diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 072c092522d..12c2535e476 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -29,10 +29,8 @@ :Description: By default, Galaxy uses a SQLite database at - 'database/universe.sqlite'. You may use a SQLAlchemy connection - string to specify an external database instead. This string takes - many options which are explained in detail in the config file - documentation. + '/universe.sqlite'. You may use a SQLAlchemy connection + string to specify an external database instead. Sample default 'sqlite:////universe.sqlite?isolation_level=IMMEDIATE' :Default: ``None`` @@ -255,7 +253,9 @@ this option is preferable. This file will be created automatically upon tool installation, whereas Galaxy will fail to start if any files in tool_config_file cannot be read. -:Default: ``config/shed_tool_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``shed_tool_conf.xml`` :Type: str @@ -284,8 +284,8 @@ 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. - Default value will be resolved to 'config/migrated_tools_conf.xml' - where 'config' is the default value of the 'config_dir' option). + The value of this option will be resolved with respect to + . :Default: ``migrated_tools_conf.xml`` :Type: str @@ -329,8 +329,8 @@ handling. If this option is set to none or an invalid path, installing tools with dependencies from the Tool Shed or in Conda will fail. - Default value will be resolved to 'database/dependencies' where - 'database' is the default value of the 'data_dir' option). + The value of this option will be resolved with respect to + . :Default: ``dependencies`` :Type: str @@ -347,7 +347,9 @@ then use Conda if available. See https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst for more information on these options. -:Default: ``config/dependency_resolvers_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``dependency_resolvers_conf.xml`` :Type: str @@ -496,7 +498,9 @@ File containing the Galaxy Tool Sheds that should be made available to install from in the admin interface (.sample used if default does not exist). -:Default: ``config/tool_sheds_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``tool_sheds_conf.xml`` :Type: str @@ -603,7 +607,8 @@ 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. - Value will be resolved with respect to ''. + The value of this option will be resolved with respect to + . :Default: ``involucro`` :Type: str @@ -696,7 +701,9 @@ installation, these entries are automatically added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. -:Default: ``config/shed_tool_data_table_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``shed_tool_data_table_conf.xml`` :Type: str @@ -747,8 +754,9 @@ ~~~~~~~~~~~~~~~~~~~~ :Description: - File containing old-style genome builds. Value will be resolved - with respect to . + File containing old-style genome builds. + The value of this option will be resolved with respect to + . :Default: ``shared/ucsc/builds.txt`` :Type: str @@ -759,7 +767,8 @@ :Description: Directory where chrom len files are kept, currently mainly used by - trackster. Value will be resolved with respect to + trackster. + The value of this option will be resolved with respect to . :Default: ``shared/ucsc/chrom`` :Type: str @@ -869,8 +878,8 @@ Each job is given a unique empty directory as its current working directory. This option defines in what parent directory those directories will be created. - Default value will be resolved to 'database/jobs_directory' where - 'database' is the default value of the 'data_dir' option). + The value of this option will be resolved with respect to + . :Default: ``jobs_directory`` :Type: str @@ -992,7 +1001,9 @@ :Description: Configuration file for the object store If this is set and exists, it overrides any other objectstore settings. -:Default: ``config/object_store_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``object_store_conf.xml`` :Type: str @@ -1325,7 +1336,7 @@ 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 ), - + 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). @@ -1340,7 +1351,9 @@ :Description: Location of the configuration file containing extra user preferences. -:Default: ``config/user_preferences_extra_conf.yml`` + The value of this option will be resolved with respect to + . +:Default: ``user_preferences_extra_conf.yml`` :Type: str @@ -2093,8 +2106,8 @@ :Description: Debug enables access to various config options useful for - development and debugging: use_lint, use_profile, use_printdebug - and use_interactive. It also causes the files used by PBS/SGE + 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. :Default: ``false`` @@ -2131,17 +2144,6 @@ :Type: bool -~~~~~~~~~~~~~~~~~~~ -``use_interactive`` -~~~~~~~~~~~~~~~~~~~ - -:Description: - Enable live debugging in your browser. This should NEVER be - enabled on a public site. -:Default: ``false`` -:Type: bool - - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``monitor_thread_join_timeout`` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2970,7 +2972,9 @@ :Description: Sets the path to OIDC configuration file. -:Default: ``config/oidc_config.xml`` + The value of this option will be resolved with respect to + . +:Default: ``oidc_config.xml`` :Type: str @@ -2980,7 +2984,9 @@ :Description: Sets the path to OIDC backends configuration file. -:Default: ``config/oidc_backends_config.xml`` + The value of this option will be resolved with respect to + . +:Default: ``oidc_backends_config.xml`` :Type: str @@ -2992,7 +2998,9 @@ XML config file that allows the use of different authentication providers (e.g. LDAP) instead or in addition to local authentication (.sample is used if default does not exist). -:Default: ``config/auth_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``auth_conf.xml`` :Type: str @@ -3213,7 +3221,9 @@ :Description: File where Tool Shed based Data Managers are configured. This file will be created automatically upon data manager installation. -:Default: ``config/shed_data_manager_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``shed_data_manager_conf.xml`` :Type: str @@ -3459,9 +3469,9 @@ :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. + (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting- + jobs-as-the-real-user) this script is used to run the job script + Galaxy generates for a tool execution. Example value 'sudo -E scripts/drmaa_external_runner.py --assign_all_groups' :Default: ``None`` @@ -3474,9 +3484,9 @@ :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). + (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting- + jobs-as-the-real-user) this script is used to kill such jobs by + Galaxy (e.g. if the user cancels the job). Example value 'sudo -E scripts/drmaa_external_killer.py' :Default: ``None`` :Type: str @@ -3488,10 +3498,10 @@ :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. + (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting- + jobs-as-the-real-user) this script is used transfer permissions + back and forth between the Galaxy user and the user that is + running the job. Example value 'sudo -E scripts/external_chown_script.py' :Default: ``None`` :Type: str @@ -3503,14 +3513,14 @@ :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 + (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 :Default: ``user_email`` @@ -3545,7 +3555,9 @@ definition. These fields will be presented to users in the tool forms and allow them to overwrite default job resources such as number of processors, memory and walltime. -:Default: ``config/job_resource_params_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``job_resource_params_conf.xml`` :Type: str @@ -3559,7 +3571,9 @@ requires both a description of the fields available (which defaults to the definitions in job_resource_params_file if not set). -:Default: ``config/workflow_resource_params_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``workflow_resource_params_conf.xml`` :Type: str @@ -3588,7 +3602,9 @@ :Description: Optional configuration file similar to `job_config_file` to specify which Galaxy processes should schedule workflows. -:Default: ``config/workflow_schedulers_conf.xml`` + The value of this option will be resolved with respect to + . +:Default: ``workflow_schedulers_conf.xml`` :Type: str diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 219a62f3d94..e3a03b801a8 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -110,10 +110,8 @@ galaxy: #data_dir: null # By default, Galaxy uses a SQLite database at - # 'database/universe.sqlite'. You may use a SQLAlchemy connection - # string to specify an external database instead. This string takes - # many options which are explained in detail in the config file - # documentation. + # '/universe.sqlite'. You may use a SQLAlchemy connection + # string to specify an external database instead. # Sample default # 'sqlite:////universe.sqlite?isolation_level=IMMEDIATE' #database_connection: null @@ -215,7 +213,9 @@ 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. - #shed_tool_config_file: config/shed_tool_conf.xml + # 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 # tool_config_files (i.e., tool_conf.xml) have been migrated from the @@ -229,8 +229,8 @@ 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. - # Default value will be resolved to 'config/migrated_tools_conf.xml' - # where 'config' is the default value of the 'config_dir' option). + # 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 @@ -253,8 +253,8 @@ galaxy: # handling. If this option is set to none or an invalid path, # installing tools with dependencies from the Tool Shed or in Conda # will fail. - # Default value will be resolved to 'database/dependencies' where - # 'database' is the default value of the 'data_dir' option). + # The value of this option will be resolved with respect to + # . #tool_dependency_dir: dependencies # The dependency resolvers config file specifies an ordering and @@ -264,7 +264,9 @@ galaxy: # Conda if available. See # https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst # for more information on these options. - #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml + # 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 # and environments are installed. @@ -328,7 +330,9 @@ 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). - #tool_sheds_config_file: config/tool_sheds_conf.xml + # 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 # file specified in tool_config_file option. If changes are found, @@ -386,7 +390,8 @@ galaxy: # 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. - # Value will be resolved with respect to ''. + # The value of this option will be resolved with respect to + # . #involucro_path: involucro # Install involucro as needed to build Docker or Singularity @@ -430,7 +435,9 @@ galaxy: # 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_config: config/shed_tool_data_table_conf.xml + # 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 # that directory and the Galaxy Community Hub for help: @@ -453,12 +460,15 @@ galaxy: # scenarios than the watchdog default. #watch_tool_data_dir: 'false' - # File containing old-style genome builds. Value will be resolved with - # respect to . + # File containing old-style genome builds. + # The value of this option will be resolved with respect to + # . #builds_file_path: shared/ucsc/builds.txt # Directory where chrom len files are kept, currently mainly used by - # trackster. Value will be resolved with respect to . + # trackster. + # The value of this option will be resolved with respect to + # . #len_file_path: shared/ucsc/chrom # Datatypes config file(s), defines what data (file) types are @@ -511,8 +521,8 @@ galaxy: # Each job is given a unique empty directory as its current working # directory. This option defines in what parent directory those # directories will be created. - # Default value will be resolved to 'database/jobs_directory' where - # 'database' is the default value of the 'data_dir' option). + # The value of this option will be resolved with respect to + # . #job_working_directory: jobs_directory # If using a cluster, Galaxy will write job scripts and stdout/stderr @@ -564,7 +574,9 @@ galaxy: # Configuration file for the object store If this is set and exists, # it overrides any other objectstore settings. - #object_store_config_file: config/object_store_conf.xml + # 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 # implementation, default is 'id' but can also be set to 'uuid' for @@ -711,14 +723,16 @@ galaxy: # 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 + # 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). #pretty_datetime_format: $locale (UTC) # Location of the configuration file containing extra user # preferences. - #user_preferences_extra_conf_path: config/user_preferences_extra_conf.yml + # 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 # end of client/galaxy/scripts/nls/locale.js. With the default value @@ -864,8 +878,8 @@ galaxy: # 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. + # to protect your users. Uncomment and leave empty to not set the + # `X-Frame-Options` header. #x_frame_options: SAMEORIGIN # nginx can also handle file uploads (user-to-Galaxy) via @@ -1041,8 +1055,8 @@ galaxy: #trust_jupyter_notebook_conversion: false # Debug enables access to various config options useful for - # development and debugging: use_lint, use_profile, use_printdebug and - # use_interactive. It also causes the files used by PBS/SGE + # 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. #debug: false @@ -1056,10 +1070,6 @@ galaxy: # Intercept print statements and show them on the returned page. #use_printdebug: true - # Enable live debugging in your browser. This should NEVER be enabled - # on a public site. - #use_interactive: false - # 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 @@ -1458,15 +1468,21 @@ galaxy: #enable_oidc: false # Sets the path to OIDC configuration file. - #oidc_config_file: config/oidc_config.xml + # 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. - #oidc_backends_config_file: config/oidc_backends_config.xml + # 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). - #auth_config_file: config/auth_conf.xml + # 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 # behalf of other users. @@ -1554,7 +1570,9 @@ galaxy: # File where Tool Shed based Data Managers are configured. This file # will be created automatically upon data manager installation. - #shed_data_manager_config_file: config/shed_data_manager_conf.xml + # 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 # tool_data_path. @@ -1680,39 +1698,38 @@ galaxy: #cleanup_job: always # 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. + # (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' #drmaa_external_runjob_script: null # 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). + # (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' #drmaa_external_killjob_script: null # 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. + # (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' #external_chown_script: null # 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 - # + # (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 #real_system_username: user_email # File to source to set up the environment when running jobs. By @@ -1731,13 +1748,17 @@ 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. - #job_resource_params_file: config/job_resource_params_conf.xml + # 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). - #workflow_resource_params_file: config/workflow_resource_params_conf.xml + # 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 # workflow resource parameter to present (typically input IDs from @@ -1752,7 +1773,9 @@ galaxy: # Optional configuration file similar to `job_config_file` to specify # which Galaxy processes should schedule workflows. - #workflow_schedulers_config_file: config/workflow_schedulers_conf.xml + # 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), # several extra database queries must be performed to determine the diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample index ab88a6689ba..a944a79f8ec 100644 --- a/lib/galaxy/config/sample/tool_shed.yml.sample +++ b/lib/galaxy/config/sample/tool_shed.yml.sample @@ -177,8 +177,8 @@ tool_shed: # 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://galaxyproject.org/admin/config - # /apache-external-user-auth/ + # For more information, see: + # https://galaxyproject.org/admin/config/apache-external-user-auth/ #use_remote_user: false # If use_remote_user is enabled, anyone who can log in to the Galaxy diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index a38d2b07859..e53eeb15724 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -1558,9 +1558,9 @@ mapping: default: false required: false desc: | - Debug enables access to various config options useful for development and - debugging: use_lint, use_profile, use_printdebug and use_interactive. It - also causes the files used by PBS/SGE (submission script, output, and error) + 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. use_lint: @@ -1584,14 +1584,6 @@ mapping: desc: | Intercept print statements and show them on the returned page. - use_interactive: - type: bool - default: false - required: false - desc: | - Enable live debugging in your browser. This should NEVER be enabled on a - public site. - monitor_thread_join_timeout: type: int default: 30