 Daniel Blankenberg
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2d5b8eca2f
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Add argument names to parameter help for GATK tools' options.
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2012-04-10 16:22:45 -04:00 |
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Daniel Blankenberg
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d38b177307
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Fix inconsequential warning about when tag when loading FreeBayes.
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2012-04-10 16:08:15 -04:00 |
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Daniel Blankenberg
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5bcce30d58
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Fix inconsequential warning about when tag when loading samtools mpileup.
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2012-04-10 16:07:19 -04:00 |
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Dannon Baker
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aafb37bd41
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Whitespace cleanup.
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2012-04-10 14:41:26 -04:00 |
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Dannon Baker
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7c2d700c43
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Fix history_contents API adding the HDA to the history twice (resulting in skipped hids)
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2012-04-10 14:32:13 -04:00 |
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Daniel Blankenberg
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7de86f1fb6
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Update argument names to parameter help for GATK Advanced options.
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2012-04-10 11:46:46 -04:00 |
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Jeremy Goecks
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23efb31da0
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Merge
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2012-04-10 11:21:37 -04:00 |
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Daniel Blankenberg
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62506054cd
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Add argument names to parameter help for GATK Advanced options.
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2012-04-10 11:20:12 -04:00 |
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Jeremy Goecks
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0a8c7565fe
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Backbone UI enhancements: create collection of tools in tool panel and use to get model when a tool link is clicked.
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2012-04-10 11:19:47 -04:00 |
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Richard Burhans
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f8037ed111
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add column names
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2012-04-10 11:03:11 -04:00 |
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Jeremy Goecks
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e0a04212f7
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Small fixes for Trackster icons
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2012-04-10 09:28:07 -04:00 |
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Daniel Blankenberg
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0372d1fe06
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Fix for BWA -R option.
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2012-04-10 09:24:25 -04:00 |
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Daniel Blankenberg
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163a2f39e1
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Do not add hidden tools to the tool panel.
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2012-04-09 23:24:31 -04:00 |
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Richard Burhans
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30c6ec3fbe
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remove Genome Diversity {test,tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository
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2012-04-09 16:34:51 -04:00 |
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Jeremy Goecks
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e0f75a6646
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Comment out recently used tool update for now because it is not implemented yet.
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2012-04-09 16:17:46 -04:00 |
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Jeremy Goecks
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2325c00b1a
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Merge
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2012-04-09 15:59:45 -04:00 |
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Jeremy Goecks
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af9ca554f9
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Tool menu changes: (a) enable Toolbox to be directly dictified; and (b) enable Toolbox to return only tools compatible with Trackster.
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2012-04-09 15:58:25 -04:00 |
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Richard Burhans
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8d4761b26e
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fix path to proprietary_datatype_module so that we get the correct error message when an import fails
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2012-04-09 15:38:05 -04:00 |
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Jeremy Goecks
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c0838a3c3b
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Fold tool panel styles back into base.css and include new style for tool panel in panel (w/o iframe).
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2012-04-09 15:20:15 -04:00 |
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Daniel Blankenberg
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59f8dd9a89
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Fix for not showing hidden tools in tool panel.
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2012-04-09 14:26:11 -04:00 |
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Jeremy Goecks
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812534f40c
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Simplify and generalize tool menu container style.
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2012-04-09 13:31:08 -04:00 |
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Nate Coraor
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cc2385220f
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Miller Lab's Genome Diversity tools moved to the Tool Shed.
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2012-04-09 13:13:44 -04:00 |
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Jeremy Goecks
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76dd928e01
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Fix bug that prevented actions from being taken on left panel.
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2012-04-09 11:02:04 -04:00 |
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Jeremy Goecks
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53db7e49dd
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Use postdraw_actions rather than predraw_init to reset track parameters after executing tool and fetching data.
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2012-04-08 12:15:54 -04:00 |
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Jeremy Goecks
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f9ddf769ec
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Do not use individual views for buttons in icon button menus.
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2012-04-08 11:44:21 -04:00 |
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Jeremy Goecks
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05f1470d9e
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Fix bugs in data fetching for tracks created via tools.
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2012-04-06 11:46:56 -04:00 |
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Jeremy Goecks
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7a11b9e51b
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Track and reuse HDA subsets in Trackster.
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2012-04-06 10:29:08 -04:00 |
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Nate Coraor
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3046e08c4b
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Fix missing import in job manager.
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2012-04-06 10:21:25 -04:00 |
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Daniel Blankenberg
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85d2692da9
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In tool_form, have call to unicode on non unicode field_html use 'replace' instead of raising a server error. Fixes issues seen with non unicode characters in history item names.
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2012-04-05 17:13:15 -04:00 |
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Daniel Blankenberg
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f304f8ab1d
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Add some missing cgi.escape calls around values in form_builder.py.
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2012-04-05 17:04:20 -04:00 |
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Jeremy Goecks
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fd8c815d2f
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Create ui.js for generic UI Backbone functionality and add models & views to display icon menus. Use new functionality for visualization menu.
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2012-04-05 15:55:47 -04:00 |
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Jeremy Goecks
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9c0ac76431
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All models have id attribute, so do not declare explicitly.
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2012-04-05 13:50:22 -04:00 |
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Jeremy Goecks
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0f46e64f3e
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Merge
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2012-04-04 21:45:44 -04:00 |
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Jeremy Goecks
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9676494356
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Pack scripts.
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2012-04-04 21:45:24 -04:00 |
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Jeremy Goecks
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01da64aa6d
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Make Trackster bookmarks compatible with recent changes to editable text elements.
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2012-04-04 21:44:49 -04:00 |
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Daniel Blankenberg
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5eb980e685
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DrillDown parameter now uses slideUp/Down.
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2012-04-04 21:12:31 -04:00 |
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Greg Von Kuster
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acd1555108
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Only include invalid tools in the metadata for the repository tip - supporting this in older revisions is a bit more complex and will be supported at a later time.
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2012-04-04 15:01:09 -04:00 |
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Greg Von Kuster
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fb96283757
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Slight fix for viewing invalid tools - allow an admin user to view only his invalid tools if requesting from the repositories view.
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2012-04-04 13:56:22 -04:00 |
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Greg Von Kuster
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656b12c316
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Apply fix for brand overflowing to the tool shed's base_panels.mako.
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2012-04-04 13:42:23 -04:00 |
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Greg Von Kuster
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a146ac6df0
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Add the ability to browse invalid tools in the tool shed - current user is restricted to seeing only their invalid tools if not an admin. Also a bit of cleanup in tool shed statistics.
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2012-04-04 13:36:37 -04:00 |
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Daniel Blankenberg
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a66adfdd1b
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Rework the display of DrillDown form elements.
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2012-04-04 12:24:43 -04:00 |
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Ross Lazarus
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8a9c206a5b
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Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py
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2012-04-05 02:16:12 +10:00 |
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Jeremy Goecks
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3d91507356
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Fix bug that scrolled Trackster on double click when completely zoomed in.
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2012-04-04 11:33:26 -04:00 |
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Dannon Baker
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55fe96c258
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Fix multi-input workflow selector to account for recent structural changes.
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2012-04-04 09:27:48 -06:00 |
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Nate Coraor
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1c676804f1
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Allow multiple output file collection from the job_working_directory.
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2012-04-03 22:07:19 -04:00 |
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Ross Lazarus
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1deefe54c2
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Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.
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2012-04-04 07:56:46 +10:00 |
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Jeremy Goecks
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2dd31018b3
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Update styles for standalone labels, tools in tool panel.
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2012-04-03 17:41:13 -04:00 |
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Jeremy Goecks
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8692f5a2e9
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Handle tool labels outside sections.
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2012-04-03 17:10:55 -04:00 |
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Ross Lazarus
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9e10f6b8f7
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branch merge
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2012-04-04 06:12:48 +10:00 |
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Ross Lazarus
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f71f0ff9d2
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Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir "${__new_file_path__}" to the command line generated. That will over-ride the default value "/tmp" for opts.tmpdir in picard_wrapper.py and solve the problem with /tmp filling reported by Matt Shirley.
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2012-04-04 06:11:54 +10:00 |
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