| a8abf0e | Dannon Baker | 23 February 2015, 16:25:45 UTC | Clone .gitignore | 23 February 2015, 16:25:45 UTC |
| 71ebf96 | John Chilton | 15 January 2015, 21:01:18 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:18 UTC |
| 48d9a82 | Daniel Blankenberg | 13 January 2015, 15:27:09 UTC | Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. | 13 January 2015, 15:27:09 UTC |
| 4589d46 | Nate Coraor | 30 July 2014, 15:02:23 UTC | Apply 2014.07.30 security fix to release_2013.11.04 | 30 July 2014, 15:02:23 UTC |
| 11853f8 | Nate Coraor | 30 July 2014, 14:57:58 UTC | Added tag latest_2013.08.12 for changeset 9ed84cd208e0 | 30 July 2014, 14:57:58 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 |
| 2219230 | Daniel Blankenberg | 27 January 2014, 14:54:34 UTC | Fix for aggregate_scores_in_intervals.py broken in 95bf71620d50c6d81248eef2001a7dc156ae1088. | 27 January 2014, 14:54:34 UTC |
| 457937c | John Chilton | 27 January 2014, 02:47:59 UTC | Bugfix: Disallow shared workflows from being inappropriately deletable... ... by user workflow is shared with via workflow API. | 27 January 2014, 02:47:59 UTC |
| 09ecc02 | Nate Coraor | 21 January 2014, 17:39:35 UTC | Add missing requirement tags to converters, fixes Trello #1349. | 21 January 2014, 17:39:35 UTC |
| de2e6d3 | Daniel Blankenberg | 16 January 2014, 21:21:41 UTC | Use toolbox.get_tool instead of toolbox.tools_by_id.get in tools api show(). | 16 January 2014, 21:21:41 UTC |
| 9902b1a | John Chilton | 13 December 2013, 21:43:26 UTC | Use null object pattern to simplify logic related to no dependency manager being set. Fixes bug introduced in 4241eff related to dependency_manager being None if tool_dependency_dir is not set. | 13 December 2013, 21:43:26 UTC |
| 3bffad2 | Daniel Blankenberg | 12 December 2013, 22:09:29 UTC | When setting external metadata using _handle_metadata_externally (e.g. local and lwr runners) use the requirments of the set metadata tool to determine dependencies. Resolves issue seen with missing samtools command when samtools is not in the path, but has been installed with the dependency system. | 12 December 2013, 22:09:29 UTC |
| c1894c3 | Daniel Blankenberg | 14 January 2014, 18:39:59 UTC | Fix for history api set_as_current(). | 14 January 2014, 18:39:59 UTC |
| 25c924f | Nate Coraor | 14 January 2014, 16:31:11 UTC | Backed out changeset c40ecf876d68 | 14 January 2014, 16:31:11 UTC |
| 07961fb | Dave Bouvier | 14 January 2014, 15:29:33 UTC | Backport fix for selecting a tool panel section when installing a repository using the API. | 14 January 2014, 15:29:33 UTC |
| 1351f2a | Dave Bouvier | 08 January 2014, 17:27:14 UTC | When a push is received in the hg controller, update the repository on disk after the push is complete. | 08 January 2014, 17:27:14 UTC |
| 5a8c645 | Nate Coraor | 09 January 2014, 15:46:01 UTC | Fix username argument to PostgreSQL connection in pgcleanup.py | 09 January 2014, 15:46:01 UTC |
| d871db6 | Daniel Blankenberg | 02 December 2013, 19:48:30 UTC | Fix for missing eggs.require in lib/galaxy/exceptions/__init__.py. | 02 December 2013, 19:48:30 UTC |
| a466686 | Dannon Baker | 07 January 2014, 14:47:37 UTC | Update cloudlaunch default AMI | 07 January 2014, 14:47:37 UTC |
| 28123bd | Aysam Guerler | 03 January 2014, 04:25:22 UTC | Fix XSS issue in former grids code | 03 January 2014, 04:25:22 UTC |
| 549461d | Dannon Baker | 19 December 2013, 19:38:03 UTC | Fix workflow import url XSS. | 19 December 2013, 19:38:03 UTC |
| 0d8fa20 | Greg Von Kuster | 19 December 2013, 00:03:05 UTC | Fix for determining a guid in the install_manager. | 19 December 2013, 00:03:05 UTC |
| e7c1cad | John Chilton | 18 December 2013, 20:59:11 UTC | Use get_history() in tools API controller. | 18 December 2013, 20:59:11 UTC |
| 607d290 | Dave Bouvier | 13 December 2013, 20:49:28 UTC | Expose the show method anonymously. | 13 December 2013, 20:49:28 UTC |
| 1e2688f | Dave Bouvier | 13 December 2013, 19:45:42 UTC | Fix API visibility for the repository_revisions index. | 13 December 2013, 19:45:42 UTC |
| 65b4f4d | Dave Bouvier | 11 December 2013, 17:43:36 UTC | When creating a repository, make sure there are no repositories with the same name, deleted or active. | 11 December 2013, 17:43:36 UTC |
| 395a06a | Nate Coraor | 06 December 2013, 21:28:31 UTC | Add missing destination long arg to cli runner's Torque plugin and fix an incorrectly used PBS option in the sample job conf. | 06 December 2013, 21:28:31 UTC |
| ee39214 | Carl Eberhard | 06 December 2013, 17:20:13 UTC | Visualizations: fixes to phyloviz to allow saving and loading as a visualization | 06 December 2013, 17:20:13 UTC |
| e197bc6 | Nate Coraor | 30 November 2013, 17:46:53 UTC | Remove broken GeneTrack tools. | 30 November 2013, 17:46:53 UTC |
| 3591c00 | John Chilton | 30 November 2013, 14:28:38 UTC | Fix from Jim Johnson for optional input handling in provenance API. | 30 November 2013, 14:28:38 UTC |
| ce31bc4 | Nate Coraor | 15 November 2013, 19:18:09 UTC | Properly handle PBS' -q argument. | 15 November 2013, 19:18:09 UTC |
| 553efe9 | John Chilton | 15 November 2013, 14:20:06 UTC | Fix small typo in 9ce5afd (tool shed autoconf action). | 15 November 2013, 14:20:06 UTC |
| a0df0c2 | Dave Bouvier | 12 November 2013, 20:36:13 UTC | Fix display of status images for installed tool shed repositories when using a proxy prefix. | 12 November 2013, 20:36:13 UTC |
| b185931 | Greg Von Kuster | 14 November 2013, 20:51:24 UTC | Display an error message rather than raising an exception when handling invalid complex repository dependencies in the Tool Shed. | 14 November 2013, 20:51:24 UTC |
| dc156fc | Jeremy Goecks | 14 November 2013, 16:00:19 UTC | Trackster: only allow datasets with proper dbkey to be added to visualization. This is a regression because summary data format [bigwig] requires a proper dbkey. | 14 November 2013, 16:00:19 UTC |
| 8e9333b | Jeremy Goecks | 13 November 2013, 23:41:23 UTC | Implement a hack to avoid infinite recursion in custom builds. | 13 November 2013, 23:41:23 UTC |
| 4bb838d | Dave Bouvier | 13 November 2013, 19:16:29 UTC | Fix for downloading jar files in tool dependencies. | 13 November 2013, 19:16:29 UTC |
| 2802936 | Aysam Guerler | 12 November 2013, 17:44:04 UTC | UI: Fix load order of masthead | 12 November 2013, 17:44:04 UTC |
| 75969b2 | John Chilton | 12 November 2013, 16:51:35 UTC | "Fix" GALAXY_SLOTS for SLURM. Your results with slurm may vary and depending how you allocate things you may want to modify this statement. | 12 November 2013, 16:51:35 UTC |
| 00a45c2 | Carl Eberhard | 12 November 2013, 16:10:04 UTC | History grid: fix logic to prevent deleting/purging a shared history | 12 November 2013, 16:10:04 UTC |
| ffd28b4 | John Chilton | 11 November 2013, 20:17:25 UTC | Revert original and documented handling of condor submission parameters. I modified the behavior unknowingly in 126d5c5b9a49. I am not sure what I was thinking when I redid the runner, perhaps I had seen an open Trello card and thought this was not implemented at all. My fault, this was implemented and looks like it was working. These should now work as documented again. | 11 November 2013, 20:17:25 UTC |
| 5b0ff95 | Jeremy Goecks | 11 November 2013, 18:32:31 UTC | Trackster visual analysis: (a) fix misreference to name and (b) do not get values for complex tool parameters. Pack script. | 11 November 2013, 18:32:31 UTC |
| c1d4a49 | Jeremy Goecks | 11 November 2013, 17:18:40 UTC | Trackster: hide tool by default. Pack script. | 11 November 2013, 17:18:40 UTC |
| 7a67c26 | Nicola Soranzo | 08 November 2013, 16:46:37 UTC | Fix min/max integer param validation when either is 0. Bug introduced in commit 5b4c4cf9bc9619d51d7f2471d64896dcdd93707c . InRangeValidator would not be appended because self.min and self.max are no more strings, but integers. Reported by: Andrea Pinna <andrea.pinna@crs4.it> | 08 November 2013, 16:46:37 UTC |
| a16d94c | Jeremy Goecks | 10 November 2013, 18:07:43 UTC | Trackster: fix bug in positioning read connector. Pack scripts. | 10 November 2013, 18:07:43 UTC |
| e2684b4 | James Taylor | 09 November 2013, 22:05:34 UTC | Fix trackster dbkey selection in safari | 09 November 2013, 22:05:34 UTC |
| bf20e2d | Jeremy Goecks | 08 November 2013, 16:14:43 UTC | Trackster: only sort amongst tracks and groups, not other items. | 08 November 2013, 16:14:43 UTC |
| dac3f9a | Carl Eberhard | 08 November 2013, 15:32:36 UTC | Tools API, show: re-add html field wrapped in try/except | 08 November 2013, 15:32:36 UTC |
| 8fda012 | Carl Eberhard | 05 November 2013, 16:33:06 UTC | History panel: fix naming bug in purge async error handling | 05 November 2013, 16:33:06 UTC |
| 2d350ef | Nate Coraor | 04 November 2013, 20:04:42 UTC | Added tag release_2013.11.04 for changeset 26f58e05aa10 | 04 November 2013, 20:04:42 UTC |
| 9ee4403 | Nate Coraor | 04 November 2013, 19:58:55 UTC | Galaxy stable release for 2013.11.04. | 04 November 2013, 19:58:55 UTC |
| 426326a | Nate Coraor | 04 November 2013, 19:57:29 UTC | Close next-stable branch. | 04 November 2013, 19:57:29 UTC |
| e8d81d7 | Nate Coraor | 04 November 2013, 19:56:17 UTC | Merge security fix for filtering tools from stable. | 04 November 2013, 19:56:17 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 |
| 8013697 | Greg Von Kuster | 02 November 2013, 15:04:47 UTC | Fix for handling a repository dependency that has a tool dependency in error because it has a missing env.sh file. | 02 November 2013, 15:04:47 UTC |
| 9571aaa | Dave Bouvier | 01 November 2013, 20:08:49 UTC | Update RSS feed filters to reflect which revisions are regularly tested and relevant to display. | 01 November 2013, 20:08:49 UTC |
| acf580f | Greg Von Kuster | 01 November 2013, 15:53:44 UTC | Return an error response rather than just logging a message when uploading a directroy or a tarball that contains a tool dependency definition that is missing wither an <actions> tag set or an <actions_group> tag set. | 01 November 2013, 15:53:44 UTC |
| 4d65e8f | Greg Von Kuster | 01 November 2013, 15:38:04 UTC | Fixes for tool_dependencies.xml files whose recipe is missing either an <actions> tag set or an <actions_group> tag set. Upon upload of a single file, an appropriate error message will be displayed (currently it is logged when uploading a tarball). In either case, when the containing repository is installed, the tool dependency will be set to an error state and and the error message will be associated with the dependency record. | 01 November 2013, 15:38:04 UTC |
| 2ef084d | Greg Von Kuster | 31 October 2013, 16:00:28 UTC | Fix for repairing a repository that has no repository dependencies. | 31 October 2013, 16:00:28 UTC |
| a9b5245 | Greg Von Kuster | 31 October 2013, 14:23:46 UTC | Move pass-through params from the request to the form data when reselecting a tool panel section when reinstalling an uninstalled tool shed repository that contains tools. | 31 October 2013, 14:23:46 UTC |
| 30aa799 | Greg Von Kuster | 31 October 2013, 02:43:02 UTC | Fix for sert_environment tag in tool dependencies definitions. | 31 October 2013, 02:43:02 UTC |
| 16a9255 | Bjoern Gruening | 23 October 2013, 12:39:49 UTC | cleanup & bugfix for R environment | 23 October 2013, 12:39:49 UTC |
| 9f5dd6b | John Chilton | 26 October 2013, 19:12:41 UTC | Fix tool shed e-mail functionality broken with 0d46133c90452dc8815de7057b13548f06beb7bb. | 26 October 2013, 19:12:41 UTC |
| 528138f | Greg Von Kuster | 25 October 2013, 19:57:06 UTC | Don't render the Import repository capsule link in the tool shed since it is still under development. | 25 October 2013, 19:57:06 UTC |
| 9ccaada | Dave Bouvier | 25 October 2013, 18:45:29 UTC | Correctly handle extracting a tarball that does contain all files and directories within a single directory at the root of the archive, but does not contain an entry for the directory itself. | 25 October 2013, 18:45:29 UTC |
| 131a2d6 | Dave Bouvier | 25 October 2013, 18:39:44 UTC | Check for matching in-memory sniffer before appending. Remove sniffer when deactivating or uninstalling a repository. Additional checks for keys existing before deleting them. | 25 October 2013, 18:39:44 UTC |
| 62326ba | Daniel Blankenberg | 25 October 2013, 15:51:37 UTC | Fix for Javascript requiring setting a user/public name during registration | 25 October 2013, 15:51:37 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 |
