From 7d7ac4111b28eafce2966841adb5894ea6fa37dd Mon Sep 17 00:00:00 2001 From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com> Date: Thu, 22 Dec 2022 16:59:27 +0100 Subject: [PATCH] rebuild config --- doc/source/admin/galaxy_options.rst | 10 +- lib/galaxy/config/sample/galaxy.yml.sample | 166 ++------------------- 2 files changed, 16 insertions(+), 160 deletions(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 2efe1c7b357..de6cb6b9144 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -5062,15 +5062,15 @@ :Type: bool -~~~~~~~~~~~~~~~ -``themes_file`` -~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~ +``themes_config_file`` +~~~~~~~~~~~~~~~~~~~~~~ :Description: Optional file containing one or more themes for galaxy. If several - themes are defined, users can choose their preferd theme in the + themes are defined, users can choose their preferred theme in the client. The value of this option will be resolved with respect to . -:Default: ``themes.yml`` +:Default: ``themes_conf.yml`` :Type: str diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 6ecf25c244e..0fae965ef56 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -20,55 +20,16 @@ # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``). gravity: - # Process manager to use. - # ``supervisor`` is the default process manager when Gravity is invoked as a non-root user. - # ``systemd`` is the default when Gravity is invoked as root. - # Valid options are: supervisor, systemd - # process_manager: - - # What command to write to the process manager configs - # `gravity` (`galaxyctl exec `) is the default - # `direct` (each service's actual command) is also supported. - # Valid options are: gravity, direct - # service_command_style: gravity - - # Use the process manager's *service instance* functionality for services that can run multiple instances. - # Presently this includes services like gunicorn and Galaxy dynamic job handlers. Service instances are only supported if - # ``service_command_style`` is ``gravity``, and so this option is automatically set to ``false`` if - # ``service_command_style`` is set to ``direct``. - # use_service_instances: true - - # umask under which services should be executed. Setting ``umask`` on an individual service overrides this value. - # umask: '022' - - # Memory limit (in GB), processes exceeding the limit will be killed. Default is no limit. If set, this is default value - # for all services. Setting ``memory_limit`` on an individual service overrides this value. Ignored if ``process_manager`` - # is ``supervisor``. - # memory_limit: - - # 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: - # Specify Galaxy's root directory. # Gravity will attempt to find the root directory, but you can set the directory explicitly with this option. # galaxy_root: - # User to run Galaxy as, required when using the systemd process manager as root. - # Ignored if ``process_manager`` is ``supervisor`` or user-mode (non-root) ``systemd``. - # galaxy_user: - - # Group to run Galaxy as, optional when using the systemd process manager as root. - # Ignored if ``process_manager`` is ``supervisor`` or user-mode (non-root) ``systemd``. - # galaxy_group: - # Set to a directory that should contain log files for the processes controlled by Gravity. - # If not specified defaults to ``/gravity/log``. + # If not specified defaults to ``/log``. # log_dir: # 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. + # If not specified, Gravity assumes all processes are on PATH. # virtualenv: # Select the application server. @@ -82,7 +43,7 @@ gravity: # this is hidden from you when running a single instance. # instance_name: _default_ - # Configuration for Gunicorn. Can be a list to run multiple gunicorns for rolling restarts. + # Configuration for Gunicorn. gunicorn: # Enable Galaxy gunicorn server. @@ -109,23 +70,6 @@ gravity: # Consumes less memory when multiple processes are configured. Default is ``false`` if using unicornherder, else ``true``. # preload: - # umask under which service should be executed - # umask: - - # Value of supervisor startsecs, systemd TimeoutStartSec - # start_timeout: 15 - - # Value of supervisor stopwaitsecs, systemd TimeoutStopSec - # stop_timeout: 65 - - # Amount of time to wait for a server to become alive when performing rolling restarts. - # restart_timeout: 300 - - # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the - # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is - # ``supervisor``. - # memory_limit: - # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -156,20 +100,6 @@ gravity: # Extra arguments to pass to Celery command line. # extra_args: - # umask under which service should be executed - # umask: - - # Value of supervisor startsecs, systemd TimeoutStartSec - # start_timeout: 10 - - # Value of supervisor stopwaitsecs, systemd TimeoutStopSec - # stop_timeout: 10 - - # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the - # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is - # ``supervisor``. - # memory_limit: - # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -187,8 +117,7 @@ gravity: # port: 4002 # Routes file to monitor. - # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if - # ``interactivetools_map is set``. + # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. # sessions: database/interactivetools_map.sqlite # Include verbose messages in gx-it-proxy @@ -206,20 +135,6 @@ gravity: # This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network. # reverse_proxy: false - # umask under which service should be executed - # umask: - - # Value of supervisor startsecs, systemd TimeoutStartSec - # start_timeout: 10 - - # Value of supervisor stopwaitsecs, systemd TimeoutStopSec - # stop_timeout: 10 - - # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the - # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is - # ``supervisor``. - # memory_limit: - # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -260,72 +175,6 @@ gravity: # Extra arguments to pass to tusd command line. # extra_args: - # umask under which service should be executed - # umask: - - # Value of supervisor startsecs, systemd TimeoutStartSec - # start_timeout: 10 - - # Value of supervisor stopwaitsecs, systemd TimeoutStopSec - # stop_timeout: 10 - - # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the - # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is - # ``supervisor``. - # memory_limit: - - # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable - # names. - # environment: {} - - # Configuration for Galaxy Reports. - reports: - - # Enable Galaxy Reports server. - # enable: false - - # Path to reports.yml, relative to galaxy.yml if not absolute - # config_file: reports.yml - - # The socket to bind. A string of the form: ``HOST``, ``HOST:PORT``, ``unix:PATH``, ``fd://FD``. An IP is a valid HOST. - # bind: localhost:9001 - - # Controls the number of Galaxy Reports application processes Gunicorn will spawn. - # It is not generally necessary to increase this for the low-traffic Reports server. - # workers: 1 - - # Gunicorn workers silent for more than this many seconds are killed and restarted. - # Value is a positive number or 0. Setting it to 0 has the effect of infinite timeouts by disabling timeouts for all workers entirely. - # timeout: 300 - - # URL prefix to serve from. - # The corresponding nginx configuration is (replace and with the values from these options): - # - # location // { - # proxy_pass http:///; - # } - # - # If is a unix socket, you will need a ``:`` after the socket path but before the trailing slash like so: - # proxy_pass http://unix:/run/reports.sock:/; - # url_prefix: - - # Extra arguments to pass to Gunicorn command line. - # extra_args: - - # umask under which service should be executed - # umask: - - # Value of supervisor startsecs, systemd TimeoutStartSec - # start_timeout: 10 - - # Value of supervisor stopwaitsecs, systemd TimeoutStopSec - # stop_timeout: 10 - - # Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the - # ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is - # ``supervisor``. - # memory_limit: - # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -2696,3 +2545,10 @@ galaxy: # Display built-in converters in the tool panel. #display_builtin_converters: true + + # Optional file containing one or more themes for galaxy. If several + # themes are defined, users can choose their preferred theme in the + # client. + # The value of this option will be resolved with respect to + # . + #themes_config_file: themes_conf.yml