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Author SHA1 Message Date
guerler 237ecc7789 Add form help class 2016-01-05 16:15:55 -05:00
John Chilton 0bad80ebdf Merge pull request #1182 from yhoogstrate/bam_cram_index_via_pysam 
cram datatype: crai index via pysam
 2016-01-05 15:21:06 -05:00
Nate Coraor 634a5b7fd9 Merge pull request #1413 from jmchilton/lib_0 
Copy pastescript's NiceConfigParser into galaxy.util.properties.
 2016-01-05 14:56:21 -05:00
Björn Grüning 6bd854ebe4 Merge pull request #1422 from dannon/interactive_tours 
Interactive Tours
 2016-01-05 20:21:46 +01:00
Dannon Baker a1a549ea67 Re-add identifiers to masthead, new ones for scratchbook (thanks @guerler) 2016-01-05 14:04:22 -05:00
Dannon Baker 3d1b3f9806 How'd that get there? 2016-01-05 13:23:03 -05:00
Dannon Baker 9416e6f3f7 Merge and resolve conflicts, rebuilding. 2016-01-05 13:18:46 -05:00
Dannon Baker 5924857c2c Fix pre/postclick that got broken somewhere along the way w/ patches&merges. 2016-01-05 13:08:33 -05:00
Dannon Baker 1876ea6bb2 Merge pull request #8 from jmchilton/interactive_tours 
Minor tweaks to interactive tours backend.
 2016-01-05 12:27:13 -05:00
Eric Rasche 1730c12f8d Merge pull request #1425 from guerler/fix_close_icon_000 
Change scratchbook close icon
 2016-01-05 10:50:16 -06:00
guerler 884b1d42db Change scratchbook close icon 2016-01-05 11:45:31 -05:00
Dannon Baker 1d97e4271e Merge dev to include menu/onclick fix. 2016-01-05 11:00:10 -05:00
Dannon Baker 5c765c0871 Merge branch 'dev' into interactive_tours 2016-01-05 10:51:54 -05:00
Aysam Guerler 099f1447a6 Merge pull request #1424 from dannon/fix_onclick 
Fix masthead/menu.js onclick functionality
 2016-01-05 10:51:10 -05:00
Dannon Baker 62b80dfcc5 Fix onclick broken in #1407 2016-01-05 10:04:03 -05:00
Dannon Baker 4ef3e21c95 Fix onclick handling broken w/ #1407 2016-01-05 09:44:06 -05:00
Dannon Baker c28d4d01ee Correctly specify default tour location. 2016-01-04 22:39:56 -05:00
John Chilton c97053a5e8 Merge pull request #1421 from galaxyproject/conda_install_fix 
Fix conda installation in debug mode
 2016-01-04 21:36:14 -05:00
John Chilton 7587809bb6 Improve tour directory logic. 
- Refactor plugin framework logic for finding configuration directories out into util.
 - Rework tours to use the plugin framework logic to parse configuration directories.
 - Rework tour logic to allow multiple tour configuration directories.
 - Fix up config.ini.sample comments on interactive environments and tours to reflect these changes and include more information like the viz directory does.
 2016-01-05 00:28:24 +00:00
Dannon Baker da8b943f53 Merge. 2016-01-04 19:23:06 -05:00
John Chilton b35a39bd55 Prefer self.app to trans.app. 
See comments here https://github.com/galaxyproject/galaxy/pull/1392#commitcomment-15141262 for instance for argument why this is superior.
 2016-01-05 00:18:22 +00:00
John Chilton 01fed4b6d4 Allow .yml extensions. 
Though not the "official" extension for YAML files, it is actually seen much more common in the wild.
 2016-01-05 00:18:22 +00:00
John Chilton b9faf84b24 Stub an API test for tours so I can refactor a little. 2016-01-05 00:18:22 +00:00
Björn Grüning 6cea5121b1 Fix conda installation in debug mode 2016-01-05 00:54:49 +01:00
Dannon Baker 0ef88e1e53 Add tour reloading API endpoint. 2016-01-04 17:17:10 -05:00
Dannon Baker e243fe3bc1 Slight refactoring, fix .yaml stripping bug. 2016-01-04 17:16:51 -05:00
Dannon Baker d235410920 Remove tour id from tour; unique and namespaced by filename and not a separate identifier. 2016-01-04 17:13:19 -05:00
Eric Rasche 5a441044fb Merge pull request #1308 from jmchilton/multi_collection_types 
Allow input collections to specify multiple collection types.
 2016-01-04 14:43:37 -06:00
Nate Coraor 4c0bb9902a Merge pull request #1347 from lparsons/galaxy_slots 
Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS
 2016-01-04 15:03:04 -05:00
Lance Parsons 9bbe4b869e Merge pull request #1 from natefoo/lparsons_galaxy_slots 
Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables.
 2016-01-04 13:22:50 -05:00
Nate Coraor 1c21ba8241 Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables. 2016-01-04 10:54:29 -05:00
Martin Cech 28cf2822f7 Merge pull request #1416 from jmchilton/workflow_missing_tool_import 
Fix importing pre-16.01 workflows with missing tools.
 2016-01-04 10:36:00 -05:00
Dannon Baker 603cb2f18d Add history tour from @bgruening 2016-01-04 09:52:47 -05:00
Björn Grüning 607db31b04 Merge pull request #1415 from guerler/fix_url_001 
Fix url formatting
 2016-01-04 15:44:43 +01:00
guerler c9870cb89d Fix url formatting 2016-01-04 08:34:56 -05:00
John Chilton bed79b5e6a Fix importing pre-16.01 workflows with missing tools. 
Fixes #1386 (thanks to @trevor for the bug report).

Test with:

```
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_import_missing_tool
```
 2016-01-04 09:58:24 +00:00
John Chilton 61f4c82642 Add test case for importing a workflow with missing tool. 2016-01-04 09:55:44 +00:00
Björn Grüning 34bb21c411 Merge pull request #1407 from guerler/revise_masthead_000 
Masthead/Scratchbook revision and test cases
 2016-01-04 01:31:44 +01:00
Björn Grüning 905adbac38 Merge pull request #1412 from jmchilton/isolate 
Isolate tool commands by default.
 2016-01-04 01:28:41 +01:00
Daniel Blankenberg 10677319f7 Merge pull request #1414 from jmchilton/lib_1 
Fix bug in db845fa187.
 2016-01-03 15:19:47 -05:00
Martin Cech 73defd48ce Merge pull request #1398 from jmchilton/toolbox_overhaul 
ToolBox Overhaul
 2016-01-03 14:08:17 -05:00
Björn Grüning 5ca71d6f29 Merge pull request #1409 from jmchilton/dep_resolution_api 
Evolving from dependency resolution to dependency management.
 2016-01-03 19:05:11 +01:00
John Chilton 308435b739 Fix bug in db845fa187. 2016-01-03 14:47:47 +00:00
John Chilton ce2795d87c Copy pastescript's NiceConfigParser into galaxy.util.properties. 
This is used in galaxy-lib and by utilities such as galaxy/main.py which has no reason to depend on pastescript.
 2016-01-03 13:58:15 +00:00
John Chilton 7cbf41feb3 Better exception when samtools is required but not on PATH. 2016-01-03 13:20:48 +00:00
John Chilton 523e2b4006 Fix shutdown of tool watcher if never activated. 
Caused a harmless, but distracting stacktrace to be printed on toolbox reload as pointed out by @bgruening https://github.com/galaxyproject/galaxy/pull/1398#issuecomment-168499678.
 2016-01-03 13:10:55 +00:00
John Chilton ce24ec6821 Remove alert from toolbox reload. 2016-01-03 13:10:55 +00:00
John Chilton eddfec36fd Refactor package_tool for better separation of concerns. 
The tool should know how to package itself, it shouldn't be the responsiblity of the toolbox. Update the code to reflect this and use more pythonic exception handling.
 2016-01-03 13:10:09 +00:00
John Chilton 8027228639 Revise tool caching for tool shed tool loading... 
The tool shed appears to load the same tool in the toolbox multiple times with different settings. Get around this by not using the cache when loading tools from a few tool shed components later in this process.
 2016-01-03 13:10:08 +00:00
John Chilton 4086dd61da Implement toolbox monitoring. 
- Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes.
 - Refactoring and test improvements for existing tool monitoring code.
 - Implement toolbox shutdown process to ensure different watchers don't compete with each other.
 - Set the default tool conf to be monitored.
 2016-01-03 13:10:08 +00:00