory", - description="""Point Galaxy at a repository consisting of a copy of the bio.tools database (e.g. -https://github.com/bio-tools/content/) to resolve bio.tools data for tool metadata. -""", + description="""Point Galaxy at a repository consisting of a copy of the bio.tools database (e.g. https://github.com/bio-tools/content/) to resolve bio.tools data for tool metadata.""", ), ] = None @@ -2042,9 +1623,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Biotools Use Api", - description="""Set this to true to attempt to resolve bio.tools metadata for tools for tool not -resovled via biotools_content_directory. -""", + description="""Set this to true to attempt to resolve bio.tools metadata for tools for tool not resolved via biotools_content_directory.""", ), ] = False @@ -2078,12 +1657,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Biotools Service Cache Url", - description="""When biotools_service_cache_type = ext:database, this is -the url of the database used by beaker for -bio.tools web service request related caching. -The application config code will set it to the -value of database_connection if this is not set. -""", + description="""When biotools_service_cache_type = ext:database, this is the url of the database used by beaker for bio.tools web service request related caching. The application config code will set it to the value of database_connection if this is not set.""", ), ] = None @@ -2091,10 +1665,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Biotools Service Cache Table Name", - description="""When biotools_service_cache_type = ext:database, this is -the database table name used by beaker for -bio.tools web service request related caching. -""", + description="""When biotools_service_cache_type = ext:database, this is the database table name used by beaker for bio.tools web service request related caching.""", ), ] = "beaker_cache" @@ -2102,10 +1673,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Biotools Service Cache Schema Name", - description="""When biotools_service_cache_type = ext:database, this is -the database table name used by beaker for -bio.tools web service request related caching. -""", + description="""When biotools_service_cache_type = ext:database, this is the database table name used by beaker for bio.tools web service request related caching.""", ), ] = None @@ -2113,10 +1681,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "file" @@ -2125,10 +1690,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CACHE_DIR, title="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. -""", + 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.""", ), ] = "citations/data" @@ -2137,10 +1699,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CACHE_DIR, title="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. -""", + 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.""", ), ] = "citations/locks" @@ -2148,11 +1707,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Citation Cache Url", - description="""When citation_cache_type = ext:database, this is -the url of the database used by beaker for citation -caching. The application config code will set it to the -value of database_connection if this is not set. -""", + description="""When citation_cache_type = ext:database, this is the url of the database used by beaker for citation caching. The application config code will set it to the value of database_connection if this is not set.""", ), ] = None @@ -2160,10 +1715,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Citation Cache Table Name", - description="""When citation_cache_type = ext:database, this is -the database table name used by beaker for -citation related caching. -""", + description="""When citation_cache_type = ext:database, this is the database table name used by beaker for citation related caching.""", ), ] = "beaker_cache" @@ -2171,10 +1723,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Citation Cache Schema Name", - description="""When citation_cache_type = ext:database, this is -the database schema name of the table used by beaker for -citation related caching. -""", + description="""When citation_cache_type = ext:database, this is the database schema name of the table used by beaker for citation related caching.""", ), ] = None @@ -2182,9 +1731,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Mulled Resolution Cache Type", - description="""Mulled resolution caching. Mulled resolution uses external APIs of quay.io, these -requests are caching using this and the following parameters -""", + description="""Mulled resolution caching. Mulled resolution uses external APIs of quay.io, these requests are caching using this and the following parameters.""", ), ] = "file" @@ -2218,11 +1765,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Mulled Resolution Cache Url", - description="""When mulled_resolution_cache_type = ext:database, this is -the url of the database used by beaker for caching mulled resolution -requests. The application config code will set it to the -value of database_connection if this is not set. -""", + description="""When mulled_resolution_cache_type = ext:database, this is the url of the database used by beaker for caching mulled resolution requests. The application config code will set it to the value of database_connection if this is not set.""", ), ] = None @@ -2230,10 +1773,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Mulled Resolution Cache Table Name", - description="""When mulled_resolution_cache_type = ext:database, this is -the database table name used by beaker for -caching mulled resolution requests. -""", + description="""When mulled_resolution_cache_type = ext:database, this is the database table name used by beaker for caching mulled resolution requests.""", ), ] = "beaker_cache" @@ -2241,10 +1781,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Mulled Resolution Cache Schema Name", - description="""When mulled_resolution_cache_type = ext:database, this is -the database schema name of the table used by beaker for -caching mulled resolution requests. -""", + description="""When mulled_resolution_cache_type = ext:database, this is the database schema name of the table used by beaker for caching mulled resolution requests.""", ), ] = None @@ -2253,9 +1790,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Object Store Config File", - description="""Configuration file for the object store -If this is set and exists, it overrides any other objectstore settings. -""", + description="""Configuration file for the object store If this is set and exists, it overrides any other objectstore settings.""", ), ] = "object_store_conf.xml" @@ -2263,18 +1798,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["auto", "external", "celery", "inprocess"]], Field( title="Object Store Cache Monitor Driver", - description="""Specify where cache monitoring is driven for caching object stores -such as S3, Azure, and iRODS. This option has no affect on disk object stores. -For production instances, the cache should be monitored by external tools such -as tmpwatch and this value should be set to 'external'. This will disable all -cache monitoring in Galaxy. Alternatively, 'celery' can monitor caches using -a periodic task or an 'inprocess' thread can be used - but this last option -seriously limits Galaxy's ability to scale. The default of 'auto' will use -'celery' if 'enable_celery_tasks' is set to true or 'inprocess' otherwise. -This option serves as the default for all object stores and can be overridden -on a per object store basis (but don't - just setup tmpwatch for all relevant -cache paths). -""", + description="""Specify where cache monitoring is driven for caching object stores such as S3, Azure, and iRODS. This option has no affect on disk object stores. For production instances, the cache should be monitored by external tools such as tmpwatch and this value should be set to 'external'. This will disable all cache monitoring in Galaxy. Alternatively, 'celery' can monitor caches using a periodic task or an 'inprocess' thread can be used - but this last option seriously limits Galaxy's ability to scale. The default of 'auto' will use 'celery' if 'enable_celery_tasks' is set to true or 'inprocess' otherwise. This option serves as the default for all object stores and can be overridden on a per object store basis (but don't - just setup tmpwatch for all relevant cache paths).""", ), ] = "auto" @@ -2282,12 +1806,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Object Store Cache Monitor Interval", - description="""For object store cache monitoring done by Galaxy, this is the interval between -cache checking steps. This is used by both inprocess cache monitors (which we -recommend you do not use) and by the celery task if it is configured (by setting -enable_celery_tasks to true and not setting object_store_cache_monitor_driver to -external). -""", + description="""For object store cache monitoring done by Galaxy, this is the interval between cache checking steps. This is used by both inprocess cache monitors (which we recommend you do not use) and by the celery task if it is configured (by setting enable_celery_tasks to true and not setting object_store_cache_monitor_driver to external).""", ), ] = 600 @@ -2296,9 +1815,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CACHE_DIR, title="Object Store Cache Path", - description="""Default cache path for caching object stores if cache not configured for -that object store entry. -""", + description="""Default cache path for caching object stores if cache not configured for that object store entry.""", ), ] = "object_store_cache" @@ -2306,9 +1823,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Object Store Cache Size", - description="""Default cache size for caching object stores if cache not configured for -that object store entry. -""", + description="""Default cache size for caching object stores if cache not configured for that object store entry.""", ), ] = -1 @@ -2316,13 +1831,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["uuid", "id"]], Field( title="Object Store Store By", - description="""What Dataset attribute is used to reference files in an ObjectStore implementation, -this can be 'uuid' or 'id'. The default will depend on how the object store is configured, -starting with 20.05 Galaxy will try to default to 'uuid' if it can be sure this -is a new Galaxy instance - but the default will be 'id' in many cases. In particular, -if the name of the directory set in is `objects`, the default will be set -to 'uuid', otherwise it will be 'id'. -""", + description="""What Dataset attribute is used to reference files in an ObjectStore implementation, this can be 'uuid' or 'id'. The default will depend on how the object store is configured, starting with 20.05 Galaxy will try to default to 'uuid' if it can be sure this is a new Galaxy instance - but the default will be 'id' in many cases. In particular, if the name of the directory set in is `objects`, the default will be set to 'uuid', otherwise it will be 'id'.""", ), ] = None @@ -2330,12 +1839,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -2343,10 +1847,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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). -""", + 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).""", ), ] = None @@ -2354,10 +1855,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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). -""", + 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).""", ), ] = None @@ -2365,7 +1863,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Smtp Ssl", - description="""If your SMTP server requires SSL from the beginning of the connection""", + description="""If your SMTP server requires SSL from the beginning of the connection.""", ), ] = False @@ -2373,9 +1871,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Mailing Join Subject", - description="""The subject of the email sent to the mailing list join address. See the -`mailing_join_addr` option for more information. -""", + description="""The subject of the email sent to the mailing list join address. See the `mailing_join_addr` option for more information.""", ), ] = "Join Mailing List" @@ -2383,9 +1879,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Mailing Join Body", - description="""The body of the email sent to the mailing list join address. See the -`mailing_join_addr` option for more information. -""", + description="""The body of the email sent to the mailing list join address. See the `mailing_join_addr` option for more information.""", ), ] = "Join Mailing List" @@ -2393,11 +1887,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -2405,12 +1895,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Email From", - description="""Email address to use in the 'From' field when sending emails for -account activations, workflow step notifications, password resets, and -tool error reports. We recommend using a string in the following format: -Galaxy Project . -If not configured, '' will be used. -""", + description="""Email address to use in the 'From' field when sending emails for account activations, workflow step notifications, password resets, and tool error reports. We recommend using a string in the following format: Galaxy Project . If not configured, '' will be used.""", ), ] = None @@ -2418,9 +1903,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Custom Activation Email Message", - description="""This text will be inserted at the end of the activation email's message, before -the 'Your Galaxy Team' signature. -""", + description="""This text will be inserted at the end of the activation email's message, before the 'Your Galaxy Team' signature.""", ), ] = None @@ -2437,13 +1920,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Email Domain Blocklist File", - description="""E-mail domains blocklist is used for filtering out users that are using -disposable email addresses at registration. If their address's base domain -matches any domain on the list, they are refused registration. Address subdomains -are ignored (both 'name@spam.com' and 'name@foo.spam.com' will match 'spam.com'). - -The value of this option will be resolved with respect to . -""", + description="""E-mail domains blocklist is used for filtering out users that are using disposable email addresses at registration. If their address's base domain matches any domain on the list, they are refused registration. Address subdomains are ignored (both 'name@spam.com' and 'name@foo.spam.com' will match 'spam.com'). The value of this option will be resolved with respect to .""", example="email_blocklist.conf", ), ] = None @@ -2452,17 +1929,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Email Domain Allowlist File", - description="""E-mail domains allowlist is used to specify allowed email address domains. -If the list is non-empty and a user attempts registration using an email -address belonging to a domain that is not on the list, registration will be -denied. Unlike which matches the address's -base domain, here email addresses are matched against the full domain (base + subdomain). -This is a more restrictive option than , and -therefore, in case is set and is not empty, - will be ignored. - -The value of this option will be resolved with respect to . -""", + description="""E-mail domains allowlist is used to specify allowed email address domains. If the list is non-empty and a user attempts registration using an email address belonging to a domain that is not on the list, registration will be denied. Unlike which matches the address's base domain, here email addresses are matched against the full domain (base + subdomain). This is a more restrictive option than , and therefore, in case is set and is not empty, will be ignored. The value of this option will be resolved with respect to .""", example="email_allowlist.conf", ), ] = None @@ -2471,11 +1938,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -2483,10 +1946,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 3 @@ -2494,11 +1954,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 0 @@ -2506,10 +1962,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 0 @@ -2517,23 +1970,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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). -""", + 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).""", ), ] = "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" @@ -2541,16 +1978,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -2566,9 +1994,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Interactivetools Proxy Host", - description="""Hostname and port of Interactive tools proxy. It is assumed to be hosted on the same hostname and port as -Galaxy by default. -""", + description="""Hostname and port of Interactive tools proxy. It is assumed to be hosted on the same hostname and port as Galaxy by default.""", ), ] = None @@ -2601,10 +2027,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Interactivetools Shorten Url", - description="""Shorten the uuid portion of the subdomain or path for interactive tools. -Especially useful for avoiding the need for wildcard certificates by keeping -subdomain under 63 chars -""", + description="""Shorten the uuid portion of the subdomain or path for interactive tools. Especially useful for avoiding the need for wildcard certificates by keeping subdomain under 63 chars.""", ), ] = False @@ -2612,12 +2035,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Retry Interactivetool Metadata Internally", - description="""Galaxy Interactive Tools (GxITs) can be stopped from within the Galaxy -interface, killing the GxIT job without completing its metadata setting post-job -steps. In such a case it may be desirable to set metadata on job outputs -internally (in the Galaxy job handler process). The default is is the value of -`retry_metadata_internally`, which defaults to `true`. -""", + description="""Galaxy Interactive Tools (GxITs) can be stopped from within the Galaxy interface, killing the GxIT job without completing its metadata setting post-job steps. In such a case it may be desirable to set metadata on job outputs internally (in the Galaxy job handler process). The default is is the value of `retry_metadata_internally`, which defaults to `true`.""", ), ] = True @@ -2627,9 +2045,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) deprecated=True, per_host=True, title="Display Galaxy Brand", - description="""This option has been deprecated, use the `logo_src` instead to change the -default logo including the galaxy brand title. -""", + description="""This option has been deprecated, use the `logo_src` instead to change the default logo including the galaxy brand title.""", ), ] = True @@ -2637,14 +2053,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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). -""", + 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), - $iso8601 (complete format string as specified by ISO 8601 international standard).""", ), ] = "$locale (UTC)" @@ -2653,14 +2062,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Trs Servers Config File", - description="""Allow import of workflows from the TRS servers configured in -the specified YAML or JSON file. The file should be a list with -'id', 'label', and 'api_url' for each entry. Optionally, -'link_url' and 'doc' may be be specified as well for each entry. - -If this is null (the default), a simple configuration containing -just Dockstore will be used. -""", + description="""Allow import of workflows from the TRS servers configured in the specified YAML or JSON file. The file should be a list with 'id', 'label', and 'api_url' for each entry. Optionally, 'link_url' and 'doc' may be be specified as well for each entry. If this is null (the default), a simple configuration containing just Dockstore will be used.""", ), ] = "trs_servers_conf.yml" @@ -2677,9 +2079,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Galaxy Url Prefix", - description="""URL prefix for Galaxy application. If Galaxy should be served under a prefix set this to -the desired prefix value. -""", + description="""URL prefix for Galaxy application. If Galaxy should be served under a prefix set this to the desired prefix value.""", ), ] = "/" @@ -2687,14 +2087,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Galaxy Infrastructure Url", - description="""URL (with schema http/https) of the Galaxy instance as accessible -within your local network. This URL is used as a default by pulsar -file staging and Interactive Tool containers for communicating back with -Galaxy via the API. - -If you plan to run Interactive Tools make sure the docker container -can reach this URL. -""", + description="""URL (with schema http/https) of the Galaxy instance as accessible within your local network. This URL is used as a default by pulsar file staging and Interactive Tool containers for communicating back with Galaxy via the API. If you plan to run Interactive Tools make sure the docker container can reach this URL.""", ), ] = "http://localhost:8080" @@ -2702,14 +2095,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 8080 @@ -2717,11 +2103,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -2729,11 +2111,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 360 @@ -2742,11 +2120,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( per_host=True, title="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. -""", + 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.""", ), ] = "static/" @@ -2755,11 +2129,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( per_host=True, title="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. -""", + 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.""", ), ] = "static/images" @@ -2768,11 +2138,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( per_host=True, title="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. -""", + 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.""", ), ] = "static/favicon.ico" @@ -2781,11 +2147,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( per_host=True, title="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. -""", + 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.""", ), ] = "static/scripts/" @@ -2794,11 +2156,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( per_host=True, title="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. -""", + 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.""", ), ] = "static/style" @@ -2807,11 +2165,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( per_host=True, title="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. -""", + 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.""", ), ] = "static/robots.txt" @@ -2827,12 +2181,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -2840,10 +2189,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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). -""", + 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).""", ), ] = None @@ -2851,11 +2197,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Upstream Gzip", - description="""If using compression in the upstream proxy server, use this option to disable -gzipping of dataset collection and library archives, since the upstream server -will do it faster on the fly. To enable compression add ``application/zip`` -to the proxy's compressable mimetypes. -""", + description="""If using compression in the upstream proxy server, use this option to disable gzipping of dataset collection and library archives, since the upstream server will do it faster on the fly. To enable compression add ``application/zip`` to the proxy's compressable mimetypes.""", ), ] = False @@ -2863,13 +2205,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Upstream Mod Zip", - description="""If using the mod-zip module in nginx, use this option to assemble -zip archives in nginx. This is preferable over the upstream_gzip option -as Galaxy does not need to serve the archive. -Requires setting up internal nginx locations to all paths that can be archived. -See https://docs.galaxyproject.org/en/master/admin/nginx.html#creating-archives-with-mod-zip -for details. -""", + description="""If using the mod-zip module in nginx, use this option to assemble zip archives in nginx. This is preferable over the upstream_gzip option as Galaxy does not need to serve the archive. Requires setting up internal nginx locations to all paths that can be archived. See https://docs.galaxyproject.org/en/master/admin/nginx.html#creating-archives-with-mod-zip for details.""", ), ] = False @@ -2877,15 +2213,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "SAMEORIGIN" @@ -2893,11 +2221,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -2905,11 +2229,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -2917,11 +2237,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -2929,10 +2245,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Tus Upload Store", - description="""The upload store is a temporary directory in which files uploaded by the -tus middleware or server will be placed. -Defaults to new_file_path if not set. -""", + description="""The upload store is a temporary directory in which files uploaded by the tus middleware or server will be placed. Defaults to new_file_path if not set.""", ), ] = None @@ -2940,13 +2253,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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). -""", + 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).""", ), ] = True @@ -2954,10 +2261,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["node", "golang"]], Field( title="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) -""", + 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) """, ), ] = "node" @@ -2966,9 +2270,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=DATA_DIR, title="Dynamic Proxy Session Map", - description="""The NodeJS dynamic proxy can use an SQLite database or a JSON file for IPC, -set that here. -""", + description="""The NodeJS dynamic proxy can use an SQLite database or a JSON file for IPC, set that here.""", ), ] = "session_map.sqlite" @@ -2976,9 +2278,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 8800 @@ -2986,9 +2286,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "0.0.0.0" @@ -3004,9 +2302,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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). -""", + description="""The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL).""", ), ] = False @@ -3014,11 +2310,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 -""", + 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 """, ), ] = "gie_proxy" @@ -3026,10 +2318,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 60 @@ -3037,10 +2326,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 10 @@ -3048,9 +2334,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "unix:///var/run/docker.sock" @@ -3058,11 +2342,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -3070,9 +2350,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + description="""If true, Galaxy will attempt to configure a simple root logger if a "loggers" section does not appear in this configuration file.""", ), ] = True @@ -3080,10 +2358,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Log Destination", - description="""Log destination, defaults to special value "stdout" that logs to standard output. If set to anything else, -then it will be interpreted as a path that will be used as the log file, and logging to stdout will be -disabled. -""", + description="""Log destination, defaults to special value "stdout" that logs to standard output. If set to anything else, then it will be interpreted as a path that will be used as the log file, and logging to stdout will be disabled.""", ), ] = "stdout" @@ -3091,11 +2366,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Log Rotate Size", - description="""Size of log file at which size it will be rotated as per the documentation in -https://docs.python.org/library/logging.handlers.html#logging.handlers.RotatingFileHandler -If log_rotate_count is not also set, no log rotation will be performed. A value of 0 (the default) means no -rotation. Size can be a number of bytes or a human-friendly representation like "100 MB" or "1G". -""", + description="""Size of log file at which size it will be rotated as per the documentation in https://docs.python.org/library/logging.handlers.html#logging.handlers.RotatingFileHandler If log_rotate_count is not also set, no log rotation will be performed. A value of 0 (the default) means no rotation. Size can be a number of bytes or a human-friendly representation like "100 MB" or "1G".""", ), ] = "0" @@ -3103,11 +2374,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Log Rotate Count", - description="""Number of log file backups to keep, per the documentation in -https://docs.python.org/library/logging.handlers.html#logging.handlers.RotatingFileHandler -Any additional rotated log files will automatically be pruned. If log_rotate_size is not also set, no log -rotation will be performed. A value of 0 (the default) means no rotation. -""", + description="""Number of log file backups to keep, per the documentation in https://docs.python.org/library/logging.handlers.html#logging.handlers.RotatingFileHandler Any additional rotated log files will automatically be pruned. If log_rotate_size is not also set, no log rotation will be performed. A value of 0 (the default) means no rotation.""", ), ] = 0 @@ -3115,10 +2382,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["NOTSET", "TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]], Field( title="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. -""", + 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.""", ), ] = "DEBUG" @@ -3127,10 +2391,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( allowempty=True, title="Logging", - description="""Controls where and how the server logs messages. If set, overrides all settings in the log_* configuration -options. Configuration is described in the documentation at: -https://docs.galaxyproject.org/en/master/admin/config_logging.html -""", + description="""Controls where and how the server logs messages. If set, overrides all settings in the log_* configuration options. Configuration is described in the documentation at: https://docs.galaxyproject.org/en/master/admin/config_logging.html """, ), ] = None @@ -3162,10 +2423,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3173,9 +2431,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Fluent Log", - description="""Fluentd configuration. Various events can be logged to the fluentd instance -configured below by enabling fluent_log. -""", + description="""Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log.""", ), ] = False @@ -3183,9 +2439,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Fluent Host", - description="""Fluentd configuration. Various events can be logged to the fluentd instance -configured below by enabling fluent_log. -""", + description="""Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log.""", ), ] = "localhost" @@ -3193,9 +2447,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Fluent Port", - description="""Fluentd configuration. Various events can be logged to the fluentd instance -configured below by enabling fluent_log. -""", + description="""Fluentd configuration. Various events can be logged to the fluentd instance configured below by enabling fluent_log.""", ), ] = 24224 @@ -3203,11 +2455,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -3215,12 +2463,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Sanitize Allowlist File", - description="""Datasets created by tools listed in this file are trusted and will not have -their HTML sanitized on display. This can be manually edited or manipulated -through the Admin control panel -- see "Manage Allowlist" - -The value of this option will be resolved with respect to . -""", + description="""Datasets created by tools listed in this file are trusted and will not have their HTML sanitized on display. This can be manually edited or manipulated through the Admin control panel -- see "Manage Allowlist" The value of this option will be resolved with respect to .""", ), ] = "sanitize_allowlist.txt" @@ -3228,11 +2471,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3240,13 +2479,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 -""", + 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 """, ), ] = None @@ -3254,12 +2487,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3267,11 +2495,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Debug", - description="""Debug enables access to various config options useful for development -and debugging: use_lint, use_profile, and use_printdebug. It also -causes the files used by PBS/SGE (submission script, output, and error) -to remain on disk after the job is complete. -""", + description="""Debug enables access to various config options useful for development and debugging: use_lint, use_profile, and use_printdebug. It also causes the files used by PBS/SGE (submission script, output, and error) to remain on disk after the job is complete.""", ), ] = False @@ -3303,14 +2527,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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`. See the -Galaxy Admin Documentation for more. -""", + 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`. See the Galaxy Admin Documentation for more.""", ), ] = 30 @@ -3318,10 +2535,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3329,10 +2543,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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 -SIGUSR1 (`kill -USR1`) to force a dump. -""", + 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 SIGUSR1 (`kill -USR1`) to force a dump.""", ), ] = 20 @@ -3348,12 +2559,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 -> Settings -> API Keys. -""", + 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 -> Settings -> API Keys.""", ), ] = None @@ -3361,9 +2567,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Sentry Event Level", - description="""Determines the minimum log level that will be sent as an event to Sentry. -Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL. -""", + description="""Determines the minimum log level that will be sent as an event to Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.""", ), ] = "ERROR" @@ -3371,10 +2575,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[float], Field( title="Sentry Traces Sample Rate", - description="""Set to a number between 0 and 1. With this option set, every transaction created -will have that percentage chance of being sent to Sentry. A value higher than 0 -is required to analyze performance. -""", + description="""Set to a number between 0 and 1. With this option set, every transaction created will have that percentage chance of being sent to Sentry. A value higher than 0 is required to analyze performance.""", ), ] = 0.0 @@ -3382,9 +2583,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Sentry Ca Certs", - description="""Use this option to provide the path to location of the CA (Certificate Authority) -certificate file if the sentry server uses a self-signed certificate. -""", + description="""Use this option to provide the path to location of the CA (Certificate Authority) certificate file if the sentry server uses a self-signed certificate.""", ), ] = None @@ -3392,13 +2591,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -3406,13 +2599,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 8125 @@ -3420,13 +2607,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "galaxy" @@ -3434,11 +2615,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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 -""", + 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 """, ), ] = False @@ -3446,9 +2623,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Statsd Mock Calls", - description="""Mock out statsd client calls - only used by testing infrastructure really. -Do not set this in production environments. -""", + description="""Mock out statsd client calls - only used by testing infrastructure really. Do not set this in production environments.""", ), ] = False @@ -3456,9 +2631,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3466,13 +2639,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="User Library Import Symlink Allowlist", - description="""For security reasons, users may not import any files that actually lie -outside of their `user_library_import_dir` (e.g. using symbolic links). A -list of directories can be allowed by setting the following option (the list -is comma-separated). Be aware that *any* user with library import permissions -can import from anywhere in these directories (assuming they are able to -create symlinks to them). -""", + description="""For security reasons, users may not import any files that actually lie outside of their `user_library_import_dir` (e.g. using symbolic links). A list of directories can be allowed by setting the following option (the list is comma-separated). Be aware that *any* user with library import permissions can import from anywhere in these directories (assuming they are able to create symlinks to them).""", ), ] = None @@ -3480,10 +2647,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3491,14 +2655,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3506,12 +2663,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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'. -""", + 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'.""", ), ] = None @@ -3520,9 +2672,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Name Boost", - description="""In tool search, a query match against a tool's name text will receive -this score multiplier. -""", + description="""In tool search, a query match against a tool's name text will receive this score multiplier.""", ), ] = 20.0 @@ -3531,9 +2681,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Name Exact Multiplier", - description="""If a search query matches a tool name exactly, the score will be -multiplied by this factor. -""", + description="""If a search query matches a tool name exactly, the score will be multiplied by this factor.""", ), ] = 10.0 @@ -3542,10 +2690,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Id Boost", - description="""In tool search, a query match against a tool's ID text will receive -this score multiplier. The query must be an exact match against ID -in order to be counted as a match. -""", + description="""In tool search, a query match against a tool's ID text will receive this score multiplier. The query must be an exact match against ID in order to be counted as a match.""", ), ] = 20.0 @@ -3554,9 +2699,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Section Boost", - description="""In tool search, a query match against a tool's section text will -receive this score multiplier. -""", + description="""In tool search, a query match against a tool's section text will receive this score multiplier.""", ), ] = 3.0 @@ -3565,9 +2708,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Description Boost", - description="""In tool search, a query match against a tool's description text will -receive this score multiplier. -""", + description="""In tool search, a query match against a tool's description text will receive this score multiplier.""", ), ] = 8.0 @@ -3576,9 +2717,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Label Boost", - description="""In tool search, a query match against a tool's label text will -receive this score multiplier. -""", + description="""In tool search, a query match against a tool's label text will receive this score multiplier.""", ), ] = 1.0 @@ -3587,10 +2726,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Stub Boost", - description="""A stub is parsed from the GUID as "owner/repo/tool_id". -In tool search, a query match against a tool's stub text will receive -this score multiplier. -""", + description="""A stub is parsed from the GUID as "owner/repo/tool_id". In tool search, a query match against a tool's stub text will receive this score multiplier.""", ), ] = 2.0 @@ -3599,9 +2735,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Help Boost", - description="""In tool search, a query match against a tool's help text will receive -this score multiplier. -""", + description="""In tool search, a query match against a tool's help text will receive this score multiplier.""", ), ] = 1.0 @@ -3610,12 +2744,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Help Bm25F K1", - description="""The lower this parameter, the greater the diminishing reward for -term frequency in the help text. A higher K1 increases the level -of reward for additional occurences of a term. The default value will -provide a slight increase in score for the first, second and third -occurrence and little reward thereafter. -""", + description="""The lower this parameter, the greater the diminishing reward for term frequency in the help text. A higher K1 increases the level of reward for additional occurences of a term. The default value will provide a slight increase in score for the first, second and third occurrence and little reward thereafter.""", ), ] = 0.5 @@ -3624,9 +2753,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Search Limit", - description="""Limits the number of results in toolbox search. Use to set the -maximum number of tool search results to display. -""", + description="""Limits the number of results in toolbox search. Use to set the maximum number of tool search results to display.""", ), ] = 20 @@ -3635,12 +2762,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Enable Ngram Search", - description="""Disabling this will prevent partial matches on tool names. -Enable/disable Ngram-search for tools. It makes tool -search results tolerant for spelling mistakes in the query, and will -also match query substrings e.g. "genome" will match "genomics" or -"metagenome". -""", + description="""Disabling this will prevent partial matches on tool names. Enable/disable Ngram-search for tools. It makes tool search results tolerant for spelling mistakes in the query, and will also match query substrings e.g. "genome" will match "genomics" or "metagenome".""", ), ] = True @@ -3667,9 +2789,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="Tool Ngram Factor", - description="""Ngram matched scores will be multiplied by this factor. Should always -be below 1, because an ngram match is a partial match of a search term. -""", + description="""Ngram matched scores will be multiplied by this factor. Should always be below 1, because an ngram match is a partial match of a search term.""", ), ] = 0.2 @@ -3677,13 +2797,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "test-data" @@ -3691,13 +2805,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 ' ' -""", + 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 ' ' """, ), ] = "USING THE DEFAULT IS NOT SECURE!" @@ -3705,10 +2813,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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). -""", + 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).""", ), ] = None @@ -3716,12 +2821,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "HTTP_REMOTE_USER" @@ -3729,13 +2829,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "USING THE DEFAULT IS NOT SECURE!" @@ -3743,10 +2837,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3755,12 +2846,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="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/ -""", + 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/""", ), ] = None @@ -3768,9 +2854,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Show User Prepopulate Form", - description="""When using LDAP for authentication, allow administrators to pre-populate users -using an additional form on 'Create new user' -""", + description="""When using LDAP for authentication, allow administrators to pre-populate users using an additional form on 'Create new user' """, ), ] = False @@ -3778,11 +2862,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3790,16 +2870,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3807,14 +2878,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Fetch Url Allowlist", - description="""List of allowed local network addresses for "Upload from URL" dialog. -By default, Galaxy will deny access to the local network address space, to -prevent users making requests to services which the administrator did not -intend to expose. Previously, you could request any network service that -Galaxy might have had access to, even if the user could not normally access it. -It should be a comma-separated list of IP addresses or IP address/mask, e.g. -10.10.10.10,10.0.1.0/24,fd00::/8 -""", + description="""List of allowed local network addresses for "Upload from URL" dialog. By default, Galaxy will deny access to the local network address space, to prevent users making requests to services which the administrator did not intend to expose. Previously, you could request any network service that Galaxy might have had access to, even if the user could not normally access it. It should be a comma-separated list of IP addresses or IP address/mask, e.g. 10.10.10.10,10.0.1.0/24,fd00::/8 """, ), ] = None @@ -3822,21 +2886,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3844,10 +2894,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Enable Beta Workflow Modules", - description="""Enable beta workflow modules that should not yet be considered part of Galaxy's -stable API. (The module state definitions may change and workflows built using -these modules may not function in the future.) -""", + description="""Enable beta workflow modules that should not yet be considered part of Galaxy's stable API. (The module state definitions may change and workflows built using these modules may not function in the future.) """, ), ] = False @@ -3855,10 +2902,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Edam Panel Views", - description="""Comma-separated list of the EDAM panel views to load - choose from merged, operations, topics. -Set to empty string to disable EDAM all together. Set default_panel_view to 'ontology:edam_topics' -to override default tool panel to use an EDAM view. -""", + description="""Comma-separated list of the EDAM panel views to load - choose from merged, operations, topics. Set to empty string to disable EDAM all together. Set default_panel_view to 'ontology:edam_topics' to override default tool panel to use an EDAM view.""", ), ] = "operations,topics" @@ -3875,10 +2919,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Panel Views Dir", - description="""Directory to check out for toolbox tool panel views. The path is relative to the -Galaxy root dir. To use an absolute path begin the path with '/'. This is a -comma-separated list. -""", + description="""Directory to check out for toolbox tool panel views. The path is relative to the Galaxy root dir. To use an absolute path begin the path with '/'. This is a comma-separated list.""", ), ] = "config/plugins/activities" @@ -3886,9 +2927,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Default Workflow Export Format", - description="""Default format for the export of workflows. Possible values are 'ga' -or 'format2'. -""", + description="""Default format for the export of workflows. Possible values are 'ga' or 'format2'.""", ), ] = "ga" @@ -3896,10 +2935,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -3907,10 +2943,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 2678400 @@ -3918,13 +2951,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 1000 @@ -3932,11 +2959,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Flush Per N Datasets", - description="""Maximum number of datasets to create before flushing created datasets to database. -This affects tools that create many output datasets. -Higher values will lead to fewer database flushes and faster execution, but require -more memory. Set to -1 to disable creating datasets in batches. -""", + description="""Maximum number of datasets to create before flushing created datasets to database. This affects tools that create many output datasets. Higher values will lead to fewer database flushes and faster execution, but require more memory. Set to -1 to disable creating datasets in batches.""", ), ] = 1000 @@ -3944,11 +2967,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="Max Discovered Files", - description="""Set this to a positive integer value to limit the number of datasets that can be discovered by -a single job. This prevents accidentally creating large numbers of datasets when running tools -that create a potentially unlimited number of output datasets, such as tools that split a file -into a collection of datasets for each line in an input dataset. -""", + description="""Set this to a positive integer value to limit the number of datasets that can be discovered by a single job. This prevents accidentally creating large numbers of datasets when running tools that create a potentially unlimited number of output datasets, such as tools that split a file into a collection of datasets for each line in an input dataset.""", ), ] = 10000 @@ -3983,10 +3002,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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). -""", + 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).""", ), ] = "auth_conf.xml" @@ -3994,9 +3010,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Api Allow Run As", - description="""Optional list of email addresses of API users who can make calls on behalf of -other users. -""", + description="""Optional list of email addresses of API users who can make calls on behalf of other users.""", ), ] = None @@ -4005,12 +3019,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( deprecated_alias="master_api_key", title="Bootstrap Admin Api Key", - description="""API key that allows performing some admin actions without actually -having a real admin user in the database and config. -Only set this if you need to bootstrap Galaxy, in particular to create -a real admin user account via API. -You should probably not set this on a production server. -""", + description="""API key that allows performing some admin actions without actually having a real admin user in the database and config. Only set this if you need to bootstrap Galaxy, in particular to create a real admin user account via API. You should probably not set this on a production server.""", ), ] = None @@ -4018,19 +3027,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Ga4Gh Service Id", - description="""Service ID for GA4GH services (exposed via the service-info endpoint for the Galaxy DRS API). -If unset, one will be generated using the URL the target API requests are made against. - -For more information on GA4GH service definitions - check out -https://github.com/ga4gh-discovery/ga4gh-service-registry -and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml - -This value should likely reflect your service's URL. For instance for usegalaxy.org -this value should be org.usegalaxy. Particular Galaxy implementations will treat this -value as a prefix and append the service type to this ID. For instance for the DRS -service "id" (available via the DRS API) for the above configuration value would be -org.usegalaxy.drs. -""", + description="""Service ID for GA4GH services (exposed via the service-info endpoint for the Galaxy DRS API). If unset, one will be generated using the URL the target API requests are made against. For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml This value should likely reflect your service's URL. For instance for usegalaxy.org this value should be org.usegalaxy. Particular Galaxy implementations will treat this value as a prefix and append the service type to this ID. For instance for the DRS service "id" (available via the DRS API) for the above configuration value would be org.usegalaxy.drs.""", ), ] = None @@ -4038,13 +3035,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Ga4Gh Service Organization Name", - description="""Service name for host organization (exposed via the service-info endpoint for the Galaxy DRS API). -If unset, one will be generated using ga4gh_service_id. - -For more information on GA4GH service definitions - check out -https://github.com/ga4gh-discovery/ga4gh-service-registry -and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml -""", + description="""Service name for host organization (exposed via the service-info endpoint for the Galaxy DRS API). If unset, one will be generated using ga4gh_service_id. For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml """, ), ] = None @@ -4052,13 +3043,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Ga4Gh Service Organization Url", - description="""Organization URL for host organization (exposed via the service-info endpoint for the Galaxy DRS API). -If unset, one will be generated using the URL the target API requests are made against. - -For more information on GA4GH service definitions - check out -https://github.com/ga4gh-discovery/ga4gh-service-registry -and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml -""", + description="""Organization URL for host organization (exposed via the service-info endpoint for the Galaxy DRS API). If unset, one will be generated using the URL the target API requests are made against. For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml """, ), ] = None @@ -4066,15 +3051,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Ga4Gh Service Environment", - description="""Service environment (exposed via the service-info endpoint for the Galaxy DRS API) for -implemented GA4GH services. - -Suggested values are prod, test, dev, staging. - -For more information on GA4GH service definitions - check out -https://github.com/ga4gh-discovery/ga4gh-service-registry -and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml -""", + description="""Service environment (exposed via the service-info endpoint for the Galaxy DRS API) for implemented GA4GH services. Suggested values are prod, test, dev, staging. For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml """, ), ] = None @@ -4082,10 +3059,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -4093,9 +3067,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Ftp Upload Dir", - description="""This should point to a directory containing subdirectories matching users' -identifier (defaults to e-mail), where Galaxy will look for files. -""", + description="""This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files.""", ), ] = None @@ -4103,11 +3075,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = "email" @@ -4115,11 +3083,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Ftp Upload Dir Template", - description="""Python string template used to determine an FTP upload directory for a -particular user. - -Defaults to '${ftp_upload_dir}/${ftp_upload_dir_identifier}'. -""", + description="""Python string template used to determine an FTP upload directory for a particular user. Defaults to '${ftp_upload_dir}/${ftp_upload_dir_identifier}'.""", ), ] = None @@ -4127,9 +3091,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Ftp Upload Purge", - description="""Set to false to prevent Galaxy from deleting uploaded FTP files -as it imports them. -""", + description="""Set to false to prevent Galaxy from deleting uploaded FTP files as it imports them.""", ), ] = True @@ -4137,10 +3099,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -4157,9 +3116,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="Expose Potentially Sensitive Job Metrics", - description="""This option allows users to see the job metrics (except for environment -variables). -""", + description="""This option allows users to see the job metrics (except for environment variables).""", ), ] = False @@ -4193,9 +3150,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=MANAGED_CONFIG_DIR, title="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. -""", + description="""File where Tool Shed based Data Managers are configured. This file will be created automatically upon data manager installation.""", ), ] = "shed_data_manager_conf.xml" @@ -4203,9 +3158,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Galaxy Data Manager Data Path", - description="""Directory to store Data Manager based tool-data. Defaults to the value of the - option. -""", + description="""Directory to store Data Manager based tool-data. Defaults to the value of the option.""", ), ] = None @@ -4214,17 +3167,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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 or the option. -""", + 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 or the option.""", ), ] = "job_conf.yml" @@ -4241,15 +3184,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[List[Any]], Field( title="Dependency Resolvers", - description="""Rather than specifying a dependency_resolvers_config_file, the definition of the -resolvers to enable can be embedded into Galaxy's config with this option. -This has no effect if a dependency_resolvers_config_file is used. - -The syntax, available resolvers, and documentation of their options is explained in detail in the -documentation: - -https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html -""", + description="""Rather than specifying a dependency_resolvers_config_file, the definition of the resolvers to enable can be embedded into Galaxy's config with this option. This has no effect if a dependency_resolvers_config_file is used. The syntax, available resolvers, and documentation of their options is explained in detail in the documentation: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html """, ), ] = None @@ -4257,11 +3192,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Dict[str, Any]], Field( title="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. -""", + 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.""", ), ] = None @@ -4269,19 +3200,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 the job config. 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 the job config - 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. -""", + 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 the job config. 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 the job config - 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.""", ), ] = None @@ -4290,9 +3209,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( deprecated=True, title="Track Jobs In Database", - description="""This option is deprecated, use the `mem-self` handler assignment option in the -job configuration instead. -""", + description="""This option is deprecated, use the `mem-self` handler assignment option in the job configuration instead.""", ), ] = True @@ -4300,10 +3217,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -4311,10 +3225,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 2 @@ -4322,12 +3233,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[float], Field( title="Job Handler Monitor Sleep", - description="""Each Galaxy job handler process runs one thread responsible for discovering jobs and -dispatching them to runners. This thread operates in a loop and sleeps for the given -number of seconds at the end of each iteration. This can be decreased if extremely high -job throughput is necessary, but doing so can increase CPU usage of handler processes. -Float values are allowed. -""", + description="""Each Galaxy job handler process runs one thread responsible for discovering jobs and dispatching them to runners. This thread operates in a loop and sleeps for the given number of seconds at the end of each iteration. This can be decreased if extremely high job throughput is necessary, but doing so can increase CPU usage of handler processes. Float values are allowed.""", ), ] = 1.0 @@ -4335,12 +3241,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[float], Field( title="Job Runner Monitor Sleep", - description="""Each Galaxy job handler process runs one thread per job runner plugin responsible for -checking the state of queued and running jobs. This thread operates in a loop and -sleeps for the given number of seconds at the end of each iteration. This can be -decreased if extremely high job throughput is necessary, but doing so can increase CPU -usage of handler processes. Float values are allowed. -""", + description="""Each Galaxy job handler process runs one thread per job runner plugin responsible for checking the state of queued and running jobs. This thread operates in a loop and sleeps for the given number of seconds at the end of each iteration. This can be decreased if extremely high job throughput is necessary, but doing so can increase CPU usage of handler processes. Float values are allowed.""", ), ] = 1.0 @@ -4348,12 +3249,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[float], Field( title="Workflow Monitor Sleep", - description="""Each Galaxy workflow handler process runs one thread responsible for -checking the state of active workflow invocations. This thread operates in a loop and -sleeps for the given number of seconds at the end of each iteration. This can be -decreased if extremely high job throughput is necessary, but doing so can increase CPU -usage of handler processes. Float values are allowed. -""", + description="""Each Galaxy workflow handler process runs one thread responsible for checking the state of active workflow invocations. This thread operates in a loop and sleeps for the given number of seconds at the end of each iteration. This can be decreased if extremely high job throughput is necessary, but doing so can increase CPU usage of handler processes. Float values are allowed.""", ), ] = 1.0 @@ -4361,15 +3257,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["directory", "extended", "directory_celery", "extended_celery", "legacy"]], Field( title="Metadata Strategy", - description="""Determines how metadata will be set. Valid values are `directory`, `extended`, -`directory_celery` and `extended_celery`. -In extended mode jobs will decide if a tool run failed, the object stores -configuration is serialized and made available to the job and is used for -writing output datasets to the object store as part of the job and dynamic -output discovery (e.g. discovered datasets , unpopulated collections, -etc) happens as part of the job. In `directory_celery` and `extended_celery` metadata -will be set within a celery task. -""", + description="""Determines how metadata will be set. Valid values are `directory`, `extended`, `directory_celery` and `extended_celery`. In extended mode jobs will decide if a tool run failed, the object stores configuration is serialized and made available to the job and is used for writing output datasets to the object store as part of the job and dynamic output discovery (e.g. discovered datasets , unpopulated collections, etc) happens as part of the job. In `directory_celery` and `extended_celery` metadata will be set within a celery task.""", ), ] = "directory" @@ -4377,12 +3265,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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). -""", + 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).""", ), ] = True @@ -4390,12 +3273,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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. -""", + 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.""", ), ] = 5242880 @@ -4403,14 +3281,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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). -""", + 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).""", ), ] = False @@ -4418,12 +3289,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[int], Field( title="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). -""", + 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).""", ), ] = 0 @@ -4431,13 +3297,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["local", "remote"]], Field( title="Tool Evaluation Strategy", - description="""Determines which process will evaluate the tool command line. If set to "local" the tool command -line, configuration files and other dynamic values will be templated in the job -handler process. If set to ``remote`` the tool command line will be built as part of the -submitted job. Note that ``remote`` is a beta setting that will be useful for materializing -deferred datasets as part of the submitted job. Note also that you have to set ``metadata_strategy`` -to ``extended`` if you set this option to ``remote``. -""", + description="""Determines which process will evaluate the tool command line. If set to "local" the tool command line, configuration files and other dynamic values will be templated in the job handler process. If set to ``remote`` the tool command line will be built as part of the submitted job. Note that ``remote`` is a beta setting that will be useful for materializing deferred datasets as part of the submitted job. Note also that you have to set ``metadata_strategy`` to ``extended`` if you set this option to ``remote``.""", ), ] = "local" @@ -4445,17 +3305,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Literal["legacy_only", "legacy_and_local", "always"]], Field( title="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). -""", + 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).""", ), ] = "legacy_only" @@ -4464,11 +3314,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( reloadable=True, title="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 -""", + 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 """, ), ] = "always" @@ -4476,12 +3322,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Drmaa External Runjob Script", - description="""When running DRMAA jobs as the Galaxy user -(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) -this script is used to run the job script Galaxy generates for a tool execution. - -Example value 'sudo -E scripts/drmaa_external_runner.py --assign_all_groups' -""", + description="""When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used to run the job script Galaxy generates for a tool execution. Example value 'sudo -E scripts/drmaa_external_runner.py --assign_all_groups' """, ), ] = None @@ -4489,13 +3330,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Drmaa External Killjob Script", - description="""When running DRMAA jobs as the Galaxy user -(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) -this script is used to kill such jobs by Galaxy (e.g. if the user cancels -the job). - -Example value 'sudo -E scripts/drmaa_external_killer.py' -""", + description="""When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used to kill such jobs by Galaxy (e.g. if the user cancels the job). Example value 'sudo -E scripts/drmaa_external_killer.py' """, ), ] = None @@ -4503,13 +3338,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="External Chown Script", - description="""When running DRMAA jobs as the Galaxy user -(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) -this script is used transfer permissions back and forth between the Galaxy user -and the user that is running the job. - -Example value 'sudo -E scripts/external_chown_script.py' -""", + description="""When running DRMAA jobs as the Galaxy user (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user) this script is used transfer permissions back and forth between the Galaxy user and the user that is running the job. Example value 'sudo -E scripts/external_chown_script.py' """, ), ] = None @@ -4517,17 +3346,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 -""", + 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 """, ), ] = "user_email" @@ -4535,16 +3354,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + 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.""", ), ] = None @@ -4553,9 +3363,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Markdown Export Css", - description="""CSS file to apply to all Markdown exports to PDF - currently used by -WeasyPrint during rendering an HTML export of the document to PDF. -""", + description="""CSS file to apply to all Markdown exports to PDF - currently used by WeasyPrint during rendering an HTML export of the document to PDF.""", ), ] = "markdown_export.css" @@ -4564,10 +3372,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Markdown Export Css Pages", - description="""CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer -markdown_export_css, but this is here for deployments that -would like to tailor different kinds of exports. -""", + description="""CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer markdown_export_css, but this is here for deployments that would like to tailor different kinds of exports.""", ), ] = "markdown_export_pages.css" @@ -4576,10 +3381,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Markdown Export Css Invocation Reports", - description="""CSS file to apply to invocation report exports to PDF. Generally prefer -markdown_export_css, but this is here for deployments that -would like to tailor different kinds of exports. -""", + description="""CSS file to apply to invocation report exports to PDF. Generally prefer markdown_export_css, but this is here for deployments that would like to tailor different kinds of exports.""", ), ] = "markdown_export_invocation_reports.css" @@ -4587,9 +3389,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) str, Field( title="Markdown Export Prologue", - description="""Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing -branded headers. -""", + description="""Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing branded headers.""", ), ] = "" @@ -4597,9 +3397,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) str, Field( title="Markdown Export Epilogue", - description="""Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing -branded footers. -""", + description="""Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing branded footers.""", ), ] = "" @@ -4615,9 +3413,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) str, Field( title="Markdown Export Prologue Invocation Reports", - description="""Alternative to markdown_export_prologue that applies just to invocation report -exports. -""", + description="""Alternative to markdown_export_prologue that applies just to invocation report exports.""", ), ] = "" @@ -4642,11 +3438,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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. -""", + 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.""", ), ] = "job_resource_params_conf.xml" @@ -4655,11 +3447,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="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). -""", + 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).""", ), ] = "workflow_resource_params_conf.xml" @@ -4667,16 +3455,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Workflow Resource Params Mapper", - description="""This parameter describes how to map users and workflows to a set of workflow -resource parameter to present (typically input IDs from workflow_resource_params_file). -If this this is a function reference it will be passed various inputs (workflow model -object and user) and it should produce a list of input IDs. If it is a path -it is expected to be an XML or YAML file describing how to map group names to parameter -descriptions (additional types of mappings via these files could be implemented but -haven't yet - for instance using workflow tags to do the mapping). - -Sample default path 'config/workflow_resource_mapper_conf.yml.sample' -""", + description="""This parameter describes how to map users and workflows to a set of workflow resource parameter to present (typically input IDs from workflow_resource_params_file). If this this is a function reference it will be passed various inputs (workflow model object and user) and it should produce a list of input IDs. If it is a path it is expected to be an XML or YAML file describing how to map group names to parameter descriptions (additional types of mappings via these files could be implemented but haven't yet - for instance using workflow tags to do the mapping). Sample default path 'config/workflow_resource_mapper_conf.yml.sample' """, ), ] = None @@ -4685,9 +3464,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Field( path_resolves_to=CONFIG_DIR, title="Workflow Schedulers Config File", - description="""Optional configuration file similar to `job_config_file` to specify -which Galaxy processes should schedule workflows. -""", + description="""Optional configuration file similar to `job_config_file` to specify which Galaxy processes should schedule workflows.""", ), ] = "workflow_schedulers_conf.xml" @@ -4695,15 +3472,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = False @@ -4711,9 +3480,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="Tool Filters", - description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) -that admins may use to restrict the tools to display. -""", + description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tools to display.""", ), ] = None @@ -4721,9 +3488,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tool labels to display.""", ), ] = None @@ -4731,9 +3496,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that admins may use to restrict the tool sections to display.""", ), ] = None @@ -4741,9 +3504,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="User Tool Filters", - description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) -that users may use to restrict the tools to display. -""", + description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tools to display.""", ), ] = "examples:restrict_upload_to_admins, examples:restrict_encode" @@ -4751,9 +3512,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tool sections to display.""", ), ] = "examples:restrict_text" @@ -4761,9 +3520,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + description="""Define toolbox filters (https://galaxyproject.org/user-defined-toolbox-filters/) that users may use to restrict the tool labels to display.""", ), ] = "examples:restrict_upload_to_admins, examples:restrict_encode" @@ -4771,9 +3528,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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. -""", + description="""The base module(s) that are searched for modules for toolbox filtering (https://galaxyproject.org/user-defined-toolbox-filters/) functions.""", ), ] = "galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters" @@ -4781,17 +3536,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[str], Field( title="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 https://docs.celeryq.dev/projects/kombu/en/stable/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). -""", + 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 https://docs.celeryq.dev/projects/kombu/en/stable/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).""", ), ] = "sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE" @@ -4799,19 +3544,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[Any], Field( title="Celery Conf", - description="""Configuration options passed to Celery. - -To refer to a task by name, use the template `galaxy.foo` where `foo` is the function name -of the task defined in the galaxy.celery.tasks module. - -The `broker_url` option, if unset, defaults to the value of `amqp_internal_connection`. -The `result_backend` option must be set if the `enable_celery_tasks` option is set. - -The galaxy.fetch_data task can be disabled by setting its route to "disabled": `galaxy.fetch_data: disabled`. -(Other tasks cannot be disabled on a per-task basis at this time.) - -For details, see Celery documentation at https://docs.celeryq.dev/en/stable/userguide/configuration.html. -""", + description="""Configuration options passed to Celery. To refer to a task by name, use the template `galaxy.foo` where `foo` is the function name of the task defined in the galaxy.celery.tasks module. The `broker_url` option, if unset, defaults to the value of `amqp_internal_connection`. The `result_backend` option must be set if the `enable_celery_tasks` option is set. The galaxy.fetch_data task can be disabled by setting its route to "disabled": `galaxy.fetch_data: disabled`. (Other tasks cannot be disabled on a per-task basis at this time.) For details, see Celery documentation at https://docs.celeryq.dev/en/stable/userguide/configuration.html.""", ), ] = {"task_routes": {"galaxy.fetch_data": "galaxy.external", "galaxy.set_job_metadata": "galaxy.external"}} @@ -4819,9 +3552,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[float], Field( title="Celery User Rate Limit", - description="""If set to a non-0 value, upper limit on number of -tasks that can be executed per user per second. -""", + description="""If set to a non-0 value, upper limit on number of tasks that can be executed per user per second.""", ), ] = 0.0 @@ -4829,10 +3560,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) Optional[bool], Field( title="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. -""", + 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.""", ), ] = True @@ -4878,9 +3606,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) path_resolves_to=CONFIG_DIR, per_host=True, title="Themes Config File", - description="""Optional file containing one or more themes for galaxy. If several themes -are defined, users can choose their preferred theme in the client. -""", + description="""Optional file containing one or more themes for galaxy. If several themes are defined, users can choose their preferred theme in the client.""", ), ] = "themes_conf.yml"