John ChiltonandClaude Opus 4.8 1981c78e84 Add developer GA4GH WES API guide ...

Client walkthrough (curl) of submit/monitor over WES v1.0.0: state mapping,
gxworkflow:// scheme, engine params, tasks, pagination, errors, limitations.
Cross-link admin <-> dev docs; point at gxy-wes / gxy-wes-bioblend examples.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-08 16:31:27 -04:00

..

special_topics

Merge branch 'release_25.1' into dev

2026-01-17 12:19:00 +00:00

_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

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

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

conda_faq.rst

A few more updates to the tool deps documentation

2021-06-07 20:54:23 -04:00

config_logging.rst

Doc fixes

2022-08-19 18:33:20 +01:00

config-template-secrets-create.png

Implement file source templates

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config-template-secrets-edit.png

Implement file source templates

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config.rst

Display 'Config Options' as subheading of 'Galaxy Configuration'

2022-09-27 15:03:03 -04:00

container_resolvers.rst

Fix bug in admin/container docs section title markup

2024-05-13 21:03:39 -04:00

data_tables.md

change text in a minor way

2024-04-18 18:55:38 +02:00

data.md

Clarifies rules for template variable requirements in docs

2026-02-11 10:04:11 +01:00

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.

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dropbox_create_app_options_1.png

Allow oauth2 file sources with Dropbox initial implementation.

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dropbox_create_button.png

Allow oauth2 file sources with Dropbox initial implementation.

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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.

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file_source_dropbox_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

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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

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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

Add developer GA4GH WES API guide

2026-06-08 16:31:27 -04:00

galaxy_options.rst

Merge branch 'release_25.1' into release_26.0

2026-02-24 13:12:42 +00:00

gen_diagrams.py

Fix isort linting

2025-05-09 12:14:20 +02:00

index.rst

Merge pull request #21335 from jmchilton/wes_implementation

2026-01-27 14:43:29 +01:00

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

fix docs for nginx

2025-08-11 11:10:50 +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.

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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

yaml_config - Add RST docs for Galaxy options.

2017-12-06 20:28:20 -05:00

production.md

Update celery section in docs

2025-09-03 10:57:50 -04:00

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

Drop uWSGI from Galaxy Reports documentation

2022-02-18 01:44:33 -05:00

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

Clarify how to separate job and workflow scheduling

2025-07-09 10:22:08 +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

tool_panel.rst

Apply suggestions from code review

2023-11-27 13:40:33 +01:00

useful_scripts.rst

Add warning, gxadmin script ref to script, docs

2025-05-09 12:19:16 +02:00

user_defined_tools.md

Add test for proposed prod-like deployment

2025-09-21 17:03:17 +02:00

user_file_source_form_full_aws_public.png

Implement file source templates

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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

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user_object_store_form_full_gcp_s3_interop.png

Implement file source templates

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