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 RViewer<http://rviewer.lbl.gov/rviewer>, Updated *IGV * <http://www.broadinstitute.org/igv/> * Visualize ENCODE<http://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 * CloudMan<http://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#Searching>for 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_Unsubscribing>mailing list Thanks for using Galaxy, The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki