*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:*
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*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/.
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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.
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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)
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*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
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*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.
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Multiple *enhancements* to the *API* http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#APItargeting user and history actions.
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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://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