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Author SHA1 Message Date
Ramkrishna Chakrabarty 4dd21d2119 fixed the svgfig egg problem in mutation viz tool 2010-08-13 08:49:09 -04:00
Kanwei Li 417d47110b Use svgfig egg instead of including it, minor fix for workflow image gen 2010-08-12 23:45:33 -04:00
Kanwei Li 37269a3a26 Add gen_image method to workflows, using svgfig library to create SVG representation of workflow 2010-08-12 19:08:49 -04:00
Ramkrishna Chakrabarty 37ff568432 Mutation visualization tool 
Added svgfig egg
 2010-08-12 14:21:59 -04:00
Jeremy Goecks 7e5a21b9a6 Framework support for importing and exporting Galaxy workflows to and from myExperiment. This commit is part of a larger effort to integrate myExperiment support into Galaxy, and it is the first piece of this effort. 
This commit includes controller methods to import/export Galaxy workflows to/from myExperiment as well as associated templates for generating the request XML. Refactoring was done so that there are now generic method to save a workflow to a json dict and recover a workflow from a json dict. These methods are used both for importing/exporting Galaxy workflows among Galaxy instances and for importing/exporting Galaxy workflows to/from myExperiment.

Caveats: (a) importing and exporting goes to the myExperiment sandbox right now rather than the official myExperiment website; (b) there is no user interface for importing/exporting workflows to myExperiment; and (c) there is no connection between Galaxy workflows and myExperiment workflows and hence no version tracking.
 2010-08-12 13:57:45 -04:00
Kelly Vincent 108ca6e24a Fixed bug in column join that mishandled trailing empty columns 2010-08-12 10:38:33 -04:00
Kelly Vincent c7f29c9d4d Fixed bug in column join that mishandled carriage returns 2010-08-12 09:54:15 -04:00
Jeremy Goecks 46be8c1223 Track tool version in workflows. 2010-08-10 15:42:47 -04:00
Dannon Baker db702de464 Force right panel reload if a dataset was visible, tracked for updates, and hidden behind the scenes. 2010-08-10 12:22:49 -04:00
Daniel Blankenberg b951bdd727 Add ToolOutputActions to set dbkey for BWA wrapper and remove no longer needed code file. 2010-08-10 11:36:50 -04:00
Daniel Blankenberg e441baa11d Remove print debug from ToolOutputActions 2010-08-10 10:49:21 -04:00
Nate Coraor ae424226f8 Single files downloaded from the library are now just named as their title 2010-08-09 22:43:58 -04:00
Jeremy Goecks 240fb5933e Enhance GFF-to-BED converter to output block data. Added test for new functionality. 2010-08-09 22:37:43 -04:00
Nate Coraor bb432dd3c5 Readded the JOB_ERROR state to galaxy.jobs since it's used by a few tools. 2010-08-09 22:33:10 -04:00
Daniel Blankenberg b8d82b9f35 Enhance Cut tool to keep column assignments for Interval datatypes. All interval datatypes will become base interval type if User specified columns contain chromosome, start and end columns; in addition to the 3 required columns, name and strand will be set when possible. 2010-08-09 21:06:37 -04:00
Daniel Blankenberg f97a380a56 Add ToolOutputActions to set dbkeys for LiftOver tool and both Bowtie wrappers; remove no longer needed code files. 2010-08-09 21:06:18 -04:00
Daniel Blankenberg e5ce8f86e4 Add ToolOutput dataset actions: change datatype, metadata, etc. 
These function similar to dynamic options for select list tool parameters. Should eliminate the need for exec_before_job code files that set output dataset attributes. More 'filter's should be defined as needed.

Examples to follow.
 2010-08-09 21:05:57 -04:00
Kanwei Li 0ec45350aa trackster: Show counts for summary view by default, but only when text can fit in. Fix summary view off-by-pixel bug. Display Mode is now only initialized once and stays the same while switching chroms. 2010-08-09 20:01:02 -04:00
Dannon Baker b476cf0c02 Merge. 2010-08-09 17:09:08 -04:00
Dannon Baker 90c2bad04e Hidden datasets will no longer show in "Show Structure" 2010-08-09 17:08:16 -04:00
Ramkrishna Chakrabarty f0a3f224d4 lims: show last update date/time in the transfer datasets grid 2010-08-09 16:33:15 -04:00
Jeremy Goecks 77a3278aa3 Fix GFF bug in interval to summary tree converter. 2010-08-09 10:36:49 -04:00
Nate Coraor 001c8dbaf5 Remove reference to the SGE job runner in config file documentation 2010-08-06 14:31:11 -04:00
Dannon Baker b972874235 EmailAction cleanup, removing history name from the message. 2010-08-06 14:25:27 -04:00
Dannon Baker 466a02cafb Email timestamp change. Year-Month-Day removed. 2010-08-06 14:05:56 -04:00
Dannon Baker 491e8c3ec3 Changed from host in the default case to usegalaxy.org to prevent 'domain not found' failure for old actions. 2010-08-06 13:56:59 -04:00
Dannon Baker dc43889d51 Email Action Bugfix. 2010-08-06 13:48:50 -04:00
Dannon Baker cf435710f3 Fix for old PJA with no host data saved for email action. 2010-08-06 13:40:53 -04:00
Dannon Baker 867ef98c6f PostJobActionAssociation created. 
Actions now execute at the job level, not the workflow level.
    Polished messages and interaction.
    Fixed Email Action.
 2010-08-06 13:25:04 -04:00
Jeremy Goecks c0ac1065b6 Update version numbers of cufflinks and tophat to reflect new tool installations. 2010-08-05 11:20:11 -04:00
Greg Von Kuster 6a5d349785 Add the ability to rate and review tools in the tool shed. 2010-08-04 15:26:55 -04:00
James Taylor 11b4b6d1c4 Missing tool data files are now a warning not a fatal error. This means that table can load but be empty, and the tool will also still load but have no options for the field that is connected to that data table. Is this too lenient? 2010-08-04 14:41:23 -04:00
Jeremy Goecks 00aace90ed merge 2010-08-04 14:36:12 -04:00
Jeremy Goecks 6d9472e9be Improvements to the GFF filtering tool. 2010-08-04 14:35:53 -04:00
James Taylor 9e25e2a944 Modified translogger middleware that properly propogates exceptions, should eliminate 'Attempt to set headers a second time w/o an exc_info' 2010-08-04 14:33:09 -04:00
Jeremy Goecks 44c69eca99 merge 2010-08-04 14:05:22 -04:00
Jeremy Goecks 508c61f532 Update gops_intersect and gops_subtract documentation to reflect that tools can accept both BED and GFF files. 2010-08-04 14:04:37 -04:00
James Taylor 6b95a1f7fd Automated merge with https://bitbucket.org/galaxy/galaxy-central/ 2010-08-04 14:01:39 -04:00
Ramkrishna Chakrabarty d4c01d8f5c lims: 
- bug fix: now a admin cannot delete a transfer dataset when the transfer has started.
- added user warning when a dataset is deleted.
 2010-08-04 09:56:51 -04:00
Kanwei Li 81b5304c4a - Fix dbkey migrate script for downgrade and rare case when config is empty 
- Fix grid sorting in "Visualize in Trackster" modal box
- Refactor out sort_order in grids, fixing a bug with sort arrow not showing
 2010-08-03 16:41:03 -04:00
Kanwei Li 1898e7712b trackster: Add new dbkey column to viz tables, finish "Visualize in Trackster" button functionality 
- Dbkey now shown in "Saved Visualizations" grid
- "Visualize in Trackster" icon in history pane for supported dataset now works, letting you add that dataset to an existing browser or to a new browser. Dbkey for existing browsers is also shown.
 2010-08-03 15:10:30 -04:00
Jeremy Goecks 1e12562272 Add a ratings framework so that users can rate shared items. All sharable items--histories, workflows, datasets, visualizations, and pages--can be rated. Main framework components are (1) database tables for storing ratings; (2) UsesItemRatings mixin that supports rating items and obtaining an item's average rating; (3) controller methods to handle rating asynchronously; and (4) jQuery star rating plugin and supporting code that enables interactive item rating. (2) and (4) can be reused in the community space. 2010-08-03 11:45:25 -04:00
Kanwei Li a1f9e6a572 Support for VCFv4.0 and misc VCF fixes [Brad Chapman] 
- Support for VCFv4.0, which should be identical to 3.3 support
- Correctly handle chromosome references when they start with 'chr' (instead of just numbers)
- Handle extra empty tabs on the header line which are present in GATK produced VCF and confuse the determination of how many sample states should be parsed.
 2010-08-03 10:43:32 -04:00
Greg Von Kuster db62fa7daf Eliminate the "menubutton split" style from library folders as well ( missed in my last commit ). Fix security checks for library popup menus - errors introduced in my last commit. Fix names produced for library datasets that are compressed by strippping off the compression extension. 2010-08-02 11:14:34 -04:00
Greg Von Kuster 66aa3b0a9c Revert code that introduced the "menubutton split" class style to the data library browser since the href link will not work when wrapped in the style ( only the popup menu works ). 2010-08-02 10:07:14 -04:00
Jeremy Goecks b090d13661 Rewrite documentation for 'users_shared_with' association proxies to make it clearer how to use them. 2010-08-01 13:33:13 -04:00
Ramkrishna Chakrabarty 6b601b83c4 lims: fixed edit samples view bug 2010-07-30 14:33:15 -04:00
Daniel Blankenberg 52acf90053 Add a 'ref_attribute' attribute to param_value dynamic option filter to allow accessing attributes of the parameter value. 2010-07-30 12:06:57 -04:00
Ramkrishna Chakrabarty e3c43d17f2 lims: cleaned up the sample datasets view for a non-admin user 2010-07-30 11:49:47 -04:00
Daniel Blankenberg 289e2828bf Bug fix for multiple_splitter dynamic option filter. 2010-07-30 11:22:21 -04:00