GotCloud

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.

Join in GotCloud mailing list

Please join in the GotCloud Google Group to ask / discuss / comment about these pipelines.

AWS Specific Setup

Preparation in AWS

You may run the GotCloud software in several modes:

• On your own hardware running Ubuntu or Redhat/CentOS. See the instructions about installing the software below.
• On any EC2 instance that uses Ubuntu or Redhat/CentOS distribution. You can install the software as described below, or create a volume using our snapshot (see Amazon Snapshot).
• On an EC2 cluster instance created by StarCluster. You can install the software as described below, or create a volume using our snapshot (see Amazon Snapshot).

Details for the Choices of Your Install

• Create a volume using our Amazon Snapshot
• Preparing a Cluster using StarCluster
• Notes on sequence data preparation in Amazon Storage.

Resources / Cost

• AWS Resources

Development Notes

• Creating an AMI on EC2
• Mount S3 Volume

General Usage

Install the Software (for AWS or a local machine)

• Installing the software as a debian package
• Installing the software as a red hat package

Run the Software

• Mapping Pipeline
• Variant Calling Pipeline (UMAKE)