 Jeremy Goecks
|
910fc94c94
|
Pack script.
|
2014-04-07 12:22:01 -04:00 |
|
|
Jeremy Goecks
|
5edebad3e6
|
Visualization client-side framework: use simpler/faster/boundary-condition insensitive calculation for extracting subsets of reference sequence data.
|
2014-04-07 12:21:43 -04:00 |
|
|
Carl Eberhard
|
b5b2635b0a
|
Fix encoding/serialization of returned data from HDA create API
|
2014-04-07 10:10:26 -04:00 |
|
|
Jeremy Goecks
|
086e37c557
|
Trackster: only draw incomplete features when displaying features, not coverage data. Pack script.
|
2014-04-04 16:33:06 -04:00 |
|
|
Greg Von Kuster
|
a5161f2c7d
|
Enhance error message displayed when installing a repository into Galaxy that has an invalid repository dependency definiton.
|
2014-04-04 11:55:24 -04:00 |
|
|
Daniel Blankenberg
|
5845ca36a3
|
Provide a full URL including protocol in activation emails.
|
2014-04-04 11:46:03 -04:00 |
|
|
Greg Von Kuster
|
5015dbcc87
|
Render tool shed features based on a combination of the webapp and a rendor_for value. Things get tricky when visiting the tool shed from galaxy to install repositories.
|
2014-04-04 11:39:48 -04:00 |
|
|
Dave Bouvier
|
db12448003
|
Fixed JAVA_JAR_PATH for realigner_target_creator.
|
2014-04-04 10:37:52 -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
|
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
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)
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;
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 |
|