6.4 Launch Amazon EC2 Spot Instances via starcluster

Finally, users can launch a Amazon EC2 Spot Instance via starcluster, to process a WGS / WES sample using the selected workflow from section 6.2. The following steps are required:

1) Users need to copy the SGE plugins into the starcluster folder in the tracking database instance:

 cp -r /path/to/vcpa-pipeline/plugins ~/.starcluster/

2) Go into the VCPA pipeline bin folder:

 cd /path/to/vcpa-pipeline/bin

3) Users can launch the Amazon EC2 spot instance to process one sample using the following command:

 starcluster start -c smallcluster --bid=${price} -U ${worflow_path} -P ${HOST_PREFIX}-${PROJECT_ID}-${SAMPLE_NAME}

price: bidding cost of the instance

workflow_path: /path/to/vcpa-pipeline/bin/${PROJECT_WORKFLOW}_aws.sh

HOST_PREFIX: host name for the tracking database

project_id: this is the project ID outputted by Section 3.2

sample_name: sample name (note this needs to match the sample name of the input file in the S3 bucket)