Difference between revisions of "GotCloud"

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Either pipeline can be run on a single machine or on a cluster of machines.
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= Genomes on the Cloud (GotCloud)=
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To handle the increasing volume of next generation sequencing and genotyping data, we created and developed software pipelines called '''Genomes on the Cloud (GotCloud)''' for:
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*Mapping
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*Variant Calling
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Key Features:
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*Scalable to tens of thousands of samples
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*Robust against unexpected system failure using GNU make
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*Massively parallel, can run hundreds of jobs
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*Easy to use - Automates series of configurable steps
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*Available on Amazon Web Services (AWS) Elastic Compute Cloud (EC2)
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*Run on local machines/clusters
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*Available via Debian Packages
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The following describes the use of this software with the Amazon Web Services (https://aws.amazon.com/),
 
The following describes the use of this software with the Amazon Web Services (https://aws.amazon.com/),
but you can just as easily use it on your own machine(s) by just installing it.
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but you can just as easily use the pipelines on your own machine(s) by just installing them.
  
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== AWS Specific Setup ==
 
'''Preparation in AWS'''
 
'''Preparation in AWS'''
  
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* Notes on sequence data preparation in [[Amazon Storage|Amazon Storage]].
 
* Notes on sequence data preparation in [[Amazon Storage|Amazon Storage]].
  
'''Install the Software'''
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'''Resources / Cost'''
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* [[AWS Rresources|AWS Resources]]
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'''Development Notes'''
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* [[Creating an AMI on EC2]]
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* [[Mount S3 Volume]]
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== General Usage ==
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'''Install the Software (for AWS or a local machine)'''
  
 
* Installing the software as a [[Pipeline Debian Package|debian package]]
 
* Installing the software as a [[Pipeline Debian Package|debian package]]
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* [[Alignment Pipeline]]  
 
* [[Alignment Pipeline]]  
 
* [[Variant Calling Pipeline (UMAKE)]]
 
* [[Variant Calling Pipeline (UMAKE)]]
 
'''Resources / Cost'''
 
 
* [[AWS Rresources|AWS Resources]]
 
 
 
 
'''Development Notes'''
 
 
* [[Creating an AMI on EC2]]
 
* [[Mount S3 Volume]]
 

Revision as of 14:45, 5 November 2012

Genomes on the Cloud (GotCloud)

To handle the increasing volume of next generation sequencing and genotyping data, we created and developed software pipelines called Genomes on the Cloud (GotCloud) for:

  • Mapping
  • Variant Calling

Key Features:

  • Scalable to tens of thousands of samples
  • Robust against unexpected system failure using GNU make
  • Massively parallel, can run hundreds of jobs
  • Easy to use - Automates series of configurable steps
  • Available on Amazon Web Services (AWS) Elastic Compute Cloud (EC2)
  • Run on local machines/clusters
  • Available via Debian Packages


The following describes the use of this software with the Amazon Web Services (https://aws.amazon.com/), but you can just as easily use the pipelines on your own machine(s) by just installing them.


AWS Specific Setup

Preparation in AWS

Resources / Cost

Development Notes

General Usage

Install the Software (for AWS or a local machine)

Run the Software