MOMMA docker container hosted on AWS ECR used to create containers in the cloud.
Please do not share this repository, algorithm code contained within, or containers with others.
Also note that all Docker containers are currently hosted in AWS. You may build the containers using the Dockerfiles located in each algorithm's directory.
Each container takes the name of a reach file as an argument. This file contains a list of reaches or sets of reaches where each reach identifier or set is on one line.
- EFS Input is mounted to the container at
/mnt/data/input - EFS Output is mounted to the container at
/mnt/data/output
AWS_BATCH_JOB_ARRAY_INDEX is used to determine the reach identifier to process for all containers. The index value is used to retrieve a line in a file that lists all reach identifiers to be processed.
There is a script to deploy the Docker container image and Terraform AWS infrastructure found in the deploy directory.
Script to deploy Terraform and Docker image AWS infrastructure
REQUIRES:
- jq (https://jqlang.github.io/jq/)
- docker (https://docs.docker.com/desktop/) > version Docker 1.5
- AWS CLI (https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html)
- Terraform (https://developer.hashicorp.com/terraform/tutorials/aws-get-started/install-cli)
Command line arguments:
[1] registry: Registry URI [2] repository: Name of repository to create [3] prefix: Prefix to use for AWS resources associated with environment deploying to [4] s3_state_bucket: Name of the S3 bucket to store Terraform state in (no need for s3:// prefix) [5] profile: Name of profile used to authenticate AWS CLI commands
Example usage: ``./deploy.sh "account-id.dkr.ecr.region.amazonaws.com" "container-image-name" "prefix-for-environment" "s3-state-bucket-name" "confluence-named-profile"`
Note: Run the script from the deploy directory.