Question: March 12, 2012 Galaxy Development News Brief
0
Jennifer Hillman Jackson ♦ 25k wrote:
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_use="" d_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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<http: wiki.g2.bx.psu.edu="" mailing%20lists#searching="">for prior Q &
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Consider *subscribing to the galaxy-dev*
<http: wiki.g2.bx.psu.edu="" mailing%20lists#subscribing_and_unsubscribi="" ng=""> mailing
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Thanks for using Galaxy,
The Galaxy team
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