Question: March 12, 2012 Galaxy Development News Brief
0
Jennifer Hillman Jackson ♦ 25k wrote:
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_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 *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
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<http: galaxyproject.org="" search="" usegalaxy=""> Galaxy
* *Consider* subscribing to the galaxy-dev
<http: wiki.g2.bx.psu.edu="" mailing%20lists#subscribing_and_unsubsc="" ribing="">mailing
list
Thanks for using Galaxy,
The Galaxy team
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