Dear Galaxy Community,
The latest Galaxy distributionhas 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 toolsXML 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 Workflowupdates 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
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* 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
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Thanks for using Galaxy,
The Galaxy team
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