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March 12, 2012 Distribution & News Brief

Complete News Brief

Highlights:

trackster-encode
* **__Emboss tools and datatypes__** __moving from the *Galaxy distribution to the [Galaxy's Main Tool Shed](http://toolshed.g2.bx.psu.edu/)__* __in the **NEXT release__**. Read more about the upcoming **[tool migrations...](/src/toolshed/migrating-tools-from-galaxy-distribution/index.md)** * Galaxy tool [XML configuration](/src/galaxy-tool-panel//index.md#xml-configuration-files-used-to-populate-your-galaxy-tool-panel), managing [tool panel layout](//src/galaxy-tool-panel//index.md#managing-the-layout-of-your-galaxy-tool-panel), and Galaxy [tool versions](/src/galaxy-tool-version-lineage/index.md). * **RNA-Seq Tools:** Added **[CuffMerge](http://cufflinks.cbcb.umd.edu/)** version 1.0.0, Updated **[TopHat](http://tophat.cbcb.umd.edu/)** default parameters * **External Display Apps:** Added **[RViewer](http://rviewer.lbl.gov/rviewer/)**, Updated **[IGV](http://www.broadinstitute.org/igv/)** * Now visualize **[ENCODE](http://genome.ucsc.edu/ENCODE/) "peak" datatype tracks** in the Galaxy Track Browser (aka Trackster) * Multiple **Workflow** updates including enhancements to input dataset options, display modes, and sharing. * **[CloudMan](http://wiki.g2.bx.psu.edu/Admin/Cloud)** now offers **[preliminary support for OpenNebula cloud type](http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py)** and a **larger default tools volume** (10GB vs old 2GB).

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 40f1816d6857

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team