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Author SHA1 Message Date
Sergey Golitsynskiy 6703584714 Fix link to requirements.txt 
Dependency files rearranged (commit 1b0ccf6, Nov. 1, 2017)
 2018-11-30 19:26:41 -05:00
Sergey Golitsynskiy 03794ce21a Fix broken links on Job Configuration page 2018-11-08 11:52:31 -05:00
Marius van den Beek 7966ca5a95 Merge pull request #6990 from jmchilton/skip_mounting_external_tmp_in_ci_tests 
Don't mount external /tmp for tests.
 2018-11-08 17:25:04 +01:00
John Chilton ebb6e78f0d Don't mount external /tmp for tests. 
Nate wants the file busy errors back ;).
 2018-11-08 09:46:04 -05:00
Nicola Soranzo f9a84b0ffe Merge pull request #6972 from Slugger70/biom_datatype_changes 
Added a metadata element to the biom1 datatype
 2018-11-08 11:36:28 +00:00
Nicola Soranzo e4c00af38d Merge branch 'release_18.09' into dev 2018-11-08 09:32:30 +00:00
Nicola Soranzo f85afad965 Merge branch 'release_18.05' into release_18.09 2018-11-08 09:31:42 +00:00
Martin Cech d28ce7686d Merge pull request #6898 from martenson/no-sanitization-db 
prevent sanitized history names being saved in database
 2018-11-07 16:31:50 -05:00
Aysam Guerler 0a6117bcda Merge pull request #6984 from dannon/fix-charts 
Fix charts entrypoint for compatibility with newer chunk changes.
 2018-11-07 16:22:20 -05:00
Martin Cech 45e475e19a Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 
[18.05] Backport commit 2d36e8955e
 2018-11-07 15:50:20 -05:00
John Chilton 5e1fb9a7a2 Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection 
[18.09] List tags as attribute of TestCollection
 2018-11-07 14:37:56 -05:00
mvdbeek 4760a0ac0f Fix recursion issue in gff_filter_by_feature_count 2018-11-07 19:26:52 +00:00
mvdbeek 5e098857e5 Display test collection input in documentation 2018-11-07 20:08:21 +01:00
Nicola Soranzo 6dd098f747 Simplify code 2018-11-07 18:57:06 +00:00
Dannon f0df34eaca Merge pull request #6967 from guerler/workflow_style_1 
Refactor workflow editor styles and move from mako to css
 2018-11-07 13:47:00 -05:00
mvdbeek bff5d51245 Use comma-separated instead of comma separated 2018-11-07 19:34:40 +01:00
Dannon Baker fcf451fb88 Fix charts entrypoint for compatibility with newer chunk changes. 2018-11-07 12:50:14 -05:00
Nicola Soranzo be87d2402d Merge branch 'release_18.09' into dev 2018-11-07 17:19:16 +00:00
Martin Cech 09186c991a Merge pull request #6982 from Nerdinacan/selenium_test_library_contents 
Update test/selenium_tests/test_library_contents.py
 2018-11-07 11:49:05 -05:00
mvdbeek 0ecb4e7c59 List tags as attribute of TestCollection 2018-11-07 11:13:02 +01:00
Mason 1b18e9ea2d More linting fun 2018-11-06 21:26:46 -08:00
Mason 10723c789f Added white space to pass linter 2018-11-06 21:24:53 -08:00
Slugger70 0bc6e35ad6 Minor alteration for flake8 2018-11-07 10:23:31 +11:00
Mason a8eb9463a6 test/selenium_tests/test_library_contents.py 2018-11-06 15:17:14 -08:00
Enis Afgan 2f2153292b Merge pull request #6583 from VJalili/cloud_download_tool 
Send data to cloud
 2018-11-06 16:36:19 -05:00
Dannon eb57469eef Merge pull request #6970 from Nerdinacan/jquery_bundle 
Normalized jquery bundle
 2018-11-06 15:13:49 -05:00
Dannon a4f21fca77 Merge pull request #6980 from bgruening/optipng 
optimize images with optipng
 2018-11-06 13:03:37 -05:00
Dannon b7c8bd47c9 Merge pull request #6979 from jmchilton/dev_merge_1 
Merge 18.09 into dev
 2018-11-06 13:00:06 -05:00
Dannon 6487d52d51 Merge pull request #6978 from nsoranzo/release_18.09_paste 
[18.09] Fix traceback when starting under Python3 with ``galaxy.ini``
 2018-11-06 10:16:41 -05:00
John Chilton 82a8eb05d6 Merge remote-tracking branch 'jmchilton/release_18.09' into dev_merge_1 2018-11-06 09:10:22 -05:00
Bjoern Gruening 443170e912 optimize images with optipng 2018-11-06 15:05:56 +01:00
Nate Coraor 9029b95e69 Merge pull request #6969 from jmchilton/ensure_better 
[18.09] In enqueue, always set an object_store_id if one isn't set.
 2018-11-06 08:46:23 -05:00
Nicola Soranzo dc9128213f Fix traceback when starting under Python3 with `galaxy.ini` 
Update `paste` requirement to 3.0.4 to include:

https://github.com/cdent/paste/pull/14

to fix the following traceback:

```
Starting server in PID 6792.
Traceback (most recent call last):
  File "./scripts/paster.py", line 27, in <module>
    serve.run()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run
    invoke(command, command_name, options, args[1:])
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke
    exit_code = runner.run(args)
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run
    result = self.command()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command
    serve()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve
    server(app)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper
    **context.local_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call
    val = callable(*args, **kw)
  File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner
    for name, value in kwargs.items():
RuntimeError: dictionary changed size during iteration
galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down
```
 2018-11-06 12:49:44 +00:00
Dannon Baker dbf5ef3360 Merge pull request #6974 from istevenshen/patch-2 
Update locale.js
 2018-11-06 07:35:09 -05:00
Slugger70 9d9bc9e272 Made changes as per review 2018-11-06 22:29:29 +11:00
Slugger70 fc53123a94 Changes as per review 2018-11-06 22:28:00 +11:00
Nicola SoranzoandSlugger70 789f7b2d8d As per review 
Co-Authored-By: Slugger70 <slugger70@gmail.com>
 2018-11-06 22:22:09 +11:00
Steven Shen 5d3d8f5559 Update locale.js 2018-11-06 17:04:21 +08:00
Slugger70 258ada862e Added a metadata element to the biom1 datatype 2018-11-06 17:50:12 +11:00
Mason 9b7b6ab04d Added jquery.custom.js to lib folder 2018-11-05 19:13:27 -08:00
Mason c42ea4d9c5 Fixed monitor Proxy set function 2018-11-05 19:06:24 -08:00
John Chilton ccb1e08000 In enqueue, always set an object_store_id if one isn't set. 
Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode.
 2018-11-05 18:50:51 -05:00
Dannon Baker 4405d15fea Merge branch 'window_monitor' into dev 2018-11-05 18:02:51 -05:00
Dannon Baker 38e9225aff Client format 2018-11-05 18:02:35 -05:00
Enis Afgan 566ffaf9d5 Update send tool help text 2018-11-05 15:53:47 -05:00
Dannon e9f2693933 Merge pull request #6729 from scrathat/admin.data.manager.vue.steps 
Vue rewrite of admin data manager (local data) in steps
 2018-11-05 15:00:20 -05:00
Dannon Baker 4b3606f1ac Target top with rerun to avoid nested Galaxy. 2018-11-05 14:47:18 -05:00
guerler 3fc6191f95 Remove unused canvas area styles 2018-11-05 13:57:02 -05:00
guerler cfc4ed8799 Move callout button specification to scss 2018-11-05 13:54:26 -05:00
guerler f19ac2d052 Remove unused panel button styles 2018-11-05 13:30:56 -05:00