Nicola Soranzo
720fae9afd
Merge branch 'release_25.1' into release_26.0
2026-02-24 13:12:42 +00:00
Nicola Soranzo
60f6185138
Merge branch 'release_25.0' into release_25.1
2026-02-24 13:11:18 +00:00
davelopez
71df52c74c
Clarifies rules for template variable requirements in docs
2026-02-11 10:04:11 +01:00
davelopez
0a1df430ed
Fix docs format
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Removes extra spaces after comment symbols in config docs
2026-02-11 10:04:10 +01:00
Marius van den Beek
ad39d779cf
Merge pull request #21335 from jmchilton/wes_implementation
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Implement GA4GH WES API
2026-01-27 14:43:29 +01:00
Marius van den Beek
d6e7db8437
Merge pull request #20924 from davelopez/explore_url_fetch_with_headers
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Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests
2026-01-27 14:21:38 +01:00
davelopez
a12a082a74
Adds docs for enabling HTTP headers in fetch
2026-01-27 11:31:35 +01:00
Marius van den Beek
26e7bd959a
Merge pull request #21594 from bernt-matthias/ext-file-source-templates
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Unify extensions of file source templates
2026-01-21 13:11:35 +01:00
davelopez
d93f093005
Rebuild config
2026-01-21 10:29:49 +01:00
Matthias Bernt
56391f903d
also update doc references
2026-01-20 21:47:49 +01:00
John Chilton and Claude
9271e56062
Implement GA4GH WES API with task logs & comprehensive test coverage
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Implement full Workflow Execution Service (WES) API support for running Galaxy
workflows via the GA4GH standard. Includes complete core functionality with run
submission, status tracking, cancellation, input/output handling, and task logs.
Core WES Features:
- 6 WES API endpoints (service-info, runs CRUD, cancel, status)
- Support for both workflow_url and workflow_attachment input methods
- Support for gxworkflow:// URI scheme for direct database workflow references
- Automatic history creation with optional custom naming
- Full workflow support: gx_workflow_ga and gx_workflow_format2
- DRS URI generation for all workflow outputs
- State mapping between Galaxy invocation states and WES states
- Cursor-based pagination for run listings
Task Log Features:
- /api/jobs/{job_id}/stdout - Job stdout as plain text
- /api/jobs/{job_id}/stderr - Job stderr as plain text
- /ga4gh/wes/v1/runs/{run_id}/tasks - Paginated task list
- /ga4gh/wes/v1/runs/{run_id}/tasks/{task_id} - Task details
- Build TaskLogs from workflow invocation steps
- Populate RunLog with task_logs list and task_logs_url
Implementation Highlights:
- Auto-generated Pydantic models from GA4GH WES OpenAPI spec
- FastAPI CBV router following Galaxy API patterns
- Service layer with full workflow submission/execution pipeline
- Shared GA4GH utilities for DRS code reuse
- Reduced test duplication with helper functions
Files Added:
- lib/galaxy/schema/wes/__init__.py - Generated Pydantic models
- lib/galaxy/webapps/galaxy/api/wes.py - WES API router
- lib/galaxy/webapps/galaxy/services/wes.py - WesService
- lib/galaxy/webapps/galaxy/services/ga4gh.py - Shared GA4GH utilities
- WES_PLAN.md - Implementation plan
🤖 Generated with [Claude Code](https://claude.com/claude-code )
Co-Authored-By: Claude <noreply@anthropic.com >
2026-01-20 13:54:01 -05:00
Nicola Soranzo
eb9fde1dcd
Drop support for Python 3.9
2026-01-19 18:39:16 +00:00
Nicola Soranzo
ace6cdbbc1
Rebuild config samples and docs
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with `make config-rebuild`
2026-01-18 18:51:57 +00:00
Nicola Soranzo
1c211faff6
Merge branch 'release_25.1' into dev
2026-01-17 12:19:00 +00:00
Marius van den Beek
8be6cfce90
Merge pull request #21563 from bernt-matthias/citation_bibtex_quotes
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[25.1] Use quotes for Galaxy citation bibtex
2026-01-15 09:44:09 +01:00
Matthias Bernt
49ddccee28
update docs
2026-01-14 10:04:36 +01:00
Arash
aabca704fa
Add documentation for the new tool credentials system in the vault
2026-01-12 17:41:56 +01:00
Dannon Baker
7279386543
Rebuild config/docs
2025-12-22 16:40:46 -05:00
Nuwan Goonasekera
666491a4e4
Also remove defunct custos vault
2025-12-02 22:13:28 +05:30
Nuwan Goonasekera
59a9c9e403
Remove defunct custos auth provider
2025-12-02 22:13:27 +05:30
mvdbeek
48c7bfe463
Various fixes around ascp file source
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- Add an ascp handler to the frontend, so users can paste ascp:// urls
- Add ssh key passphrase config option, without this downloads hang
waiting for password
- Bypass is_dir / is_file checks, they'll always fail. We assume files
for now.
- Implement top-level get_file. `_get_file` would require implementing
`get_info` which doesn't really make sense for this file source.
2025-12-01 15:17:34 +01:00
Danielle Callan
04c5b460af
fix ascp fsspec import and improve related docs
2025-11-25 16:44:18 -05:00
Danielle Callan
8d984a22a8
simplify ssh key management for ascp plugin
2025-11-25 09:33:30 -05:00
Danielle Callan
2268ca292f
docs ascp plugin
2025-11-24 18:40:42 -05:00
Matthias Bernt
029a5409f4
reformulate
2025-11-20 15:33:06 +01:00
davelopez
45d5bc3da6
Refactors template variable validation to use tool_util validators
2025-10-30 15:08:21 +01:00
davelopez
5eb0aa5792
Adds documentation for template variable validators
2025-10-30 15:08:21 +01:00
Matthias Bernt
29bc617bac
add missing enable_beta_tool_formats config option
2025-10-29 13:46:18 +01:00
davelopez
856e0eff6c
Update config samples from schema
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Some leftovers after running `make config-rebuild`.
2025-10-14 16:41:20 +02:00
Uwe Winter
09a4b5272a
rebuild-config
2025-09-29 17:41:48 -05:00
Uwe Winter
815f26d5bf
Rename allow_user_creation to allow_local_account_creation
2025-09-29 17:41:40 -05:00
Uwe Winter
68b4a0c948
Add Config opion disable_local_accounts
2025-09-29 17:40:47 -05:00
Aysam Guerler
8ec885eda0
Merge pull request #20868 from ahmedhamidawan/move_tour_generator_webhook_to_core
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Replace tour_generator webhook with internal API and frontend
2025-09-26 07:45:08 +03:00
Dannon
8ebc13e047
Merge pull request #20361 from scottcain/update-admin-doc-index
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Remove 8 year old note that points at a non-existent subdomain
2025-09-23 14:38:38 -04:00
Ahmed Awan and Björn Grüning
e9710be048
set enable_tool_generated_tours to true by default
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Co-authored-by: Björn Grüning <469983+bgruening@users.noreply.github.com >
2025-09-23 08:41:29 -05:00
Ahmed Awan
8e47e1638d
add enable_tool_generated_tours config option
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Doesn't do anything yet
2025-09-23 08:41:27 -05:00
mvdbeek
0c09aa9e5c
Add test for proposed prod-like deployment
2025-09-21 17:03:17 +02:00
Ahmed Hamid Awan
2d513e834c
Merge pull request #20911 from ahmedhamidawan/merge_25.0_into_dev_sept
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Merge 25.0 into dev
2025-09-15 21:06:30 -05:00
marius-mather
1f4cd32967
Rebuild config and skip pre-commit changes
2025-09-16 08:58:52 +10:00
Ahmed Awan
f823afcc2a
Merge remote-tracking branch 'upstream/release_25.0' into merge_25.0_into_dev_sept
2025-09-15 14:46:12 -05:00
marius-mather
c11e7529c8
Merge remote-tracking branch 'upstream/dev' into oidc-pipeline-config
2025-09-15 11:05:44 +10:00
marius-mather
6d7deabdb7
Rebuild config docs
2025-09-15 10:49:45 +10:00
John Davis
ddee1a2a90
Merge branch 'release_24.2' into release_25.0
2025-09-10 09:54:38 -04:00
Tim Kok
cc6da148c1
Add support for hierarchical module systems in lmod + modules dependency resolvers
2025-09-05 09:04:31 +02:00
John Davis
c87d5391d6
Update celery section in docs
2025-09-03 10:57:50 -04:00
mvdbeek
ba5122a724
Drop configfiles not supported from docs
2025-09-01 17:36:10 +02:00
Nicola Soranzo and Marius van den Beek
be6a0dee57
Drop unnecessary "just"
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2025-08-27 19:18:20 +01:00
Nicola Soranzo
7fa47d4ba6
Update Python instructions for admins
2025-08-27 16:30:39 +01:00
Matthias Bernt
70444d3177
Merge branch 'release_25.0' into dev
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# Conflicts:
# client/package.json
# lib/galaxy/version.py
# package.json
# packages/app/HISTORY.rst
# packages/app/setup.cfg
# packages/auth/HISTORY.rst
# packages/auth/setup.cfg
# packages/config/HISTORY.rst
# packages/config/setup.cfg
# packages/data/HISTORY.rst
# packages/data/setup.cfg
# packages/files/HISTORY.rst
# packages/files/setup.cfg
# packages/job_execution/HISTORY.rst
# packages/job_execution/setup.cfg
# packages/job_metrics/HISTORY.rst
# packages/job_metrics/setup.cfg
# packages/meta/HISTORY.rst
# packages/meta/setup.cfg
# packages/navigation/HISTORY.rst
# packages/navigation/setup.cfg
# packages/objectstore/HISTORY.rst
# packages/objectstore/setup.cfg
# packages/schema/HISTORY.rst
# packages/schema/setup.cfg
# packages/selenium/HISTORY.rst
# packages/selenium/setup.cfg
# packages/test_api/HISTORY.rst
# packages/test_api/setup.cfg
# packages/test_base/HISTORY.rst
# packages/test_base/setup.cfg
# packages/test_driver/HISTORY.rst
# packages/test_driver/setup.cfg
# packages/tool_shed/HISTORY.rst
# packages/tool_shed/setup.cfg
# packages/tool_shed_schema/HISTORY.rst
# packages/tool_shed_schema/setup.cfg
# packages/tool_util/HISTORY.rst
# packages/tool_util/setup.cfg
# packages/tool_util_models/HISTORY.rst
# packages/tool_util_models/setup.cfg
# packages/tours/HISTORY.rst
# packages/tours/setup.cfg
# packages/util/HISTORY.rst
# packages/util/setup.cfg
# packages/web_apps/HISTORY.rst
# packages/web_apps/setup.cfg
# packages/web_client/HISTORY.rst
# packages/web_client/setup.cfg
# packages/web_framework/HISTORY.rst
# packages/web_framework/setup.cfg
# packages/web_stack/HISTORY.rst
# packages/web_stack/setup.cfg
2025-08-13 14:34:10 +02:00
Martin Cech
fe5315d74d
fix docs for nginx
2025-08-11 11:10:50 +02:00
Nicola Soranzo