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 = 8 # Number of nodes
CLUSTER_SHELL = bash
# This is the 64 bit AMI from starcluster
NODE_IMAGE_ID = ami-c6bd50f6
AVAILABILITY_ZONE = us-west-2a # Region again!
NODE_INSTANCE_TYPE = m1.large # 8G memory should work for Pipeline
