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
40,845 Commits 69 Branches 243 Tags
5db219b1d2f991e36ce144fc29a6196767a4546a
Commit Graph
40845 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Martin Cech 5db219b1d2 add 19.05 RN to index 2019-06-05 15:53:05 -04:00
Dannon b74c288f41 Merge pull request #8101 from WilliamHolden/remove_unresolved_function 
Remove unresolved function causing console error
 2019-06-05 15:30:20 -04:00
Martin Cech 31b7fb0356 Merge pull request #8051 from jmchilton/galaxy_util_libs 
Prepare all packages/ for actual releases.
 2019-06-05 15:29:08 -04:00
Martin Cech 9c2f142fb8 Merge pull request #8044 from jmchilton/job_metrics_component_3 
Update JobMetrics component to use a Vuex Store + vuex-cache...
 2019-06-05 15:18:25 -04:00
Martin Cech cb35ec38b4 Merge branch 'release_19.05' into dev 2019-06-05 15:07:12 -04:00
Martin Cech b0dc3feded Merge branch 'release_19.01' into release_19.05 2019-06-05 15:06:43 -04:00
Martin Cech cb53c7390e Merge pull request #8085 from dannon/fix-multipanel-history-search 
[19.01] Fix multipanel history search.
 2019-06-05 15:04:58 -04:00
will 8488a9340b prefer let and const over var 2019-06-05 11:49:27 -04:00
will 7e8ed9d0b7 remove hover function that calls unresolved function hoverImage on mouse in 2019-06-05 11:46:05 -04:00
Nicola Soranzo 1279a2074c Merge branch 'release_19.05' into dev 2019-06-05 15:17:43 +01:00
Nicola Soranzo 7aa5d562e1 Merge branch 'release_19.01' into release_19.05 2019-06-05 15:16:13 +01:00
Marius van den Beek 2a19b2151f Merge pull request #8097 from bgruening/fix_macro_backport_19.01 
[19.01] Fix nested macro/token expansion
 2019-06-05 15:48:00 +02:00
Nicola Soranzo fc2bff63b3 Remove recursion from `expand_nested_tokens()` 
Also add test for recursive nested token.
 2019-06-05 13:54:18 +02:00
mvdbeek 574d9ad1f5 Fix nested macro/token expansion on python 3 
I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced.
It's surprising that this didn't cause any issues on python 2,
but might have to do with the iteration order changes.
 2019-06-05 13:44:46 +02:00
John Chilton 3f1487a7b1 Merge pull request #8094 from nsoranzo/dockerfile_fixes 
Small Dockerfile fixes
 2019-06-04 18:32:56 -04:00
Nicola Soranzo abe695cd77 Small Dockerfile fixes 
- `MAINTAINER` is deprecated
- Ports for `EXPOSE` don't need a starting colon
- We use the `psycopg2-binary` wheel in
  `lib/galaxy/dependencies/conditional-requirements.txt`
 2019-06-04 19:55:40 +01:00
Dannon Baker 8edffb118a const, formatting 2019-06-04 11:47:21 -04:00
Dannon Baker b732950c70 Actually search in onfirstsearch of history search in multipanel 2019-06-04 11:46:24 -04:00
Dannon Baker edcce00aab Fix multipanel history search. 2019-06-04 11:46:24 -04:00
Aysam Guerler 3de955731d Merge pull request #7825 from martenson/tool-install-interface 
Beta tool install interface improvements
 2019-06-04 07:53:17 -04:00
Nicola Soranzo fdd28253f0 Merge branch 'release_19.05' into dev 2019-06-03 18:16:17 +01:00
Nicola Soranzo 4a87bb42e6 Merge branch 'release_19.01' into release_19.05 2019-06-03 18:13:05 +01:00
Nicola Soranzo fd02b745c3 Merge branch 'release_18.09' into release_19.01 2019-06-03 18:06:45 +01:00
John Chilton 2a0f04e82e Merge pull request #8076 from martenson/allow-quoted-query 
allow for filter values in repository search to be quoted
 2019-06-03 10:05:48 -04:00
John Chilton 35b547f65a Merge pull request #8070 from mvdbeek/backport_data_source_fix_and_database_operation_tools 
[19.05] Backport #8050 and #8038: data source fix and database operation tools
 2019-06-03 10:04:18 -04:00
John Chilton 115157cdf9 Merge pull request #8071 from dannon/axios-sec-upgrade 
[19.05] Upgrade axios to handle CVE-2019-10742
 2019-06-03 10:00:38 -04:00
John Chilton f4ea424015 Merge pull request #8077 from mvdbeek/include_shell_for_tool_script_sh 
Call tool_script.sh with shell
 2019-06-03 09:59:40 -04:00
John Chilton 6f88c4455f Merge pull request #8082 from nuwang/fix_k8s_runner_wording 
Fix wording for pod retries while maintaining backward compatibility
 2019-06-03 09:56:38 -04:00
Nuwan Goonasekera 4a7708b7e0 Fix wording for pod retries while maintaining backward compatibility 2019-06-03 14:36:44 +05:30
mvdbeek bf31260192 Call tool_script.sh with shell 2019-06-01 13:24:51 +02:00
Björn Grüning 84063a2bfc Fix link formats for mulled_containers.rst, minor rewording (#8075) 
Fix link formats for mulled_containers.rst, minor rewording
 2019-06-01 10:53:51 +02:00
Björn Grüning 2f21e73ff4 [18.09] Backport 8023: Fix ColumnSetAction post job action (#8069) 
[18.09] Backport 8023: Fix ColumnSetAction post job action
 2019-06-01 10:50:02 +02:00
Martin Cech 2dc6998eaa allow for filter values in repository search to be quoted 
i.e. they can contain space(s)
 2019-05-31 15:58:25 -04:00
Enis Afgan 90f56ebc40 Fix link formats for mulled_containers.rst, minor rewording 2019-05-31 15:32:23 -04:00
Dannon Baker b346565402 Upgrade axios to handle https://snyk.io/vuln/SNYK-JS-AXIOS-174505 2019-05-31 07:55:21 -04:00
mvdbeek 58189a6d9e Fix stream_to_open_named_file for non-utf8 text 
We only recode the file if a target encoding is given,
and make the assumption that the file is not binary
or compressed if a target encoding is set.

This is required to upload the imzml test data by url
in https://github.com/galaxyproject/galaxy/issues/7412#issuecomment-469379295
 2019-05-31 11:00:57 +02:00
mvdbeek 2e25b50c62 Add testcase for new tag from file behavior 2019-05-31 10:59:21 +02:00
mvdbeek f248961d26 Convert tags starting with # to name: tags 
I think we want name tags to be `name:` tags in the backend,
this keeps processing more uniform.
 2019-05-31 10:59:21 +02:00
Steffen Neumann 926b096cd0 Update help text for Relabel List Identifiers 
This addresses https://github.com/galaxyproject/galaxy/issues/6156#issuecomment-494290527.
The rest of #6156 might require python-hacking. Yours, Steffen
 2019-05-31 10:59:21 +02:00
mvdbeek 44256971eb Fix ColumnSetAction post job action 
If columns are specified as integers this would fail currently.
Reported by Peter Briggs on the [mailing list](https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/thread/PXLCVKIZ5LW3MLI6333PFMANYGOCDLD2/)
 2019-05-31 10:44:45 +02:00
Aysam Guerler a763c89180 Merge pull request #8035 from martenson/changesets-search-index 
enhance TS repo search capabilities
 2019-05-30 23:25:14 -04:00
Nate Coraor 51b39b82e6 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-30 15:03:50 -04:00
Nate Coraor bff203f48c Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-30 15:03:00 -04:00
Martin Cech 91041c2ba4 minor refactoring 2019-05-30 14:27:59 -04:00
John Chilton bef00770ba Merge pull request #8036 from WilliamHolden/update_layout_folder_es6 
Prefer const and let over var in layout folder
 2019-05-30 14:16:21 -04:00
John Chilton 9c960c2db8 Merge pull request #8056 from mvdbeek/possibly_fix_amqp_issue_on_mules 
[19.05] Release ampq connection after initial connect
 2019-05-30 14:15:21 -04:00
Martin Cech 7addeb952f the alphabet 2019-05-30 13:51:25 -04:00
Nicola Soranzo c7decb1d3c Merge pull request #8061 from natefoo/max-grab-typo 
Fix typo grap -> grab
 2019-05-30 16:43:39 +01:00
Martin Cech 2eb02c613c refactor filtering method and add doctest 2019-05-30 11:24:26 -04:00
Björn Grüning da0f5f290c [19.01] Document the handler max_grab config param (#8060) 
[19.01] Document the handler max_grab config param
 2019-05-30 17:16:06 +02:00