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Nov 14, 2012 Distribution & News Brief

Complete News Brief

dist-readthedocs
Read the DocsSphinx Python Documentation Generator
**Highlights:** * **NGS: Picard (beta)** tools have moved from the **[Galaxy distribution](https://bitbucket.org/galaxy/galaxy-dist)** to the **[Galaxy Main Tool Shed](http://toolshed.g2.bx.psu.edu/)**. * The **Galaxy Project** is now using *[Sphinx](http://sphinx-doc.org/) Python* hosted at [Read the Docs](http://readthedocs.org) to document the **[galaxy-central](http://galaxy-central.readthedocs.org)** and **[galaxy-dist](http://galaxy-dist.readthedocs.org)** code base. That's a peek on the right → * The **[Intergalactic Utilities Commission](http://wiki.g2.bx.psu.edu/ReviewingToolShedRepositories)** will soon begin reviewing repositories in the **[Galaxy Main Tool Shed](http://toolshed.g2.bx.psu.edu/)** (better repos, better tools) * **[Tool Shed](http://toolshed.g2.bx.psu.edu/)** **"best practice"** advice: [a single tool or a suite of tools per repository?](http://wiki.galaxyproject.org/AToolOrASuitePerRepository) * **[Tophat](http://tophat.cbcb.umd.edu/)**, **[Tophat2](http://tophat.cbcb.umd.edu/manual.html)**, and **[Cuffdiff](http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff)** **updated** to accept gene annotations in **[GFF3](http://wiki.galaxyproject.org/Learn/Datatypes#GFF3)** format. * Multiple **enhancements** to the **[API](/src/archive/dev-news-briefs/2012-11-14/index.md#api)** targeting user and history actions. * Plus **updates to** **[CloudLaunch](http://usegalaxy.org/cloud)**, new **[Security Fixes](/src/archive/dev-news-briefs/2012-11-14/index.md#security-fixes)**, and several usability enhancements for **Datasets**, **Datatypes**, **Tools**, and **Tool Shed** functions.

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r 5dcbbdfe1087

Thanks for using Galaxy!

The Galaxy Team