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Revision Author Date Message Commit Date
c139790 Nate Coraor 15 December 2016, 19:09:48 UTC Update version to 16.10 15 December 2016, 19:09:48 UTC
5c01c01 Nate Coraor 15 December 2016, 19:07:00 UTC Add security disclosure to release notes 15 December 2016, 19:07:00 UTC
42cda96 Nate Coraor 15 December 2016, 18:07:39 UTC Merge branch 'release_16.07' into release_16.10 15 December 2016, 18:07:39 UTC
22fda44 Nate Coraor 15 December 2016, 18:05:22 UTC Merge branch 'release_16.04' into release_16.07 15 December 2016, 18:05:22 UTC
4cf70ae Nate Coraor 15 December 2016, 18:04:29 UTC Merge branch 'release_16.01' into release_16.04 15 December 2016, 18:04:29 UTC
4c07734 Nate Coraor 15 December 2016, 17:55:39 UTC Merge branch 'release_15.10' into release_16.01 15 December 2016, 17:55:39 UTC
95daf69 Nate Coraor 15 December 2016, 17:49:39 UTC Merge branch 'release_15.07' into release_15.10 15 December 2016, 17:49:39 UTC
790e60a Nate Coraor 15 December 2016, 17:46:17 UTC Merge branch 'release_15.05' into release_15.07 15 December 2016, 17:46:17 UTC
7c443ed Nate Coraor 15 December 2016, 17:38:28 UTC Merge branch 'release_15.03' into release_15.05 15 December 2016, 17:38:28 UTC
da7afb4 Nate Coraor 15 December 2016, 17:37:10 UTC Merge branch 'release_15.01' into release_15.03 15 December 2016, 17:37:10 UTC
9ee3d01 Nate Coraor 15 December 2016, 17:36:21 UTC Merge branch 'release_14.10' into release_15.01 15 December 2016, 17:36:21 UTC
c1e3087 Nate Coraor 15 December 2016, 17:34:18 UTC Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. 15 December 2016, 17:34:18 UTC
d2ab7e7 Bjoern Gruening 14 December 2016, 21:46:36 UTC build the client 14 December 2016, 21:46:36 UTC
3ab4e1d Dannon Baker 14 December 2016, 20:59:18 UTC The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming / 14 December 2016, 20:59:18 UTC
329108f Nate Coraor 14 December 2016, 18:44:44 UTC Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. 14 December 2016, 18:44:44 UTC
bb8a5a2 John Chilton 13 December 2016, 18:36:24 UTC [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. 13 December 2016, 18:36:53 UTC
2c83349 John Chilton 12 December 2016, 03:48:29 UTC Merge pull request #3287 from guerler/fix_chart_datatypes [16.10] Rely on tabular subclass matching through vizframework layer 12 December 2016, 03:48:29 UTC
22c7fcf John Chilton 12 December 2016, 03:40:00 UTC Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes [16.10] Tool install fixes 12 December 2016, 03:40:00 UTC
9dda310 John Chilton 12 December 2016, 03:39:21 UTC Merge pull request #3296 from dannon/workflow_editor_toolsearch_messagebox_fix [16.10] Workflow editor 'messagebox' fix. 12 December 2016, 03:39:21 UTC
5a7f9e8 Nicola Soranzo 09 December 2016, 12:38:35 UTC Correctly update TS repo status Execute build_dependency_cache() only if using a cached dependency manager. Set tool versions only if the TS repo contains tools. Raise exception if fetch_tool_versions() fails, previously the error message never reached the UI. 11 December 2016, 20:31:38 UTC
d6d2a12 Nicola Soranzo 09 December 2016, 17:09:28 UTC Merge branch 'release_16.07' into release_16.10 Conflicts: client/galaxy/scripts/mvc/upload/composite/composite-row.js client/galaxy/scripts/mvc/upload/default/default-row.js static/maps/mvc/upload/composite/composite-row.js.map static/maps/mvc/upload/default/default-row.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/scripts/mvc/upload/composite/composite-row.js static/scripts/mvc/upload/default/default-row.js 09 December 2016, 17:09:28 UTC
602f2f2 Nate Coraor 09 December 2016, 16:53:23 UTC Merge pull request #3292 from dannon/backport_upload_fn_escape [16.07] Upload file escaping backport. 09 December 2016, 16:53:23 UTC
7c9d9d2 Dannon Baker 09 December 2016, 14:56:29 UTC Apply a fix similar to 36134bca694c9dc6b2584fb661dfbce4ddb793e6 for the workflow editor. Not ideal, but this is old code we're replacing as the editor is overhauled. 09 December 2016, 14:56:29 UTC
879e3d6 Nicola Soranzo 07 December 2016, 21:50:53 UTC Skip building cache if force_rebuild is False Also: - re-raise exception if rmtree() fails - change hash(ed)_requirements to hash(ed)_dependencies 09 December 2016, 11:45:14 UTC
2268741 Nicola Soranzo 07 December 2016, 20:48:10 UTC Ensure Conda prefix and cached environment are absolute paths Otherwise when Conda commands are executed from the job working directory, they will break. 09 December 2016, 11:45:14 UTC
ca99753 Martin Cech 08 December 2016, 22:17:09 UTC Merge pull request #3281 from nsoranzo/release_16.10_fix_doc_Makefile [16.10] Use OSX-compatible sed syntax 08 December 2016, 22:17:09 UTC
13ae374 Nicola Soranzo 08 December 2016, 20:45:43 UTC Move sed commands to a script to resolve interferences with Make which happen only under OSX 08 December 2016, 20:46:06 UTC
c315f1d Dannon Baker 08 December 2016, 20:31:59 UTC Upload file escaping backport. 08 December 2016, 20:31:59 UTC
4431d73 guerler 08 December 2016, 16:22:13 UTC Extend list of tabular datatypes for bar diagrams 08 December 2016, 17:08:58 UTC
2cbf9a9 John Chilton 08 December 2016, 16:00:12 UTC Merge pull request #3284 from martenson/notes-tinies [16.10] add small touches to release notes 08 December 2016, 16:00:12 UTC
c01e25d Martin Cech 08 December 2016, 15:41:26 UTC missing articles 08 December 2016, 15:41:26 UTC
e3fbbc5 Martin Cech 08 December 2016, 15:37:44 UTC add small touches to release notes 08 December 2016, 15:37:44 UTC
9c43568 Dannon Baker 07 December 2016, 21:31:02 UTC Don't rely on complex, absolute selector, use local element.find() 07 December 2016, 21:31:02 UTC
83de83e John Chilton 07 December 2016, 21:27:11 UTC Merge pull request #3282 from martenson/release_16.10 [16.10] work on release notes 16.10 07 December 2016, 21:27:11 UTC
5784a83 Martin Cech 07 December 2016, 20:41:37 UTC fix bad merge 07 December 2016, 20:41:37 UTC
739fb59 Martin Cech 07 December 2016, 20:39:20 UTC fix the fix 07 December 2016, 20:39:20 UTC
3e0e966 Martin Cech 07 December 2016, 20:23:53 UTC add work on release notes 16.10, improve docs for webhooks Conflicts: doc/source/releases/16.10.rst doc/source/releases/16.10_announce.rst 07 December 2016, 20:37:44 UTC
d0f39ce Martin Cech 07 December 2016, 20:29:56 UTC Merge pull request #3270 from jmchilton/16.10_release_notes_0 [16.10] Add 16.10 release notes. 07 December 2016, 20:29:56 UTC
128a317 Nicola Soranzo 07 December 2016, 19:59:14 UTC Use OSX-compatible sed syntax 07 December 2016, 20:24:34 UTC
70fc43b Martin Cech 07 December 2016, 19:44:14 UTC Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink [16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink. 07 December 2016, 19:44:14 UTC
f6b94dc Daniel Blankenberg 07 December 2016, 18:30:21 UTC Fix for ToolShed install when copied sample data target exists, but is broken symlink. 07 December 2016, 18:30:21 UTC
75d327f Aysam Guerler 07 December 2016, 18:00:14 UTC Merge pull request #3278 from dannon/upload_escape_filename [16.10] Escape filename in upload dialog, default and composite. 07 December 2016, 18:00:14 UTC
13ab070 Dannon Baker 07 December 2016, 12:53:34 UTC Use consistent spacing. 07 December 2016, 12:53:34 UTC
8766e12 Dannon Baker 07 December 2016, 12:48:34 UTC Escape filename in upload dialog, default and composite. Pointed out by David Wyde. 07 December 2016, 12:48:34 UTC
8a5ff5d Martin Cech 07 December 2016, 01:27:47 UTC Merge pull request #3277 from dannon/fix_tour_welcome_1610 [16.10] port Fix tour URLs in welcome 07 December 2016, 01:27:47 UTC
a1e3965 Dannon Baker 06 December 2016, 15:07:32 UTC Fix tour URLs in welcome 07 December 2016, 00:18:05 UTC
d0ad2ae Björn Grüning 06 December 2016, 12:01:51 UTC Merge pull request #3272 from mvdbeek/fix_superfluous_brackets [16.10] Simplify dependency list for cached environemnts (many thanks @nsoranzo) 06 December 2016, 12:01:51 UTC
7fa10aa mvdbeek 06 December 2016, 11:07:48 UTC Simplify dependency list for cached environemnts (many thanks @nsoranzo) 06 December 2016, 11:07:48 UTC
a84601b John Chilton 05 December 2016, 21:26:12 UTC Add 16.10 release notes. 06 December 2016, 00:38:19 UTC
622f299 Martin Cech 05 December 2016, 18:02:57 UTC Merge pull request #3262 from mvdbeek/conda_only_improvements [16.10] Display tool requirements for conda-only tools 05 December 2016, 18:02:57 UTC
f20c478 mvdbeek 03 December 2016, 18:07:49 UTC Use Tool Shed instead of toolshed 03 December 2016, 19:19:46 UTC
72f417e mvdbeek 03 December 2016, 17:14:46 UTC Display requirement status on TS install This commit displays tool requirements as defined in the tool xml during the install confirmation dialog. If a tool dependency is defined in the tool XML, but not in a tool_dependencies.xml, a warning is shown if conda is not activated. This should close #3257. 03 December 2016, 19:19:46 UTC
bab709c mvdbeek 03 December 2016, 10:56:19 UTC Request information about tool dependencies from toolshed and make available in prepare_for_install 03 December 2016, 19:19:46 UTC
888a8f9 John Chilton 30 November 2016, 12:10:04 UTC Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8 [16.10] Pin flake8 and flake8-import-order 30 November 2016, 12:10:04 UTC
a26568b Nicola Soranzo 30 November 2016, 11:04:47 UTC Pin flake8 and flake8-import-order Do not pin when forward-merging to dev branch! 30 November 2016, 11:04:47 UTC
be6a2f8 Dannon Baker 29 November 2016, 22:00:20 UTC Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history 29 November 2016, 22:00:20 UTC
d6f0e6b Martin Cech 29 November 2016, 21:21:49 UTC Merge pull request #3227 from mvdbeek/cached_deps_16.10 [16.10] Backport #3106 and #3222: Cached conda environments and API to manage them 29 November 2016, 21:21:49 UTC
e3f8b72 John Chilton 29 November 2016, 18:41:52 UTC Merge pull request #3226 from martenson/16-10-install-ux [16.10] admin installation ux 29 November 2016, 18:41:52 UTC
2a4ccac mvdbeek 27 November 2016, 23:07:40 UTC Connect `clean` endpoint properly and add `-y` to exec_clean 29 November 2016, 16:42:09 UTC
1efd4d4 Bjoern Gruening 16 September 2016, 16:46:37 UTC add a conda clean function to remove downloaded tarballs after installation 29 November 2016, 16:42:09 UTC
16b49d9 mvdbeek 27 November 2016, 22:16:56 UTC Add dependency_resolvers/clean endpoint 29 November 2016, 16:42:09 UTC
045a2f0 mvdbeek 27 November 2016, 17:39:13 UTC Add `force_rebuild` param to build_dependency_cache This will remove a pre-existing cached dependency directory. 29 November 2016, 16:42:09 UTC
f10fd79 mvdbeek 27 November 2016, 17:15:22 UTC Install the correct converter dependency 29 November 2016, 16:42:09 UTC
cc7cd47 mvdbeek 27 November 2016, 16:49:59 UTC Add integration test-case for install tool dependency API endpoint 29 November 2016, 16:42:09 UTC
cf769dd mvdbeek 27 November 2016, 15:38:34 UTC Add API to install resolver tool dependencies and to build a tool dependency cache (if activated in galaxy.ini). An example to install dependencies for the twobit converter: ``` import bioblend.galaxy url = 'http://localhost:8080/' api_key = 'admin_api_key' tool_id = 'CONVERTER_fasta_to_2bit' endpoint = "api/tools/%s/install_dependencies" % tool_id gi = bioblend.galaxy.GalaxyInstance(url, api_key) gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` If `use_cached_dependency_manager` is activated in the galaxy.ini, a cached environment can be built like this: ``` endpoint = "api/tools/%s/build_dependency_cache" % tool_id gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` 29 November 2016, 16:42:08 UTC
64bc924 mvdbeek 23 November 2016, 10:03:14 UTC Fix NameError 29 November 2016, 16:41:06 UTC
82f30e7 mvdbeek 04 November 2016, 14:21:45 UTC Only attempt to build cache once per install and override __eq__ for ToolRequirement, to simplify checking if ToolRequirements are already installed/cached. 29 November 2016, 16:41:06 UTC
f919a98 mvdbeek 02 November 2016, 10:59:10 UTC Build dependency cache at install time and only activate cached environments if they exist. 29 November 2016, 16:41:06 UTC
2b17657 mvdbeek 28 October 2016, 16:30:47 UTC Rework cached dependencies to be more robust to updates or changes in depedencies, folder structure and resolver configuration. Instead of hashing name, type and version of a dependency, hash the json representation of the dependencies returned by the dependency resolver, which include the path to the environment and the depedency type. This is only applied to resolvers whose cacheable attribute is set to True (conda-only, currently). 29 November 2016, 16:41:06 UTC
0a9b6d8 mvdbeek 28 October 2016, 16:22:36 UTC Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) 29 November 2016, 16:41:06 UTC
94edc94 mvdbeek 28 October 2016, 09:48:17 UTC Add cached dependency manager Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement a mechanism that allows tool dependencies to be cached. If the `use_cached_dependency_manager` option is set to True in galaxy.ini, we build a hash of the combination of a tools' requirements, and store the resulting environment in a directory specified by the `tool_dependency_cache_dir` option in galaxy.ini. 29 November 2016, 16:41:06 UTC
83e1392 Dannon Baker 29 November 2016, 15:02:27 UTC Standard styles inclusion in .less, more styling to match rounded edges and spacing. 29 November 2016, 15:02:27 UTC
4b79472 Martin Cech 28 November 2016, 21:42:10 UTC fix a bug that renders conda dependency selection everytime 28 November 2016, 21:42:10 UTC
73d010e Martin Cech 28 November 2016, 20:54:39 UTC fix another test 28 November 2016, 20:54:39 UTC
706bc3f Martin Cech 28 November 2016, 20:20:48 UTC fix test and hide shed_conf select udner details 28 November 2016, 20:20:48 UTC
29cf718 Dannon Baker 28 November 2016, 19:59:41 UTC Minor styling tweaks -- todo: swap from inline to class-based. 28 November 2016, 19:59:41 UTC
068ee6b Martin Cech 28 November 2016, 19:41:28 UTC fix install repo test 28 November 2016, 19:41:28 UTC
9a2bae7 Martin Cech 28 November 2016, 19:19:29 UTC simplify the UI of deps installation by hiding the details under toggle button 28 November 2016, 19:19:29 UTC
ce320b6 Dannon Baker 28 November 2016, 18:32:00 UTC A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes. 28 November 2016, 18:32:00 UTC
0b2d0c1 John Chilton 22 November 2016, 20:17:55 UTC Merge pull request #3210 from guerler/fix_output_label_handler [16.10] Preserve custom event handler for form inputs 22 November 2016, 20:17:55 UTC
a9dab63 guerler 22 November 2016, 19:24:54 UTC Preserve custom event handler for form inputs 22 November 2016, 19:24:54 UTC
ec08ec6 Martin Cech 21 November 2016, 22:18:31 UTC Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. 21 November 2016, 22:18:31 UTC
74d8faa Daniel Blankenberg 21 November 2016, 19:37:54 UTC Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. 21 November 2016, 19:37:54 UTC
aadc14d Martin Cech 21 November 2016, 19:09:01 UTC Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories 21 November 2016, 19:09:01 UTC
5ba8201 Daniel Blankenberg 21 November 2016, 16:02:20 UTC Pack scripts 21 November 2016, 16:02:20 UTC
548d3e6 Daniel Blankenberg 21 November 2016, 15:53:37 UTC Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d 21 November 2016, 15:53:37 UTC
3f27777 Dannon Baker 18 November 2016, 16:19:33 UTC Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override 18 November 2016, 16:19:33 UTC
5c4ac18 Martin Cech 18 November 2016, 16:05:28 UTC remove unused override this caused Help/Search to point at /root/tool_search 18 November 2016, 16:05:28 UTC
6fd58af Dannon Baker 17 November 2016, 11:10:18 UTC Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 17 November 2016, 11:10:18 UTC
9d45f1e Dannon Baker 17 November 2016, 11:03:36 UTC Update version to 16.10.rc1 17 November 2016, 11:03:36 UTC
d8c75e2 Dannon Baker 17 November 2016, 10:51:11 UTC Merge pull request #3187 from mvdbeek/samtools_1_3_fix Make sam to bam converter tool compatible with samtools >= 1.3 17 November 2016, 10:51:11 UTC
8ace021 mvdbeek 17 November 2016, 09:06:07 UTC Single quote variables in sam-to-bam conversion 17 November 2016, 09:06:07 UTC
164a0ad Martin Cech 16 November 2016, 21:19:35 UTC Merge pull request #3188 from dannon/startup_output_tweaks Slight clarification of run.sh messaging when using conda. 16 November 2016, 21:19:35 UTC
0b395a7 Dannon Baker 16 November 2016, 21:16:33 UTC Slight clarification of run.sh messaging when using conda. 16 November 2016, 21:16:33 UTC
592f15c mvdbeek 16 November 2016, 21:01:47 UTC Add sam-to-bam conversion test tool 16 November 2016, 21:01:47 UTC
92105d9 Martin Cech 16 November 2016, 21:01:12 UTC Merge pull request #2818 from erasche/rstudio-1610 Return of RStudio 16 November 2016, 21:01:12 UTC
31b73fd Nicola Soranzo 16 November 2016, 20:53:49 UTC Merge pull request #3180 from dannon/venv_over_conda Prefer existing .venv over conda, when both are available. 16 November 2016, 20:53:49 UTC
0b8fc7c Dannon Baker 16 November 2016, 20:43:32 UTC Merge remote-tracking branch 'guerler/validate_workflow' into dev 16 November 2016, 20:43:32 UTC
efde00d mvdbeek 16 November 2016, 20:10:17 UTC Handle samtools 0.x 16 November 2016, 20:37:43 UTC
e5b69a7 John Chilton 16 November 2016, 20:20:41 UTC Merge pull request #2966 from dannon/workflow_intermediates_ux Change wording to be more clear about how workflow output cleanup wor… 16 November 2016, 20:20:41 UTC
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