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Author SHA1 Message Date
guerler 0a506dc561 Workflow editor adjustments 2015-05-02 16:00:38 -04:00
Nate Coraor eba280515a Merge branch 'release_15.05' into dev 2015-05-01 12:12:39 -04:00
Nate Coraor 16d1d32d54 Merge branch 'release_15.03' into release_15.05 2015-05-01 12:12:26 -04:00
Nate Coraor 4c7c2955cb Merge pull request #195 from natefoo/fix_galaxy_lib_dir 
[STABLE] Ensure JobWrapper.galaxy_lib_dir is set
 2015-05-01 12:11:19 -04:00
Nate Coraor f7e43384a2 Ensure JobWrapper.galaxy_lib_dir is set, necessary for locally setting 
metadata externally with Pulsar, which (sometimes?) does not call the
wrapper's prepare() method.
 2015-05-01 11:48:04 -04:00
Dannon Baker 17dba34f93 Merge pull request #194 from dannon/release_15.05 
Sanity check PR for manual merge (due to conflicts) of #188
 2015-04-30 16:00:43 -04:00
Dannon Baker e9becad552 Merge branch 'guerler-expand_optionals' into release_15.05 2015-04-30 15:55:13 -04:00
Dannon Baker c87c2a90a4 Merge branch 'expand_optionals' of https://github.com/guerler/galaxy into guerler-expand_optionals 
Conflicts:
	static/maps/mvc/form/form-section.js.map
	static/scripts/mvc/form/form-section.js
 2015-04-30 15:52:35 -04:00
Dannon Baker 535302b2d9 Merge pull request #190 from martenson/more-welcoming 
include more information in default welcome.html
 2015-04-30 14:07:27 -04:00
Martin Cech be4f3a40c6 nicer wording 2015-04-30 14:02:33 -04:00
Martin Cech 4386ffdf30 abandon our old CS habits 2015-04-30 13:23:29 -04:00
Dannon Baker fa3842ad3d Merge pull request #186 from carlfeberhard/vis.registry 
Promote visualization plugins to a class
 2015-04-30 13:15:03 -04:00
Martin Cech 2d97aa2938 Merge pull request #189 from guerler/label_fallback 
[15.05] Allow fallback to name for missing tool parameter labels
 2015-04-30 11:48:03 -04:00
Martin Cech 6b796503fd include more information in default welcome.html 2015-04-30 11:30:27 -04:00
guerler d9b857ee13 Fix typo 2015-04-29 21:25:05 -04:00
guerler 83750b418b Allow fallback to name for missing tool parameter labels 2015-04-29 21:09:48 -04:00
guerler 2f714044c9 Expand optional parameters, disable collapsing 2015-04-29 20:55:23 -04:00
Carl Eberhard d848ff861c Visualizations registry: remove class level debugging switch for config parser 2015-04-29 15:03:26 -04:00
Carl Eberhard c15573bfee Visualizations registry: remove 'show_deprecations until we get a better way to configure that, remove lambdas where builtins are available 2015-04-29 14:59:42 -04:00
Carl Eberhard 43a6c0ba21 Visualizations registry: correctly use config (and not kwargs) to build plugin rendering resources 2015-04-29 14:16:44 -04:00
Carl Eberhard 7fd6cc3704 Visualization registry: move tests into directory matching lib/galaxy/visualization/plugins 2015-04-29 13:46:51 -04:00
Carl Eberhard 41abb7d000 Visualization registry: expand plugin testing 2015-04-29 13:40:57 -04:00
Carl Eberhard af1f9db527 Visualizations registry: a bit more shuffling between methods and between plugins and the visualization controller 2015-04-29 11:53:05 -04:00
Dannon Baker b3596d5b17 Merge pull request #172 from dannon/testing_updates 
[WIP] Nose update with --debug option added to run_tests
 2015-04-29 09:30:19 -04:00
Daniel Blankenberg 91feaacbf4 Merge pull request #163 from nekrut/bcf_metadata 
[WIP] Added default indexing for bcf files
 2015-04-28 16:43:25 -04:00
Dannon Baker 11fe79fbc4 Merge pull request #181 from kellrott/workflow-instance-data 
Re-issue of PR #176 now targeting dev, without additional commits
 2015-04-28 16:17:38 -04:00
Nate Coraor 1b2cabc4b0 Merge branch 'release_15.05' into dev 2015-04-28 16:13:43 -04:00
Carl Eberhard dab23a747c Visualizations Registry: fix broken test that was sending mock template py files to the actual template cache dir 2015-04-28 16:05:25 -04:00
Kyle Ellrott 21a4927d4b Making changes based on PR comments 2015-04-28 13:03:03 -07:00
Kyle Ellrott d1b939136b Adding dataset uuid information to job and workflow invocation calls. Adding output mapping data to workflow invocation steps. 2015-04-28 13:02:38 -07:00
John Chilton 485bdafa35 Merge pull request #159 from abretaud/dev 
Significant speedup of tool panel/homepage loading
 2015-04-28 14:55:51 -05:00
Dannon Baker 494f5dc643 Merge branch 'release_15.03' into release_15.05 2015-04-28 15:48:08 -04:00
Dannon Baker f472d9b3c1 Merge pull request #178 from natefoo/release_15.03 
[STABLE] Fix job stopping under some conditions
 2015-04-28 15:47:17 -04:00
Carl Eberhard ed36e625bb Visualizations registry: refactor the relationship between plugins, the visualization controller, rendering, and rendering saved visualizations, minor fixes; Extend testing; Scatterplot: fix baseUrl resolution when used in own window 2015-04-28 15:41:01 -04:00
Nate Coraor 3211466d68 Don't use a bare except 2015-04-28 15:26:29 -04:00
Dannon Baker b65921645c Merge pull request #179 from martenson/fix-library-duplication 
[15.05] fix for UI duplication bug reported by Bjorn
 2015-04-28 14:56:55 -04:00
John Chilton 6e71a90cdd Merge pull request #151 from natefoo/runtime_stats 
A command line script for collecting stats on job runtimes
 2015-04-28 13:11:33 -05:00
anton 41343e4b41 Added test for bcf index creation. 2015-04-28 13:45:33 -04:00
Martin Cech 357d5f2e44 fix for UI duplication bug reported bo Bjorn 
occured when folder contents were re-sorted
 2015-04-28 12:37:23 -04:00
Nate Coraor f0fc892089 Fix job stopping under some conditions: 
1. track_jobs_in_database is False
2. Jobs being stopped were in the local runner
3. Jobs were deleted with the deleted state and not deleted_new
 2015-04-28 11:49:18 -04:00
Dannon Baker 374a1826f6 Merge pull request #160 from vavrusa/drmaa-external-jobs 
Fixes for DRMAA when Galaxy instance isn't on a shared volume with compute nodes
 2015-04-27 17:57:28 -04:00
John Chilton 72fe730d6c Merge pull request #168 from galaxyproject/fix_numeric_parameters_1 
[STABLE] Fix empty default values for numeric parameters with min/max
 2015-04-27 14:45:01 -05:00
Nate Coraor 32775e9692 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 2015-04-27 15:22:47 -04:00
Nate Coraor 7861ef5f8c Merge branch 'release_15.05' into dev 2015-04-27 15:20:42 -04:00
Martin Cech 8065fb8c25 Merge pull request #171 from dannon/release_15.05 
Merging several #stable changes forward to 15.05
 2015-04-27 15:17:08 -04:00
Dannon Baker cda6af165a Merge branch 'release_15.03' into release_15.05 2015-04-27 15:10:41 -04:00
Dannon Baker 78aa8e017d Merge pull request #174 from natefoo/fix_shed_check 
[STABLE] Make the `enable_tool_shed_check` option perform as advertised in the sample config file, disable checks at startup.
 2015-04-27 15:07:25 -04:00
Nate Coraor ffbfcc68a4 Make the enable_tool_shed_check option perform as advertised in the 
sample config file. Also disables checks at startup.
 2015-04-27 14:56:30 -04:00
Carl Eberhard 1cf6e64abf Visualization registry: update test so that mako caching occurs in the proper place 2015-04-27 10:57:42 -04:00
Dannon Baker 4693a948e1 Merge pull request #173 from carlfeberhard/grunt.decompress 
Client build: add grunt command 'grunt decompress' to copy decompressed ...
 2015-04-27 10:48:19 -04:00