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GotCloud: Amazon Demo (view source)

Revision as of 12:55, 31 October 2014

381 bytes removed ,  12:55, 31 October 2014
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* [[SeqShop: Variant Calling and Filtering for INDELs Practical]]
 
* [[SeqShop: Variant Calling and Filtering for INDELs Practical]]
 
* [[SeqShop: Analysis of Structural Variation Practical]]
 
* [[SeqShop: Analysis of Structural Variation Practical]]
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To run this Demo on an Amazon Cluster rather than on a single node, see: [[StarCluster#Run_GotCloud_Demo_Using_StarCluster|StarCluster -> Run GotCloud Demo Using StarCluster]]
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== Starting up a Node ==
 
== Starting up a Node ==
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#:[[File:SnpSummary.png|700px]]
 
#:[[File:SnpSummary.png|700px]]
 
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
 
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
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=== Run GotCloud ldrefine ===
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Now run GotCloud ldrefine
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# <pre>gotcloud ldrefine --conf example/test.conf --outdir output --numjobs 8</pre>
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#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
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#: [[File:RunIndel.png|700px]]
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#:* This will take a few minutes to run.
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#:* GotCloud first generates a makefile, and then runs the makefile
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# When complete, GotCloud ldrefine will indicate success/failure
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#:[[File:LdrefineSuccess.png|700px]]
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==== Examining ldrefine Output ====
       
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11927...11931"

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