*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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