From 066a9bc78a47223b33c967b71f247cd4a14e070e Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Thu, 22 Oct 2020 22:00:10 -0400 Subject: [PATCH] Generate path resolution note for sample file, docs --- doc/source/admin/galaxy_options.rst | 104 +++++++++++++++++- lib/galaxy/config/config_manage.py | 13 ++- lib/galaxy/config/sample/galaxy.yml.sample | 91 ++++++++++++++- lib/galaxy/config/sample/tool_shed.yml.sample | 6 + 4 files changed, 210 insertions(+), 4 deletions(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 4921c3bff8c..592c12e8979 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -240,6 +240,8 @@ 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 value of this option will be resolved with respect to + . :Default: ``objects`` :Type: str @@ -252,6 +254,8 @@ Where temporary files are stored. It must be accessible at the same path on any cluster nodes that will run Galaxy jobs, unless using Pulsar. + The value of this option will be resolved with respect to + . :Default: ``tmp`` :Type: str @@ -267,6 +271,8 @@ config/tool_conf.xml does not exist). Can be a single file, a list of files, or (for backwards compatibility) a comma-separated list of files. + The value of this option will be resolved with respect to + . :Default: ``tool_conf.xml`` :Type: any @@ -285,6 +291,8 @@ this option is preferable. This file will be created automatically upon tool installation, whereas Galaxy will fail to start if any files in tool_config_file cannot be read. + The value of this option will be resolved with respect to + . :Default: ``shed_tool_conf.xml`` :Type: str @@ -314,6 +322,8 @@ migration scripts to install tools that have been migrated to the tool shed upon a new release, they will be added to this tool config file. + The value of this option will be resolved with respect to + . :Default: ``migrated_tools_conf.xml`` :Type: str @@ -377,6 +387,8 @@ then use Conda if available. See https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst for more information on these options. + The value of this option will be resolved with respect to + . :Default: ``dependency_resolvers_conf.xml`` :Type: str @@ -482,6 +494,8 @@ Path to a file that provides a mapping from abstract packages to concrete conda packages. See `config/local_conda_mapping.yml.sample` for examples. + The value of this option will be resolved with respect to + . :Default: ``local_conda_mapping.yml`` :Type: str @@ -494,6 +508,8 @@ Path to a file that provides a mapping from abstract packages to locally installed modules. See `config/environment_modules_mapping.yml.sample` for examples. + The value of this option will be resolved with respect to + . :Default: ``environment_modules_mapping.yml`` :Type: str @@ -550,6 +566,8 @@ File containing the Galaxy Tool Sheds that should be made available to install from in the admin interface (.sample used if default does not exist). + The value of this option will be resolved with respect to + . :Default: ``tool_sheds_conf.xml`` :Type: str @@ -637,6 +655,8 @@ :Description: Configured FileSource plugins. + The value of this option will be resolved with respect to + . :Default: ``file_sources_conf.yml`` :Type: str @@ -745,6 +765,8 @@ XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator (.sample used if default does not exist). + The value of this option will be resolved with respect to + . :Default: ``tool_data_table_conf.xml`` :Type: str @@ -761,6 +783,8 @@ installation, these entries are automatically added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. + The value of this option will be resolved with respect to + . :Default: ``shed_tool_data_table_conf.xml`` :Type: str @@ -826,6 +850,8 @@ :Description: File that defines the builds (dbkeys) available at sites used by display applications and the URL to those sites. + The value of this option will be resolved with respect to + . :Default: ``build_sites.yml`` :Type: str @@ -865,6 +891,8 @@ If a datatype appears in multiple files, the last definition is used (though the first sniffer is used so limit sniffer definitions to one file). + The value of this option will be resolved with respect to + . :Default: ``datatypes_conf.xml`` :Type: str @@ -972,6 +1000,8 @@ :Description: If using a cluster, Galaxy will write job scripts and stdout/stderr to this directory. + The value of this option will be resolved with respect to + . :Default: ``pbs`` :Type: str @@ -983,6 +1013,8 @@ :Description: Mako templates are compiled as needed and cached for reuse, this directory is used for the cache + The value of this option will be resolved with respect to + . :Default: ``compiled_templates`` :Type: str @@ -1045,6 +1077,8 @@ stored at this path. Per tool_conf cache locations can be configured in (shed_)tool_conf.xml files using the tool_cache_data_dir attribute. + The value of this option will be resolved with respect to + . :Default: ``tool_cache`` :Type: str @@ -1054,7 +1088,8 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Directory in which the toolbox search index is stored. + Directory in which the toolbox search index is stored. The value + of this option will be resolved with respect to . :Default: ``tool_search_index`` :Type: str @@ -1093,6 +1128,8 @@ fetched from external sources such as https://doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. + The value of this option will be resolved with respect to + . :Default: ``citations/data`` :Type: str @@ -1106,6 +1143,8 @@ fetched from external sources such as https://doi.org/ by Galaxy - the following parameters can be used to control the caching used to store this information. + The value of this option will be resolved with respect to + . :Default: ``citations/locks`` :Type: str @@ -1129,6 +1168,8 @@ :Description: Data directory used by beaker for caching mulled resolution requests. + The value of this option will be resolved with respect to + . :Default: ``mulled/data`` :Type: str @@ -1140,6 +1181,8 @@ :Description: Lock directory used by beaker for caching mulled resolution requests. + The value of this option will be resolved with respect to + . :Default: ``mulled/locks`` :Type: str @@ -1151,6 +1194,8 @@ :Description: Configuration file for the object store If this is set and exists, it overrides any other objectstore settings. + The value of this option will be resolved with respect to + . :Default: ``object_store_conf.xml`` :Type: str @@ -1483,6 +1528,8 @@ :Description: Map for interactivetool proxy. + The value of this option will be resolved with respect to + . :Default: ``interactivetools_map.sqlite`` :Type: str @@ -1575,6 +1622,8 @@ 'doc' may be be specified as well for each entry. If this is null (the default), a simple configuration containing just Dockstore will be used. + The value of this option will be resolved with respect to + . :Default: ``trs_servers_conf.yml`` :Type: str @@ -1586,6 +1635,8 @@ :Description: Location of the configuration file containing extra user preferences. + The value of this option will be resolved with respect to + . :Default: ``user_preferences_extra_conf.yml`` :Type: str @@ -2025,6 +2076,8 @@ :Description: The NodeJS dynamic proxy can use an SQLite database or a JSON file for IPC, set that here. + The value of this option will be resolved with respect to + . :Default: ``session_map.sqlite`` :Type: str @@ -2636,6 +2689,19 @@ :Type: float +~~~~~~~~~~~~~~~~~ +``tool_id_boost`` +~~~~~~~~~~~~~~~~~ + +:Description: + Boosts are used to customize this instance's toolbox search. The + higher the boost, the more importance the scoring algorithm gives + to the given field. Section refers to the tool group in the tool + panel. Rest of the fields are tool's attributes. +:Default: ``9.0`` +:Type: float + + ~~~~~~~~~~~~~~~~~~~~~~ ``tool_section_boost`` ~~~~~~~~~~~~~~~~~~~~~~ @@ -3213,6 +3279,8 @@ :Description: Sets the path to OIDC configuration file. + The value of this option will be resolved with respect to + . :Default: ``oidc_config.xml`` :Type: str @@ -3223,6 +3291,8 @@ :Description: Sets the path to OIDC backends configuration file. + The value of this option will be resolved with respect to + . :Default: ``oidc_backends_config.xml`` :Type: str @@ -3235,6 +3305,8 @@ XML config file that allows the use of different authentication providers (e.g. LDAP) instead or in addition to local authentication (.sample is used if default does not exist). + The value of this option will be resolved with respect to + . :Default: ``auth_conf.xml`` :Type: str @@ -3279,6 +3351,8 @@ :Description: If OpenID is enabled, consumer cache directory to use. + The value of this option will be resolved with respect to + . :Default: ``openid_consumer_cache`` :Type: str @@ -3456,6 +3530,8 @@ :Description: XML config file that contains the job metric collection configuration. + The value of this option will be resolved with respect to + . :Default: ``job_metrics_conf.xml`` :Type: str @@ -3498,6 +3574,8 @@ :Description: File where Data Managers are configured (.sample used if default does not exist). + The value of this option will be resolved with respect to + . :Default: ``data_manager_conf.xml`` :Type: str @@ -3509,6 +3587,8 @@ :Description: File where Tool Shed based Data Managers are configured. This file will be created automatically upon data manager installation. + The value of this option will be resolved with respect to + . :Default: ``shed_data_manager_conf.xml`` :Type: str @@ -3539,6 +3619,8 @@ Jobs are run locally on the system on which Galaxy is started. Advanced job running capabilities can be configured through the job configuration file. + The value of this option will be resolved with respect to + . :Default: ``job_conf.xml`` :Type: str @@ -3866,6 +3948,8 @@ CSS file to apply to all Markdown exports to PDF - currently used by WeasyPrint during rendering an HTML export of the document to PDF. + The value of this option will be resolved with respect to + . :Default: ``markdown_export.css`` :Type: str @@ -3878,6 +3962,8 @@ CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer markdown_export_css, but this is here for deployments that would like to tailor different kinds of exports. + The value of this option will be resolved with respect to + . :Default: ``markdown_export_pages.css`` :Type: str @@ -3890,6 +3976,8 @@ CSS file to apply to invocation report exports to PDF. Generally prefer markdown_export_css, but this is here for deployments that would like to tailor different kinds of exports. + The value of this option will be resolved with respect to + . :Default: ``markdown_export_invocation_reports.css`` :Type: str @@ -3969,6 +4057,8 @@ definition. These fields will be presented to users in the tool forms and allow them to overwrite default job resources such as number of processors, memory and walltime. + The value of this option will be resolved with respect to + . :Default: ``job_resource_params_conf.xml`` :Type: str @@ -3983,6 +4073,8 @@ requires both a description of the fields available (which defaults to the definitions in job_resource_params_file if not set). + The value of this option will be resolved with respect to + . :Default: ``workflow_resource_params_conf.xml`` :Type: str @@ -4014,6 +4106,8 @@ :Description: Optional configuration file similar to `job_config_file` to specify which Galaxy processes should schedule workflows. + The value of this option will be resolved with respect to + . :Default: ``workflow_schedulers_conf.xml`` :Type: str @@ -4268,6 +4362,8 @@ removed from the recommendations and another is for adding additional tools to be recommended along side those from the deep learning model. + The value of this option will be resolved with respect to + . :Default: ``tool_recommendations_overwrite.yml`` :Type: str @@ -4293,6 +4389,8 @@ :Description: Path to error reports configuration file. + The value of this option will be resolved with respect to + . :Default: ``error_report.yml`` :Type: str @@ -4305,6 +4403,8 @@ Path to container interface configuration file. The containers interface is only used if `enable_beta_containers_interface` config option is set. + The value of this option will be resolved with respect to + . :Default: ``containers_conf.yml`` :Type: str @@ -4315,6 +4415,8 @@ :Description: Path to dynamic tool destinations configuration file. + The value of this option will be resolved with respect to + . :Default: ``tool_destinations.yml`` :Type: str diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py index b8e6dfd87ba..16a2288381c 100644 --- a/lib/galaxy/config/config_manage.py +++ b/lib/galaxy/config/config_manage.py @@ -407,7 +407,7 @@ def _write_option_rst(args, rst, key, heading_level, option_value): heading = heading_level * len(title) rst.write(f"{heading}\n{title}\n{heading}\n\n") option, value = _parse_option_value(option_value) - desc = option["desc"] + desc = _get_option_desc(option) rst.write(":Description:\n") # Wrap and indent desc, replacing whitespaces with a space, except # for double newlines which are replaced with a single newline. @@ -733,7 +733,7 @@ def _write_header(f, section_header): def _write_option(args, f, key, option_value, as_comment=False, uwsgi_hack=False): option, value = _parse_option_value(option_value) - desc = option["desc"] + desc = _get_option_desc(option) comment = "" if desc and args.add_comments: # Wrap and comment desc, replacing whitespaces with a space, except @@ -802,6 +802,15 @@ def _warn(message): print("WARNING: %s" % message) +def _get_option_desc(option): + desc = option["desc"] + parent_dir = option.get("path_resolves_to") + if parent_dir: + path_resolves = f"The value of this option will be resolved with respect to <{parent_dir}>." + return f"{desc}\n{path_resolves}" if desc else path_resolves + return desc + + ACTIONS = { "convert": _run_conversion, "build_sample_yaml": _build_sample_yaml, diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index b0fe163e6d8..cbaccfe8f8b 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -215,11 +215,15 @@ galaxy: # 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 value of this option will be resolved with respect to + # . #file_path: objects # Where temporary files are stored. It must be accessible at the same # path on any cluster nodes that will run Galaxy jobs, unless using # Pulsar. + # The value of this option will be resolved with respect to + # . #new_file_path: tmp # Tool config files, defines what tools are available in Galaxy. Tools @@ -228,6 +232,8 @@ galaxy: # config/tool_conf.xml does not exist). Can be a single file, a list # of files, or (for backwards compatibility) a comma-separated list of # files. + # The value of this option will be resolved with respect to + # . #tool_config_file: tool_conf.xml # Tool config file for tools installed from the Galaxy Tool Shed. Must @@ -239,6 +245,8 @@ galaxy: # preferable. This file will be created automatically upon tool # installation, whereas Galaxy will fail to start if any files in # tool_config_file cannot be read. + # The value of this option will be resolved with respect to + # . #shed_tool_config_file: shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed @@ -253,6 +261,8 @@ galaxy: # migration scripts to install tools that have been migrated to the # tool shed upon a new release, they will be added to this tool config # file. + # The value of this option will be resolved with respect to + # . #migrated_tools_config: migrated_tools_conf.xml # File that contains the XML section and tool tags from all tool panel @@ -288,6 +298,8 @@ galaxy: # Conda if available. See # https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst # for more information on these options. + # The value of this option will be resolved with respect to + # . #dependency_resolvers_config_file: dependency_resolvers_conf.xml # conda_prefix is the location on the filesystem where Conda packages @@ -329,11 +341,15 @@ galaxy: # Path to a file that provides a mapping from abstract packages to # concrete conda packages. See `config/local_conda_mapping.yml.sample` # for examples. + # The value of this option will be resolved with respect to + # . #local_conda_mapping_file: local_conda_mapping.yml # Path to a file that provides a mapping from abstract packages to # locally installed modules. See # `config/environment_modules_mapping.yml.sample` for examples. + # The value of this option will be resolved with respect to + # . #modules_mapping_files: environment_modules_mapping.yml # Certain dependency resolvers (namely Conda) take a considerable @@ -362,6 +378,8 @@ galaxy: # File containing the Galaxy Tool Sheds that should be made available # to install from in the admin interface (.sample used if default does # not exist). + # The value of this option will be resolved with respect to + # . #tool_sheds_config_file: tool_sheds_conf.xml # Monitor the tools and tool directories listed in any tool config @@ -407,6 +425,8 @@ galaxy: #legacy_eager_objectstore_initialization: false # Configured FileSource plugins. + # The value of this option will be resolved with respect to + # . #file_sources_config_file: file_sources_conf.yml # Enable Galaxy to fetch containers registered with quay.io generated @@ -459,6 +479,8 @@ galaxy: # XML config file that contains data table entries for the # ToolDataTableManager. This file is manually # maintained by the # Galaxy administrator (.sample used if default does not exist). + # The value of this option will be resolved with respect to + # . #tool_data_table_config_path: tool_data_table_conf.xml # XML config file that contains additional data table entries for the @@ -468,6 +490,8 @@ galaxy: # these entries are automatically added to the following file, which # is parsed and applied to the ToolDataTableManager at server start # up. + # The value of this option will be resolved with respect to + # . #shed_tool_data_table_config: shed_tool_data_table_conf.xml # Directory where data used by tools is located. See the samples in @@ -498,6 +522,8 @@ galaxy: # File that defines the builds (dbkeys) available at sites used by # display applications and the URL to those sites. + # The value of this option will be resolved with respect to + # . #build_sites_config_file: build_sites.yml # File containing old-style genome builds. @@ -516,6 +542,8 @@ galaxy: # a datatype appears in multiple files, the last definition is used # (though the first sniffer is used so limit sniffer definitions to # one file). + # The value of this option will be resolved with respect to + # . #datatypes_config_file: datatypes_conf.xml # Enable sniffing of compressed datatypes. This can be @@ -567,10 +595,14 @@ galaxy: # If using a cluster, Galaxy will write job scripts and stdout/stderr # to this directory. + # The value of this option will be resolved with respect to + # . #cluster_files_directory: pbs # Mako templates are compiled as needed and cached for reuse, this # directory is used for the cache + # The value of this option will be resolved with respect to + # . #template_cache_path: compiled_templates # Set to false to disable various checks Galaxy will do to ensure it @@ -598,9 +630,12 @@ galaxy: # stored at this path. Per tool_conf cache locations can be configured # in (shed_)tool_conf.xml files using the tool_cache_data_dir # attribute. + # The value of this option will be resolved with respect to + # . #tool_cache_data_dir: tool_cache - # Directory in which the toolbox search index is stored. + # Directory in which the toolbox search index is stored. The value of + # this option will be resolved with respect to . #tool_search_index_dir: tool_search_index # Set this to true to delay parsing of tool inputs and outputs until @@ -618,12 +653,16 @@ galaxy: # from external sources such as https://doi.org/ by Galaxy - the # following parameters can be used to control the caching used to # store this information. + # The value of this option will be resolved with respect to + # . #citation_cache_data_dir: citations/data # Citation related caching. Tool citations information maybe fetched # from external sources such as https://doi.org/ by Galaxy - the # following parameters can be used to control the caching used to # store this information. + # The value of this option will be resolved with respect to + # . #citation_cache_lock_dir: citations/locks # Mulled resolution caching. Mulled resolution uses external APIs of @@ -633,14 +672,20 @@ galaxy: # Data directory used by beaker for caching mulled resolution # requests. + # The value of this option will be resolved with respect to + # . #mulled_resolution_cache_data_dir: mulled/data # Lock directory used by beaker for caching mulled resolution # requests. + # The value of this option will be resolved with respect to + # . #mulled_resolution_cache_lock_dir: mulled/locks # Configuration file for the object store If this is set and exists, # it overrides any other objectstore settings. + # The value of this option will be resolved with respect to + # . #object_store_config_file: object_store_conf.xml # What Dataset attribute is used to reference files in an ObjectStore @@ -799,6 +844,8 @@ galaxy: #interactivetools_proxy_host: null # Map for interactivetool proxy. + # The value of this option will be resolved with respect to + # . #interactivetools_map: interactivetools_map.sqlite # Show visualization tab and list in masthead. @@ -834,10 +881,14 @@ galaxy: # 'doc' may be be specified as well for each entry. # If this is null (the default), a simple configuration containing # just Dockstore will be used. + # The value of this option will be resolved with respect to + # . #trs_servers_config_file: trs_servers_conf.yml # Location of the configuration file containing extra user # preferences. + # The value of this option will be resolved with respect to + # . #user_preferences_extra_conf_path: user_preferences_extra_conf.yml # Default localization for Galaxy UI. Allowed values are listed at the @@ -1030,6 +1081,8 @@ galaxy: # The NodeJS dynamic proxy can use an SQLite database or a JSON file # for IPC, set that here. + # The value of this option will be resolved with respect to + # . #dynamic_proxy_session_map: session_map.sqlite # Set the port and IP for the dynamic proxy to bind to, this must @@ -1588,14 +1641,20 @@ galaxy: #enable_oidc: false # Sets the path to OIDC configuration file. + # The value of this option will be resolved with respect to + # . #oidc_config_file: oidc_config.xml # Sets the path to OIDC backends configuration file. + # The value of this option will be resolved with respect to + # . #oidc_backends_config_file: oidc_backends_config.xml # XML config file that allows the use of different authentication # providers (e.g. LDAP) instead or in addition to local authentication # (.sample is used if default does not exist). + # The value of this option will be resolved with respect to + # . #auth_config_file: auth_conf.xml # Optional list of email addresses of API users who can make calls on @@ -1612,6 +1671,8 @@ galaxy: #enable_openid: false # If OpenID is enabled, consumer cache directory to use. + # The value of this option will be resolved with respect to + # . #openid_consumer_cache_path: openid_consumer_cache # Enable tool tags (associating tools with tags). This has its own @@ -1691,6 +1752,8 @@ galaxy: # XML config file that contains the job metric collection # configuration. + # The value of this option will be resolved with respect to + # . #job_metrics_config_file: job_metrics_conf.xml # This option allows users to see the job metrics (except for @@ -1705,10 +1768,14 @@ galaxy: # File where Data Managers are configured (.sample used if default # does not exist). + # The value of this option will be resolved with respect to + # . #data_manager_config_file: data_manager_conf.xml # File where Tool Shed based Data Managers are configured. This file # will be created automatically upon data manager installation. + # The value of this option will be resolved with respect to + # . #shed_data_manager_config_file: shed_data_manager_conf.xml # Directory to store Data Manager based tool-data. Defaults to the @@ -1725,6 +1792,8 @@ galaxy: # are run locally on the system on which Galaxy is started. Advanced # job running capabilities can be configured through the job # configuration file. + # The value of this option will be resolved with respect to + # . #job_config_file: job_conf.xml # Description of job running configuration, can be embedded into @@ -1896,16 +1965,22 @@ galaxy: # CSS file to apply to all Markdown exports to PDF - currently used by # WeasyPrint during rendering an HTML export of the document to PDF. + # The value of this option will be resolved with respect to + # . #markdown_export_css: markdown_export.css # CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer # markdown_export_css, but this is here for deployments that would # like to tailor different kinds of exports. + # The value of this option will be resolved with respect to + # . #markdown_export_css_pages: markdown_export_pages.css # CSS file to apply to invocation report exports to PDF. Generally # prefer markdown_export_css, but this is here for deployments that # would like to tailor different kinds of exports. + # The value of this option will be resolved with respect to + # . #markdown_export_css_invocation_reports: markdown_export_invocation_reports.css # Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing @@ -1936,12 +2011,16 @@ galaxy: # These fields will be presented to users in the tool forms and allow # them to overwrite default job resources such as number of # processors, memory and walltime. + # The value of this option will be resolved with respect to + # . #job_resource_params_file: job_resource_params_conf.xml # Similar to the above parameter, workflows can describe parameters # used to influence scheduling of jobs within the workflow. This # requires both a description of the fields available (which defaults # to the definitions in job_resource_params_file if not set). + # The value of this option will be resolved with respect to + # . #workflow_resource_params_file: workflow_resource_params_conf.xml # This parameter describes how to map users and workflows to a set of @@ -1959,6 +2038,8 @@ galaxy: # Optional configuration file similar to `job_config_file` to specify # which Galaxy processes should schedule workflows. + # The value of this option will be resolved with respect to + # . #workflow_schedulers_config_file: workflow_schedulers_conf.xml # If using job concurrency limits (configured in job_config_file), @@ -2070,6 +2151,8 @@ galaxy: # removed from the recommendations and another is for adding # additional tools to be recommended along side those from the deep # learning model. + # The value of this option will be resolved with respect to + # . #admin_tool_recommendations_path: tool_recommendations_overwrite.yml # Overwrite or append to the tool recommendations by the deep learning @@ -2081,13 +2164,19 @@ galaxy: #overwrite_model_recommendations: false # Path to error reports configuration file. + # The value of this option will be resolved with respect to + # . #error_report_file: error_report.yml # Path to container interface configuration file. The containers # interface is only used if `enable_beta_containers_interface` config # option is set. + # The value of this option will be resolved with respect to + # . #containers_config_file: containers_conf.yml # Path to dynamic tool destinations configuration file. + # The value of this option will be resolved with respect to + # . #tool_destinations_config_file: tool_destinations.yml diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample index bb8a1f791eb..eb3774e34b9 100644 --- a/lib/galaxy/config/sample/tool_shed.yml.sample +++ b/lib/galaxy/config/sample/tool_shed.yml.sample @@ -408,6 +408,8 @@ tool_shed: # XML config file that allows the use of different authentication # providers (e.g. LDAP) instead or in addition to local authentication # (.sample is used if default does not exist). + # The value of this option will be resolved with respect to + # . #auth_config_file: auth_conf.xml # XML config file that contains additional data table entries for the @@ -417,6 +419,8 @@ tool_shed: # these entries are automatically added to the following file, which # is parsed and applied to the ToolDataTableManager at server start # up. + # The value of this option will be resolved with respect to + # . #shed_tool_data_table_config: shed_tool_data_table_conf.xml # Datatypes config file(s), defines what data (file) types are @@ -424,5 +428,7 @@ tool_shed: # a datatype appears in multiple files, the last definition is used # (though the first sniffer is used so limit sniffer definitions to # one file). + # The value of this option will be resolved with respect to + # . #datatypes_config_file: datatypes_conf.xml