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July 20, 2012 Distribution & News Brief

Complete News Brief

**Highlights:** * **[Freebayes](http://bioinformatics.bc.edu/marthlab/FreeBayes)** has moved from the *Galaxy distribution to the [Galaxy's Main Tool Shed](http://toolshed.g2.bx.psu.edu/)* * **[EMBOSS](http://emboss.sourceforge.net/)** version 5.0.0 tool dependencies in the `emboss_5` repository of the Galaxy Main Tool Shed updated to include information for automatically installing. * **Tool Shed** now also supports specifying the third party tool dependencies to be automatically installed in new repositories * **Admin Genome Indexing** is now in *BETA*. Download, index, and track progress right from the admin UI! That's a screen shot on the right -> * **Improved Error Handling** that captures `EXIT` codes, `STDOUT`, and `STDERR` from tools in XML. Be sure to read full details. * **[TopHat2](/TopHat2/)/Bowtie2** latest support includes option to 'report discordant pairs', updated tests, and more preset options. * **Trackster** new parameter space visualization. *BRAND NEW!!* More details coming soon, but give a test drive now.


new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r ec29ce8e27a1

Thanks for using Galaxy! We hope to see everyone in Chicago @ GCC2012!!

Jennifer Jackson

Galaxy Team