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galaxy/doc/source/admin
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Dannon Baker efa5e9b233 Harden agent retries config resolution 
Two follow-ups on the configurable-retries change. A shared `default` block
`retries` was silently overriding custom_tool's producer-0, which would
re-enable pydantic-ai's generic retry loop inside the producer's own reflection
loop. The producer's 0 is a correctness requirement, not a tunable, so it now
honors only an explicit `custom_tool.retries` and ignores the default block.
Separately, a non-numeric or blank `retries` value used to blow up with a bare
TypeError/ValueError at agent construction -- which the manager mistook for an
unknown-agent fallback and double-faulted on -- so it now raises a clear
ConfigurationError.
2026-06-12 12:59:27 -04:00
..
special_topics
Add Hashicorp Vault token renewal support
2026-03-30 12:27:04 +02:00
_inc_proxy_prereq.md
Migrate to MyST-Parser for Markdown docs
2023-03-27 15:01:27 +01:00
_inc_proxy_serving_root.md
Migrate to MyST-Parser for Markdown docs
2023-03-27 15:01:27 +01:00
_inc_proxy_ssl.md
Migrate to MyST-Parser for Markdown docs
2023-03-27 15:01:27 +01:00
ai_agents.md
Update admin docs and 26.0 release notes for the GalaxyAI rebrand
2026-05-20 11:35:01 -04:00
apache.md
Migrate to MyST-Parser for Markdown docs
2023-03-27 15:01:27 +01:00
authentication.md
Fix `'myst' cross-reference target not found` warnings
2023-03-27 15:07:21 +01:00
carbon_emissions.md
Move carbon intensity reference data to backend and add admin docs
2023-06-24 13:53:34 +02:00
cluster.md
cleanups, test cleanups
2026-05-08 00:00:08 +02:00
conda_faq.rst
…
config_logging.rst
Doc fixes
2022-08-19 18:33:20 +01:00
config-template-secrets-create.png
Implement file source templates
2024-05-20 12:18:47 -04:00
config-template-secrets-edit.png
Implement file source templates
2024-05-20 12:18:47 -04:00
config.rst
Display 'Config Options' as subheading of 'Galaxy Configuration'
2022-09-27 15:03:03 -04:00
container_resolvers.rst
Add namespace stripping to CachedExplicitSingularityContainerResolver
2026-06-11 15:57:08 +02:00
data_tables.md
doc: add missing value examples and Flux XML filter example
2026-04-17 12:16:53 +02:00
data.md
fixes after review
2026-04-09 17:20:51 +10:00
db_migration.md
Add documentation on handling a deadlock error during db migration
2025-02-05 15:03:33 -05:00
dependency_resolvers.rst
Add support for hierarchical module systems in lmod + modules dependency resolvers
2025-09-05 09:04:31 +02:00
dropbox_callback.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
dropbox_client_creds.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
dropbox_create_app_options_1.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
dropbox_create_button.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
dropbox_scopes.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
enable_headers_in_fetch_requests.md
Adds docs for enabling HTTP headers in fetch
2026-01-27 11:31:35 +01:00
file_source_azure_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_azure_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_dropbox_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_dropbox_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_elabftw_configuration_template.png
Set writable: true in file source template for eLabFTW
2025-02-13 15:33:56 +01:00
file_source_elabftw_configuration.png
Set writable: true in file source template for eLabFTW
2025-02-13 15:33:56 +01:00
file_source_ftp_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_ftp_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_invenio_configuration_template.png
Add InvenioRDM file source configuration documentation and templates
2025-02-17 13:44:19 +01:00
file_source_invenio_configuration.png
Add InvenioRDM file source configuration documentation and templates
2025-02-17 13:44:19 +01:00
file_source_posix_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_posix_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_rspace_configuration_template.png
Implement file source to integrate Galaxy with RSpace
2025-05-09 12:04:46 +02:00
file_source_rspace_configuration.png
Implement file source to integrate Galaxy with RSpace
2025-05-09 12:04:46 +02:00
file_source_s3fs_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_s3fs_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_templates.png
Implement file source to integrate Galaxy with RSpace
2025-05-09 12:04:46 +02:00
file_source_webdav_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_webdav_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
file_source_zenodo_configuration_template.png
Add Zenodo file source template documentation
2025-02-19 10:36:33 +01:00
file_source_zenodo_configuration.png
Add Zenodo file source template documentation
2025-02-19 10:36:33 +01:00
framework_dependencies.rst
Replace poetry with uv
2024-10-31 10:22:52 +00:00
ga4gh.md
Implement GA4GH WES API with task logs & comprehensive test coverage
2026-01-20 13:54:01 -05:00
galaxy_options.rst
Harden agent retries config resolution
2026-06-12 12:59:27 -04:00
gen_diagrams.py
Use `os.path.join() or pathlib.Path` instead of f-strings for filesystem paths
2026-02-27 19:48:46 +00:00
index.rst
Add admin docs for SSE-driven real-time updates
2026-04-28 19:15:24 +02:00
job_metrics.rst
Support setting and displaying timezone with the core metrics plugin
2025-05-06 11:45:51 -04:00
jobs.md
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-21 16:58:21 +02:00
migrating_to_gunicorn.md
Migrate to MyST-Parser for Markdown docs
2023-03-27 15:01:27 +01:00
mq.md
Update Celery and Kombu links
2022-05-06 13:29:14 +01:00
nginx.md
Add admin docs for SSE-driven real-time updates
2026-04-28 19:15:24 +02:00
object_store_aws_s3_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_aws_s3_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_azure_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_azure_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_boto3_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_boto3_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_disk_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_disk_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_generic_s3_configuration_template.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_generic_s3_configuration.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
object_store_templates.png
Allow oauth2 file sources with Dropbox initial implementation.
2024-10-14 15:16:41 +02:00
options.rst
…
production.md
Document per-user rate limiting and concurrency limiting in production guide
2026-04-07 14:47:36 +02:00
proxy_package_layout.rst
Drop remaining references to uWSGI
2022-03-21 13:44:37 +01:00
python.md
Drop support for Python 3.9
2026-01-19 18:39:16 +00:00
reports_options.rst
Remove old WSGI middleware that is no longer useful.
2022-11-10 05:28:24 -05:00
reports.rst
…
s3_configuration_template.png
Implement file source templates
2024-05-20 12:18:47 -04:00
s3_configuration.png
Implement file source templates
2024-05-20 12:18:47 -04:00
scaling.md
Add admin docs for SSE-driven real-time updates
2026-04-28 19:15:24 +02:00
search_for_new_screenshots.py
Implement file source to integrate Galaxy with RSpace
2025-05-09 12:04:46 +02:00
security.md
Migrate to MyST-Parser for Markdown docs
2023-03-27 15:01:27 +01:00
sse_updates.md
Add admin docs for SSE-driven real-time updates
2026-04-28 19:15:24 +02:00
tool_panel.rst
Address gx-arch-review feedback on PR #22212
2026-05-19 11:43:34 +02:00
useful_scripts.rst
Add warning, gxadmin script ref to script, docs
2025-05-09 12:19:16 +02:00
user_defined_tools.md
narrow YAML tool parameter schema for UserToolSource
2026-04-15 15:36:56 -04:00
user_file_source_form_full_aws_public.png
Implement file source templates
2024-05-20 12:18:47 -04:00
user_file_source_form_full_azure.png
Implement file source templates
2024-05-20 12:18:47 -04:00
user_file_source_form_full_elabftw.png
Update eLabFTW file source template docs
2025-02-17 13:10:32 +01:00
user_file_source_form_full_ftp.png
Implement file source templates
2024-05-20 12:18:47 -04:00
user_file_source_form_full_invenio.png
Add InvenioRDM file source configuration documentation and templates
2025-02-17 13:44:19 +01:00
user_file_source_form_full_rspace.png
Implement file source to integrate Galaxy with RSpace
2025-05-09 12:04:46 +02:00
user_file_source_form_full_webdav.png
Add images of the webdav conf and template and update file source templates image
2024-10-10 10:40:58 +00:00
user_file_source_form_full_zenodo.png
Add Zenodo file source template documentation
2025-02-19 10:36:33 +01:00
user_object_store_form_full_aws_s3.png
Implement file source templates
2024-05-20 12:18:47 -04:00
user_object_store_form_full_azure.png
Implement file source templates
2024-05-20 12:18:47 -04:00
user_object_store_form_full_gcp_s3_interop.png
Implement file source templates
2024-05-20 12:18:47 -04:00