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Author SHA1 Message Date
Martin Cech 86158cbc7f Merge pull request #1487 from dannon/release_16.01 
[16.01] Cherrypick of pep8 fixes.
 2016-01-13 11:18:50 -05:00
Dannon Baker 2f1dbeee68 Address W503 and E721 errors now enforced by pep8 1.7. 2016-01-13 10:41:27 -05:00
Dannon Baker b559cf303c Drop E731 from flake8 enforcement (though we should revisit this and see if we *do* want to follow this or not) 2016-01-13 10:41:19 -05:00
Martin Cech 24cb97cdbf Merge pull request #1462 from jmchilton/release_16.01_merge_4 
[16.01] Full merge of 15.10 into 16.01.
 2016-01-11 12:22:13 -05:00
Dannon Baker cea1f9e617 Merge pull request #1468 from carlfeberhard/fix.multihistory-drop 
[16.01] UI, Multi-history: fix drop event handler to use dataTransfer of orig…
 2016-01-11 12:07:15 -05:00
Dannon Baker 107ce1986f Merge pull request #1464 from bgruening/tours+ 
Improve default tours
 2016-01-11 10:39:42 -05:00
carlfeberhard 54dca064fa UI, Multi-history: fix drop event handler to use dataTransfer of original event 2016-01-11 10:21:06 -05:00
Björn Grüning d2702e9e44 Fix spelling mistake spotted by Nicola 2016-01-11 16:17:09 +01:00
John Chilton 3dda415fb9 Merge remote-tracking branch 'jmchilton/release_16.01' into release_16.01_merge_4 
Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
 2016-01-11 12:15:14 +00:00
Bjoern Gruening 252586f86c improve default tours 2016-01-10 23:26:55 +01:00
John Chilton 71aef50d25 Merge pull request #1461 from jmchilton/release_16.01 
[16.01] Merge more of 15.10 forward.
 2016-01-08 17:06:18 -05:00
Dannon Baker 0403a3175c Fix refactoring from 7587809b 2016-01-08 16:35:52 -05:00
John Chilton bb8f0f75ef Merge pull request #1455 from jmchilton/release_16.01_merge_1 
[16.01] Merge #1314 forward into 16.01.
 2016-01-08 15:18:37 -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 c13b1c088c Merge pull request #1458 from jmchilton/release_15.10_merge_0 
[15.10] Merge 15.07 into 15.10.
 2016-01-08 15:17:38 -05:00
John Chilton e36d33ce74 Merge pull request #1451 from jmchilton/release_16.01_merge_0 
[16.01] Empty cherry-pick of 93c6d05 to cleanup merge 15.10 -> 16.01
 2016-01-08 12:57:40 -05:00
Daniel Blankenberg 88a1e636b8 Merge pull request #1448 from jmchilton/watcher_fix 
[16.01] Fix optional watchdog handling.
 2016-01-08 12:27:20 -05:00
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
John Chilton 90bed00ebe Merge 15.07 into 15.10. 
Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10

Conflicts:
	client/galaxy/scripts/mvc/history/multi-panel.js
	lib/galaxy/webapps/galaxy/controllers/external_service.py
	lib/galaxy/webapps/galaxy/controllers/forms.py
	lib/galaxy/webapps/galaxy/controllers/library_admin.py
	lib/galaxy/webapps/galaxy/controllers/request_type.py
	lib/galaxy/webapps/galaxy/controllers/requests_admin.py
	lib/galaxy/webapps/galaxy/controllers/requests_common.py
	lib/galaxy/webapps/galaxy/controllers/visualization.py
	lib/galaxy/webapps/reports/controllers/jobs.py
	lib/galaxy/webapps/reports/controllers/sample_tracking.py
	lib/galaxy/webapps/reports/controllers/workflows.py
	lib/tool_shed/grids/admin_grids.py
	lib/tool_shed/grids/repository_grids.py
	lib/tool_shed/grids/repository_review_grids.py
	static/maps/mvc/history/multi-panel.js.map
	static/maps/mvc/ui/ui-select-default.js.map
	static/scripts/mvc/collection/list-collection-creator.js
	static/scripts/mvc/collection/list-of-pairs-collection-creator.js
	static/scripts/mvc/dataset/dataset-li-edit.js
	static/scripts/mvc/dataset/dataset-li.js
	static/scripts/mvc/history/history-panel.js
	static/scripts/mvc/history/multi-panel.js
	static/scripts/mvc/list/list-panel.js
	static/scripts/mvc/ui/ui-select-default.js
 2016-01-08 15:14:52 +00:00
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 d05ee50725 Empty cherry-pick of 93c6d05 to cleanup merge. 2016-01-08 12:54:39 +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
Martin Cech 5d32c9f8fc Merge pull request #1439 from jmchilton/backport_casper_fixes 
[16.01] Fix casper tests.
 2016-01-06 14:14:43 -05:00
Dave B 073609d005 Fix casper tests. 2016-01-06 13:58:13 +00:00
John Chilton 291d775170 Merge pull request #1430 from natefoo/version-16.01 
[16.01] Update version to 16.01.rc1
 2016-01-05 18:04:38 -05:00
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
Nate Coraor ddc2a12eb1 Merge pull request #1428 from guerler/add_pseudo_class_000 
Add form help class
 2016-01-05 16:31:02 -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
guerler 237ecc7789 Add form help class 2016-01-05 16:15:55 -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
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
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