diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 60b91c44a99..8f922c5526c 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -3816,9 +3816,9 @@ :Type: bool -~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ ``prefer_oidc_login`` -~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ :Description: Controls the order of the login page to prefer OIDC-based login @@ -3834,7 +3834,7 @@ :Description: Allow unregistered users to create new local (non-OIDC) accounts (otherwise, they will have to be created by an admin). This option - will be overridden to false in case disable_local_accounts is set + will be overridden to false in case disable_local_accounts is set to true. :Default: ``true`` :Type: bool @@ -3846,7 +3846,7 @@ :Description: Disable local accounts. If this option is set to true, at least - one OIDC provider needs to be configured and will serve as the + one OIDC provider needs to be configured and will serve as the account provider. If this option is set to true, allow_local_account creation will be overridden with false. :Default: ``false`` diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 30a3eb9763b..df7c57d9a77 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -47,6 +47,11 @@ gravity: # is ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB), processes exceeding the limit are throttled and put under heavy reclaim pressure. + # If set, this is the default value for all services. Setting ``memory_high`` on an individual service overrides this + # value. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Specify Galaxy config file (galaxy.yml), if the Gravity config is separate from the Galaxy config. Assumed to be the # same file as the Gravity config if a ``galaxy`` key exists at the root level, otherwise, this option is required. # galaxy_config_file: @@ -67,6 +72,11 @@ gravity: # If not specified defaults to ``/gravity/log``. # log_dir: + # Run Galaxy processes in the specified journal namespace (sets the value of ``LogNamespace=`` in the systemd service + # units). This allows you to keep Galaxy log messages separate in the system journal from other log messages. Ignored if + # ``process_manager`` is not ``systemd``. See ``systemd.exec(5)`` for details. + # log_namespace: + # Set to Galaxy's virtualenv directory. # If not specified, Gravity assumes all processes are on PATH. This option is required in most circumstances when using # the ``systemd`` process manager. @@ -74,9 +84,7 @@ gravity: # Select the application server. # ``gunicorn`` is the default application server. - # ``unicornherder`` is a production-oriented manager for (G)unicorn servers that automates zero-downtime Galaxy server restarts, - # similar to uWSGI Zerg Mode used in the past. - # Valid options are: gunicorn, unicornherder + # Valid options are: gunicorn # app_server: gunicorn # Override the default instance name. @@ -107,8 +115,8 @@ gravity: # extra_args: # Use Gunicorn's --preload option to fork workers after loading the Galaxy Application. - # Consumes less memory when multiple processes are configured. Default is ``false`` if using unicornherder, else ``true``. - # preload: + # Consumes less memory when multiple processes are configured. + # preload: true # umask under which service should be executed # umask: @@ -127,6 +135,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -171,6 +184,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -224,6 +242,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -286,6 +309,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -338,6 +366,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -2111,19 +2144,19 @@ galaxy: # page (even if require_login is true). #show_welcome_with_login: false - # Controls the order of the login page to prefer OIDC-based login - # and registration. + # Controls the order of the login page to prefer OIDC-based login and + # registration. #prefer_oidc_login: false # Allow unregistered users to create new local (non-OIDC) accounts # (otherwise, they will have to be created by an admin). This option - # will be overridden to false in case disable_local_accounts is set - # to true. + # will be overridden to false in case disable_local_accounts is set to + # true. #allow_local_account_creation: true # Disable local accounts. If this option is set to true, at least one - # OIDC provider needs to be configured and will serve as the account - # provider. If this option is set to true, allow_local_account + # OIDC provider needs to be configured and will serve as the account + # provider. If this option is set to true, allow_local_account # creation will be overridden with false. #disable_local_accounts: false diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample index f7e2ac55872..9a4b9a26aab 100644 --- a/lib/galaxy/config/sample/tool_shed.yml.sample +++ b/lib/galaxy/config/sample/tool_shed.yml.sample @@ -23,6 +23,12 @@ tool_shed: # without authentication. #config_hg_for_dev: null + # The base URL of the Tool Shed server used for generating clone URLs + # and repository hostnames. If set, this value will be used instead of + # deriving the URL from the incoming request. + # Example: https://toolshed.g2.bx.psu.edu + #tool_shed_url: null + # Where Tool Shed repositories are stored. #file_path: database/community_files