December 3, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_03_DistributionNewsBrief>

*
Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_03>*


*
Highlights:*

 *

   *NGS: Mapping* tools *Bowtie
   <http://bowtie-bio.sourceforge.net/index.shtml>* and *Lastz
   <http://www.bx.psu.edu/%7Ersharris/lastz/>* have moved from the
   *Galaxy distribution <https://bitbucket.org/galaxy/galaxy-dist>* to
   the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>*.

 *

   Improvements in the display of *Tool Shed
   <http://wiki.galaxyproject.org/Tool%20Shed>* repository dependencies
   and contents.

 *

   More *Tool Shed <http://toolshed.g2.bx.psu.edu/>* updates including
   details of the Functional test framework
   
<http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framework_for_the_tool_shed>,
   a new hgweb.config file and HgWebConfigManager tool, plus other
   management features.

 *

   Updated *UI* display and functionality for datasets and histories:
   new *paused* state and "resume/paused" toggle, new *History menu
   options*, and improved *Scatterplot* visualizations.

 *

   The *SGE* job runner has now been fully deprecated and replaced with
   *DRMAA*.

 *

   Several enhancements to aid with *reproducibility*: "Re-run" and
   "Extract workflow" validates datasets and tools, respectively, and a
   new data tables registry within the Administration menu, along with
   associated tools, corrects or warns about tool migration issues.

 *

   Highlights from the new Galaxy *CloudMan
   <http://usegalaxy.org/cloud>* release and /*December 2012 Galaxy
   Update <http://wiki.galaxyproject.org/GalaxyUpdates/2012_12>*/.

*
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 f364d992270c

*
Thanks for using Galaxy!*


The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>


--
Jennifer Jackson
http://galaxyproject.org

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