Dear Galaxy Community,
The *latest Galaxy distribution* has been released: March 12, 2012 Galaxy Development News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12
*Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857
*Important Upcoming Changes to Tool Organization: *
The _*Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised *"Migrating tools"* http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed section of the Galaxy tool shed wiki to understand how this process will work:
*Migrating tools from the Galaxy distribution to the Galaxy Main tool shed http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed*
/(Summary)/ In 2012, the Galaxy development team will begin the process of /migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed/. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed
*Release Highlights: *
* *Galaxy tools:* XML configuration http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_populate_your_Galaxy_tool_panel, managing tool panel layout http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel, and Galaxy tool versions http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions
* *RNA-Seq Tools:* Added *CuffMerge* http://cufflinks.cbcb.umd.edu version 1.0.0, Updated *TopHat* http://tophat.cbcb.umd.edu default parameters
* *External Display Apps:* Added RViewerhttp://rviewer.lbl.gov/rviewer, Updated *IGV * http://www.broadinstitute.org/igv/
* Visualize ENCODEhttp://genome.ucsc.edu/ENCODE "peak" datatype tracks in the Galaxy Track Browser (aka Trackster)
* Multiple *Workflow* updates including enhancements to/input dataset options, display modes, and sharing
* CloudManhttp://wiki.g2.bx.psu.edu/Admin/Cloud now offers /preliminary support for OpenNebula cloud type http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py/ and a larger default tools volume(10GB vs old 2GB)
*Need help with a local instance? *
* *Installation* and *Admin* Instructions: http://getgalaxy.org
* *Search* with our custom google tools:
* All Galaxy mailings lists http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searchingfor prior Q & A * Information about deploying, developing, customizing, and administering http://galaxyproject.org/search/getgalaxy Galaxy * Information about using http://galaxyproject.org/search/usegalaxy Galaxy
* *Consider* subscribing to the galaxy-dev http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribingmailing list
Thanks for using Galaxy,
The Galaxy team
http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki