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Talk:GotCloud (view source)

Revision as of 00:17, 8 January 2016

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The main page is http://genome.sph.umich.edu/wiki/GotCloud .
 
The main page is http://genome.sph.umich.edu/wiki/GotCloud .
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Setup instructions:
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Setup instructions and documentation:
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Binary_Releases
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Binary_Releases
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Source_Releases
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Source_Releases
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** http://genome.sph.umich.edu/wiki/StarCluster
 
** http://genome.sph.umich.edu/wiki/StarCluster
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Documentation of steps in the GotCloud pipeline:
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Documentation of pieces of GotCloud:
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions)
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions)
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline
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** http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Sub-Pipelines
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options
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* http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Filters
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Filters
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* http://genome.sph.umich.edu/wiki/VcfCooker
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* http://genome.sph.umich.edu/wiki/Understanding_VerifyBamID_output
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* http://genome.sph.umich.edu/wiki/Understanding_QPLOT_output
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* http://genome.sph.umich.edu/wiki/Understanding_vcf-summary_output
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* http://genome.sph.umich.edu/wiki/GotCloud:_GenomeSTRiP_Pipeline
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* http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline
    
Configuration:
 
Configuration:
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Tutorials:
 
Tutorials:
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo
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* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo_Setup
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* http://genome.sph.umich.edu/wiki/Tutorial:_Low_Pass_Sequence_Analysis
    
Pages for developers:
 
Pages for developers:
 
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud
 
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud
 
* http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2
 
* http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2
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Other:
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* http://genome.sph.umich.edu/wiki/GotCloud:_FAQs
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* http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions
    
Event-specific pages:
 
Event-specific pages:
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* http://genome.sph.umich.edu/wiki/Short_Workshops lists all of these
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* http://genome.sph.umich.edu/wiki/SeqShop:_May_2015 (and sub-pages)
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* http://genome.sph.umich.edu/wiki/SeqShop:_December_2014 (and sub-pages)
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* http://genome.sph.umich.edu/wiki/SeqShop:_June_2014 (and sub-pages)
 
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG
 
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG
 
* http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM
 
* http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM
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** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8
 
** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8
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Pages that ought to be hidden or deleted:
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Pages of which some ought to be hidden, deleted, or heavily re-worked:
 
* http://genome.sph.umich.edu/wiki/GotCloud:_RedHat_Package
 
* http://genome.sph.umich.edu/wiki/GotCloud:_RedHat_Package
 
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud
 
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud
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* http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2
 
* http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (<code>FA_REF</code> has since been renamed.)
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (<code>FA_REF</code> has since been renamed.)
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* http://genome.sph.umich.edu/wiki/UMAKE
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* http://genome.sph.umich.edu/wiki/Mount_S3_Volume
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* http://genome.sph.umich.edu/wiki/GotCloud:_AMIs
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* http://genome.sph.umich.edu/wiki/GBR60vc.conf
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