Question: March 12, 2012 Galaxy Development News Brief
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gravatar for Jennifer Hillman Jackson
6.4 years ago by
United States
Jennifer Hillman Jackson25k 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 * *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_unsubsc="" ribing="">mailing list Thanks for using Galaxy, The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki
rna-seq cuffmerge cufflinks • 859 views
ADD COMMENTlink written 6.4 years ago by Jennifer Hillman Jackson25k
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