*Galaxy November 14, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_11_14_DistributionNewsBrief>*

*
Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14>
*

*Highlights:*

 *

   *NGS: Picard (beta)* 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/ to document the *galaxy-central
   <http://galaxy-central.readthedocs.org>* and *galaxy-dist*
   <http://galaxy-dist.readthedocs.org> code base.

 *

   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*
   <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#API>targeting user
   and history actions.

 *

   Plus *updates to* *CloudLaunch <http://usegalaxy.org/cloud>*, new
   *Security Fixes*
   <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#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!*

Jennifer Jackson <http://wiki.galaxyproject.org/JenniferJackson> & the Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

/http://galaxyproject.org/

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