Steck

Project Logan assembly analysis toolkit Adapted from https://gitlab.pasteur.fr/rchikhi_pasteur/logan-analysis/

Warning / Costs

Running this system costs real $'s in your AWS bill. Spot instances with local disk are 0.0022$ per vCPU-hour (https://instances.vantage.sh/aws/ec2/c5d.4xlarge). E.g. a 10,000 vCPU workload during 10 hours is 220$ total. Do a test run and use AWS Cost Explorer 24 hours later to see real costs.

Initialize Steck

1. 1_deploy_container.sh push : Build the container defined in env/Dockerfile, importing reference sequence sets from ref/. Deploy the the Steck ECR.

2. 2_form_cloud.sh : Build the Steck-batch cloud environment using CloudFormation YAML.

Running Steck

1. run_steck.sh <runs/job_parameters.list> : Submits a job-queue for Steck to submit jobss.

Notes:

Where dest_bucket is the name of the destination bucket, and nb_jobs is the number of jobs to submit (can't exceed 10000). The more jobs, the faster it will be. Each job takes 1 vcpu and 1.5G memory. Destination bucket file structure is decided by the task.

Tests

• env/1_deploy_contiainer.sh test : Run a local unit test of the steck-container
• env/0_run-test.sh : Run a test of Batch jobs

Clean-up

Manually delete the CloudFormation stack. Also delete the ECR image.