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Author SHA1 Message Date
Martin Cech 2e62388b2f Merge pull request #1494 from jmchilton/tool_command_integrity 
[16.01] Fix to ensure integrity of tool_script.sh also.
 2016-01-14 00:41:57 -05:00
Dannon Baker 9d52a4a31d Merge pull request #1493 from guerler/undo_user_000 
[16.01] Undo user icon in masthead
 2016-01-13 18:46:11 -05:00
guerler 37f8038d63 Undo user icon in masthead 2016-01-13 14:31:40 -05:00
Nate Coraor becffe93a3 Merge pull request #1485 from jmchilton/common_startup_fixes 
[16.01] Fix common_startup options for planemo.
 2016-01-13 14:20:56 -05:00
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
John Chilton 55677f2d3d Fix to ensure integrity of tool_script.sh also. 
Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected.

Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable.
 2016-01-13 14:58:28 +00:00
John Chilton 8fd83df665 Allow override of location of virtual env Galaxy manages. 2016-01-13 13:55:36 +00:00
John Chilton 9dc9ddf8cd Add --replace-pip option to common_startup.sh. 
Needed to restore correct functionality to planemo.
 2016-01-13 13:55:35 +00:00
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