Commits

Author Commit Message Labels Comments Date
ichorny
add actual user changes to galaxy-central
Daniel Blankenberg
On edit attributes page, make the info field a textarea. Also HTML escape the contents of data_annotation and info textareas.
Greg Von Kuster
Fix a type related to handling tool data table when uploading to a tool shed repository, and if conditions allow for it, reset all metadta on all changeset revisions of a tool shed repsoitory whenever a new change set is introduced. This will result in a more standardized set of valid changeset revisions that can be installed.
Daniel Blankenberg
Have GOPs Concatenate tool always respect the provided strand column.
jeremy goecks
Update Tophat tests for v1.4.0
Greg Von Kuster
Fix for getting a tool in the API workflow component.
Daniel Blankenberg
Better handling of JEXL expressions in GATK.
Greg Von Kuster
Fix for loading tools - bug introduced in my last commit...
Greg Von Kuster
Enhance the process used by objects to retrieve tools from the tools_by_id dictionary. This allows for workflows that were built with tools originally included in the Galaxy distribution but later moved to the tool shed to function correctly if the tools are installed from the tool shed using Galaxy's update manager. In addition, workflows that were built using locally developed and hosted tools, but the tools were included in a tool shed repository, removed from the local instanc…
Nate Coraor
Fix a bug with object store and metadata files.
Greg Von Kuster
Enhance the process of deactivating / activating installed tool shed repositories by handling the deactivation / reactivation of proprietary datatypes, datatype converters and display applications.
jeremy goecks
Remove spurious export in run functional tests scripts.
jeremy goecks
Update functional tests to be compatible with 0d1d62b8be2e
jeremy goecks
Subset GFF datasets correctly when running tools in Trackster.
jeremy goecks
Trackster: true replacement of a track with a group when running a tool.
jeremy goecks
Trackster: fixes for running tools.
Nate Coraor
Avoid annoying errors produced by the Googlebot hitting the import library datasets to history page (it doesn't have a history).
Nate Coraor
Filesystem free space checking for the object store.
jeremy goecks
Trackster: bug fix for showing 'more data' icons. Pack scripts.
Greg Von Kuster
Fix for reloading a tool in the tool panel - make sure to keep the tool's tool shed related attributes when the tool is reloaded. Also make sure to send the guid attribute when loading a tool into the tool panel if the tool is contained in an installed tool shed repository.
jeremy goecks
Add href to trackster icons in history pane so that browser treats it as a URL and not an anchor.
Greg Von Kuster
Fixes for Galaxy instance ,=> tool shed communciation where Galaxy instance is running behind apache with rewrite rules.
Greg Von Kuster
Add the ability to deactivate / activate installed tool shed repositories. When a repository is deactivated, it's contained tools are eliminated from the tool panel on the fly. Similarly, if a deactivated repository is activated, it's contained tools are loaded into the tool panel on the fly. This works for tools contained in sections or outside sections in the tool panel. Also fix a bug which resulted in a server error when installing a tool shed repository that includs a .loc.sample file.
jeremy goecks
Trackster: fix reference track display bug.
Nate Coraor
Bugfix for distributed object store that prevented certain kwargs from being passed to certain methods in the backend store.
Nate Coraor
Add missing distributed object store config file option to the sample universe_wsgi.ini.
jeremy goecks
Fix jQuery 1.7 compatibility bug so that multi-selects are not replaced by search+select and pack scripts.
jeremy goecks
Trackster: bug fix when padding tiles for display.
Dannon Baker
PostJobAction execution on job failure - uses association correctly now, renamed for clarity.
jeremy goecks
Pack trackster script.
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