Commits

Author Commit Message Labels Comments Date
Greg Von Kuster
Add baseline support for handling data types included in tool shed repositories, add the ability to upload files to tool shed repositories by entering a URL in the upload form, provide much better file content checking when uploading either single files or archives to a tool shed repository (niether html content nor images are currently allowed), enhance error messaging when tool config parameter tags are not functionally correct.
Daniel Blankenberg
Tool help updates.
jeremy goecks
Make history UI icons compatible with changes in 9dbc82483bd2.
Daniel Blankenberg
Fixes for Data source async controller.
Greg Von Kuster
Fix for renaming a tool shed repository - hopefully resolves race condition.
Ross Lazarus
Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.
Ross Lazarus
branch merge
Ross Lazarus
Some minor additional cleanup to the picard suite
Ross Lazarus
Updates for picard tools 1.56 - they changed the params for CollectInsertSizeMetrics.jar - bless them - so
Greg Von Kuster
Fix grid operations for use in UserListGrid to allow for Delete, Undelete, Purge of users if the allow_user_deletion config setting is true.
jeremy goecks
Trackster: use icon to set track mode.
jeremy goecks
Make toggle icons use black and white and color on hover to match other Trackster icons.
Dannon Baker
Fix for slug check flag pointed out by Andrew Warren.
Nate Coraor
Fix an exception class that doesn't exist. Thanks Oleksandr Moskalenko.
Greg Von Kuster
Eliminate the non-functional PacBio tools from the distribution and the sample tool config.
Daniel Blankenberg
Update GeneTrack help.
Greg Von Kuster
Add the ability to enter a new tool panel section label when installing repositories with tools from a tool shed in addition to being able to choose an existing tool panel section for containing the tools. Also clean up code related to message displayed when a local Galaxy instance is missing tools required by an imported workflow.
Dannon Baker
Repack of .js
Nate Coraor
Merged in jdlogicman/galaxy-central (pull request #15)
John Duddy
Fix copy/paste errors in histry contents API
Daniel Blankenberg
Remove "-targetNotSorted" argument from GATK indel realigner: vanished without warning or notice.
Daniel Blankenberg
Update FASTQ Groomer tool help to indicate that Illumina 1.8+ is Sanger encoded.
Greg Von Kuster
Add locale files for Chinese provided by hanfeisun.
Greg Von Kuster
Fix for generating metadata in tool shed repositories for a tool that does not use a tool_data_table entry for a dynamic SelectField input parameter.
Greg Von Kuster
Fix importing library datasets into multiple histories - library datasets will now only be imported into those checked.
James Taylor
Trackster: dense mode features are full height again, don't draw strand indicators when drawing squished features.
James Taylor
Automated merge with ssh://bitbucket.org/galaxy/galaxy-central
James Taylor
Trackster: fix strand drawing for single blocks with no thin/thick part
James Taylor
Trackster: code for adding multiple bookmarks from a dataset. Currently the button is commented out until this can be made more usable
James Taylor
Trackster: fix loading of track connector style when initializing from saved
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