Rebuild config including gravity stuff

2026-09-24 16:30:27 +08:00 · 2022-12-22 21:25:41 -05:00
parent fd7aef5e42
commit 9de4e72563
2 changed files with 165 additions and 10 deletions
@@ -5074,3 +5074,6 @@
    <config_dir>.
 :Default: ``themes_conf.yml``
 :Type: str
+
+
+
@@ -1,35 +1,74 @@
 # Galaxy is configured by default to be usable in a single-user development
 # environment.  To tune the application for a multi-user production
 # environment, see the documentation at:
-#
+# 
 #  https://docs.galaxyproject.org/en/master/admin/production.html
-#
+# 
 # Throughout this sample configuration file, except where stated otherwise,
 # uncommented values override the default if left unset, whereas commented
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
-#
+# 
 # Examples of many of these options are explained in more detail in the Galaxy
 # Community Hub.
-#
+# 
 #   https://galaxyproject.org/admin/config
-#
+# 
 # Config hackers are encouraged to check there before asking for help.
-#
+# 
 # Configuration for Gravity process manager.
 # ``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 <service-name>`) 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 ``<state_dir>/log``.
+  # If not specified defaults to ``<galaxy_data_dir>/gravity/log``.
  # log_dir:

  # Set to Galaxy's virtualenv directory.
-  # If not specified, Gravity assumes all processes are on PATH.
+  # If not specified, Gravity assumes all processes are on PATH. This option is required in most circumstances when using
+  # the ``systemd`` process manager.
  # virtualenv:

  # Select the application server.
@@ -43,7 +82,7 @@ gravity:
  # this is hidden from you when running a single instance.
  # instance_name: _default_

-  # Configuration for Gunicorn.
+  # Configuration for Gunicorn. Can be a list to run multiple gunicorns for rolling restarts.
  gunicorn:

    # Enable Galaxy gunicorn server.
@@ -70,6 +109,23 @@ 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: {}
@@ -100,6 +156,20 @@ 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: {}
@@ -117,7 +187,8 @@ gravity:
    # port: 4002

    # Routes file to monitor.
-    # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section.
+    # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if
+    # ``interactivetools_map is set``.
    # sessions: database/interactivetools_map.sqlite

    # Include verbose messages in gx-it-proxy
@@ -135,6 +206,20 @@ 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: {}
@@ -175,6 +260,72 @@ 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 <url_prefix> and <bind> with the values from these options):
+    #
+    # location /<url_prefix>/ {
+    #     proxy_pass http://<bind>/;
+    # }
+    #
+    # If <bind> 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: {}
@@ -2552,3 +2703,4 @@ galaxy:
  # The value of this option will be resolved with respect to
  # <config_dir>.
  #themes_config_file: themes_conf.yml
+