opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:03:57 +08:00
Code Issues Packages Projects Releases Wiki Activity
38,341 Commits 63 Branches 243 Tags
5d771424bf8f7a3e783c86e91c90eefdd200bcc9
Commit Graph
38341 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Dannon Baker 5d771424bf Drop debug github object print 2019-03-19 10:24:55 -04:00
Helena Rasche ea0700a032 fix some small bugs 2019-03-14 10:09:36 +01:00
Helena Rasche ec086c1e8b Attempt to automate this? 2019-03-14 10:02:23 +01:00
Helena Rasche df7904dd7b Add user facing release notes 2019-03-14 10:02:15 +01:00
Nicola Soranzo aef53f6cde Merge branch 'release_18.09' into release_19.01 2019-03-10 21:39:24 +00:00
Nicola Soranzo 8e125b7698 Merge branch 'release_18.05' into release_18.09 2019-03-10 21:36:15 +00:00
Dannon 0ab05b3ce6 Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 
[18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins
 2019-03-10 16:18:56 -04:00
Nicola Soranzo c1a9095ad4 Restrict loading of JSON files on the server via the workflow API to Galaxy admins 
Fix https://github.com/galaxyproject/security/issues/29
 2019-03-10 12:52:02 +00:00
Dannon 9c711e7efa Merge pull request #7458 from mvdbeek/fix_broken_hidden_parameter 
[19.01] Fix hidden parameter use in workflows
 2019-03-05 08:33:56 -05:00
mvdbeek b5bbdfd89f Also use correct image 2019-03-04 19:00:56 +01:00
mvdbeek 76be1263ca Test that workflows with hidden params can be run 2019-03-04 18:41:51 +01:00
mvdbeek 1a636c376f Fix HiddenParameter use 
Broken in
https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5d1e1288315e1
Fixes https://github.com/galaxyproject/galaxy/issues/7454
 2019-03-04 17:39:57 +01:00
Nicola Soranzo 91e49acf37 Merge branch 'release_18.09' into release_19.01 2019-03-03 15:52:13 +00:00
Martin Cech 996d7c9a60 Merge pull request #7448 from mvdbeek/fix_when_default_label_is_none 
[18.09] Fix loading workflows with steps without default label
 2019-03-03 10:49:49 -05:00
Martin Cech 6c80ca50a4 Merge pull request #7449 from mvdbeek/remove_broken_tool_submission_burst 
[18.09] Remove broken tool_submission_burst
 2019-03-03 10:46:11 -05:00
Martin Cech d96034062a fix lint 2019-03-02 12:03:10 -05:00
mvdbeek bc8cf37d09 Remove broken tool_submission_burst 2019-03-02 16:53:36 +01:00
mvdbeek 5142d0df07 Fix loading workflows with steps without default label 
Prior to https://github.com/galaxyproject/galaxy/pull/7422
we'd call str(default_label), so if `default_label` was None
we'd get 'None'. Fixes part of https://github.com/galaxyproject/galaxy/issues/7447
 2019-03-02 16:13:54 +01:00
mvdbeek 739bb6310c Merge branch 'release_18.09' into release_19.01 2019-03-01 18:04:44 +01:00
John Chilton a12d9e367c Merge pull request #7438 from mvdbeek/fix_shell_runner 
[18.09] Fix LocalShellRunner
 2019-03-01 11:40:35 -05:00
mvdbeek e8f5a13f3b Fix LocalShellRunner 
All the `cmd` coming from the plugins are strings, so if cmd is
a string we use `shell=True`, brings this on par
with the Remote Shell plugins (which consume strings).
Should fix https://github.com/galaxyproject/galaxy/issues/7269.
 2019-03-01 14:45:32 +01:00
Marius van den Beek c40689dbd5 Merge pull request #7432 from martenson/fix-lib-paths 
[19.01] send post data in payload
 2019-03-01 09:51:28 +01:00
Nicola Soranzo 64a0152a6b Merge branch 'release_18.09' into release_19.01 2019-03-01 00:16:18 +00:00
Nicola Soranzo 68e3568bb2 Merge pull request #7429 from natefoo/slurm-cgroup-message-fix 
[18.09] Catch another Slurm memory cgroup creation error message
 2019-03-01 00:03:03 +00:00
Martin Cech 2039376ddf send post data in payload per @mvdbeek suggestion 2019-02-28 14:20:36 -05:00
Nate Coraor 9a26de1b4b Catch another Slurm memory cgroup creation error message 2019-02-28 11:51:36 -05:00
Martin Cech 13c175a809 Merge pull request #7422 from mvdbeek/fix_workflow_loading 
[18.09] Fix workflow loading on systems with ASCII locale
 2019-02-28 10:16:44 -05:00
mvdbeek 9e0d3b69ca Fix workflow loading on systems with ASCII locale 
Fixes https://github.com/galaxyproject/galaxy/issues/7421,
though it's very likely Galaxy won't play well when python
is falling back to ASCII as default encoding.

WorkflowStep.label is backed by a 255 character unicode string,
but tool_inputs is JSONType, which might have integer or float values
(in principle), so we play it safe by casting to unicode.
 2019-02-27 18:02:55 +01:00
Martin Cech 4dae35ea67 Merge pull request #7418 from mvdbeek/fix_install_through_managment_ui 
[19.01] Fix dependency installation in UI
 2019-02-27 09:58:28 -05:00
mvdbeek 51d167b85d Fix dependency installation in UI 
We need to pass the install kwarg here.
Broken in https://github.com/galaxyproject/galaxy/commit/2d3ab4ce1205aec24664225d74b2a851cb94b2b0
 2019-02-27 14:15:52 +01:00
John Chilton fdb18045b7 Update version to 19.01 v19.01 2019-02-26 14:28:25 -05:00
John Chilton 7553326ba1 Merge pull request #7415 from dannon/fix-workflow-drop-hack 
[19.01] Fix workflow list drop-to-upload
 2019-02-26 14:23:03 -05:00
Dannon Baker 1583eecfdb Client formatting sync for 19.01 2019-02-26 11:14:36 -05:00
Dannon Baker 14f3ce3b50 Fix workflow interface drop to import 2019-02-26 11:12:22 -05:00
Martin Cech bd25ff919c Merge pull request #7414 from mvdbeek/fix_analyze_75 
[19.01] Fix analyze 75 datatype upload
 2019-02-26 10:40:01 -05:00
mvdbeek ed375993eb Fix analyze75 hdr file upload when convert newlines is on 2019-02-26 12:22:46 +01:00
mvdbeek 47ed81feb9 Remove unreachable print statement 
I don't think an exception could ever occur here.
 2019-02-26 12:06:07 +01:00
Nate Coraor 808aa5bef7 Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 2019-02-22 13:23:16 -05:00
Nicola Soranzo 9b72f5a880 Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments 
[18.09] Update configuration samples
 2019-02-22 18:16:25 +00:00
John Chilton 8651e1eea3 Merge branch 'release_18.09' into release_19.01 2019-02-22 13:12:16 -05:00
John Chilton 2f973ac7fa Merge branch 'release_18.05' into release_18.09 2019-02-22 13:11:49 -05:00
John Chilton 1529758ecb Merge branch 'release_18.01' into release_18.05 2019-02-22 13:11:19 -05:00
John Chilton 656b3c2f87 Refactor dataset fetching in get/set dataset method in web controller. 2019-02-22 13:10:12 -05:00
Marius van den Beek 5fc5b4aaab Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments 
Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions
 2019-02-22 17:41:24 +01:00
Nate Coraor a83eb67775 Slight rewording of the cookie_path option description, and corrections 
to file_path and new_file_path descriptions.
 2019-02-22 11:31:44 -05:00
Nicola Soranzo 351c188830 Remove `filter-with and update cookie_path` options also for Tool Shed and Reports 2019-02-22 12:07:16 +00:00
Martin Cech 1a0f067590 change config schema to reflect removing paste options 2019-02-21 12:26:31 -05:00
Martin Cech 4ad4fe59be Merge pull request #7399 from dannon/bump_yarn_network_tolerance 
[19.01] Bump yarn network tolerance
 2019-02-21 11:57:49 -05:00
Dannon Baker 726ad9a0f6 Bump yarn's network timeout from 2 minutes to 5 minutes. 2019-02-21 11:48:11 -05:00
mvdbeek 8c9c27b7f6 Drop filter-with from docs / .sample 2019-02-21 17:45:56 +01:00