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 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 starcluster config file with care.

####################################
## StarCluster Configuration File ##
####################################
[global]
DEFAULT_TEMPLATE=myexample

#############################################
## AWS Credentials Settings
#############################################
[aws info]
AWS_ACCESS_KEY_ID = AKImyexample8FHJJF2Q
AWS_SECRET_ACCESS_KEY = fthis_was_my_example_secretMqkMIkJjFCIGf
AWS_USER_ID=199998888709 

AWS_REGION_NAME = us-west-2                 # Choose your own region
AWS_REGION_HOST = ec2.us-west-2.amazonaws.com
AWS_S3_HOST = s3-us-west-2.amazonaws.com

###########################
## EC2 Keypairs
###########################
[key west2_starcluster]
KEY_LOCATION = ~/.ssh/AWS/west2_starcluster_key.rsa   # Same region

###########################################
## Define Cluster
##   starcluster start -c west2_starcluster  nameichose4cluster
###########################################
[cluster myexample]
KEYNAME = west2_starcluster                 # Name I chose
CLUSTER_SIZE = 4                            # Number of nodes
CLUSTER_SHELL = bash

#  Choose the base AMI:  starcluster listpublic
#   (http://star.mit.edu/cluster/docs/0.93.3/faq.html)
NODE_IMAGE_ID = ami-c6bd30f6
AVAILABILITY_ZONE = us-west-2a              # Region again!
NODE_INSTANCE_TYPE = m1.medium              # 4G memory should work for Pipeline

Create Your Cluster

 starcluster start -c myexample myseq-example
 StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
 Software Tools for Academics and Researchers (STAR)
 Please submit bug reports to starcluster@mit.edu

 >>> Validating cluster template settings...
 >>> Cluster template settings are valid
 >>> Starting cluster...
     [lines deleted]

Set Up Master Node, Login as root

 starcluster sshmaster myseq-example
 StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
 Software Tools for Academics and Researchers (STAR)
   [lines deleted]

 #   Install Pipeline software just like says in debian package
 mkdir debs
 cd debs
 wget ftp://share.sph.umich.edu/biopipe/current-align.deb
   [lines deleted]
 wget ftp://share.sph.umich.edu/biopipe/current-umake.deb
   [lines deleted]

 dpkg -i debs/current-align*.deb debs/current-umake*.deb
   [lines deleted]