Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[24.0] Rebuild config samples #17911

Merged
merged 1 commit into from
Apr 5, 2024
Merged

[24.0] Rebuild config samples #17911

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 35 additions & 6 deletions doc/source/admin/galaxy_options.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1453,7 +1453,7 @@
This option has no effect if the file specified by
object_store_config_file exists. Otherwise, if this option is set,
it overrides any other objectstore settings.
The syntax, available instrumenters, and documentation of their
The syntax, available storage plugins, and documentation of their
options is explained in detail in the object store sample
configuration file, `object_store_conf.sample.yml`
:Default: ``None``
Expand Down Expand Up @@ -2606,8 +2606,20 @@

:Description:
The upload store is a temporary directory in which files uploaded
by the tus middleware or server will be placed. Defaults to
new_file_path if not set.
by the tus middleware or server for user uploads will be placed.
Defaults to new_file_path if not set.
:Default: ``None``
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tus_upload_store_job_files``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
The upload store is a temporary directory in which files uploaded
by the tus middleware or server for remote job files (Pulsar) will
be placed. Defaults to tus_upload_store if not set.
:Default: ``None``
:Type: str

Expand Down Expand Up @@ -4030,6 +4042,23 @@
:Type: str


~~~~~~~~~~~~~~~~~~~~~
``oidc_scope_prefix``
~~~~~~~~~~~~~~~~~~~~~

:Description:
Sets the prefix for OIDC scopes specific to this Galaxy instance.
If an API call is made against this Galaxy instance using an OIDC
bearer token, any scopes must be prefixed with this value e.g.
https://galaxyproject.org/api. More concretely, to request all
permissions that the user has, the scope would have to be
specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
Currently, only * is recognised as a valid scope, and future
iterations may provide more fine-grained scopes.
:Default: ``https://galaxyproject.org/api``
:Type: str


~~~~~~~~~~~~~~~~~~~~
``auth_config_file``
~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -5439,9 +5468,9 @@
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``help_forum_tool_panel_integration_enabled``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_help_forum_tool_panel_integration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
Enable the integration of the Galaxy Help Forum in the tool panel.
Expand Down
67 changes: 40 additions & 27 deletions lib/galaxy/config/sample/galaxy.yml.sample
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
# 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:
Expand Down Expand Up @@ -181,7 +181,7 @@ gravity:
# enable: false

# gx-it-proxy version
# version: '>=0.0.5'
# version: '>=0.0.6'

# Public-facing IP of the proxy
# ip: localhost
Expand Down Expand Up @@ -248,6 +248,14 @@ gravity:
# Must match ``tus_upload_store`` setting in ``galaxy:`` section.
# upload_dir:

# Value of tusd -hooks-httpd option
#
# the default of is suitable for using tusd for Galaxy uploads and should not be changed unless you are using tusd for
# other purposes such as Pulsar staging.
#
# The value of galaxy_infrastructure_url is automatically prepended if the option starts with a `/`
# hooks_http: /api/upload/hooks

# Comma-separated string of enabled tusd hooks.
#
# Leave at the default value to require authorization at upload creation time.
Expand Down Expand Up @@ -333,15 +341,9 @@ gravity:
# names.
# environment: {}

# Configure dynamic handlers in this section. Below is a simple example
# Configure dynamic handlers in this section.
# See https://docs.galaxyproject.org/en/latest/admin/scaling.html#dynamically-defined-handlers for details.
#handlers:
# handler:
# processes: 3
# pools:
# - job-handlers
# - workflow-schedulers

# handlers: {}
galaxy:

# The directory that will be prepended to relative paths in options
Expand Down Expand Up @@ -1030,7 +1032,7 @@ galaxy:
# This option has no effect if the file specified by
# object_store_config_file exists. Otherwise, if this option is set,
# it overrides any other objectstore settings.
# The syntax, available instrumenters, and documentation of their
# The syntax, available storage plugins, and documentation of their
# options is explained in detail in the object store sample
# configuration file, `object_store_conf.sample.yml`
#object_store_config: null
Expand Down Expand Up @@ -1067,6 +1069,13 @@ galaxy:
# for that object store entry.
#object_store_cache_size: -1

# Set this to true to indicate in the UI that a user's object store
# selection isn't simply a "preference" that job destinations often
# respect but in fact will always be respected. This should be set to
# true to simplify the UI as long as job destinations never override
# 'object_store_id's for a jobs.
#object_store_always_respect_user_selection: false

# What Dataset attribute is used to reference files in an ObjectStore
# implementation, this can be 'uuid' or 'id'. The default will depend
# on how the object store is configured, starting with 20.05 Galaxy
Expand Down Expand Up @@ -1304,9 +1313,6 @@ galaxy:
# The value of this option will be resolved with respect to
# <data_dir>.
#interactivetools_map: interactivetools_map.sqlite
# Note: the following config should still be used due to lack of
# support of data_dir resolution in gx-it-proxy and gravity:
#interactivetools_map: database/interactivetools_map.sqlite

# Prefix to use in the formation of the subdomain or path for
# interactive tools
Expand Down Expand Up @@ -1547,10 +1553,15 @@ galaxy:
#nginx_upload_job_files_path: null

# The upload store is a temporary directory in which files uploaded by
# the tus middleware or server will be placed. Defaults to
# new_file_path if not set.
# the tus middleware or server for user uploads will be placed.
# Defaults to new_file_path if not set.
#tus_upload_store: null

# The upload store is a temporary directory in which files uploaded by
# the tus middleware or server for remote job files (Pulsar) will be
# placed. Defaults to tus_upload_store if not set.
#tus_upload_store_job_files: null

# Galaxy can upload user files in chunks without using nginx. Enable
# the chunk uploader by specifying a chunk size larger than 0. The
# chunk size is specified in bytes (default: 10MB).
Expand Down Expand Up @@ -2189,12 +2200,13 @@ galaxy:
# <config_dir>.
#oidc_backends_config_file: oidc_backends_config.xml

# Sets the prefix for OIDC scopes specific to this Galaxy instance.
# If an API call is made against this Galaxy instance using an OIDC bearer token,
# any scopes must be prefixed with this value e.g. https://galaxyproject.org/api.
# More concretely, to request all permissions that the user has, the scope
# would have to be specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
# Currently, only * is recognised as a valid scope, and future iterations may
# Sets the prefix for OIDC scopes specific to this Galaxy instance. If
# an API call is made against this Galaxy instance using an OIDC
# bearer token, any scopes must be prefixed with this value e.g.
# https://galaxyproject.org/api. More concretely, to request all
# permissions that the user has, the scope would have to be specified
# as "<prefix>:*". e.g "https://galaxyproject.org/api:*". Currently,
# only * is recognised as a valid scope, and future iterations may
# provide more fine-grained scopes.
#oidc_scope_prefix: https://galaxyproject.org/api

Expand Down Expand Up @@ -2897,3 +2909,4 @@ galaxy:
# Enable the integration of the Galaxy Help Forum in the tool panel.
# This requires the help_forum_api_url to be set.
#enable_help_forum_tool_panel_integration: false

Loading