StarCluster

Back to the beginning [1]

If you have access to your own cluster, your task will be much simpler. Install the Pipeline software (links at [2]) and run it as descibed on the same pages.

For those who are not so lucky to have access to a cluster, AWS provides an alternative. You may run the pipeline software on a cluster created in AWS. One tool that makes the creation of a cluster of AMIs (Amazon Machine Instances) is StarCluster (see http://star.mit.edu/cluster/).

The following shows an example of how you might use starcluster to create and AWS cluster and set it up to run the Pipeline.

We will use starcluster to launch a set of AWS instances. There are many details setting up starcluster and this is not intended to explain all of the many variations you might choose, but should provide you a working example.

The tasks to be completed are:

• Install and configure starcluster on a machine you use.
• Create an AWS cluster
• Install the Pipeline software on the master node
• Create storage for your sequence data and make it available for the software
• Run the Pipeline software

Installing and configuring starcluster on your machine is described at http://star.mit.edu/cluster/. Only the second step will be covered here, as the others are described at [3].

StarCluster Configuration Example

StarCluster creates a model configuration file in ~/.starcluster/config and you are instructed to edit this and set the correct values for the variables. Here is an example of a config file that we used (with some details changed of course).