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
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