[galaxy-announce] March 12, 2012 Galaxy Development News Brief

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[galaxy-announce] March 12, 2012 Galaxy Development News Brief

Jennifer Jackson
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_panel>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#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/getgalaxy>y
  * Information about using Galaxy
    <http://galaxyproject.org/search/usegalaxy>


*Consider****subscribing to the galaxy-dev *mailing list
<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing>


Thanks for using Galaxy,

The Galaxy team


-------
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org