| 3edcc3f | Dannon Baker | 23 February 2015, 16:25:34 UTC | Clone .gitignore | 23 February 2015, 16:25:34 UTC |
| b954cca | John Chilton | 15 January 2015, 21:01:13 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:13 UTC |
| a32fca7 | Daniel Blankenberg | 13 January 2015, 15:26:56 UTC | Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. | 13 January 2015, 15:26:56 UTC |
| 4263ff5 | Nate Coraor | 30 July 2014, 14:57:52 UTC | Apply 2014.07.30 security fix to release_2013.08.12 | 30 July 2014, 14:57:52 UTC |
| f179f9d | Nate Coraor | 30 July 2014, 14:56:05 UTC | Added tag latest_2013.06.03 for changeset 9713d86392ef | 30 July 2014, 14:56:05 UTC |
| 653b73b | Nate Coraor | 30 July 2014, 14:55:57 UTC | Apply 2014.07.30 security fix to release_2013.06.03 | 30 July 2014, 14:55:57 UTC |
| 35cf1e3 | Nate Coraor | 30 July 2014, 14:53:14 UTC | Added tag latest_2013.04.01 for changeset 425009b3ff4d | 30 July 2014, 14:53:14 UTC |
| 7313176 | Nate Coraor | 30 July 2014, 14:53:01 UTC | Apply 2014.07.30 security fix to release_2013.04.01 | 30 July 2014, 14:53:01 UTC |
| 4425904 | Nate Coraor | 30 July 2014, 14:44:55 UTC | Added tag latest_2013.02.08 for changeset 3e62060b14b9 | 30 July 2014, 14:44:55 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 |
| 4fb2b89 | John Chilton | 04 November 2013, 19:55:00 UTC | White-list expressions executed by filtering and dna_filtering tools. | 04 November 2013, 19:55:00 UTC |
| 188e50d | Daniel Blankenberg | 29 September 2013, 06:04:31 UTC | Add additional check and slice to _sniffnfix_pg9_hex(). Fixes issue seen when attempting to view saved visualizations. Further investigation may be needed. | 29 September 2013, 06:04:31 UTC |
| 4850745 | Nate Coraor | 26 September 2013, 15:02:58 UTC | Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. | 26 September 2013, 15:02:58 UTC |
| b741f55 | Nate Coraor | 23 September 2013, 23:38:30 UTC | Remove unmaintained RGENETICS tools from Galaxy Main | 23 September 2013, 23:38:30 UTC |
| 4986d53 | Jeremy Goecks | 11 September 2013, 20:06:32 UTC | Pack script. | 11 September 2013, 20:06:32 UTC |
| 4bc809d | Jeremy Goecks | 11 September 2013, 20:00:19 UTC | Trackster: fix data-mode compatibility test; this fixes mode changing from coverage to dense/squish/pack. | 11 September 2013, 20:00:19 UTC |
| c9d4426 | Jeremy Goecks | 11 September 2013, 16:22:16 UTC | Close branch 10517:97d020901403 | 11 September 2013, 16:22:16 UTC |
| 65e1fcc | Carl Eberhard | 09 September 2013, 15:20:40 UTC | Fix to dbkey select in library upload when 'unspecified' is not in dbkey list | 09 September 2013, 15:20:40 UTC |
| 5e4ec92 | Dave Bouvier | 04 September 2013, 18:30:49 UTC | Fix for duplicate records created when a repository is installed from the tool shed, and the same repository had previously been installed and uninstalled. | 04 September 2013, 18:30:49 UTC |
| 56bb537 | Nate Coraor | 28 August 2013, 20:02:16 UTC | Logic on DiskObjectStore's empty() method was reversed (previously returned True when non-empty). | 28 August 2013, 20:02:16 UTC |
| a012e23 | Daniel Blankenberg | 23 August 2013, 13:07:28 UTC | Fix for ToolParameterValueWrapper.get_display_text() due to inconsistent behavior between Python2.7 and lower for empty strings. expected quoted empty string: $ python2.7 Python 2.7.5 (default, Aug 1 2013, 00:59:24) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pipes >>> print pipes.quote('') '' >>> repr( pipes.quote('') ) '"\'\'"' >>> python < 2.7: $ python2.6 Python 2.6.1 (r261:67515, Aug 2 2010, 20:10:18) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pipes >>> print pipes.quote('') >>> repr( pipes.quote('') ) "''" >>> | 23 August 2013, 13:07:28 UTC |
| d26b5ed | Greg Von Kuster | 20 August 2013, 15:13:54 UTC | Fix for retrieving an installed tool shed repository record from the Galaxy database during installation of a repository dependency where the dependency definition defines a changeset_revision that is older than the changeset_revision associated with the installed repository. This occurs only with repositories of type tool_dependency_definition. | 20 August 2013, 15:13:54 UTC |
| 7adc736 | Dave Bouvier | 19 August 2013, 17:06:17 UTC | Fix for case where running functional tests might overwrite certain files in database/files. | 19 August 2013, 17:06:17 UTC |
| 338517b | Nate Coraor | 12 August 2013, 15:55:41 UTC | Added tag release_2013.08.12 for changeset 1ae95b3aa98d | 12 August 2013, 15:55:41 UTC |
| 707326b | Nate Coraor | 12 August 2013, 15:54:39 UTC | Merge next-stable to stable. | 12 August 2013, 15:54:39 UTC |
| 8a90830 | Nate Coraor | 12 August 2013, 15:53:34 UTC | Close next-stable branch for merge to stable. | 12 August 2013, 15:53:34 UTC |
| bac95b8 | Nate Coraor | 08 August 2013, 19:40:00 UTC | Define the ActionInputError exception that was being caught in the quotas API controller. Thanks Jim Johnson. | 08 August 2013, 19:40:00 UTC |
| 4054f6c | Carl Eberhard | 08 August 2013, 14:40:27 UTC | History view: fix broken scrollbar | 08 August 2013, 14:40:27 UTC |
| 7dfc3c2 | Daniel Blankenberg | 07 August 2013, 19:23:30 UTC | Fix for Datatype.matches_any() introduced in 10027:b999689a0130. Fixes issue seen where external display applications requiring format conversions would always fail with server error. | 07 August 2013, 19:23:30 UTC |
| 40897ad | Jeremy Goecks | 06 August 2013, 22:06:45 UTC | Update citation for Tophat2. | 06 August 2013, 22:06:45 UTC |
| 8e35f12 | Jeremy Goecks | 06 August 2013, 20:34:20 UTC | Add Bowtie2 wrapper to main's tool conf. | 06 August 2013, 20:34:20 UTC |
| 20196a6 | Jeremy Goecks | 06 August 2013, 15:01:31 UTC | Add tophat2 to main tool conf. | 06 August 2013, 15:01:31 UTC |
| 1cfcf5b | Jeremy Goecks | 06 August 2013, 14:59:43 UTC | Add requirements tags to tophat wrapper. | 06 August 2013, 14:59:43 UTC |
| 0dd2f9a | John Chilton | 06 August 2013, 05:01:44 UTC | Slight simplification of logic related to implementation of tool.requires_login. | 06 August 2013, 05:01:44 UTC |
| ae1d7da | John Chilton | 06 August 2013, 04:50:04 UTC | Fix tool.requires_login behvaior broken with dynamic tool box filters (sorry again Dan and thanks for the bug report). | 06 August 2013, 04:50:04 UTC |
| b88be23 | Nate Coraor | 05 August 2013, 21:15:12 UTC | Bugfix for stopping jobs with the PBS plugin. | 05 August 2013, 21:15:12 UTC |
| b5cfae7 | Nate Coraor | 05 August 2013, 20:06:55 UTC | Bug fix for job recovery in the Condor runner. | 05 August 2013, 20:06:55 UTC |
| ee763fe | Nate Coraor | 05 August 2013, 20:06:31 UTC | 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. | 05 August 2013, 20:06:31 UTC |
| b8045f2 | Nate Coraor | 02 August 2013, 20:39:05 UTC | Merge changes from stable. | 02 August 2013, 20:39:05 UTC |
| 1a88188 | Jeremy Goecks | 01 August 2013, 23:38:24 UTC | Fix imports and parentheses spacing. | 01 August 2013, 23:38:24 UTC |
| f81c33b | Jeremy Goecks | 31 July 2013, 17:00:23 UTC | Fix bug in Pages' link creation and pack scripts. | 31 July 2013, 17:00:23 UTC |
| 181293f | Dave Bouvier | 31 July 2013, 14:38:40 UTC | Fix server error when displaying a tool with conditionals in the tool shed. | 31 July 2013, 14:38:40 UTC |
| 4b2b096 | Nate Coraor | 30 July 2013, 16:56:17 UTC | Open next-stable for the next release. | 30 July 2013, 16:56:17 UTC |
| caa16ac | Nate Coraor | 30 July 2013, 16:54:02 UTC | See previous commit message. | 30 July 2013, 16:54:02 UTC |
| 900cf1a | Nate Coraor | 30 July 2013, 16:50:29 UTC | 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. | 30 July 2013, 16:50:29 UTC |
| 812aebd | Nate Coraor | 30 July 2013, 16:44:05 UTC | 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. | 30 July 2013, 16:44:05 UTC |
| ae28586 | Nate Coraor | 30 July 2013, 16:32:17 UTC | Merge closed branch. | 30 July 2013, 16:32:17 UTC |
| 0f32b50 | Nate Coraor | 30 July 2013, 16:31:59 UTC | Close branch. | 30 July 2013, 16:31:59 UTC |
| 3a71ed6 | Dave Bouvier | 30 July 2013, 14:32:31 UTC | Fix for revision select on repositories with multiple installable revisions. | 30 July 2013, 14:32:31 UTC |
| fdc46aa | Dave Bouvier | 30 July 2013, 13:23:39 UTC | Clear tool test results when the skip tool tests option is enabled. | 30 July 2013, 13:23:39 UTC |
| 8944c1a | Jeremy Goecks | 30 July 2013, 02:38:17 UTC | Move welcome_url setting to 'UI Localization' section of the config file. | 30 July 2013, 02:38:17 UTC |
| f34f529 | Jeremy Goecks | 29 July 2013, 21:37:14 UTC | Automated merge | 29 July 2013, 21:37:14 UTC |
| a1714c4 | Jeremy Goecks | 29 July 2013, 21:36:39 UTC | Add and document welcome_url config option. | 29 July 2013, 21:36:39 UTC |
| f87221e | Dave Bouvier | 29 July 2013, 19:25:08 UTC | Define a CSS class that applies to all tool test results subfolders. | 29 July 2013, 19:25:08 UTC |
| a4313a3 | Dave Bouvier | 29 July 2013, 17:50:55 UTC | 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. | 29 July 2013, 17:50:55 UTC |
| bb30319 | Dave Bouvier | 29 July 2013, 16:01:24 UTC | Do not truncate tool test input dataset names, as Galaxy no longer displays them truncated. | 29 July 2013, 16:01:24 UTC |
| 10ed6d9 | Greg Von Kuster | 26 July 2013, 13:10:23 UTC | Fix import in the tool shed's commit_util. | 26 July 2013, 13:10:23 UTC |
| c011564 | Jeremy Goecks | 25 July 2013, 23:45:29 UTC | Add --no-effective-length-correction parameter to Cufflinks wrapper | 25 July 2013, 23:45:29 UTC |
| 3794972 | Jeremy Goecks | 25 July 2013, 16:56:30 UTC | Change ToolInput to ToolParameter in JavaScript tools implementation to match language used in model. | 25 July 2013, 16:56:30 UTC |
| 12c61c4 | Dave Bouvier | 25 July 2013, 15:37:13 UTC | 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. | 25 July 2013, 15:37:13 UTC |
| 9d7cd8a | Greg Von Kuster | 25 July 2013, 15:01:18 UTC | A bit of refactoring of the tool shed's repository controller. | 25 July 2013, 15:01:18 UTC |
| 8a44bdb | Greg Von Kuster | 24 July 2013, 20:36:52 UTC | 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. | 24 July 2013, 20:36:52 UTC |
| 5a9caf6 | Dave Bouvier | 24 July 2013, 19:19:38 UTC | Tool shed functional tests for repairing an installed repository. | 24 July 2013, 19:19:38 UTC |
| 0883b48 | Dave Bouvier | 24 July 2013, 17:39:47 UTC | Tool shed functional tests for the $ENV[] environment variable inheritance feature. | 24 July 2013, 17:39:47 UTC |
| 2cc5caf | Carl Eberhard | 24 July 2013, 15:06:51 UTC | History panel: remove profiling methods | 24 July 2013, 15:06:51 UTC |
| a9fc6aa | Dave Bouvier | 24 July 2013, 14:58:05 UTC | Merged in changes. | 24 July 2013, 14:58:05 UTC |
| ab43ff0 | Dave Bouvier | 24 July 2013, 14:54:37 UTC | Tool shed functional tests for the repository type feature. | 24 July 2013, 14:54:37 UTC |
| 66d7a1f | Greg Von Kuster | 24 July 2013, 14:51:30 UTC | Apply Peter Cock's patch for appending a .rst extension to readme file names in tool shed repositories. | 24 July 2013, 14:51:30 UTC |
| 53562a4 | Greg Von Kuster | 24 July 2013, 14:34:21 UTC | Render tool shed repository readme files as rst only if the file name ends with .rst. | 24 July 2013, 14:34:21 UTC |
| 81feb44 | Dave Bouvier | 24 July 2013, 14:17:03 UTC | Fix to correctly handle comments in repository dependency definitions. | 24 July 2013, 14:17:03 UTC |
| 74218ce | Carl Eberhard | 23 July 2013, 17:55:39 UTC | base controller, get_history_dataset_association: remove deleted=False flag; api/histories, update: remove deleted flag; casperjs tests: update for previous and remove tool iframe code | 23 July 2013, 17:55:39 UTC |
| 48de95c | Carl Eberhard | 23 July 2013, 14:12:59 UTC | api/genomes, create: update docs | 23 July 2013, 14:12:59 UTC |
| e54aa39 | Carl Eberhard | 23 July 2013, 13:32:22 UTC | History panel: disable (w/ message) display button for uploading files | 23 July 2013, 13:32:22 UTC |
| e6d42fd | Carl Eberhard | 22 July 2013, 21:04:52 UTC | API histories, delete: ensure HTTPExceptions are raised, better return values; API workflows delete: add code 400 to not found clause, change to code 403 for not accessible clause | 22 July 2013, 21:04:52 UTC |
| 676ee26 | Carl Eberhard | 22 July 2013, 19:48:50 UTC | library upload: sort dbkeys, default to unspecified, remove unneeded call to replace_big_select_inputs | 22 July 2013, 19:48:50 UTC |
| f48f7f7 | Dave Bouvier | 22 July 2013, 17:14:58 UTC | Wrap the repository type select in form tags so that Twill will correctly parse the HTML on the browse repository files page. This resolves failing functional tests in the test_0440_deleting_dependency_definitions script. | 22 July 2013, 17:14:58 UTC |
| b45e763 | Nate Coraor | 19 July 2013, 20:52:50 UTC | Merged in mepcotterell/galaxy-central/mepcotterell/allow-pip-to-run-when-venv_directory-con-1373715782557 (pull request #195) allow pip to run when venv_directory contains spaces | 19 July 2013, 20:52:50 UTC |
| f796406 | Greg Von Kuster | 19 July 2013, 19:19:04 UTC | Enhance the change_directory action for installing tool dependencies via fabric to allow for changing the current directory to a location above the current working directory as long as the location is still within the defined working_directory. | 19 July 2013, 19:19:04 UTC |
| fe04835 | Aysam Guerler | 19 July 2013, 18:56:39 UTC | bowtie2 wrapper update | 19 July 2013, 18:56:39 UTC |
| 3367d43 | Aysam Guerler | 19 July 2013, 18:30:38 UTC | bowtie2 tool wrapper update | 19 July 2013, 18:30:38 UTC |
| a3ce4e6 | Greg Von Kuster | 19 July 2013, 18:14:59 UTC | More fixes for managing tool dependencies for installed tool shed repositories. | 19 July 2013, 18:14:59 UTC |
| ed12a58 | Greg Von Kuster | 19 July 2013, 17:57:31 UTC | Fixes for managing the tool dependencies of an installed tool shed repository. | 19 July 2013, 17:57:31 UTC |
| 18a5d59 | Daniel Blankenberg | 19 July 2013, 17:40:39 UTC | Fix server error when an invalid locale is provided by a clients browser. Better handling of locales provided with surrounding whitespace. | 19 July 2013, 17:40:39 UTC |
| a34b360 | Daniel Blankenberg | 19 July 2013, 17:40:39 UTC | Fix server error when an invalid locale is provided by a clients browser. Better handling of locales provided with surrounding whitespace. | 19 July 2013, 17:40:39 UTC |
| 1673e06 | Greg Von Kuster | 19 July 2013, 13:47:41 UTC | Filter out repository dependencies that have been deleted from the repository grids in the tool shed. | 19 July 2013, 13:47:41 UTC |
| 6ad1eb0 | Carl Eberhard | 18 July 2013, 20:27:38 UTC | Visualizations registry: turned off by default in main .ini | 18 July 2013, 20:27:38 UTC |
| 3766616 | Carl Eberhard | 18 July 2013, 20:24:18 UTC | Visualizations registry: move built-in vis config files to sample, copying them over on registry start; add vis xml files to .hgignore; fix test data in scatterplot.xml | 18 July 2013, 20:24:18 UTC |
| e98313a | Carl Eberhard | 18 July 2013, 19:52:38 UTC | Visualizations registry: break visualizations_conf.xml into one xml file per visualization and place in config/visualizations | 18 July 2013, 19:52:38 UTC |
| a114d1c | Carl Eberhard | 18 July 2013, 16:46:21 UTC | Dataproviders: change 'map' providers to 'dict' for better consistency w/ python | 18 July 2013, 16:46:21 UTC |
| 337be8e | Greg Von Kuster | 18 July 2013, 14:57:29 UTC | Fix for discovering types to which a repository can be set. | 18 July 2013, 14:57:29 UTC |
| e35c46f | Greg Von Kuster | 18 July 2013, 14:51:23 UTC | Enhance messaging in the tool shed as a result of the introduction of support for repository types. | 18 July 2013, 14:51:23 UTC |
| 292b568 | Carl Eberhard | 17 July 2013, 22:46:42 UTC | Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True | 17 July 2013, 22:46:42 UTC |
| 4de7530 | Carl Eberhard | 17 July 2013, 22:42:46 UTC | Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True | 17 July 2013, 22:42:46 UTC |
| b14d7e1 | Aysam Guerler | 17 July 2013, 20:58:56 UTC | Dataset display eye-icon, fix context menu | 17 July 2013, 20:58:56 UTC |
| cfcf08b | Greg Von Kuster | 17 July 2013, 19:34:54 UTC | Fixes when pushing changes to a repository in the tool shed from the command line: (a) only allow changes to a single file named tool_dependencies.xml to be pushed to a repository whose type is "Tool dependency definition" and (b) for any changes that are made to dependency definition files, validate the attributes of any <repository> tags, making sure that all required attributes (toolshed, name, owner, changeset_revision) are defined since automatically populating these attributes is supported only when using the tool shed's upload utility. | 17 July 2013, 19:34:54 UTC |
| e3dd18f | Carl Eberhard | 17 July 2013, 15:42:14 UTC | api/histories.delete: wrap purge in try/catch, raise HTTPForbidden if config.allow_user_dataset_purge == False and purge == True | 17 July 2013, 15:42:14 UTC |
| cbc0a13 | Greg Von Kuster | 15 July 2013, 15:28:41 UTC | Only allow a single file named tool_dependencies.xml to be committed to a repository in the tool shed whose type is tool_dependency_definition. | 15 July 2013, 15:28:41 UTC |
| 927164b | Greg Von Kuster | 15 July 2013, 14:10:12 UTC | Display the new request type in appropriate tool shed girds. | 15 July 2013, 14:10:12 UTC |
