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/galaxygalaxy-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#XML_configuration_files_used_to_populate_your_Galaxy_tool_panel*http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_populate_your_Galaxy_tool_panelsection 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#XML_configuration_files_used_to_populate_your_Galaxy_tool_panel
(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#XML_configuration_files_used_to_populate_your_Galaxy_tool_panel
*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 https://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 Galax http://galaxyproject.org/search/getgalaxyy * Information about using Galaxy http://galaxyproject.org/search/usegalaxy
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Thanks for using Galaxy,
The Galaxy team
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