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DevNewsBriefs/2015_01_13_StableAdditions

Updates added to the last Galaxy Distribution listed below

These represent changes introduced after the initial release. May also be tracked in Trello.

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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 new DataManager 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




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