Development News Brief
Updates added to the last Galaxy Distribution listed below
These represent changes introduced after the initial release. May also be tracked in Trello.
Review prior distribution
New
Improved
- Made installation of tool repositories more robust by setting time to "Epoch" instead of throwing server error when
repository_metadata.time_last_tested
is unset. o09VBhr1 - Updated the Tuxedo RNA-seq tools to version 2.2.1 and created new wrappers for Cuffquant and Cuffnorm. In the Tool Shed and installed on http://usegalaxy.org. bfr0jKut
- Enhanced the
DataManagers
reference genome retrieval protocol to function better with UCSC's updated file naming/paths. Created a newDataManager
for dbkeys/Genome Builds. Find these in the Tool Shed. kPkwDHmi pmd6gSS6 - Change to allow anonymous users (those not logged into a Galaxy account) to view Pages with embedded Histories. 9Om6Odj2
Bug Fixes
- Fixed a GATK Evaluation Bug. PXClb3PT
- Corrected an "over-sanitized" info message after renaming a history (html was displaying). MtAQNOqC
- Discovered and fixed issue with Paired list collection creator (key renaming broken). QklilFk3
- Fix for preventing non-admins from running Data Managers through the API.EeHJP167
- Egg-fetching related bugfixes. 9L0HlQ0u
- Fixes for resetting metadata on ToolShed Repositories. lGmlkvdr
- Small fixes for updated workflow scheduler. fF7pUNIG
- Change to use samtools version 1.x to generate BAM indexes if it is first in $PATH. UOVlg7nL
- Removed displayed paragraph tags from history/rename feedback messages V4VMvDeY
- Fixed Picard index Data Manager so that it no longer indicates failure (red dataset result in admin history) when it is actually successful. b1cHiIw0
Security
- Various low-vulnerability-level security fixes. U6yj2pPr