🧬 Kubefold Manager

A utility service for managing protein folding tasks with AWS infrastructure support.

About

Kubefold Manager is a versatile utility designed to handle various aspects of protein folding workflows. It provides functionality for:

1. Handling and validating input data
2. Uploading prediction artifacts to S3
3. Sending SMS notifications about task completion

Developed as part of the Kubefold project ecosystem for protein structure prediction.

Usage

Environment Variables

The application is configured using the following environment variables:

Required for all operations:

• INPUT_PATH: Directory path where input files are located
• OUTPUT_PATH: Directory path where output files are generated

For input processing:

• ENCODED_INPUT: Base64-encoded JSON input data for folding tasks

For artifact uploading:

• BUCKET: S3 bucket name where artifacts will be uploaded

For notifications:

• NOTIFICATION_PHONES: Comma-separated list of phone numbers to notify
• NOTIFICATION_MESSAGE: Custom message to send in the notification

Docker

docker run -e INPUT_PATH=/data/input \
           -e OUTPUT_PATH=/data/output \
           -e BUCKET=my-result-bucket \
           -v /local/input:/data/input \
           -v /local/output:/data/output \
           kubefold/manager

AWS Credentials

For S3 uploads and SNS notifications, the application uses the AWS SDK's default credential provider chain. Ensure appropriate AWS credentials are available through:

• Environment variables (AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY)
• AWS credentials file
• IAM roles for Amazon EC2 or ECS tasks

Features

• Process and validate protein folding input data
• Upload prediction results to Amazon S3
• Send SMS notifications via Amazon SNS
• Containerized for easy deployment in cloud environments

Building from Source

git clone https://github.com/kubefold/manager.git
cd manager
go build -o manager ./cmd/main.go

Related Projects

• kubefold/downloader: Utility for downloading protein databases