Greg Von Kuster
399f5508f6
Merged next-stable
2014-04-03 17:41:18 -04:00
Greg Von Kuster
2abe24b292
Better fix than ea1fbe9 and handle first discovered unhandled secure / insecure protocol issue when messing with the tool shed url for installed repositories.
2014-04-03 17:40:44 -04:00
Jeremy Goecks
e630fb10c8
Automated merge of next-stable to default
2014-04-03 14:34:17 -04:00
Jeremy Goecks
18c2e3fc71
Trackster: fixes for creating and resizing composite line tracks.
2014-04-03 14:33:48 -04:00
Nate Coraor
dfb34ae108
Open next-stable branch.
2014-04-03 12:02:24 -04:00
Greg Von Kuster
9f5f3a93e1
Add exception handling when updating an installed repository to a revision that include newly defined dependency definitions.
2014-04-03 12:00:25 -04:00
Daniel Blankenberg
a5b23557bf
Change Biostar 'submit' parameter to be called 'action'. Resolves needing to use workaround of 'click()' on submit button instead of submit() on form.
2014-04-03 11:17:47 -04:00
Greg Von Kuster
8f031dfd7b
Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to "False") to the <repository> tag when a repository was exported.
2014-04-03 10:19:46 -04:00
Dave Bouvier
463b50bb1d
Use correct revisions of best_regression_subsets and weightedaverage.
2014-04-03 09:45:51 -04:00
Greg Von Kuster
971e9d6f88
Don't add unnecessary (and problematic) prior_installation_required attributes to repository dependency definitions when exporting a repository and its dependencies into a capsule.
2014-04-03 09:31:43 -04:00
Martin Cech
1758f3d63a
libraries: removed unused and deprecated function
2014-04-02 17:21:06 -04:00
Martin Cech
5f928cd92d
libraries: more refactoring fun; full UI for permissions handling; repainting from cache
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should be ready for stable
2014-04-02 17:18:51 -04:00
Dave Bouvier
b6af887925
Corrected an error in the analyze_covariates tool shed repository.
2014-04-02 16:05:57 -04:00
Greg Von Kuster
ffa19b77a5
Add a new RepositoryGridFilterManager to the Tool Shed framework to support filtering the repositories displayed in the many Tool Shed grids. The current filters are CERTIFIED_LEVEL_ONE, CERTIFIED_LEVEL_ONE_SUITE and CERTIFIED_LEVEL_TWO, CERTIFIED_LEVEL_TWO_SUITE. The "level one" filters display repositories or suites that have been certified by the Tool Shed's install and test framework. The "level two" filters are not yet supported (the query enhancements are trivial, but not yet done) since no repositories in the test or main Tool Shed have been certified at this level (this level requires reviews and approvals by IUC members). When set, filters are stored in session cookies. Filters are easy to set. The Javascript event handler (e.g. checking a filter checkbox) would make a call something like: trans.app.repository_grid_filter_manager.set_filter( trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE ).
2014-04-02 15:18:40 -04:00
Daniel Blankenberg
ba7a5c7b08
When a tool dependency has failed to install, display the error message as pretty escaped html.
2014-04-02 15:15:00 -04:00
Martin Cech
8d2a8f9b7b
libraries: more refactoring; basic UI based on role handling; attaching to global Galaxy object; persistent lib preferences
2014-04-02 11:07:04 -04:00
Jeremy Goecks
579ebf5157
Circster fixes: (a) make compatible with new config object; (b) fix formatting issue with negative values; and (c) clean up debugging statements. Pack scripts.
2014-04-02 10:15:54 -04:00
Dave Bouvier
0994d4c2bd
Fix issue in migrations where the same complex repository would be installed once for each repository that depends on it.
2014-04-02 09:13:33 -04:00
Jeremy Goecks
867df48180
Automated merge
2014-04-02 09:12:22 -04:00
Jeremy Goecks
fee4cb7333
Trackster: CompositeTrack fixes for recent refactoring. Pack script.
2014-04-02 09:12:07 -04:00
Greg Von Kuster
7e9f07c9d3
Don't require categories and status attributes to be associated with a repository being imported from a capsule, although they should always exist.
2014-04-02 07:22:01 -04:00
Jeremy Goecks
573456d475
Trackster: show drawn reads across all tiles by pooling incompletely drawn reads and drawing them at the end.
2014-04-01 16:21:32 -04:00
Jeremy Goecks
2ebd82519e
Automated merge.
2014-04-01 15:09:45 -04:00
Jeremy Goecks
e2f56b50f2
Trackster: drawing performance improvement. Packed scripts.
2014-04-01 15:09:30 -04:00
Dave Bouvier
f807d8f406
Remove escaped double quotes from setup_virtualenv action.
2014-04-01 14:48:48 -04:00
Jeremy Goecks
67288cb54f
Fix for 615d504: do not use downsampling when all reads can be returned.
2014-04-01 14:45:34 -04:00
Daniel Blankenberg
01a77cc319
Update Biostar question posting to use POST. Have biostar bug reports automatically post.
2014-04-01 14:11:56 -04:00
Dave Bouvier
10cda06773
Pass shell=True to subprocess.Popen, which eliminates the need to escape double quotes and prepend /bin/sh -c to a tool dependency shell command.
2014-04-01 13:08:02 -04:00
Dave Bouvier
2f2e163df7
Remove migrated tools from main's tool conf.
2014-04-01 11:05:31 -04:00
Dave Bouvier
83af05b1f2
Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
2014-04-01 11:04:32 -04:00
Jeremy Goecks
75d9496e10
Genome data providers: (a) organize imports and (b) implement random and nth read iterators to downsample deep coverage regions. Use nth read iterator by default because it is the fastest.
2014-04-01 10:30:12 -04:00
Aysam Guerler
82a9a3dc7a
Charts: Show/hide optional settings, switch to auto-axis by default
2014-03-31 17:35:49 -04:00
Nate Coraor
8614373698
Merge branch close.
2014-03-31 16:43:05 -04:00
Nate Coraor
f16c8ce6f4
Close inactive branch.
2014-03-31 16:42:43 -04:00
Martin Cech
a1e9cf6f07
data libraries, don't allow showing deleted libraries to non-admins; provide information what actions user is allowed to do on library;
2014-03-31 15:36:49 -04:00
Dannon Baker
d10be6b718
Merged in nsoranzo/galaxy-central (pull request #355 )
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Workflow API: show also workflow owner, so a user can check it before importing.
2014-03-31 13:21:49 -04:00
Martin Cech
14760aba92
added is_admin to the javascript user object for UI rendering purposes;
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modified is_admin_user in masthead config to be consistent with standard is_admin check
2014-03-31 12:55:06 -04:00
Carl Eberhard
b1b00a9562
Fix base-mvc SessionStorageModel to require an id; Show alert on disabled sessionStorage
2014-03-31 12:08:21 -04:00
Carl Eberhard
2bb923e892
Fix to add spacing in hda-edit deleted/hidden info boxes between added sentences
2014-03-31 11:21:14 -04:00
Greg Von Kuster
8254c7a62c
Eliminate unused method in the tool shed's repository controller.
2014-03-31 08:00:19 -04:00
Greg Von Kuster
45ec91d466
Improvements for populating the tool panel when installing a repository containing a version of a tool alreadly loaded in the tool panel.
2014-03-31 07:37:45 -04:00
Greg Von Kuster
8420fc65cd
When multiple versions of the same tool are loaded into the Galaxy tool panel, make sure the newest version of the tool is displayed by default in the tool version select list on the tool form when it is initially loaded.
2014-03-30 22:48:17 -04:00
Greg Von Kuster
4bcb1f8a4c
Don't call the tool shed when loading the Galaxy tool panel at server startup.
2014-03-30 17:42:22 -04:00
Greg Von Kuster
a1c9b006e8
Really fix broken tool shed functional test.
2014-03-30 16:35:44 -04:00
Greg Von Kuster
ff46b3d37c
Fix broken tool shed functional test.
2014-03-30 16:33:56 -04:00
Greg Von Kuster
2ff422d6f2
Fix for installing a repository into Galaxy that contains a tool to be loaded into the tool panel where another version in the tool's lineage chain is already loaded into the tool panel. An additional entry will no longer be made. Instead, a single entry will exist for the entire lineage chain.
2014-03-30 16:25:25 -04:00
John Chilton
d590921b6f
Add unit test for extra primary dataset collection.
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Tests overridding various output properties (ext, dbkey, name, visible) with file name and galaxy.json, collecting from new_file_path versus job_working_directory, setting job output associations, and logic related to adding outputs to copied histories.
2014-03-28 18:33:03 -05:00
John Chilton
aae9c9ca94
Bugfix: Problem with primary dataset collection on cloned histories.
2014-03-28 17:49:50 -05:00
Nate Coraor
0c6876f68d
Merged in natefoo/galaxy-central (pull request #340 )
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Rename ucsc_build_sites.txt to .sample.
2014-03-28 16:44:54 -04:00
Nate Coraor
1c217f5eda
Disable manage_dependency_relationships by default to improve startup time.
2014-03-28 16:36:47 -04:00
Greg Von Kuster