Aysam Guerler
bc5b2f5953
Unification and refactoring of front end templating for js-visualizations (trackster, circster, etc.)
2013-08-05 17:02:05 -04:00
Greg Von Kuster
31d457cfc5
Include a file name export_info.xml to repository archives for repositories exported from the tool shed.
2013-08-05 16:45:16 -04:00
Nate Coraor
9ba86a1438
Merge next-stable.
2013-08-05 16:08:10 -04:00
Nate Coraor
b5cfae7b62
Bug fix for job recovery in the Condor runner.
2013-08-05 16:06:55 -04:00
Nate Coraor
ee763fea19
Don't allow exceptions in set_metadata.py to hang the process when the distributed object store's free space monitor is in use. Also, don't run the monitor unless the object store is started inside the Galaxy application.
2013-08-05 16:06:31 -04:00
Greg Von Kuster
ba17fe567b
Enhance the generated name of the archive file created when exporting a tool shed repository.
2013-08-05 15:59:49 -04:00
Greg Von Kuster
fff79bb54a
Do not display the same repository multiple times on the Monitor installing tool shed repositories page when installing / reinstalling repositories into Galaxy.
2013-08-05 14:05:38 -04:00
Dave Bouvier
8114490771
Fix issue where a tool shed functional test was failing. Only allow hours between check to be less than 1 when running functional tests.
2013-08-05 10:17:10 -04:00
Andrew Robinson
ba2e2924ed
Fixed a clobbering of 'util' package in the permissions API.
...
- used a qualified import to avoid a module name clobbering. This addresses the "AttributeError: 'module' object has no attribute 'Params'" exception when updating permissions via the GalaxyAPI.
2013-08-05 12:17:52 +10:00
Greg Von Kuster
cf96dccddb
Add the ability to export a specified repository revision from the tool shed to a gzip compressed archive saved locally. The ability to import this archive to the same or another tool shed is not yet implemented, but coming soon. All of the repository's repository dependencies can optionally be exported into the same archive. The archive includes a manifest.xml file that contains the order in whcih the repositories in the archive must be imported.
...
This feature is now available for any installable revision of a repository using the new "Export this revision" option in the Repository actions menu in the browser. It is also available via the Tool Shed API using a command like the following:
export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
2013-08-02 19:30:03 -04:00
Nate Coraor
3036d2e2f5
Merge stable.
2013-08-02 16:39:52 -04:00
Nate Coraor
b8045f20ce
Merge changes from stable.
2013-08-02 16:39:05 -04:00
Daniel Blankenberg
26bfa7b1ed
Explicitly set TEMP dir in Local Runner, when a temp dir value is not already set.
2013-08-02 13:28:22 -04:00
Dave Bouvier
ac5ac91ebd
Explicitly set the test_install_error in the automated testing framework when a repository installs and passes or fails functional tests.
2013-08-02 13:13:07 -04:00
Dave Bouvier
f016d2cfef
Fix the install and test framework's handling of external metadata.
2013-08-02 10:53:41 -04:00
Jeremy Goecks
80cfe1c1de
Automated merge of next-stable branch
2013-08-01 19:38:49 -04:00
Jeremy Goecks
1a881886f3
Fix imports and parentheses spacing.
2013-08-01 19:38:24 -04:00
Carl Eberhard
c0339bbe0b
API Documentation: small fixes for histories, history_contents
2013-08-01 15:35:45 -04:00
Carl Eberhard
f7d664aed0
API Documentation: libraries, library_contents
2013-08-01 15:21:46 -04:00
Dave Bouvier
93ca584fc2
Add a sanity check to the twobit sniffer.
2013-08-01 15:03:37 -04:00
Jeremy Goecks
269c246bc4
Cuffdiff wrapper: add option to output read group datasets.
2013-08-01 14:51:06 -04:00
Dave Bouvier
352ae2ebf0
Implement baseline support for defining a tool dependency that downloads a precompiled binary for the target platform.
2013-08-01 11:05:34 -04:00
Carl Eberhard
21dae3dca1
API Documentation: histories, history_contents
2013-07-31 16:55:50 -04:00
Carl Eberhard
63658c75c1
Unit tests: add base dataprovider unit tests
2013-07-31 14:07:01 -04:00
Jeremy Goecks
b33ab4b947
Automated merge of next-stable
2013-07-31 13:00:52 -04:00
Jeremy Goecks
f81c33b3c3
Fix bug in Pages' link creation and pack scripts.
2013-07-31 13:00:23 -04:00
Dave Bouvier
8adaaa5d1e
Merge in bugfix from next-stable.
2013-07-31 10:40:15 -04:00
Dave Bouvier
181293f054
Fix server error when displaying a tool with conditionals in the tool shed.
2013-07-31 10:38:40 -04:00
Jeremy Goecks
5ac47c9d8c
New version of Cuffdiff wrapper: (a) remove obsolete wrapper script; (b) rework steps to specify conditions and replicates; and (c) remove deprecated options.
2013-07-31 09:50:00 -04:00
Nate Coraor
4b2b0966eb
Open next-stable for the next release.
2013-07-30 12:56:17 -04:00
Nate Coraor
caa16ac59e
See previous commit message.
2013-07-30 12:54:02 -04:00
Nate Coraor
900cf1a98b
See previous commit message. Note that cufflinks reverts to 0.0.6, not 0.0.7, due to a version increase that came after the changes that are being rolled back.
2013-07-30 12:50:29 -04:00
Nate Coraor
812aebdd62
Backout af20b15f7eda, these changes will be reapplied after tools using the sam_fa_indices data table have been migrated to the Tool Shed in their original state and updated to use the new table format.
2013-07-30 12:44:05 -04:00
Nate Coraor
ae285864f1
Merge closed branch.
2013-07-30 12:32:17 -04:00
Nate Coraor
0f32b50f97
Close branch.
2013-07-30 12:31:59 -04:00
Dave Bouvier
3a71ed6ebc
Fix for revision select on repositories with multiple installable revisions.
2013-07-30 10:32:31 -04:00
Dave Bouvier
fdc46aac91
Clear tool test results when the skip tool tests option is enabled.
2013-07-30 09:23:39 -04:00
Jeremy Goecks
8944c1ac30
Move welcome_url setting to 'UI Localization' section of the config file.
2013-07-29 22:38:17 -04:00
Jeremy Goecks
f34f5292d5
Automated merge
2013-07-29 17:37:14 -04:00
Jeremy Goecks
a1714c4ad2
Add and document welcome_url config option.
2013-07-29 17:36:39 -04:00
Dave Bouvier
f87221e850
Define a CSS class that applies to all tool test results subfolders.
2013-07-29 15:25:08 -04:00
Dave Bouvier
a4313a37f3
When checking tool shed repositories for functional tests and test data, explicitly filter out metadata records that have been specified not to be tested by the repository owner.
2013-07-29 13:50:55 -04:00
Dave Bouvier
bb30319154
Do not truncate tool test input dataset names, as Galaxy no longer displays them truncated.
2013-07-29 12:01:24 -04:00
Greg Von Kuster
10ed6d92f1
Fix import in the tool shed's commit_util.
2013-07-26 09:10:23 -04:00
Jeremy Goecks
c011564812
Add --no-effective-length-correction parameter to Cufflinks wrapper
2013-07-25 19:45:29 -04:00
Jeremy Goecks
379497217c
Change ToolInput to ToolParameter in JavaScript tools implementation to match language used in model.
2013-07-25 12:56:30 -04:00
Dave Bouvier
12c61c47c2
Fix for installing a repository with a complex tool dependency where the dependent repository's tool dependency definition does not define any set_environment actions.
2013-07-25 11:37:13 -04:00
Greg Von Kuster
9d7cd8ae2a
A bit of refactoring of the tool shed's repository controller.
2013-07-25 11:01:18 -04:00
Greg Von Kuster
8a44bdbea2
Add the ability to display tool form components that are inside conditionals for tools contained in repositories in the tool shed. Also fix tool shed functional tests I recently broke sue to messing with rendering readme files in tool shed repositories.
2013-07-24 16:36:52 -04:00
Dave Bouvier
5a9caf6f7f
Tool shed functional tests for repairing an installed repository.
2013-07-24 15:19:38 -04:00
Aysam Guerler