John Chilton
c3e99bc384
Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.
...
Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app.
Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh
Added usage documentation to run_reports.sh.
Added extension points to tweak pid and log location for reports application via environment variables.
2012-09-21 22:04:15 -05:00
Carl Eberhard
5b14ebfaa3
fixes to ae57c837ab03
2012-09-21 18:39:04 -04:00
Jeremy Goecks
479de769d2
Circster: add support for drawing a generic quantitative track and draw summary tree data using a single path.
2012-09-21 17:44:41 -04:00
Carl Eberhard
ff3f630b03
fixed(?) weird permissions on jquery-ui; scatterplot: major adjustments;
2012-09-21 16:42:29 -04:00
Jeremy Goecks
2e310f6cc6
Small additions based on bdd35af2a18a
2012-09-21 14:05:37 -04:00
Jeremy Goecks
6fefb40d4b
Viz framework: (a) push data provider creation to registry to simplify provider creation; (b) fix bugs in filters module naming; (c) enable deeper sampling in BBI data provider.
2012-09-21 14:00:09 -04:00
Jeremy Goecks
36e589d845
Push data sources/converter methods from controller mixin to dataset object.
2012-09-21 11:52:47 -04:00
Greg Von Kuster
f3070824b1
Add the ability to review tools migration stages that are available for the current Galaxy instance.
2012-09-21 11:21:38 -04:00
Jeremy Goecks
95b945b184
Place track filters in their own file.
2012-09-21 11:14:56 -04:00
Jeremy Goecks
75f936db5f
Add requireJS support for data, visualization, tools and update dependencies.
2012-09-21 10:12:01 -04:00
Dannon Baker
924cd349d3
Workflows: Viewing and Downloading of workflows with missing tools now handled gracefully.
2012-09-20 17:10:52 -04:00
Jeremy Goecks
53f26307c2
Add utility function to circster that determines whether an element is visible.
2012-09-20 15:39:57 -04:00
Greg Von Kuster
1b9513293c
Display warning or error message if attempting to install tool dependencies defined in a tool shed repository when the tool_dependency_dir config setting is not set in the Galaxy config.
2012-09-20 14:41:33 -04:00
Dannon Baker
8fec516f19
Workflows: Fix for 0ba260ea43c4 to correctly display error message when attempting to run a workflow missing tools.
2012-09-20 14:11:19 -04:00
Greg Von Kuster
9b063e395d
Fixes for viewing tool metadata in a tool shed repository for tools the require data index (.loc) files.
2012-09-20 13:43:42 -04:00
Greg Von Kuster
452249f806
Fix for viewing tool metadata defined for tools in a repository that use the Galaxy ToolDataTableManager.
2012-09-20 10:58:05 -04:00
Jeremy Goecks
1dd49b9ed4
Circster: render wiggle data as a single path rather than many small paths.
2012-09-19 18:31:30 -04:00
Greg Von Kuster
946fe73a82
Fix and enhance the features for resetting a repository that encounted errors during the cloning process so the Galaxy admin can make another attempt to install it.
2012-09-19 16:35:49 -04:00
Dannon Baker
1d67ba66b0
Revert previous change to message.mako for now -- we do use html in the message box elsewhere (links, etc) and this breaks them.
2012-09-19 13:20:45 -04:00
Dannon Baker
f1670541bf
Prevent reflective XSS through message display.
2012-09-19 10:32:19 -04:00
Dannon Baker
03694c29b2
Cloud Launch - Fix for rare instance udpate() that happens when (rarely) Amazon doesn't have the instance fully registered before update() is called.
2012-09-19 00:10:47 -04:00
Jeremy Goecks
ff226c3a4b
Fix bug in setting dbkey for new track browser.
2012-09-18 22:33:49 -04:00
Dannon Baker
ba6114ca3e
Fix create_all_fasta_loc to work when inspect_dir is not set.
2012-09-18 20:49:29 -04:00
Jeremy Goecks
b1d9046175
Tophat2 wrapper fixes. Thanks to Jim Johnson and Lance Parsons.
2012-09-18 17:11:18 -04:00
Jeremy Goecks
7bd55e2928
Wrap Sweepster in a requireJS module and add needed module qualifications. Pack scripts.
2012-09-18 16:50:45 -04:00
Scott McManus
0b221fee66
Fixed call to check_tool_output for TaskWrapper.
2012-09-18 14:10:56 -04:00
Greg Von Kuster
565fbaff4b
Fix for getting updates for tool shed repositories installed into a local Galaxy instance.
2012-09-18 13:54:19 -04:00
Jeremy Goecks
49632eab74
Fix bugs in Trackster refactoring.
2012-09-18 13:48:06 -04:00
Jeremy Goecks
79d9d25daa
Remove dubugging statement from last commit.
2012-09-18 13:14:49 -04:00
Jeremy Goecks
6d6b972951
Enhancements for finding available visualizations: (a) use dataset rather than datatype and (b) only show scatterplot for tabular datasets with >=2 numerical columns.
2012-09-18 13:10:04 -04:00
Carl Eberhard
8810a1c680
fix to apply tooltips to running/queued datasets in history panel
2012-09-18 12:39:13 -04:00
Nate Coraor
949ffbfe20
Add $__user_name__ to job template.
2012-09-18 12:13:02 -04:00
Jeremy Goecks
93f6810ed5
Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.
2012-09-18 11:40:57 -04:00
Dannon Baker
91ddfaff28
Grammar. it's -> its in admin panel (and tests)
2012-09-18 09:34:51 -04:00
Greg Von Kuster
ca4034cd32
Apply fix from Jim Johnson for rendering tool dependencies defined in a tool shed repository.
2012-09-18 09:03:39 -04:00
Jeremy Goecks
c66679cb26
Fix bugs when converting BED to FLI and JS module references.
2012-09-17 17:36:40 -04:00
Carl Eberhard
5d9348f1f2
scatterplot.mako: some cleanup
2012-09-17 17:19:53 -04:00
Carl Eberhard
68be41d2a9
initial, un-wired prototype for scatterplot visualization
2012-09-17 17:12:42 -04:00
James Taylor
a4216b5a74
pack
2012-09-17 16:24:27 -04:00
James Taylor
d8dac5bfcc
trackster: moving more stuff out of mako into javascript
2012-09-17 16:24:13 -04:00
James Taylor
bb08862dc6
pack scripts
2012-09-17 16:15:09 -04:00
James Taylor
8fbf7a3b0a
trackster: misc fixes and reorganization
2012-09-17 16:14:52 -04:00
James Taylor
893a610e8d
trackster: fix adding bookmarks
2012-09-17 15:41:35 -04:00
James Taylor
ae1a8a894c
trackster: fix groups
2012-09-17 15:38:46 -04:00
James Taylor
3fa6a8ab4e
trackster fixes
2012-09-17 15:36:11 -04:00
James Taylor
2297b49262
trackster: adding packed scripts
2012-09-17 15:23:45 -04:00
Nate Coraor
3bb0588147
I missed some missing indexes...
2012-09-17 14:23:00 -04:00
Nate Coraor
c51a9fb9fb
Index galaxy_user.email and add a bunch of indexes for columns added to existing tables that were supposed to be indexed.
2012-09-17 13:54:28 -04:00
Dannon Baker
987f9ad5fd
Set header 'X-Content-Type-Options: nosniff' for dataset display. This will prevent IE8 from trying to render as html datasets served as text/plain.
2012-09-17 13:19:32 -04:00
Nate Coraor
459d3a2c1d
More pgcleanup.py fixes and addition of cleanup event tables for library items.
2012-09-17 12:51:17 -04:00
John Chilton