| 0637e0a | Dannon Baker | 12 February 2015, 13:28:37 UTC | Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers. | 05 March 2015, 14:58:28 UTC |
| ff7b3eb | Dannon Baker | 23 February 2015, 16:26:12 UTC | Clone .gitignore | 23 February 2015, 16:26:12 UTC |
| ca34200 | John Chilton | 15 January 2015, 21:01:27 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:27 UTC |
| 4ab1216 | Daniel Blankenberg | 13 January 2015, 15:27:27 UTC | Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. | 13 January 2015, 15:27:27 UTC |
| 5ae1915 | Nate Coraor | 30 July 2014, 15:07:29 UTC | Apply 2014.07.30 security fix to release_2014.04.14 | 30 July 2014, 15:07:29 UTC |
| 08279ce | Nate Coraor | 30 July 2014, 15:04:48 UTC | Added tag latest_2014.02.10 for changeset 2a756ca2cb18 | 30 July 2014, 15:04:48 UTC |
| 93173c3 | Nate Coraor | 30 July 2014, 15:04:40 UTC | Apply 2014.07.30 security fix to release_2014.02.10 | 30 July 2014, 15:04:40 UTC |
| db6c0f0 | Nate Coraor | 30 July 2014, 15:02:24 UTC | Added tag latest_2013.11.04 for changeset 81fbe25bd02e | 30 July 2014, 15:02:24 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 |
| adcacf6 | Nate Coraor | 02 June 2014, 20:24:53 UTC | Added tag latest_2014.04.14 for changeset 68a8b0397947 | 02 June 2014, 20:24:53 UTC |
| b04eb27 | Nicola Soranzo | 19 May 2014, 16:03:21 UTC | Fix for "'HistoryTagsController' object has no attribute 'security_check'". Trying to access /api/histories/$history_id/tags gives this error: Execption in get_object check for History 1723db999e478a37: 'HistoryTagsController' object has no attribute 'security_check' Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 233, in get_object check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 131, in get_object self.security_check( trans, item, check_ownership, check_accessible ) AttributeError: 'HistoryTagsController' object has no attribute 'security_check' The same happens for workflow tags. | 19 May 2014, 16:03:21 UTC |
| 55a2098 | John Chilton | 12 May 2014, 18:32:34 UTC | Fixes for DRMAA submission failures. Mark job as failed once Galaxy is done attempting to submit the job, catch and retry drmaa.DeniedByDrmException like drmaa.InternalException. | 12 May 2014, 18:32:34 UTC |
| 2432115 | Dannon Baker | 07 May 2014, 13:45:53 UTC | Force an absolute path for the temp directory in the local runner | 07 May 2014, 13:45:53 UTC |
| 53cc897 | Dave Bouvier | 23 April 2014, 20:24:11 UTC | Fix server error when attempting to update a repository that defines set_environment tool dependency types. | 23 April 2014, 20:24:11 UTC |
| 70ecfdf | Dannon Baker | 23 April 2014, 13:44:28 UTC | Merged in jmchilton/galaxy-central-fork-1/stable (pull request #373) [stable] Bugfix for multiple input data parameters. | 23 April 2014, 13:44:28 UTC |
| 2a1ff52 | Martin Cech | 22 April 2014, 14:53:35 UTC | rename biostar menu link | 22 April 2014, 14:53:35 UTC |
| 8c5f1d1 | Dannon Baker | 22 April 2014, 14:01:58 UTC | Merged in dan/galaxy-central-stable-prs/stable (pull request #374) Prevent redirect misuse on user log in. | 22 April 2014, 14:01:58 UTC |
| 5ae1c9b | Daniel Blankenberg | 21 April 2014, 16:12:03 UTC | Fix for masthead link for biostar mainpage. | 21 April 2014, 16:12:03 UTC |
| bebfa2b | Daniel Blankenberg | 21 April 2014, 16:12:03 UTC | Fix for masthead link for biostar mainpage. | 21 April 2014, 16:12:03 UTC |
| 9db12a5 | Daniel Blankenberg | 21 April 2014, 16:11:49 UTC | Prevent redirect misuse on user log in. | 21 April 2014, 16:11:49 UTC |
| 84fcb55 | John Chilton | 19 April 2014, 19:37:02 UTC | Bugfix for multiple input data parameters. Workflow editor would drop all but one multiple input data connections if and when the parameter itself was nested in repeats/conds. | 19 April 2014, 19:37:02 UTC |
| 0c1c0ad | Dave Bouvier | 18 April 2014, 17:58:51 UTC | If a tool shed repository was updated after a tool migration without a new installable changeset revision being generated, for example by adding or removing a readme file, the migration install framework would be unable to find repository dependencies. This changeset resolves that. | 18 April 2014, 17:58:51 UTC |
| 960cf07 | John Chilton | 17 April 2014, 20:02:44 UTC | Merged in dan/galaxy-central-stable-prs/stable (pull request #369) BioStar fixes | 17 April 2014, 20:02:44 UTC |
| 9aa9f7d | Daniel Blankenberg | 17 April 2014, 19:38:42 UTC | Add an option to biostar integration to never authenticate. | 17 April 2014, 19:38:42 UTC |
| 53a154d | John Chilton | 17 April 2014, 18:46:57 UTC | Fix library permissions API controller. | 17 April 2014, 18:46:57 UTC |
| 69924df | Daniel Blankenberg | 17 April 2014, 17:03:02 UTC | Remove 'galaxy' tag as default now that we are using a custom biostar site. | 17 April 2014, 17:03:02 UTC |
| 322a9b9 | Daniel Blankenberg | 17 April 2014, 16:34:33 UTC | Allow disabling biostar bug reports through config settings. | 17 April 2014, 16:34:33 UTC |
| 343c174 | Daniel Blankenberg | 16 April 2014, 17:28:22 UTC | Fix for bug reporting in Chrome (webkit), due to it not properly handling forms with disabled submit buttons. | 16 April 2014, 17:28:22 UTC |
| f15d461 | Daniel Blankenberg | 16 April 2014, 14:50:23 UTC | Manually graft IGB updates to stable, since the old display applications now no longer work properly. | 16 April 2014, 14:50:23 UTC |
| 86d7cf5 | Nate Coraor | 14 April 2014, 23:28:10 UTC | Added tag release_2014.04.14 for changeset 9e53251b0b7e | 14 April 2014, 23:28:10 UTC |
| 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 |
