Talk:GotCloud

Organization of the GotCloud pages on this wiki

The main page is http://genome.sph.umich.edu/wiki/GotCloud .

Setup instructions and documentation:

• 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:_Reference_Files
• http://genome.sph.umich.edu/wiki/AWS_Resources
  • http://genome.sph.umich.edu/wiki/Amazon_Single_Node
  • http://genome.sph.umich.edu/wiki/Amazon_Storage
  • http://genome.sph.umich.edu/wiki/StarCluster

Documentation of steps in the GotCloud 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:_Variant_Calling_Pipeline
• http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options
• http://genome.sph.umich.edu/wiki/GotCloud:_GenomeSTRiP_Pipeline
• http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline

Documentation of pieces of GotCloud:

• http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling
• http://genome.sph.umich.edu/wiki/GotCloud:_Filters
• http://genome.sph.umich.edu/wiki/VcfCooker
• http://genome.sph.umich.edu/wiki/Understanding_VerifyBamID_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/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions)

Configuration:

• http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers BATCH_OPTS)

Tutorials:

• http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo
• http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo_Setup
• http://genome.sph.umich.edu/wiki/Tutorial:_Low_Pass_Sequence_Analysis

Pages for developers:

• http://genome.sph.umich.edu/wiki/Releasing_GotCloud
• http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2

Other:

• http://genome.sph.umich.edu/wiki/GotCloud:_FAQs
• http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions

Event-specific pages:

• http://genome.sph.umich.edu/wiki/Short_Workshops links to all of them (or their parents)

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/Tutorial:_GotCloud
• http://genome.sph.umich.edu/wiki/AWS_Resources
• http://genome.sph.umich.edu/wiki/Amazon_Snapshot
• http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2
• http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (FA_REF has since been renamed.)
• http://genome.sph.umich.edu/wiki/UMAKE
• http://genome.sph.umich.edu/wiki/Mount_S3_Volume
• http://genome.sph.umich.edu/wiki/GotCloud:_AMIs
• http://genome.sph.umich.edu/wiki/GBR60vc.conf