opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
77,490 Commits 69 Branches 243 Tags
db7395b42378fe8aec00a5d25e452e033bc19164
Commit Graph
1032 Commits
Author SHA1 Message Date
Nicola Soranzo af9b9efdd6 Remove conda defaults channel from more places 2024-10-21 21:31:56 +02:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
mvdbeek 7c6fc1800f Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc 2024-06-21 16:58:21 +02:00
Bjoern Gruening 5eec5cc7ae rebuild Galaxy config 2024-06-04 21:30:24 +02:00
John Chilton b598bff3e0 Big warning box about distributed object stores being required. 2024-05-20 12:19:01 -04:00
John Chilton 29ea0ba522 Implement many PR comments around Vue stuff and docs. 2024-05-20 12:19:01 -04:00
John Chilton f95da89b3d Implement file source templates 2024-05-20 12:18:47 -04:00
John Davis 076f298a99 Merge pull request #18079 from jdavcs/dev_userless_history_script_and_tests 
Script for deleting userless histories from database + testing + drop unused model testing code
 2024-05-14 13:48:24 -04:00
John Davis 3904681f40 Provide an example of ISO format 2024-05-14 13:47:35 -04:00
John Davis 77d8d61e90 Add documentation 2024-05-13 22:17:21 -04:00
John Davis 54bb8a9a06 Fix bug in admin/container docs section title markup 2024-05-13 21:03:39 -04:00
tianzedavid 04bfa209e7 chore: remove repetitive words 
Signed-off-by: tianzedavid <cuitianze@aliyun.com>
 2024-05-02 21:30:03 +08:00
Nicola Soranzo 1d64120a00 Merge branch 'release_24.0' into dev 2024-04-25 14:32:52 +01:00
mvdbeek f26e90f712 Log start and end of request 
Configurable via `use_access_logging_middleware`.
Looks like this:

```
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:43,776 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:48,719 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435 200
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,767 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,786 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4 200
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:53,139 [pN:main,p:73562,tN:MainThread] GET /api/entry_points?running=true 763693e9-4fd3-4a97-a100-a3c259b4b4c8
```
 2024-04-24 17:08:06 +02:00
Martin Cech ffc66f2c28 Merge pull request #17585 from bernt-matthias/admin-doc-data-tables 
Add some admin facing docs on data tables
 2024-04-18 18:55:55 +02:00
Martin Cech abad770d5a change text in a minor way 2024-04-18 18:55:38 +02:00
davelopez dbdd5bca81 Add dispatch_notifications_interval config option 2024-04-16 17:06:19 +02:00
davelopezandNicola Soranzo 3bb49cab8e Move result_backend comment to celery_conf 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2024-04-11 09:21:27 +02:00
davelopez 514df55323 Add broker and backend defaults as null 
This will keep the values in the sample config.
 2024-04-10 18:23:52 +02:00
davelopez a739ed1cb8 Rebuild config samples 2024-04-10 17:56:52 +02:00
davelopezandNicola Soranzo 4ec8cef337 Reword sentence 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2024-04-10 17:03:55 +02:00
davelopez ac526184e8 Make sure data_dir is used for default result backend DB 2024-04-10 15:27:13 +02:00
davelopez 9d9630dc1c Replace sample Celery result_backend in config 2024-04-09 17:33:29 +02:00
davelopez 2f4bc1a600 Update config docs to mention the celery result_backend 2024-04-05 17:09:28 +02:00
davelopez 9fb43e58b2 Update production docs to mention Celery 2024-04-05 17:08:28 +02:00
davelopez eed755a3f7 Reorder enable_celery_tasks in config schema 
This is the main flag and it makes sense to set it before the rest of the configuration.
 2024-04-05 16:16:03 +02:00
davelopez d43b826666 Run make config-rebuild 2024-04-05 16:14:24 +02:00
davelopez a6ddaac915 Run make config-rebuild 2024-04-05 11:31:11 +02:00
mvdbeek 3669caee17 Merge branch 'release_23.2' into release_24.0 2024-03-28 09:29:33 +01:00
mvdbeek 2ce2686205 Proxy Access-Control-* headers when using x-accel-redirect 2024-03-26 10:54:29 +01:00
John Chilton 13cce38dd9 Allow admin to sharpen language about selected object stores. 2024-03-22 10:41:59 -04:00
Matthias Bernt e5a56addd3 Merge branch 'admin-doc-data-tables' of https://github.com/bernt-matthias/galaxy into admin-doc-data-tables 2024-03-06 13:18:04 +01:00
Matthias Bernt c964d89ba3 try to use terms properly 
loc files and tool data tables should now be used as they should be
 2024-03-06 13:15:21 +01:00
M BerntandNicola Soranzo f15426c56b Improve wording 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-03-05 08:28:56 +01:00
Matthias Bernt de34121ae1 add some admin facing docs on data tables 2024-03-04 16:03:30 +01:00
Matthias Bernt c3ff77512e add documentation on how to use vault keys in file sources 2024-02-19 19:39:55 +01:00
Nate Coraor a65dd8ae49 Support configuring object store inline 2023-12-20 14:11:22 -05:00
mvdbeek 5d401923fc Merge branch 'release_23.2' into dev 2023-12-14 11:44:09 +01:00
Nate Coraor 0598a4be81 Document falsey values of job_metrics 2023-12-12 16:53:54 -05:00
Nate Coraor 91ef184f39 Support configuring job metrics inline, update documentation 2023-12-12 14:56:38 -05:00
Dannon 426e24ff24 Merge pull request #16954 from common-workflow-lab/python3.8 
Python 3.8 as minimum
 2023-11-28 23:53:14 -05:00
Dannon f2034f6cb4 Merge pull request #16798 from ElectronicBlueberry/galaxy-help-forum-integration 
[EGD 2023 Cofest] Galaxy help forum integration
 2023-11-28 09:57:33 -05:00
M BerntandNicola Soranzo 378a144597 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-11-27 13:40:33 +01:00
davelopez ccbac95e85 Rename config option 2023-11-27 11:25:52 +01:00
davelopez 885ceb2d8e Add config options for help forum integration 2023-11-27 11:25:51 +01:00
Michael R. Crusoe c00967cca4 Python 3.8 as new minimum version 
Fixes: https://github.com/galaxyproject/galaxy/issues/16394

Also upgrade code to Python 3.8 syntax with:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|lib/tool_shed_client/schema/trs.*.py\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs pyupgrade --py38-plus
```
 2023-11-26 18:34:09 +00:00
Matthias Bernt 878e9fd10d reorder elements of tool conf description 2023-11-24 16:56:17 +01:00
M BerntandNicola Soranzo c6bb6767ab Reformulations 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-11-24 16:53:57 +01:00
M BerntandNicola Soranzo 8a87d75b8d reformulation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-11-24 16:24:33 +01:00
Matthias Bernt 16b2bf20b2 add docs for tool panel and panel view administration 2023-11-24 12:37:55 +01:00