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Author SHA1 Message Date
John Chilton a6f3b255cb Merge pull request #11764 from mvdbeek/fix_format_input_implicit_conversion 
[21.01] Fix format="input" with implicit conversions
 2021-04-01 10:45:55 -04:00
Marius van den Beek b6c24cfce0 Merge pull request #11765 from almahmoud/webapp 
[21.01] galaxy.webapps.tool_shed to webapp.tool_shed
 2021-04-01 16:32:53 +02:00
Marius van den Beek 9711b31eba Merge pull request #11763 from abretaud/pulsar_flood 
[21.01] Pulsar: mark cancelled jobs as finished
 2021-04-01 15:30:45 +02:00
almahmoud 619f1e7a11 galaxy.webapps.tool_shed to webapp.tool_shed 2021-03-31 17:37:36 -04:00
mvdbeek 7eb853d703 Fix format="input" with implicit conversions 
where the implicit converter uses galaxy.json.

Add test, fix fix
 2021-03-31 22:06:39 +02:00
Anthony Bretaudeau 8d7736d0a5 catch cancelled state for pulsar jobs 2021-03-31 17:23:59 +02:00
Marius van den Beek 69d6e78a3d Merge pull request #11599 from abretaud/pulsar_tool_dir 
[21.01] Fix bug with Pulsar and $__tool_directory__
 2021-03-31 15:37:23 +02:00
Anthony Bretaudeau b5e2ea9877 try something else 2021-03-31 13:42:17 +02:00
Anthony Bretaudeau b9c6fc6b23 debug unending ci 2021-03-31 12:09:15 +02:00
Dannon 56db84fa4c Merge pull request #11753 from mvdbeek/create_ts_database_if_no_install_database 
[21.01] Create install database with create_db.sh
 2021-03-30 09:41:30 -04:00
mvdbeek ca6f2fa68e Create install database with create_db.sh 2021-03-30 13:44:36 +02:00
John Chilton 1f8aac784a Merge pull request #11741 from jmchilton/fix_mo_tools 
[21.01] Fix a bug when unzipping collections with nametags.
 2021-03-27 16:41:18 -04:00
John Chilton f360f6498f Fix copy tags bug - broken in #10761 I think. 2021-03-26 16:48:15 -04:00
John Chilton d983fc72e8 Exhibit bug when unzipping collections with nametags. 2021-03-26 15:43:12 -04:00
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 BeekandOleg 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). 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). 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