Anthony Bretaudeau
b9c6fc6b23
debug unending ci
2021-03-31 12:09:15 +02:00
Anthony Bretaudeau
4adeca0e86
Merge remote-tracking branch 'upstream/release_21.01' into pulsar_tool_dir
2021-03-25 16:53:34 +01:00
Marius van den Beek
91aeaa3f8a
Merge pull request #11728 from abretaud/refgenie_table_del
...
[21.01] Refgenie table del
2021-03-25 16:36:47 +01:00
Anthony Bretaudeau
b5ad804b64
lint
2021-03-25 14:08:14 +01:00
Anthony Bretaudeau
340caa1174
add more tests
2021-03-25 14:01:17 +01:00
Anthony Bretaudeau
7e136c83b3
fix
2021-03-25 14:01:12 +01:00
Marius van den Beek
c4ca1a612a
Merge pull request #11724 from assuntad23/hotfix/remove-extensions-console-error
...
[21.01] Removedreference to remove-extensions
2021-03-24 20:34:44 +01:00
Björn Grüning
b0b3d4bf0a
Merge pull request #11718 from mvdbeek/library_elements
...
[21.01] Fix importing collections to new history and import correct elements
2021-03-24 18:30:25 +01:00
Assunta DeSanto
1f7170ff66
removed reference to remove-extensions
2021-03-24 12:21:25 -04:00
Marius van den Beek and Oleg Zharkov
5292bedabd
Switch to newly created history
...
Co-authored-by: Oleg Zharkov <jos.to.new@gmail.com >
2021-03-24 14:54:24 +01:00
mvdbeek
ba6dbe9513
Fix importing collection from library into new history
2021-03-24 11:51:45 +01:00
mvdbeek
cf647412fb
Make sure elements are ldda when importing from library
2021-03-24 11:51:45 +01:00
Anthony Bretaudeau
cbf3a62ef8
Don't block data table deletion when using refgenie
2021-03-24 11:42:35 +01:00
Anthony Bretaudeau
703406efe6
empty lines
2021-03-24 10:52:43 +01:00
Anthony Bretaudeau
ffcbb4ee98
simpler solution
2021-03-24 10:51:15 +01:00
mvdbeek
1ffd226625
Merge branch 'release_20.09' into release_21.01
2021-03-23 17:24:10 +01:00
Anthony Bretaudeau
73208d1fb8
possible fix for failing test
2021-03-23 17:05:23 +01:00
John Chilton
4bc8b9a868
Merge pull request #11708 from mvdbeek/make_all_extra_user_preferences_behave_like_defaultdict
...
[20.09] Make extra user preferences behave like defaultdict
2021-03-23 09:05:05 -04:00
mvdbeek
27b7d57080
Make extra user preferences behave like defaultdict
...
This was the intention in
https://github.com/galaxyproject/galaxy/pull/10747 and is an alternative
to https://github.com/galaxyproject/galaxy/pull/11707
To test this, enable the file sources, and make sure you add a plugin
you haven't configured in your user preferences.
2021-03-23 12:04:49 +01:00
Dannon
d6b16b43e5
Merge pull request #11661 from bgruening/hrr_datatype
...
[21.01] Add HHR datatype
2021-03-22 17:44:35 -04:00
Björn Grüning
1784941533
Merge pull request #11700 from assuntad23/hotfix/paired-list-builder-from-data-library
...
[21.01] Hotfix/paired list builder from data library
2021-03-22 19:30:06 +01:00
John Chilton
f08861afb7
Merge pull request #11692 from mvdbeek/fix_data_column_parameter
...
[21.01] Fix displaying data column parameters in workflow editor
2021-03-22 13:35:31 -04:00
Assunta DeSanto
cc6f978266
fixing some names to actually create list of pairs
2021-03-22 12:53:56 -04:00
Assunta DeSanto
4066588c7f
fixed call to create paired list collection from data library
2021-03-22 12:38:41 -04:00
Marius van den Beek
0f8aca6e22
Merge pull request #11669 from dannon/single_user
...
[21.01] Single User Mode - Disable irrelevant and broken options
2021-03-22 15:33:33 +01:00
Dannon
29945c0294
Merge pull request #11694 from bgruening/meryldb
...
[21.01] add meryldb datatype
2021-03-22 09:08:40 -04:00
mvdbeek
a9389ecd08
Drop test that does not apply to multiple="true" data_column parameters
2021-03-22 09:28:47 +01:00
mvdbeek
70934cd276
Add selenium test for data column parameters in workflow editor
2021-03-19 22:42:57 +01:00
mvdbeek
9bd9ac3abf
Fix displaying data column parameters in workflow editor
...
Fixes https://github.com/galaxyproject/galaxy/issues/11672
2021-03-19 22:42:57 +01:00
Björn Grüning
b62f8206f0
Merge pull request #11684 from mvdbeek/redraw_connections
...
[21.01] Redraw connections when adding or removing inputs
2021-03-19 21:38:18 +01:00
Dannon
353f2fc087
Merge pull request #11673 from mvdbeek/fix_fail_job_cycle
...
[21.01] Prevent endless fail_job cycles
2021-03-19 16:08:22 -04:00
Bjoern Gruening
38816d3043
add meryldb
2021-03-19 20:44:55 +01:00
John Chilton
3e0a5d7b06
Starting work on tool-util 21.1.1
2021-03-19 14:27:29 -04:00
John Chilton
883a4b9641
Version 21.1.0 of tool-util (tag galaxy-tool-util-21.1.0).
2021-03-19 14:27:10 -04:00
John Chilton
9486d96b3b
Starting work on containers 21.1.1
2021-03-19 14:21:42 -04:00
John Chilton
a3e2698bd6
Version 21.1.0 of containers (tag galaxy-containers-21.1.0).
2021-03-19 14:21:21 -04:00
John Chilton
1a9433b298
Starting work on util 21.1.1
2021-03-19 14:18:57 -04:00
John Chilton
4c06212424
Version 21.1.0 of util (tag galaxy-util-21.1.0).
2021-03-19 14:18:27 -04:00
John Chilton
3fe054b7e6
Prepare for 21.1.0 release of galaxy-util.
2021-03-19 14:14:08 -04:00
John Chilton
45700e9f18
Merge pull request #11689 from nsoranzo/release_21.01_backport_11655
...
[21.01] Backport #11655 "update to cope with impending changes to cwltool internals"
2021-03-19 13:42:38 -04:00
Rupert Nash
14fe8188b8
update to cope with impending changes to cwltool internals
2021-03-19 16:28:34 +00:00
John Chilton
50eaca7b3f
Merge pull request #11678 from mvdbeek/give_some_guidance_on_hidden_runtime_bug
...
[21.01] Use Modal to show wrong RuntimeValue
2021-03-19 10:27:49 -04:00
mvdbeek
47bcb9a243
Redraw connections when adding or removing inputs
2021-03-19 14:07:04 +01:00
mvdbeek
446efc67b7
Replace RuntimeParameter for hidden parameter
...
This will warn the user when opening the workflow editor and shows the
"Some tools in this workflow may have changed since it was last saved or
some errors were found. The workflow may still run, but any new options
will have default values." message.
2021-03-19 11:11:37 +01:00
mvdbeek
8895eb14df
Use Modal to alter to wrong RuntimeValue
...
Since these parameters are not visible just highlighting them won't cut
it.
2021-03-18 22:16:15 +01:00
Marius van den Beek
6b8508e756
Merge pull request #11670 from jmchilton/fix_rename
...
[21.01] Fix workflow rename dropping metadata.
2021-03-18 17:21:34 +01:00
mvdbeek
79dc34f134
Prevent endless fail_job cycles
...
That should fix https://github.com/galaxyproject/galaxy/issues/9272 for
good.
2021-03-18 16:48:24 +01:00
Björn Grüning
f6598593a2
Update datatypes_conf.xml.sample
2021-03-18 15:39:53 +01:00
John Chilton
470baa5921
Fix workflow rename dropping metadata.
2021-03-18 10:16:29 -04:00
Marius van den Beek
01ffe5b7bd
Merge pull request #11663 from davelopez/fix_missing_tags_imported_workflow
...
[21.01] Fix tags not included when importing shared workflow
2021-03-18 15:16:03 +01:00
Anthony Bretaudeau