| 21aa78c | Nate Coraor | 14 April 2014, 23:27:21 UTC | Update stable branch from next-stable for release. | 14 April 2014, 23:27:21 UTC |
| 7af851b | Nate Coraor | 14 April 2014, 23:26:24 UTC | Close next-stable branch. | 14 April 2014, 23:26:24 UTC |
| 71dd34c | Daniel Blankenberg | 14 April 2014, 20:33:57 UTC | Remove duplicated enable_unique_workflow_defaults from universe_wsgi.ini.sample. | 14 April 2014, 20:33:57 UTC |
| f5d289c | Daniel Blankenberg | 14 April 2014, 20:29:46 UTC | Fix for rerun of unvalidated parameters for multiple selects. | 14 April 2014, 20:29:46 UTC |
| 2cf20cc | Daniel Blankenberg | 14 April 2014, 19:44:36 UTC | Fix for workflow editor in call to check_param on input parameters that need late validation but were attempting to run validators. | 14 April 2014, 19:44:36 UTC |
| 7007f85 | Dave Bouvier | 14 April 2014, 17:17:12 UTC | Fixed tool help image for gops complement. | 14 April 2014, 17:17:12 UTC |
| c7e6181 | Dave Bouvier | 14 April 2014, 13:32:41 UTC | Fix issues with tool migration stage 10. | 14 April 2014, 13:32:41 UTC |
| d87eca5 | Carl Eberhard | 11 April 2014, 20:46:50 UTC | Pack data.js from 86f93a1 | 11 April 2014, 20:46:50 UTC |
| cf0e061 | Carl Eberhard | 11 April 2014, 20:22:11 UTC | PR #366 from Jian-Long Huang: to next-stable | 11 April 2014, 20:22:11 UTC |
| 28ddf4b | Jeremy Goecks | 10 April 2014, 21:21:00 UTC | Updates to Sweepster to get it working again. | 10 April 2014, 21:21:00 UTC |
| c5f3f75 | Daniel Blankenberg | 10 April 2014, 20:48:07 UTC | Fix for route used in displaying images on tool installed from a toolshed. | 10 April 2014, 20:48:07 UTC |
| 7da3f0a | Dave Bouvier | 10 April 2014, 17:59:40 UTC | Corrected version for migrated tools. | 10 April 2014, 17:59:40 UTC |
| e83208a | Daniel Blankenberg | 10 April 2014, 17:39:41 UTC | When posting to BioStar include a ToolShed url, as applicable. | 10 April 2014, 17:39:41 UTC |
| d197d2c | Daniel Blankenberg | 10 April 2014, 17:38:44 UTC | Include tool version information in bug reports. | 10 April 2014, 17:38:44 UTC |
| 38452da | Jeremy Goecks | 09 April 2014, 16:53:34 UTC | SAM/BAM data provider: fix bug and streamline code to support both genomes with reference data and those without. | 09 April 2014, 16:53:34 UTC |
| c892a67 | Jeremy Goecks | 09 April 2014, 14:47:22 UTC | Genome data provider: (a) handle regions with no mapped reads and (b) clean up trailing whitespace. | 09 April 2014, 14:47:22 UTC |
| 6c704a4 | Daniel Blankenberg | 08 April 2014, 21:05:09 UTC | fix tab spaces in javascript | 08 April 2014, 21:05:09 UTC |
| cee2ac4 | Daniel Blankenberg | 08 April 2014, 21:03:19 UTC | When submiting bug reports disable submit buttons while form is being submitted. When submiting bug report to Biostar, have user confirm that they are posting to a public forum. | 08 April 2014, 21:03:19 UTC |
| d7dda26 | Carl Eberhard | 08 April 2014, 18:14:17 UTC | Remove debugging statements | 08 April 2014, 18:14:17 UTC |
| 9d64557 | Jeremy Goecks | 08 April 2014, 16:07:50 UTC | Trackster: update jQuery selector so that all tool inputs are updated on change rather only <input> elements. Pack script. | 08 April 2014, 16:07:50 UTC |
| 04b2d95 | Aysam Guerler | 07 April 2014, 17:53:14 UTC | Charts: Fix api call | 07 April 2014, 17:53:14 UTC |
| 910fc94 | Jeremy Goecks | 07 April 2014, 16:22:01 UTC | Pack script. | 07 April 2014, 16:22:01 UTC |
| 5edebad | Jeremy Goecks | 07 April 2014, 16:21:43 UTC | Visualization client-side framework: use simpler/faster/boundary-condition insensitive calculation for extracting subsets of reference sequence data. | 07 April 2014, 16:21:43 UTC |
| b5b2635 | Carl Eberhard | 07 April 2014, 14:10:26 UTC | Fix encoding/serialization of returned data from HDA create API | 07 April 2014, 14:10:26 UTC |
| 086e37c | Jeremy Goecks | 04 April 2014, 20:33:06 UTC | Trackster: only draw incomplete features when displaying features, not coverage data. Pack script. | 04 April 2014, 20:33:06 UTC |
| a5161f2 | Greg Von Kuster | 04 April 2014, 15:55:24 UTC | Enhance error message displayed when installing a repository into Galaxy that has an invalid repository dependency definiton. | 04 April 2014, 15:55:24 UTC |
| 5845ca3 | Daniel Blankenberg | 04 April 2014, 15:46:03 UTC | Provide a full URL including protocol in activation emails. | 04 April 2014, 15:46:03 UTC |
| 5015dbc | Greg Von Kuster | 04 April 2014, 15:39:48 UTC | 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. | 04 April 2014, 15:39:48 UTC |
| db12448 | Dave Bouvier | 04 April 2014, 14:37:52 UTC | Fixed JAVA_JAR_PATH for realigner_target_creator. | 04 April 2014, 14:37:52 UTC |
| 2abe24b | Greg Von Kuster | 03 April 2014, 21:40:44 UTC | Better fix than ea1fbe9 and handle first discovered unhandled secure / insecure protocol issue when messing with the tool shed url for installed repositories. | 03 April 2014, 21:40:44 UTC |
| 18c2e3f | Jeremy Goecks | 03 April 2014, 18:33:48 UTC | Trackster: fixes for creating and resizing composite line tracks. | 03 April 2014, 18:33:48 UTC |
| dfb34ae | Nate Coraor | 03 April 2014, 16:02:24 UTC | Open next-stable branch. | 03 April 2014, 16:02:24 UTC |
| 9f5f3a9 | Greg Von Kuster | 03 April 2014, 16:00:25 UTC | Add exception handling when updating an installed repository to a revision that include newly defined dependency definitions. | 03 April 2014, 16:00:25 UTC |
| a5b2355 | Daniel Blankenberg | 03 April 2014, 15:17:47 UTC | Change Biostar 'submit' parameter to be called 'action'. Resolves needing to use workaround of 'click()' on submit button instead of submit() on form. | 03 April 2014, 15:17:47 UTC |
| 8f031df | Greg Von Kuster | 03 April 2014, 14:19:46 UTC | Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to "False") to the <repository> tag when a repository was exported. | 03 April 2014, 14:19:46 UTC |
| 463b50b | Dave Bouvier | 03 April 2014, 13:45:51 UTC | Use correct revisions of best_regression_subsets and weightedaverage. | 03 April 2014, 13:45:51 UTC |
| 971e9d6 | Greg Von Kuster | 03 April 2014, 13:31:43 UTC | Don't add unnecessary (and problematic) prior_installation_required attributes to repository dependency definitions when exporting a repository and its dependencies into a capsule. | 03 April 2014, 13:31:43 UTC |
| 1758f3d | Martin Cech | 02 April 2014, 21:21:06 UTC | libraries: removed unused and deprecated function | 02 April 2014, 21:21:06 UTC |
| 5f928cd | Martin Cech | 02 April 2014, 21:18:51 UTC | libraries: more refactoring fun; full UI for permissions handling; repainting from cache should be ready for stable | 02 April 2014, 21:18:51 UTC |
| b6af887 | Dave Bouvier | 02 April 2014, 20:05:57 UTC | Corrected an error in the analyze_covariates tool shed repository. | 02 April 2014, 20:05:57 UTC |
| ffa19b7 | Greg Von Kuster | 02 April 2014, 19:18:40 UTC | 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 ). | 02 April 2014, 19:18:40 UTC |
| ba7a5c7 | Daniel Blankenberg | 02 April 2014, 19:15:00 UTC | When a tool dependency has failed to install, display the error message as pretty escaped html. | 02 April 2014, 19:15:00 UTC |
| 8d2a8f9 | Martin Cech | 02 April 2014, 15:07:04 UTC | libraries: more refactoring; basic UI based on role handling; attaching to global Galaxy object; persistent lib preferences | 02 April 2014, 15:07:04 UTC |
| 579ebf5 | Jeremy Goecks | 02 April 2014, 14:15:54 UTC | Circster fixes: (a) make compatible with new config object; (b) fix formatting issue with negative values; and (c) clean up debugging statements. Pack scripts. | 02 April 2014, 14:15:54 UTC |
| 0994d4c | Dave Bouvier | 02 April 2014, 13:13:33 UTC | Fix issue in migrations where the same complex repository would be installed once for each repository that depends on it. | 02 April 2014, 13:13:33 UTC |
| 867df48 | Jeremy Goecks | 02 April 2014, 13:12:22 UTC | Automated merge | 02 April 2014, 13:12:22 UTC |
| fee4cb7 | Jeremy Goecks | 02 April 2014, 13:12:07 UTC | Trackster: CompositeTrack fixes for recent refactoring. Pack script. | 02 April 2014, 13:12:07 UTC |
| 7e9f07c | Greg Von Kuster | 02 April 2014, 11:22:01 UTC | Don't require categories and status attributes to be associated with a repository being imported from a capsule, although they should always exist. | 02 April 2014, 11:22:01 UTC |
| 573456d | Jeremy Goecks | 01 April 2014, 20:21:32 UTC | Trackster: show drawn reads across all tiles by pooling incompletely drawn reads and drawing them at the end. | 01 April 2014, 20:21:32 UTC |
| 2ebd825 | Jeremy Goecks | 01 April 2014, 19:09:45 UTC | Automated merge. | 01 April 2014, 19:09:45 UTC |
| e2f56b5 | Jeremy Goecks | 01 April 2014, 19:09:30 UTC | Trackster: drawing performance improvement. Packed scripts. | 01 April 2014, 19:09:30 UTC |
| f807d8f | Dave Bouvier | 01 April 2014, 18:48:48 UTC | Remove escaped double quotes from setup_virtualenv action. | 01 April 2014, 18:48:48 UTC |
| 67288cb | Jeremy Goecks | 01 April 2014, 18:45:34 UTC | Fix for 615d504: do not use downsampling when all reads can be returned. | 01 April 2014, 18:45:34 UTC |
| 01a77cc | Daniel Blankenberg | 01 April 2014, 18:11:56 UTC | Update Biostar question posting to use POST. Have biostar bug reports automatically post. | 01 April 2014, 18:11:56 UTC |
| 10cda06 | Dave Bouvier | 01 April 2014, 17:08:02 UTC | 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. | 01 April 2014, 17:08:02 UTC |
| 2f2e163 | Dave Bouvier | 01 April 2014, 15:05:31 UTC | Remove migrated tools from main's tool conf. | 01 April 2014, 15:05:31 UTC |
| 83af05b | Dave Bouvier | 01 April 2014, 15:04:32 UTC | Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation. | 01 April 2014, 15:04:32 UTC |
| 75d9496 | Jeremy Goecks | 01 April 2014, 14:30:12 UTC | 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. | 01 April 2014, 14:30:12 UTC |
| 82a9a3d | Aysam Guerler | 31 March 2014, 21:35:49 UTC | Charts: Show/hide optional settings, switch to auto-axis by default | 31 March 2014, 21:35:49 UTC |
| 8614373 | Nate Coraor | 31 March 2014, 20:43:05 UTC | Merge branch close. | 31 March 2014, 20:43:05 UTC |
| f16c8ce | Nate Coraor | 31 March 2014, 20:42:43 UTC | Close inactive branch. | 31 March 2014, 20:42:43 UTC |
| a1e9cf6 | Martin Cech | 31 March 2014, 19:36:49 UTC | data libraries, don't allow showing deleted libraries to non-admins; provide information what actions user is allowed to do on library; | 31 March 2014, 19:36:49 UTC |
| d10be6b | Dannon Baker | 31 March 2014, 17:21:49 UTC | Merged in nsoranzo/galaxy-central (pull request #355) Workflow API: show also workflow owner, so a user can check it before importing. | 31 March 2014, 17:21:49 UTC |
| 14760ab | Martin Cech | 31 March 2014, 16:55:06 UTC | 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 | 31 March 2014, 16:55:06 UTC |
| b1b00a9 | Carl Eberhard | 31 March 2014, 16:08:21 UTC | Fix base-mvc SessionStorageModel to require an id; Show alert on disabled sessionStorage | 31 March 2014, 16:08:21 UTC |
| 2bb923e | Carl Eberhard | 31 March 2014, 15:21:14 UTC | Fix to add spacing in hda-edit deleted/hidden info boxes between added sentences | 31 March 2014, 15:21:14 UTC |
| 8254c7a | Greg Von Kuster | 31 March 2014, 12:00:19 UTC | Eliminate unused method in the tool shed's repository controller. | 31 March 2014, 12:00:19 UTC |
| 45ec91d | Greg Von Kuster | 31 March 2014, 11:37:45 UTC | Improvements for populating the tool panel when installing a repository containing a version of a tool alreadly loaded in the tool panel. | 31 March 2014, 11:37:45 UTC |
| 8420fc6 | Greg Von Kuster | 31 March 2014, 02:48:17 UTC | 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. | 31 March 2014, 02:48:17 UTC |
| 4bcb1f8 | Greg Von Kuster | 30 March 2014, 21:42:22 UTC | Don't call the tool shed when loading the Galaxy tool panel at server startup. | 30 March 2014, 21:42:22 UTC |
| a1c9b00 | Greg Von Kuster | 30 March 2014, 20:35:44 UTC | Really fix broken tool shed functional test. | 30 March 2014, 20:35:44 UTC |
| ff46b3d | Greg Von Kuster | 30 March 2014, 20:33:56 UTC | Fix broken tool shed functional test. | 30 March 2014, 20:33:56 UTC |
| 2ff422d | Greg Von Kuster | 30 March 2014, 20:25:25 UTC | 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. | 30 March 2014, 20:25:25 UTC |
| d590921 | John Chilton | 28 March 2014, 23:33:03 UTC | Add unit test for extra primary dataset collection. 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. | 28 March 2014, 23:33:03 UTC |
| aae9c9c | John Chilton | 28 March 2014, 22:49:50 UTC | Bugfix: Problem with primary dataset collection on cloned histories. | 28 March 2014, 22:49:50 UTC |
| 0c6876f | Nate Coraor | 28 March 2014, 20:44:54 UTC | Merged in natefoo/galaxy-central (pull request #340) Rename ucsc_build_sites.txt to .sample. | 28 March 2014, 20:44:54 UTC |
| 1c217f5 | Nate Coraor | 28 March 2014, 20:36:47 UTC | Disable manage_dependency_relationships by default to improve startup time. | 28 March 2014, 20:36:47 UTC |
| 1295b78 | Daniel Blankenberg | 28 March 2014, 19:53:19 UTC | Add some missing semi-colons to javascript on templates/user/register.mako | 28 March 2014, 19:53:19 UTC |
| 5255559 | Daniel Blankenberg | 28 March 2014, 19:52:08 UTC | Use encoded HDA ID in dataset/errors.mako | 28 March 2014, 19:52:08 UTC |
| 8dd9edc | Aysam Guerler | 28 March 2014, 18:38:36 UTC | Charts: Add processing queue | 28 March 2014, 18:38:36 UTC |
| 37650b8 | Martin Cech | 28 March 2014, 18:33:27 UTC | libraries storage prefs: name default prefs for libraries | 28 March 2014, 18:33:27 UTC |
| 4931d47 | Martin Cech | 28 March 2014, 18:17:57 UTC | libraries: some serious refactoring, caching of subviews; base-mvc initialAttrs default setting (empty object) | 28 March 2014, 18:17:57 UTC |
| f675ffa | Dave Bouvier | 28 March 2014, 17:42:08 UTC | Correctly detect when a mercurial request is a fresh checkout of a tool shed repository. | 28 March 2014, 17:42:08 UTC |
| bc7ddb6 | Nicola Soranzo | 28 March 2014, 11:54:53 UTC | Workflow API: show also workflow owner, so a user can check it before importing. | 28 March 2014, 11:54:53 UTC |
| 64f05a9 | Aysam Guerler | 28 March 2014, 06:16:57 UTC | Charts: Improve event deferral | 28 March 2014, 06:16:57 UTC |
| e785177 | Greg Von Kuster | 27 March 2014, 20:03:53 UTC | Add the new repository type "Repository suite definition". This new type is associated with repositories that will contain a single file named repository_dependencies.xml that defines simple repository dependency relationships to a collection of repositories that contain related Galaxy utilities. The chemicaltoolbox repository is an example. | 27 March 2014, 20:03:53 UTC |
| 91338a4 | Carl Eberhard | 27 March 2014, 17:19:11 UTC | Fix: use preventDefault when trying to add display or visualizations to galaxy.frame | 27 March 2014, 17:19:11 UTC |
| 212e7d1 | Carl Eberhard | 27 March 2014, 16:57:54 UTC | Fix to 7155334: add user model to AMD chain for history panel | 27 March 2014, 16:57:54 UTC |
| 4529d00 | Dannon Baker | 27 March 2014, 16:37:21 UTC | Merged in nsoranzo/galaxy-central (pull request #353) Add BCF datatype sniffing, so BCF files are not uncompressed during upload. | 27 March 2014, 16:37:21 UTC |
| 2ae82ed | Nicola Soranzo | 27 March 2014, 16:19:39 UTC | Use new Bcf class. | 27 March 2014, 16:19:39 UTC |
| 5c02088 | Carl Eberhard | 27 March 2014, 16:17:18 UTC | History/HDA API: normalize exceptions and exception codes; Fix ability to history/view a history shared with another user | 27 March 2014, 16:17:18 UTC |
| de8f25c | Nicola Soranzo | 27 March 2014, 16:03:16 UTC | Add BCF datatype sniffing, so BCF files are not uncompressed during upload. | 27 March 2014, 16:03:16 UTC |
| 152fa0d | Aysam Guerler | 27 March 2014, 03:00:42 UTC | Trackster: Fix trackster button in tabular data viewer | 27 March 2014, 03:00:42 UTC |
| e329872 | Jeremy Goecks | 27 March 2014, 02:15:12 UTC | Pack script. | 27 March 2014, 02:15:12 UTC |
| 597b88a | Jeremy Goecks | 27 March 2014, 02:14:10 UTC | Trackster: (a) default read track block colors to gray in order to show variants; (b) do not set default height of variant track. | 27 March 2014, 02:14:10 UTC |
| ebaa1c3 | Jeremy Goecks | 26 March 2014, 21:53:07 UTC | Visualization JS: fix incorrect method call. Pack script. | 26 March 2014, 21:53:07 UTC |
| f0e4046 | Jeremy Goecks | 26 March 2014, 21:39:58 UTC | Pack scripts. | 26 March 2014, 21:39:58 UTC |
| c461e68 | Jeremy Goecks | 26 March 2014, 21:38:22 UTC | Automated merge of local changesets with -default | 26 March 2014, 21:38:22 UTC |
| cba7a66 | Jeremy Goecks | 26 March 2014, 21:37:03 UTC | Trackster: fix offset bug that was rendering bases incorrectly. | 26 March 2014, 21:37:03 UTC |
| 8a019c0 | John Chilton | 26 March 2014, 21:28:31 UTC | Fix broken import with workflow PR. | 26 March 2014, 21:28:31 UTC |
