Commits

Author Commit Message Labels Comments Date
ichorny
added altered config.py
ichorny
merge with galaxy central
ichorny
add actual user changes to galaxy-central
Daniel Blankenberg
Update generic GATK command line options.
Nate Coraor
John Duddy
Correct indentation, only access summary if it is set!
John Duddy
Fix API code errors, add ability to set ldda associations, fixed misc error in util
Greg Von Kuster
Fixes for searching for and installing tools from a tool shed. The value of the webapp request parameter is heavily used throughout this process, and has been added to all grid forms that include operation buttons.
Daniel Blankenberg
Update sff extractor to version 0.2.10.
Daniel Blankenberg
First pass at updating GATK tools to version 1.2. Changes are not backwards compatible with workflows. Still considered BETA, and so future changes are like to also not be backwards compatible.
Daniel Blankenberg
Allow toolbox tests to test 0 instances of a repeat.
Daniel Blankenberg
Allow specifying a help attribute for repeat parameter grouping.
Greg Von Kuster
Enhanced Galaxy instance <=> Galaxy tool shed integration: 1. All accessible tool sheds are now displayed in a mako template in teh Admin view rather than the left tool panel 2. From Galaxy you can now search for tools by id, name, version in a selected Galaxy tool shed. 3. Tools found using the above search can now be installed in the local Galaxy instance.
Daniel Blankenberg
Add dataset_metadata_in_data_table validator. Mimics behavior of dataset_metadata_in_file, but uses data tables.
Greg Von Kuster
Fixes and code cleanup for searching for tools in tool shed repositories.
Greg Von Kuster
Add new tool attributes to hold information about tools installed from a Galaxy tool shed. Enhance the toolbox's <tool> tag parser to handle these new tool attributes for installed tools. Enhance the Workflow import and load functions to search these new attributes when looking for required tools in the Galaxy instance.
jeremy goecks
Bug fixes to Trackster ReferenceDataManager.
Daniel Blankenberg
Fix for job.compute_outputs() when outputs_to_working_directory is True.
Greg Von Kuster
Make sure the same key is used in encoding and decoding between Galaxy and the tool sheds.
jeremy goecks
Better handling of reference data in Trackster read tracks.
Greg Von Kuster
Encode the tool shed repository information and include in the request when installing into local Galaxy instances rather than using cookies.
jeremy goecks
Fix Trackster bug that prevented differences from being displayed in mapped reads.
jeremy goecks
Improvements to Trackster filters: (a) scaler framework replaces generator framework; (b) addition of height scaler to set feature height based on attributes; and (c) no transparency for feature labels.
Nate Coraor
PBS cluster error user messages now suggest retrying the job.
Greg Von Kuster
Fix for loading a workflow that contains tools whose tools ids are the old version of tools ids, but whose available tools use the new tool guids as the tool id because the tools were installed from a Galaxy tool shed.
Greg Von Kuster
Enhance automatic tool shed repository installation to enable installation of multiple repositories using a multi-select frid layout instead of installing just a single repository at a time.
Greg Von Kuster
Enhance tool searching in tool shed repositories to enable multiple values in any of tool_id, tool_name, tool_version. In the tool shed search form, taking advantage of this feature requires comma-separated lists to be entered in the form fields.
Nate Coraor
Merged in jmchilton/umn-galaxy-central (pull request #10)
John Chilton
Re merged with galaxy central.
John Chilton
Merged galaxy-central.
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