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and run it as descibed on the same pages.
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.
For those who are not so lucky to have access to a cluster, Amazon Web Services (AWS) provides an alternative.
You may run the pipeline software on a cluster created in AWS.
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
One tool that makes the creation of a cluster of AMIs (Amazon Machine Instances) is
The tasks to be completed are:
The tasks to be completed are:
* Install and configure starcluster on a machine you use.
* Install the ec2 tools package (ec2-api-tools for Ubuntu) on your machine (optional)
* Install and configure starcluster on your machine (required)
* Create an EBS volume based on the GotCloud snapshot
* Configure StarCluster to use the volume just created
* Create an AWS cluster
* Create an AWS cluster
* 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/.
Installing and configuring StarCluster on your machine is described at http://star.mit.edu/cluster/.
'''StarCluster Configuration Example'''
'''StarCluster Configuration Example'''
to edit this and set the correct values for the variables.
to edit this and set the correct values for the variables.
Here is a highly simplified example of a config file that should work.
Here is a highly simplified example of a config file that should work.
Please note there are many things you might want to choose, so craft the
Please note there are many things you might want to choose, so craft the config file with care.
You'll need to specify nodes with 4GB of memory (type m1.medium) and make sure each node has access to the input and output data for the step being run.
<code>
<code>
###########################################
###########################################
[cluster <font color='red'>myexample</font>]
[cluster <font color='red'>myexample</font>]
KEYNAME = west2_starcluster # Name I chose
KEYNAME = westcluster # Name I chose
CLUSTER_SIZE = 4 # Number of nodes
CLUSTER_SIZE = 4 # Number of nodes
CLUSTER_SHELL = bash
CLUSTER_SHELL = bash
# Choose the base AMI: starcluster listpublic
# Choose the base AMI using starcluster listpublic
# (http://star.mit.edu/cluster/docs/0.93.3/faq.html)
# (http://star.mit.edu/cluster/docs/0.93.3/faq.html)
NODE_IMAGE_ID = ami-c6bd30f6
NODE_IMAGE_ID = ami-c6bd30f6
<code>
<code>
'''starcluster start -c <font color='red'>myexample</font> myseq-example'''
'''starcluster start -c <font color='red'>westcluster</font> myseq-example'''
StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
Software Tools for Academics and Researchers (STAR)
Software Tools for Academics and Researchers (STAR)
