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Merge pull request #48 from aws-solutions-library-samples/dev
v1.13.3 maintenance release
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‎.gitignore‎

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tests/data/
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data/*
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.scratch
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release.sh

‎.gitlab-ci.yml‎

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‎.taskcat.yml‎

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‎CHANGELOG.md‎

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---
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## [1.13.3] - 2025-10-14
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### 1.13.3 Updates
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- Added region-specific deployment buttons to README.
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### 1.13.3 Fixed
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- Resolved container issues with AlphaFold2 and OpenFold
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---
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## [1.13.2] - 2025-09-10
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### 1.13.2 Fixed
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- Fix multiple issues with ESMFold inference script
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- Fix issue with version of numpy in RFDiffusion ontainer
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## [1.13.1] - 2025-05-28

‎README.md‎

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> [!IMPORTANT]
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> The examples provided in this repository are for experimental and educational purposes only. They demonstrate concepts and techniques but are not intended for direct use in production environments.
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> [!IMPORTANT]
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> The CloudFormation templates included in this repository only support deployment to the us-east-1, and us-east-2, eu-west-1, eu-west-2, eu-central-1, and ap-southwest-1 regions. For additional options, please refer to the [Drug Discovery Workflows for AWS HealthOmics](https://github.com/aws-samples/drug-discovery-workflows) project.
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## Contents
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1. [Overview](#1-overview)
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## 2. Quick Start
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NOTE: This procedure only supports the following AWS regions: eu-west-1, eu-west-2, eu-central-1, ap-southwest-1, us-east-1, and us-east-2
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1. Choose **Launch Stack** and (if prompted) log into your AWS account:
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[![Launch Stack](imgs/LaunchStack.jpg)](https://console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://aws-hcls-ml.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml)
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2. For **Stack Name**, enter a value unique to your account and region. Leave the other parameters as their default values and select **Next**.
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| Region | Launch URL |
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| ------ | ---------- |
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| eu-west-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-west-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-west-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
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| eu-west-2 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-west-2.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-west-2.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
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| eu-central-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-central-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-central-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
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| ap-southeast-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://ap-southeast-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-ap-southeast-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
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| us-east-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://us-east-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-us-east-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
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| us-west-2 | [![Launch Stack](imgs/LaunchStack.jpg)](https://us-west-2.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-us-west-2.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
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2. For **Stack Name**, enter a value unique to your account and region. Also update the *DeploymentRegion** parameter with the name of your current AWS region. Leave the other parameters as their default values and select **Next**.
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![Provide a stack name](imgs/name.png)
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3. Select **I acknowledge that AWS CloudFormation might create IAM resources with custom names**.
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4. Choose **Create stack**.
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### 4.2. AlphaFold
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[Version 2.3.2](https://github.com/deepmind/alphafold/releases/tag/v2.3.2) from 4/5/2023.
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Please visit [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold) for more information about the AlphaFold2 algorithm.
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Due to updates to the OpenMM module, GPU-accelerated relaxation is no longer available. All alphafold jobs now default to `use_gpu_relax=False`.
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The original AlphaFold 2 citation is
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```text

‎deploy.sh‎

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[ -z "$CODE_REPO_S3_BUCKET_NAME" ] && { CODE_REPO_S3_BUCKET_NAME="5d1a4b76751b4c8a994ce96bafd91ec9"; }
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zip -r code.zip * -x .\*/\* -x random_commands.sh -x analysis\* -x build\*
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aws s3 cp code.zip s3://$BUCKET_NAME/main/batch-protein-folding.zip
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aws s3 cp code.zip s3://${BUCKET_NAME}-${REGION}/main/batch-protein-folding.zip
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rm code.zip
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aws cloudformation package --template-file infrastructure/cloudformation/batch-protein-folding-cfn-root.yaml --output-template infrastructure/cloudformation/batch-protein-folding-cfn-packaged.yaml --region $REGION --s3-bucket $BUCKET_NAME --s3-prefix cfn

‎infrastructure/cloudformation/batch-protein-folding-cfn-container.yaml‎

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CodeRepoS3BucketName:
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Description: S3 Bucket Name to retrieve code zip
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Type: String
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Default: "aws-hcls-ml"
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Default: "5d1a4b76751b4c8a994ce96bafd91ec9-us-east-1"
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S3BucketARN:
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Description: S3 Bucket ARN
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Type: String

‎infrastructure/cloudformation/batch-protein-folding-cfn-root.yaml‎

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Parameters:
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ApplicationName:
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Description: Name for your application stack
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Type: String
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Default: BatchProteinFolding
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DeploymentRegion:
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Description: AWS region name for deployment. If deploying using the AWS console, this should match the region currently selected in the header menu.
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Type: String
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AllowedValues: ["ap-southeast-1", "eu-central-1", "eu-west-1", "eu-west-2", "us-east-1", "us-west-2"]
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LaunchSageMakerNotebook:
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Type: String
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Default: Y
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Type: String
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AllowedValues: [Y, N]
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CodeRepoS3BucketName:
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Description: S3 Bucket Name to retrieve code .zip
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CodeRepoS3BucketRootName:
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Description: S3 Bucket root name. This will be appended with the region name and used to retrieve the code .zip archive for CodeBuild
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CodeRepoS3BucketName: !Sub "${CodeRepoS3BucketRootName}-${DeploymentRegion}"
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CodeRepoS3BucketName: !Sub "${CodeRepoS3BucketRootName}-${DeploymentRegion}"
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CodeRepoS3BucketName: !Sub "${CodeRepoS3BucketRootName}-${DeploymentRegion}"
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CodeRepoS3BucketName: !Sub "${CodeRepoS3BucketRootName}-${DeploymentRegion}"
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CodeRepoS3BucketName: !Sub "${CodeRepoS3BucketRootName}-${DeploymentRegion}"
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