| 8b7e2af | Dannon Baker | 23 February 2015, 16:23:38 UTC | Clone .gitignore | 23 February 2015, 16:23:38 UTC |
| f5282fa | Daniel Blankenberg | 13 January 2015, 15:26:12 UTC | Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. | 13 January 2015, 15:26:12 UTC |
| e2cf60e | Nate Coraor | 30 July 2014, 14:44:41 UTC | Apply 2014.07.30 security fix to release_2013.02.08 | 30 July 2014, 14:44:41 UTC |
| 4cc2067 | Nate Coraor | 30 July 2014, 14:40:27 UTC | Added tag latest_2013.01.13 for changeset 6b0bd93038a8 | 30 July 2014, 14:40:27 UTC |
| 926c1b1 | Nate Coraor | 30 July 2014, 14:40:05 UTC | Fix a critical security vulnerability with handling pickled data. Thanks to Inge Alexander Raknes for reporting the isssue. | 30 July 2014, 14:40:05 UTC |
| b7c256d | Daniel Blankenberg | 22 March 2013, 16:23:05 UTC | Do not display old-style display links in server-side history when they are disabled. | 22 March 2013, 16:23:05 UTC |
| 88238a1 | Daniel Blankenberg | 22 March 2013, 15:43:42 UTC | Allow old-style display applications to be disabled. | 22 March 2013, 15:43:42 UTC |
| ed606d4 | Daniel Blankenberg | 06 March 2013, 18:47:00 UTC | Fix display bug for DrillDown Fields and parameters. | 06 March 2013, 18:47:00 UTC |
| 3407ef7 | Nate Coraor | 06 March 2013, 17:40:31 UTC | Make maf-to-bed object-store aware | 06 March 2013, 17:40:31 UTC |
| 2124845 | Daniel Blankenberg | 22 February 2013, 22:03:49 UTC | Fix for displaying error messages on DataToolParameter where optional=True. | 22 February 2013, 22:03:49 UTC |
| 622cd9a | Daniel Blankenberg | 21 February 2013, 20:26:15 UTC | Fix for display_in_upload | 21 February 2013, 20:26:15 UTC |
| 0d9b986 | Greg Von Kuster | 21 February 2013, 16:49:21 UTC | Add styles to the readme container. | 21 February 2013, 16:49:21 UTC |
| 8d35648 | Dave Bouvier | 21 February 2013, 16:06:11 UTC | Changed to_safe_string to use markupsafe.escape for unsafe characters. | 21 February 2013, 16:06:11 UTC |
| c88a954 | Jeremy Goecks | 17 February 2013, 19:59:02 UTC | Move grid element initialization to main body to prevent it from happening too early. Pack scripts. | 17 February 2013, 19:59:02 UTC |
| eaa7abf | Dave Bouvier | 20 February 2013, 13:56:36 UTC | Fix missing import in repository controller. | 20 February 2013, 13:56:36 UTC |
| 578e6da | Dave Bouvier | 19 February 2013, 17:29:29 UTC | Fix for installing a repository that only contains a workflow, then importing that workflow to Galaxy. | 19 February 2013, 17:29:29 UTC |
| 134b115 | Greg Von Kuster | 18 February 2013, 20:28:06 UTC | Fix for installing a repository from the tool shed that includes a repository dependency defintion where the required repository is owned by a user other than the dependent repository. | 18 February 2013, 20:28:06 UTC |
| 12ccf10 | Greg Von Kuster | 18 February 2013, 16:04:29 UTC | Fix for handling proprietary datatyps definitions in repositories being installed from the tool shed when only datatyes that subclass from those in the Galaxy frameowrk are defined (i.e., there are no proprietary datatype class files for the datatypes). In addition, this changeset now properly handles installing a tool shed repository that included prioretary datatype definitions (they were failing due to a bug in this same method). | 18 February 2013, 16:04:29 UTC |
| 348f07d | Nate Coraor | 15 February 2013, 15:53:20 UTC | Handle the Torque 'E' job state in the CLI runner. | 15 February 2013, 15:53:20 UTC |
| 2590523 | Nate Coraor | 12 February 2013, 13:46:28 UTC | Allow the CLI runner to handle command stdout >65K. | 12 February 2013, 13:46:28 UTC |
| e1d02e9 | Nate Coraor | 08 February 2013, 16:23:04 UTC | Added tag release_2013.02.08 for changeset 1c7174911392 | 08 February 2013, 16:23:04 UTC |
| 7fd8dfc | Nate Coraor | 08 February 2013, 16:21:50 UTC | merge changes from next-stable branch | 08 February 2013, 16:21:50 UTC |
| 3bcea4f | Nate Coraor | 08 February 2013, 16:20:41 UTC | close next-stable branch for release | 08 February 2013, 16:20:41 UTC |
| 09a59a2 | Nate Coraor | 08 February 2013, 16:20:41 UTC | merge closed branch | 08 February 2013, 16:20:41 UTC |
| 9852cb4 | Nate Coraor | 08 February 2013, 16:20:38 UTC | merge closed branch | 08 February 2013, 16:20:38 UTC |
| c5e4765 | Nate Coraor | 08 February 2013, 16:20:36 UTC | merge closed branch | 08 February 2013, 16:20:36 UTC |
| a581fa6 | Nate Coraor | 08 February 2013, 16:20:33 UTC | merge closed branch | 08 February 2013, 16:20:33 UTC |
| 6c8e9d0 | Nate Coraor | 08 February 2013, 16:20:31 UTC | merge closed branch | 08 February 2013, 16:20:31 UTC |
| 7f5e0ef | Nate Coraor | 08 February 2013, 16:20:28 UTC | merge changes from stable branch | 08 February 2013, 16:20:28 UTC |
| f8265a7 | James Taylor | 02 February 2013, 20:38:58 UTC | merge | 02 February 2013, 20:38:58 UTC |
| dae6692 | James Taylor | 02 February 2013, 20:37:21 UTC | jobs bugfix: fix syntax error in light weight runner init | 02 February 2013, 20:37:21 UTC |
| 423cfa1 | James Taylor | 02 February 2013, 19:10:47 UTC | Added tag release_2013.01.13 for changeset a4113cc1cb5e | 02 February 2013, 19:10:47 UTC |
| 53f51ac | Dave Bouvier | 04 February 2013, 19:00:31 UTC | Updated BWA's tool_dependencies.xml to no longer rely on a network connection to correctly complete functional tests. | 04 February 2013, 19:00:31 UTC |
| e34bc17 | Dave Bouvier | 04 February 2013, 16:51:42 UTC | Tool shed functional tests for complex repository dependencies, detection and setting of metadata for invalid repository dependencies. Fixes for detecting and displaying invalid repository dependencies. | 04 February 2013, 16:51:42 UTC |
| d9a3f29 | Daniel Blankenberg | 01 February 2013, 23:13:05 UTC | Fix for workflow parameters. | 01 February 2013, 23:13:05 UTC |
| 57e27e2 | Nate Coraor | 01 February 2013, 21:19:55 UTC | Merged changes from the default branch. | 01 February 2013, 21:19:55 UTC |
| e7ca9f2 | Greg Von Kuster | 01 February 2013, 21:13:15 UTC | Add an enhanced version of the cirable URLs for tool shed repositories contributed by Peter Cock. | 01 February 2013, 21:13:15 UTC |
| 2fb29b1 | Nate Coraor | 01 February 2013, 21:06:33 UTC | Created next-stable branch. | 01 February 2013, 21:06:33 UTC |
| f397718 | Nate Coraor | 01 February 2013, 21:03:14 UTC | Created stable branch. | 01 February 2013, 21:03:14 UTC |
| 826e8db | Dave Bouvier | 01 February 2013, 20:31:33 UTC | Removed log.debug. | 01 February 2013, 20:31:33 UTC |
| f09555e | Dave Bouvier | 01 February 2013, 20:28:43 UTC | Fix detection of invalid repository dependencies on upload. | 01 February 2013, 20:28:43 UTC |
| b6226ab | Dave Bouvier | 01 February 2013, 18:37:38 UTC | Fix for installing a complex dependency that has not been previously installed. | 01 February 2013, 18:37:38 UTC |
| bb7a0b6 | Greg Von Kuster | 01 February 2013, 18:13:09 UTC | When resetting all metadata on a repository in the tool shed, restrict display of error messages to those associated with the tip. | 01 February 2013, 18:13:09 UTC |
| aee8516 | Dave Bouvier | 01 February 2013, 16:43:40 UTC | Uncommented cleanup method in functional_tests.py. | 01 February 2013, 16:43:40 UTC |
| c11ea0e | Dave Bouvier | 01 February 2013, 16:42:18 UTC | Tool shed functional tests for complex repository dependencies. Tool shed functional tests for reserved strings in repository and user names. Tool shed functional test enhancements. | 01 February 2013, 16:42:18 UTC |
| dc7f156 | Greg Von Kuster | 01 February 2013, 16:31:59 UTC | Generate metadata for repository dependencies even if their definitions are invalid. | 01 February 2013, 16:31:59 UTC |
| 8172179 | Greg Von Kuster | 01 February 2013, 15:50:38 UTC | Improved messaging for invalid repository dependency definitions. | 01 February 2013, 15:50:38 UTC |
| 2fcf3b1 | Greg Von Kuster | 01 February 2013, 14:40:22 UTC | Handle invalid complex repository dependency definitions. | 01 February 2013, 14:40:22 UTC |
| a2eb678 | Greg Von Kuster | 31 January 2013, 16:47:32 UTC | Automatically create missing required tool shed files from samples when startign the tool shed server. | 31 January 2013, 16:47:32 UTC |
| fa0959f | Greg Von Kuster | 31 January 2013, 16:39:12 UTC | Uncomment the default sqlite database connection string in community_wsgi.ini.sample. | 31 January 2013, 16:39:12 UTC |
| d7a6fd5 | Greg Von Kuster | 31 January 2013, 16:33:15 UTC | Allow a Galaxy admin to select a shed-related tool panel config file whose tool_path setting will be used to installed repositories into Galaxy for those repositories with which a tool panel selection is not necessary. | 31 January 2013, 16:33:15 UTC |
| 1f55cc5 | Greg Von Kuster | 31 January 2013, 14:28:40 UTC | Restrict the ability to use reserved words in the tool shed for repository names and public user names. | 31 January 2013, 14:28:40 UTC |
| b115ab8 | Greg Von Kuster | 30 January 2013, 21:47:20 UTC | Dont' assume a complex repository dependency was properly defined. | 30 January 2013, 21:47:20 UTC |
| 332f497 | Greg Von Kuster | 30 January 2013, 21:29:37 UTC | Support for installation and administration of complex repository dependencies in Galaxy. | 30 January 2013, 21:29:37 UTC |
| 478c3be | Dannon Baker | 30 January 2013, 20:57:10 UTC | Merge Pull Request #114 https://bitbucket.org/galaxy/galaxy-central/pull-request/114/fixed-error-when-retrieving-workflows-via/ Adjusted spacing. | 30 January 2013, 20:57:10 UTC |
| e3de29e | Richard Park | 30 January 2013, 20:48:54 UTC | Fixed error when retrieving workflows via API. Added additional tab to lines 88 and 89, to fix error when trying to refer to variable "step." | 30 January 2013, 20:48:54 UTC |
| e0a308f | Dave Bouvier | 30 January 2013, 19:57:16 UTC | Pass in a temporary file as migrated_tools_conf, so repositories without tools end up in the right location. | 30 January 2013, 19:57:16 UTC |
| eb10beb | Dave Bouvier | 30 January 2013, 19:55:08 UTC | Enable running tool shed functional tests with run_functional_tests.sh. | 30 January 2013, 19:55:08 UTC |
| 25f019a | Dave Bouvier | 30 January 2013, 19:54:41 UTC | Enable specifying the location of the migrated tools' XML file. | 30 January 2013, 19:54:41 UTC |
| 382a7e5 | Daniel Blankenberg | 30 January 2013, 18:49:43 UTC | Add a util.move_merge() function that makes moving directories more consistent. | 30 January 2013, 18:49:43 UTC |
| caf527e | Daniel Blankenberg | 30 January 2013, 18:40:23 UTC | Allow DiskObjectStore.update_from_file() to optionally preserve symlinks. | 30 January 2013, 18:40:23 UTC |
| e09138d | Daniel Blankenberg | 30 January 2013, 18:40:22 UTC | Add a util.force_symlink() helper method. | 30 January 2013, 18:40:22 UTC |
| baf3017 | Daniel Blankenberg | 30 January 2013, 18:30:00 UTC | Show Galaxy Tool Version (job.tool_version) in addition to Tool Version (hda.tool_version) in dataset show_params. | 30 January 2013, 18:30:00 UTC |
| 7538091 | Jeremy Goecks | 30 January 2013, 17:55:49 UTC | Change order of Bowtie2 output datasets to put aligned reads at top of history. | 30 January 2013, 17:55:49 UTC |
| d0768ba | Jeremy Goecks | 30 January 2013, 17:22:59 UTC | Collect and output comments when reading unordered GTF. Handle comments when converting from GTF to FLI. | 30 January 2013, 17:22:59 UTC |
| 517fb61 | Jeremy Goecks | 30 January 2013, 15:54:15 UTC | Fixes for 149f0fc and pack scripts. | 30 January 2013, 15:54:15 UTC |
| 7f079a8 | James Taylor | 30 January 2013, 15:32:16 UTC | web.framework: remove stray print | 30 January 2013, 15:32:16 UTC |
| af3724c | Jeremy Goecks | 30 January 2013, 14:03:27 UTC | Add missing output file for new trimmer test. | 30 January 2013, 14:03:27 UTC |
| 3dd11e9 | Joachim Jacob | 30 January 2013, 09:38:58 UTC | Adjusted trimming tool to include negative positions. Modified help and test. | 30 January 2013, 09:38:58 UTC |
| e2a1d18 | Dannon Baker | 29 January 2013, 23:08:43 UTC | Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #87) Refactoring Task Splitting Toward Per-Job Definitions (in Addition to Current Per-Tool Definitions) | 29 January 2013, 23:08:43 UTC |
| 122d274 | Jeremy Goecks | 29 January 2013, 21:41:04 UTC | Add metadata support to JavaScript dataset objects. | 29 January 2013, 21:41:04 UTC |
| 5996602 | Jeremy Goecks | 29 January 2013, 21:40:04 UTC | Fixes for packing metadata in HDA api values. | 29 January 2013, 21:40:04 UTC |
| 3bd5cae | Jeremy Goecks | 29 January 2013, 19:34:42 UTC | Documentation fix. | 29 January 2013, 19:34:42 UTC |
| ea8d337 | Jeremy Goecks | 29 January 2013, 15:37:16 UTC | Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well. | 29 January 2013, 15:37:16 UTC |
| e31e6fa | Jeremy Goecks | 28 January 2013, 21:36:02 UTC | Language improvements for tophat wrappers. | 28 January 2013, 21:36:02 UTC |
| ba73ae7 | Carl Eberhard | 28 January 2013, 21:22:47 UTC | history panel: log responseText of history-model update errors; pack scripts | 28 January 2013, 21:22:47 UTC |
| 3deac8e | Carl Eberhard | 28 January 2013, 21:20:49 UTC | History grid, view: allow user to view their own histories | 28 January 2013, 21:20:49 UTC |
| 409ba63 | Jeremy Goecks | 28 January 2013, 19:02:25 UTC | Grid framework refactoring to increase speed and ease of debugging: (1) create and use Backbone object for grid; (2) move grid javascript to its own file; (3) remove webapp parameter; (4) augment search box style so that search button does not wrap. Pack scripts. | 28 January 2013, 19:02:25 UTC |
| 0ca2a01 | Dannon Baker | 28 January 2013, 18:56:01 UTC | Merged in kellrott/galaxy-central (pull request #105) Adding UUIDType to data model and uuid column to dataset table. | 28 January 2013, 18:56:01 UTC |
| 6773daa | Dannon Baker | 28 January 2013, 17:57:28 UTC | Merged in kellrott/galaxy-central (pull request #92) Adding handler for httpexceptions.HTTPFound, so that the redirect tool will work (rather then causing an error) | 28 January 2013, 17:57:28 UTC |
| 4b6fb05 | John Chilton | 16 January 2013, 22:22:55 UTC | Merge with latest galaxy-central to resolve conflict introduced with 4bd4197. | 16 January 2013, 22:22:55 UTC |
| ca26e14 | Greg Von Kuster | 16 January 2013, 20:39:22 UTC | Properly handle updates which have become available for tool shed repositories while they were ninstalled when reinstalling them. | 16 January 2013, 20:39:22 UTC |
| e6f32ac | Dave Bouvier | 16 January 2013, 20:14:36 UTC | Fix missing import that was breaking unit tests. | 16 January 2013, 20:14:36 UTC |
| 4bc0312 | Dave Bouvier | 16 January 2013, 18:19:45 UTC | Tool shed functional test enhancements. Tests for installing repositories via the tool search. Tests for reviewing repository components. | 16 January 2013, 18:19:45 UTC |
| dd4e359 | Dave Bouvier | 16 January 2013, 17:36:19 UTC | Fix server error when trying to create a component review for a repository when one already exists for that changeset revision. | 16 January 2013, 17:36:19 UTC |
| f695f8f | Dave Bouvier | 16 January 2013, 17:35:36 UTC | Fix for removing roles from users in the tool shed. | 16 January 2013, 17:35:36 UTC |
| 1ad4152 | Nate Coraor | 16 January 2013, 17:30:24 UTC | Remove spurious debugging statement. | 16 January 2013, 17:30:24 UTC |
| 6d323f2 | Jeremy Goecks | 15 January 2013, 22:17:32 UTC | Update history functional tests for changes in f93113b | 15 January 2013, 22:17:32 UTC |
| b7c4932 | Dannon Baker | 15 January 2013, 22:09:33 UTC | Merged in jmchilton/galaxy-central-hgignore-fixes (pull request #100: Add more commonly generated Galaxy runtime files to .hgignore.) | 15 January 2013, 22:09:33 UTC |
| 27dc7a7 | Daniel Blankenberg | 15 January 2013, 21:46:47 UTC | Make galaxy.tools.Tool a new-style class. | 15 January 2013, 21:46:47 UTC |
| b831d61 | Jeremy Goecks | 15 January 2013, 21:16:55 UTC | Change 'clone workflow/visualization' to 'copy workflow/visualization' in user interface and associated code. | 15 January 2013, 21:16:55 UTC |
| 0d016d5 | Jeremy Goecks | 15 January 2013, 15:48:35 UTC | Change 'clone history' to 'copy history' in user interface and associated code. | 15 January 2013, 15:48:35 UTC |
| fbe969d | Dannon Baker | 15 January 2013, 15:34:58 UTC | page controller: fix invalid error syntax, remove unused import. | 15 January 2013, 15:34:58 UTC |
| 9fed9f6 | Jeremy Goecks | 15 January 2013, 02:07:11 UTC | Remove tipsy classes from base css. | 15 January 2013, 02:07:11 UTC |
| c851778 | Dave Clements | 15 January 2013, 01:01:17 UTC | Update Sphinx RST structural doc to reflect recent code changes. | 15 January 2013, 01:01:17 UTC |
| f706f34 | Dave Clements | 15 January 2013, 00:13:54 UTC | Replaced "query" with "dataset" in a number of tool definition XML files. I got tired of coming across "query" when doing workshops. | 15 January 2013, 00:13:54 UTC |
| 3e1cdcf | Greg Von Kuster | 14 January 2013, 22:15:46 UTC | Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled. | 14 January 2013, 22:15:46 UTC |
| b2af07c | Greg Von Kuster | 14 January 2013, 20:16:06 UTC | Get updates to the latest changset revision and reset metadata when reinstalling an uninstalled tool shed repository in Galaxy. | 14 January 2013, 20:16:06 UTC |
| 5864d5f | Jeremy Goecks | 14 January 2013, 19:14:41 UTC | Add tool id for when clause warnings that are output when tool XML is parsed. | 14 January 2013, 19:14:41 UTC |
| f7c1999 | Jeremy Goecks | 14 January 2013, 19:00:21 UTC | Remove unused test parameter. | 14 January 2013, 19:00:21 UTC |
