[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 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

Searchwith 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


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