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Talk:GotCloud (view source)

Revision as of 16:40, 1 April 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 and documentation:
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Pages that document or help with installation:
 
* 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 pieces of GotCloud:
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Pages that document steps in the GotCloud pipeline:
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* 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
 
** http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Sub-Pipelines
 
** 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
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* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options
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** http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options (sub-page)
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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
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Pages that document pieces of GotCloud:
 
* http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling
 
* 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/Understanding_QPLOT_output
 
* http://genome.sph.umich.edu/wiki/Understanding_QPLOT_output
 
* http://genome.sph.umich.edu/wiki/Understanding_vcf-summary_output
 
* 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:_Genetic_Reference_and_Resource_Files (documentation and instructions)
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* http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline
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Configuration:
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Pages that explain configuration:
 
* http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers <code>BATCH_OPTS</code>)
 
* http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers <code>BATCH_OPTS</code>)
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Pages for developers:
 
Pages for developers:
 
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud
 
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud
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* http://genome.sph.umich.edu/wiki/Git_FAQs
 
* 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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Other pages:
 
* http://genome.sph.umich.edu/wiki/GotCloud:_FAQs
 
* http://genome.sph.umich.edu/wiki/GotCloud:_FAQs
 
* http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions
 
* 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/Short_Workshops links to all of them (or their parents)
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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)
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* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG
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* 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_2
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** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_5
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** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_6
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** http://genome.sph.umich.edu/wiki/Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8
      
Pages of which some ought to be hidden, deleted, or heavily re-worked:
 
Pages of which some ought to be hidden, deleted, or heavily re-worked:
Pjvh
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