Construction of viral contigs using [Minia/coronaSPAdes]+CheckV on AWS Batch

Source

Taken from: "Orchestrating an Application Process with AWS Batch using AWS CloudFormation"

But I removed all the CodeCommit stuff (replaced by deploy-docker.sh manual deployment to ECR).

Amazon Elastic Container Registry (ECR) is used as the Docker container registry. An AWS Batch job is manually triggered by submit_job.py.

Provided CloudFormation template has all the services (VPC, Batch managed, IAM roles, EC2 env)

Installation

Execute the below commands to spin up the infrastructure cloudformation stack.

./spinup.sh
./deploy-docker.sh

If you ever recreate the stack (e.g. after cleanup.sh), you don't need to run deploy-docker.sh unless the Dockerfile or scripts in src/ were modified.

Running an assembly job

1. ./submit_job.py SRRxxxxxx
2. In AWS Console > Batch, monitor how the job runs.

Code Cleanup

In short:

./cleanup.sh

Which deletes the CloudFormation stack.

What it doesn't do (need sto be done manually):

AWS Console > ECR - serratus-batch-assembly-job - delete the image(s) that are pushed to the repository

License

This library is licensed under the MIT-0 License. See the LICENSE file.