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Dec 3, 2012 Distribution & News Brief

Complete News Brief

**Highlights:** * **NGS: Mapping** tools **[Bowtie](http://bowtie-bio.sourceforge.net/index.shtml)** and **[Lastz](http://www.bx.psu.edu/~rsharris/lastz/)** have moved from the **[Galaxy distribution](https://bitbucket.org/galaxy/galaxy-dist)** to the **[Galaxy Main Tool Shed](http://toolshed.g2.bx.psu.edu/)**. * Improvements in the display of **[http://wiki.galaxyproject.org/ToolShed](http://wiki.galaxyproject.org/ToolShed)** repository dependencies and contents. * More **[Tool Shed](http://toolshed.g2.bx.psu.edu/)** updates including details of the [Functional test framework](http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framework_for_the_tool_shed), a new hgweb.config file and `HgWebConfigManager` tool, plus other management features. * Updated **UI** display and functionality for datasets and histories: new **paused** state and "resume/paused" toggle, new **History menu options** (seen at right →), and improved **Scatterplot** visualizations. * The **SGE** job runner has now been fully deprecated and replaced with **DRMAA**. * Several enhancements to aid with **reproducibility**: "Re-run" and "Extract workflow" validates datasets and tools, respectively, and a new data tables registry within the Administration menu, along with associated tools, corrects or warns about tool migration issues. * Highlights from the new Galaxy **[CloudMan](http://usegalaxy.org/cloud)** release and ***[December 2012 Galaxy Update](http://wiki.galaxyproject.org/GalaxyUpdates/2012-12)***.




new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r f364d992270c

Thanks for using Galaxy!

The Galaxy Team