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11061 Commits
Author SHA1 Message Date
Dannon Baker 95d00b4174 Fix MIMEText usage in galaxy.util 2016-01-14 11:04:33 -05:00
Dannon Baker 2f1dbeee68 Address W503 and E721 errors now enforced by pep8 1.7. 2016-01-13 10:41:27 -05:00
John Chilton f8a7ac0820 Merge release_15.10 into release_16.01. 
Conflicts:
	eggs.ini
	lib/galaxy/tools/__init__.py
	lib/galaxy/tools/actions/__init__.py
	lib/galaxy/tools/toolbox/base.py
	static/maps/mvc/collection/list-collection-creator.js.map
	static/maps/mvc/library/library-foldertoolbar-view.js.map
	static/maps/utils/uploadbox.js.map
	static/scripts/mvc/collection/list-collection-creator.js
	static/scripts/mvc/library/library-foldertoolbar-view.js
	static/scripts/utils/uploadbox.js
	test/base/twilltestcase.py
	test/functional/tools/samples_tool_conf.xml
 2016-01-08 18:06:28 +00:00
John Chilton dff94d743f "Fix" collection outputs to hide the HDAs in the history. 
Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also.

Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem.

xref https://github.com/galaxyproject/tools-iuc/pull/412/files

Conflicts:
	lib/galaxy/tools/actions/__init__.py
 2016-01-08 17:04:51 +00:00
Dannon Baker 0403a3175c Fix refactoring from 7587809b 2016-01-08 16:35:52 -05:00
Nicola Soranzo e8e01bdfb1 When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. 
Workaround for issue #1283, which causes the loaded tool to have a
StockLineage instead of a ToolShedLineage, thus creating multiple entries
for the tool in the panel.

Conflicts:
	lib/galaxy/tools/toolbox/base.py
 2016-01-08 14:17:12 +00:00
Nicola Soranzo 47361f12ec Reduce code duplication by reusing get_installed_repository() function. 
Conflicts:
	lib/galaxy/tools/toolbox/base.py
 2016-01-08 14:17:12 +00:00
John Chilton e611b8fdb8 Use a more typical optional default value for optional import in watcher.py. 
Thanks to @nsoranzo for the advice - https://github.com/galaxyproject/galaxy/pull/1448#discussion_r49210125.
 2016-01-08 12:00:50 +00:00
John Chilton 7a3cc41054 Fix optional watchdog handling. 
Broken with 4086dd61da.

Thanks for bug report from @nsoranzo.
 2016-01-08 11:45:42 +00:00
Nate Coraor a0610ecdc0 Update version to 16.01.rc1 2016-01-05 16:39:53 -05:00
Nate Coraor b4fe6e2c3d Merge pull request #1393 from erasche/requirements-hashes-round-3 
Added hashes
 2016-01-05 16:33:25 -05:00
Nate Coraor 0ae86f59a1 Merge pull request #1429 from dannon/interactive_tours 
fix title_default to work as a default and not an override
 2016-01-05 16:33:01 -05:00
Dannon Baker 1568c0db80 fix title_default to work as a default and not an override 2016-01-05 16:28:51 -05:00
Nate Coraor 8bd293683b Merge pull request #1427 from jmchilton/lib-deps 
Revise galaxy-lib dependencies.
 2016-01-05 16:12:42 -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
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
Dannon Baker 5c765c0871 Merge branch 'dev' into interactive_tours 2016-01-05 10:51:54 -05:00
John Chilton 951b95e079 Make wchartype an optional dependency of galaxy-lib. 2016-01-05 15:38:46 +00:00
John Chilton 39f5c5d207 Make docutils an optional dependency of galaxy-lib. 2016-01-05 15:38:46 +00:00
John Chilton c416426522 Remove dup NiceConfigParser from loadwsgi.py. 
We are really adopting pastescript as our own.
 2016-01-05 15:38:46 +00:00
Dannon Baker c28d4d01ee Correctly specify default tour location. 2016-01-04 22:39:56 -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
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
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
Nate Coraor 1c21ba8241 Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables. 2016-01-04 10:54:29 -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
Björn Grüning 905adbac38 Merge pull request #1412 from jmchilton/isolate 
Isolate tool commands by default.
 2016-01-04 01:28:41 +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 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
John Chilton 864cc32892 Allow toolbox reloading via app, UI, and API. 
Introduce an app ToolCache to help ensure this operation remains speedy.
 2016-01-03 13:10:08 +00:00
John Chilton b68991c4ca Allow loading tool confs written in YAML and JSON. 
Because lets say someone was writing a programatic way to manage elements in a tool conf, that hypothetical person probably shouldn't be writing XML.
 2016-01-03 13:10:08 +00:00
John Chilton fcc83d4e09 Introduce ToolBox parser. 
Abstract simpler ToolBox interactions to separate XML representation from handling. Doesn't cover tool shed operations since the tool shed explicitly writes XML.
 2016-01-03 13:10:08 +00:00
John Chilton db845fa187 Refactor loader_directory to support beta formats in other ways. 2016-01-03 13:10:08 +00:00
John Chilton 2054f538be Infrastructure for parsing CWL tools. 2016-01-03 13:10:08 +00:00
John Chilton a9d4783f2c Add CWL suppoort to tool checking and parsing. 
To be clear, this provides none of the infrastructure for running the tools. This is just so that planemo and future tool registry efforts can have a unified interface for accessing and reasoning about tools using the same methods Galaxy does.
 2016-01-03 13:10:07 +00:00
John Chilton 0da66ee8dc Small improvements to load_directory for downstream extension. 2016-01-03 13:10:07 +00:00
John Chilton 4650d77bd9 Fix listing conda requirements if conda hasn't been installed. 
Fix problem discovered by @bgruening.
 2016-01-03 12:33:11 +00:00
John Chilton ef9e1876a2 Fixup dependency module and API comments. 
Thanks to suggestions by @bgruening.
 2016-01-03 12:29:15 +00:00