StarCluster: Difference between revisions
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The tasks to be completed are: | The tasks to be completed are: | ||
* Install starcluster on a machine you use | * Install and configure starcluster on a machine you use. | ||
* Create an AWS cluster | * Create an AWS cluster | ||
* Install the Pipeline software on the master node | * Install the Pipeline software on the master node | ||
* Create storage for your sequence data and make it available for the software | * Create storage for your sequence data and make it available for the software | ||
* Run the Pipeline 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 [http://genome.sph.umich.edu/wiki/Pipelines]. | |||
'''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). | |||
<code> | |||
</code> | |||
Revision as of 10:48, 29 October 2012
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).
