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/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%20sh="" ed#xml_configuration_files_used_to_populate_your_galaxy_tool_panel="">sec tion 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_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 <https: bitbucket.org="" galaxy="" cloudman="" src="" tip="" cm="" clouds="" opennebul="" a.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_unsubscribi="" ng=""> Thanks for using Galaxy, The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki
rna-seq cuffmerge cufflinks • 812 views
ADD COMMENTlink written 6.4 years ago by Jennifer Hillman Jackson25k
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