Aysam Guerler
3b59f94d57
Pack scripts
2014-02-20 20:11:07 -05:00
Aysam Guerler
44cfdc11d4
Ui: Add portlet to ui library and use it in charts app
2014-02-20 20:09:44 -05:00
Dave Bouvier
85add8fc6d
Fix path for bowtie2.
2014-02-20 23:01:05 +00:00
Carl Eberhard
4b2b3af5ce
(Fix to 8e4196a) Histories embedded in pages: first pass at using panel
2014-02-20 17:44:04 -05:00
John Chilton
9a06cdd454
Fix mock-requests PUT action.
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Should fix failing history import/export test on buildbot server that doesn't have requests dependency available.
2014-02-20 15:28:06 -06:00
John Chilton
e7140af07a
Fix failing api search test.
2014-02-20 15:18:37 -06:00
Dave Bouvier
3d807b3b73
Merged in davebgx/galaxy-central/central-eliminate-fabric (pull request #330 )
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Eliminate use of fabric when executing tool dependency recipes' shell_command actions.
2014-02-20 16:27:11 -05:00
Martin Cech
d54136101d
Merge
2014-02-20 16:24:56 -05:00
Martin Cech
9c45e67d88
bugfix: reverted showing of terms_url
2014-02-20 16:21:45 -05:00
Dave Bouvier
ac2d39eb90
Use the provided use_fabric parameter in handle_command.
2014-02-20 16:00:21 -05:00
Carl Eberhard
8fd3ccb584
Remove debugging statement
2014-02-20 15:59:22 -05:00
Dave Bouvier
afa3088ed0
Merge stable.
2014-02-20 15:52:09 -05:00
Dave Bouvier
db55ca3bc2
Code cleanup, documentation.
2014-02-20 15:45:42 -05:00
Carl Eberhard
00b02bc69d
Fix to persistance between page loads of tags, annotations shown/hidden in history panel
2014-02-20 14:03:21 -05:00
Aysam Guerler
832ed95e7c
Fix default parameter in universe config
2014-02-20 13:27:57 -05:00
Dannon Baker
cc03a9b144
Add PyYAML 3.10 egg.
2014-02-20 13:10:00 -05:00
Carl Eberhard
cdae2d44c1
Browser tests: update empty history message
2014-02-20 11:56:45 -05:00
Daniel Blankenberg
2849660333
Fix for ToolEvaluator with optional Dataset Input selected with multiple inputs.
2014-02-20 11:52:52 -05:00
John Chilton
f8bf5f4d8e
Merged in clayton_turner/galaxy-central (pull request #322 )
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Added "ignore lines starting with specific characters" to group tool
2014-02-20 10:35:58 -06:00
Carl Eberhard
2a28ef005a
History published/shared/display as slug: use annotated-history-panel, search open by default, preserve whitespace in annotations, replace import button with 'switch to' if owned by user viewing; Annotated History Panel: panel view of history that shows datasets as a table with additional dataset info in a left cell
2014-02-20 11:34:19 -05:00
Daniel Blankenberg
42bd248b93
Rework logic for setting selection of DataToolParameter. Fixes issue seen with rerun where incorrect options were selected.
2014-02-20 11:31:07 -05:00
Dave Bouvier
b7fb1c33ce
Enable specifying the install database connection when executing the install and test framework.
2014-02-20 11:18:30 -05:00
Greg Von Kuster
ea2f6b3d80
Merged in trevorw/galaxy-central-2/trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 (pull request #326 )
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specify third-party cookies must not be blocked - repository.py
2014-02-20 11:14:38 -05:00
Daniel Blankenberg
994737422d
Fix for ToolEvaluator with optional Dataset Input selected.
2014-02-20 11:07:16 -05:00
Nate Coraor
8331e4358d
Remove empty/renamed sections in tool_conf.xml.main
2014-02-20 10:52:31 -05:00
Nate Coraor
4ea6abbc79
Minor updates to comments/documentation in universe_wsgi.ini.sample
2014-02-20 10:52:19 -05:00
Nate Coraor
38f36eb88f
Remove obsolete DRMAA_python egg from eggs.ini.
2014-02-20 10:51:42 -05:00
Trevor Wennblom
59c29d1f75
specify third-party cookies must not be blocked - repository.py
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third-party cookies are normally (and hopefully) disabled for privacy
2014-02-20 15:27:57 +00:00
John Chilton
214d1f89bb
Update LWR client through LWR changeset 51f097d.
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Add RemoteTransferAction - to allow LWR server to stage files up and down by downloading/uploading them. Still need to augment Galaxy to support such an endpoint for job-related files.
2014-02-20 09:23:52 -06:00
Dave Bouvier
63adb743a2
Eliminate the use of fabric when executing commands defined in an <action type="shell_command"> tag.
2014-02-20 09:47:35 -05:00
Dave Bouvier
89eaa9181b
Created new branch central-eliminate-fabric
2014-02-20 14:28:11 +00:00
Dannon Baker
c6d9b53ce5
Update boto to 2.25.0 in anticipation of supporting VPC
2014-02-19 19:33:27 -05:00
Dave Bouvier
915cfe0cfc
Merge with a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21
2014-02-19 16:34:22 -05:00
Dave Bouvier
23889efef6
Ensure that symlinks are moved before regular files, since this can in some cases causes a 'No such file or directory' error when the symlink target is moved before the symlink itself.
2014-02-19 16:34:01 -05:00
Daniel Blankenberg
b60aba259e
Fix for DatasetListWrapper with optional inputs.
2014-02-19 16:15:48 -05:00
Dave Bouvier
665099efa4
Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script.
2014-02-19 15:23:45 -05:00
Dave Bouvier
a878c87720
Fix for situation where duplicate database records would be created if a repository was uninstalled and reinstalled after getting updates from the tool shed.
2014-02-19 15:21:12 -05:00
Dave Bouvier
3da1ca8fec
Fix for situation where duplicate database records would be created if a repository was uninstalled and reinstalled after getting updates from the tool shed.
2014-02-19 15:21:12 -05:00
Dannon Baker
7474579310
Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1.
2014-02-19 14:27:10 -05:00
Carl Eberhard
e3c2f5bee5
History panel: remove anonymous template
2014-02-19 13:54:55 -05:00
Martin Cech
80bf252219
removing bug with not rendering when there is exactly one tool present; https://trello.com/c/6nJIhOdJ/1166-valid-tool-conf-xml-file-with-a-single-entry-renders-nothing-in-the-galaxy-tool-panel ;
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tool_menu.mako edited online with Bitbucket
2014-02-19 18:29:36 +00:00
Aysam Guerler
b1b88f9189
Grids: Fix negative page numbers
2014-02-19 13:20:42 -05:00
Aysam Guerler
9e77ce9ad8
Merge
2014-02-19 13:18:37 -05:00
Aysam Guerler
f96e3eee5a
Grids: Fix negative page numbers
2014-02-19 13:16:36 -05:00
Dave Bouvier
8bcd251be5
Merge bugfix from stable.
2014-02-19 13:09:03 -05:00
Greg Von Kuster
19ab47d1a8
Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances.
2014-02-19 13:05:25 -05:00
Greg Von Kuster
dda9905cef
Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances.
2014-02-19 13:05:25 -05:00
Nate Coraor
4e5e7bd21e
merge.
2014-02-19 12:02:12 -06:00
Nate Coraor
069c52523b
merge.
2014-02-19 12:01:03 -06:00
Nate Coraor
8ecae313d8
Stop jobs when all output datasets are deleted via the API.
2014-02-19 12:00:33 -06:00
Aysam Guerler