Difference between revisions of "GotCloud"
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Please join in the [http://groups.google.com/group/GotCloud GotCloud Google Group] to ask / discuss / comment about these pipelines. | Please join in the [http://groups.google.com/group/GotCloud GotCloud Google Group] to ask / discuss / comment about these pipelines. | ||
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== Setup == | == Setup == | ||
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* Notes on sequence data preparation in [[Amazon Storage|Amazon Storage]]. | * Notes on sequence data preparation in [[Amazon Storage|Amazon Storage]]. | ||
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* [[Mapping Pipeline]] | * [[Mapping Pipeline]] | ||
* [[Variant Calling Pipeline (UMAKE)]] | * [[Variant Calling Pipeline (UMAKE)]] | ||
Revision as of 15:58, 19 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.
Join in GotCloud mailing list
Please join in the GotCloud Google Group to ask / discuss / comment about these pipelines.
Setup
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
- Install the software as a debian package
- Install the software as a red hat package
- Create a volume using our Amazon Snapshot
- Create an EC2 cluster instance using StarCluster
Resources / Cost
Development Notes
- Creating an AMI on EC2
- Mount S3 Volume
- Notes on sequence data preparation in Amazon Storage.
