Save These Dates! July 25-27: Galaxy Community Conference
Hello all, I am pleased to announce that the 2012 Galaxy Community Conference (GCC2012) has been scheduled for July 25-27, 2012 at the University of Illinois Chicago. See http://galaxyproject.org/wiki/Events/GCC2012 for more information on the meeting, and for sponsorship opportunities. Abstract submission and registration deadlines will be announced in the coming months. Please reserve July 25-27 on your calendar now, and hope to see you in Chicago next summer! Dave Clements PS: If your curious to know what goes on at a Galaxy meeting, see the GCC2011 page for an idea: http://galaxyproject.org/wiki/Events/GCC2011 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/
Hello all, I am trying to run through the GATK pipeline on the Galaxy Test page. I have a question related to the UnifiedGenotyper wrapper page. At the bottom of the page, I choose the "Advanced" tab for "Basic or Advanced Analysis options." After the automatically refreshed, I choose the "Annotation Types" that I was interested in. Then below that are options for "Annotation Interfaces/Groups:" What are these options used for? I have looked all over the web, on the GATK wiki and at the GATK Q&A page (located at getsatisaction.com) without any luck. Are these options important? The description located at the bottom of the page lists: Group - One or more classes/groups of annotations to apply to variant calls. What type of group or class is "Standard", "Experiments" or "WorkInProgress?" Does "class" refer to a Java "class" in a similar way that annotations are "arguments?" Any clarification would be very helpful. Thanks, Mike
Hi Mike, Apologies for the delay in reply, your message was threaded under an announcement (perhaps accidentally sent as a reply to that thread?). For GATK, we are not offering support yet as the pipeline is still considered beta. Most tool that are only on Test, and not on Main, are considered to be the same. That said, I can let you know that the tool is under active development, may change at any time, and comments about the current implementation is welcomed at galaxy development list. http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result Take care, Jen Galaxy team On 11/15/11 12:31 PM, Mike Dufault wrote:
Hello all, I am trying to run through the GATK pipeline on the Galaxy Test page. I have a question related to the UnifiedGenotyper wrapper page. At the bottom of the page, I choose the "Advanced" tab for "Basic or Advanced Analysis options." After the automatically refreshed, I choose the "Annotation Types" that I was interested in. Then below that are options for "Annotation Interfaces/Groups:" What are these options used for? I have looked all over the web, on the GATK wiki and at the GATK Q&A page (located at getsatisaction.com) without any luck. Are these options important? The description located at the bottom of the page lists: Group - One or more classes/groups of annotations to apply to variant calls. What type of group or class is "Standard", "Experiments" or "WorkInProgress?" Does "class" refer to a Java "class" in a similar way that annotations are "arguments?" Any clarification would be very helpful. Thanks, Mike
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participants (3)
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Dave Clements -
Jennifer Jackson -
Mike Dufault