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Rebuild config schema.
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@jmchilton
jmchilton committed Oct 17, 2023
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72 changes: 45 additions & 27 deletions doc/source/admin/galaxy_options.rst
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Expand Up @@ -1650,13 +1650,26 @@
~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
URL of the support resource for the galaxy instance. Used in
activation emails.
URL of the support resource for the galaxy instance. Used outside
of web contexts such as in activation emails and in Galaxy
markdown report generation.
Example value 'https://galaxyproject.org/'
:Default: ``None``
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~
``instance_access_url``
~~~~~~~~~~~~~~~~~~~~~~~

:Description:
URL used to access this Galaxy server. Used outside of web
contexts such as in Galaxy markdown report generation.
Example value 'https://usegalaxy.org'
:Default: ``None``
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``email_domain_blocklist_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -4036,54 +4049,59 @@
:Type: str


~~~~~~~~~~~~~~~~~~~~
``ga4gh_service_id``
~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~
``organization_name``
~~~~~~~~~~~~~~~~~~~~~

:Description:
Service ID for GA4GH services (exposed via the service-info
endpoint for the Galaxy DRS API). If unset, one will be generated
using the URL the target API requests are made against.
The name of the organization that operates this Galaxy instance.
Serves as the default for the GA4GH service organization name and
can be exposed through Galaxy markdown for reports and such. For
instance, "Not Evil Corporation".
For GA4GH APIs, this is exposed via the service-info endpoint for
the Galaxy DRS API. If unset, one will be generated using
ga4gh_service_id (but only in the context of GA4GH APIs).
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
This value should likely reflect your service's URL. For instance
for usegalaxy.org this value should be org.usegalaxy. Particular
Galaxy implementations will treat this value as a prefix and
append the service type to this ID. For instance for the DRS
service "id" (available via the DRS API) for the above
configuration value would be org.usegalaxy.drs.
:Default: ``None``
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``ga4gh_service_organization_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~
``organization_url``
~~~~~~~~~~~~~~~~~~~~

:Description:
Service name for host organization (exposed via the service-info
endpoint for the Galaxy DRS API). If unset, one will be generated
using ga4gh_service_id.
The URL of the organization that operates this Galaxy instance.
Serves as the default for the GA4GH service organization name and
can be exposed through Galaxy markdown for reports and such. For
instance, "notevilcorp.com".
For GA4GH APIs, this is exposed via the service-info endpoint.
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
:Default: ``None``
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``ga4gh_service_organization_url``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~
``ga4gh_service_id``
~~~~~~~~~~~~~~~~~~~~

:Description:
Organization URL for host organization (exposed via the
service-info endpoint for the Galaxy DRS API). If unset, one will
be generated using the URL the target API requests are made
against.
Service ID for GA4GH services (exposed via the service-info
endpoint for the Galaxy DRS API). If unset, one will be generated
using the URL the target API requests are made against.
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
This value should likely reflect your service's URL. For instance
for usegalaxy.org this value should be org.usegalaxy. Particular
Galaxy implementations will treat this value as a prefix and
append the service type to this ID. For instance for the DRS
service "id" (available via the DRS API) for the above
configuration value would be org.usegalaxy.drs.
:Default: ``None``
:Type: str

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48 changes: 30 additions & 18 deletions lib/galaxy/config/sample/galaxy.yml.sample
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Expand Up @@ -1116,11 +1116,17 @@ galaxy:
# message, before the 'Your Galaxy Team' signature.
#custom_activation_email_message: null

# URL of the support resource for the galaxy instance. Used in
# activation emails.
# URL of the support resource for the galaxy instance. Used outside
# of web contexts such as in activation emails and in Galaxy markdown
# report generation.
# Example value 'https://galaxyproject.org/'
#instance_resource_url: null

# URL used to access this Galaxy server. Used outside of web contexts
# such as in Galaxy markdown report generation.
# Example value 'https://usegalaxy.org'
#instance_access_url: null

# E-mail domains blocklist is used for filtering out users that are
# using disposable email addresses at registration. If their
# address's base domain matches any domain on the list, they are
Expand Down Expand Up @@ -2187,6 +2193,28 @@ galaxy:
# production server.
#bootstrap_admin_api_key: null

# The name of the organization that operates this Galaxy instance.
# Serves as the default for the GA4GH service organization name and
# can be exposed through Galaxy markdown for reports and such. For
# instance, "Not Evil Corporation".
# For GA4GH APIs, this is exposed via the service-info endpoint for
# the Galaxy DRS API. If unset, one will be generated using
# ga4gh_service_id (but only in the context of GA4GH APIs).
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#organization_name: null

# The URL of the organization that operates this Galaxy instance.
# Serves as the default for the GA4GH service organization name and
# can be exposed through Galaxy markdown for reports and such. For
# instance, "notevilcorp.com".
# For GA4GH APIs, this is exposed via the service-info endpoint.
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#organization_url: null

# Service ID for GA4GH services (exposed via the service-info endpoint
# for the Galaxy DRS API). If unset, one will be generated using the
# URL the target API requests are made against.
Expand All @@ -2201,22 +2229,6 @@ galaxy:
# be org.usegalaxy.drs.
#ga4gh_service_id: null

# Service name for host organization (exposed via the service-info
# endpoint for the Galaxy DRS API). If unset, one will be generated
# using ga4gh_service_id.
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#ga4gh_service_organization_name: null

# Organization URL for host organization (exposed via the service-info
# endpoint for the Galaxy DRS API). If unset, one will be generated
# using the URL the target API requests are made against.
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#ga4gh_service_organization_url: null

# Service environment (exposed via the service-info endpoint for the
# Galaxy DRS API) for implemented GA4GH services.
# Suggested values are prod, test, dev, staging.
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48 changes: 48 additions & 0 deletions lib/galaxy/config/sample/tool_shed.yml.sample
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,10 @@ tool_shed:
# installation directory.
#hgweb_config_dir: null

# Allow pushing directly to mercurial repositories directly and
# without authentication.
#config_hg_for_dev: null

# Where Tool Shed repositories are stored.
#file_path: database/community_files

Expand Down Expand Up @@ -188,6 +192,50 @@ tool_shed:
# Address to join mailing list
#mailing_join_addr: galaxy-announce-join@bx.psu.edu

# Service ID for GA4GH services.
# If unset, one will be generated using the URL the target API
# requests are made against.
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
# This value should likely reflect your service's URL. For instance
# for usegalaxy.org this value should be org.usegalaxy. Particular
# Galaxy implementations will treat this value as a prefix and append
# the service type to this ID. For instance for the DRS service "id"
# (available via the DRS API) for the above configuration value would
# be org.usegalaxy.drs.
#ga4gh_service_id: null

# The name of the organization that operates this Galaxy instance.
# Serves as the default for the GA4GH service organization name and
# can be exposed through Galaxy markdown for reports and such. For
# instance, "Not Evil Corporation".
# For GA4GH APIs, this is exposed via the service-info endpoint for
# the Galaxy DRS API. If unset, one will be generated using
# ga4gh_service_id (but only in the context of GA4GH APIs).
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#organization_name: null

# The URL of the organization that operates this Galaxy instance.
# Serves as the default for the GA4GH service organization name and
# can be exposed through Galaxy markdown for reports and such. For
# instance, "notevilcorp.com".
# For GA4GH APIs, this is exposed via the service-info endpoint.
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#organization_url: null

# Service environment (exposed via the service-info endpoint for the
# Galaxy DRS API) for implemented GA4GH services.
# Suggested values are prod, test, dev, staging.
# For more information on GA4GH service definitions - check out
# https://github.com/ga4gh-discovery/ga4gh-service-registry and
# https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
#ga4gh_service_environment: null

# Write thread status periodically to 'heartbeat.log' (careful, uses
# disk space rapidly!)
#use_heartbeat: true
Expand Down

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