Atlas AWS Auto Download

A Python tool for automatically downloading BGI sequencing data from AWS S3 bucket with configuration file support.

Features

• 🔬 BGI Specific: Optimized for downloading BGI sequencing data from AWS S3
• 🔐 Secure: Supports AWS access keys and region configuration
• 📁 Flexible: Configurable S3 bucket and folder paths for different projects
• 📝 Logging: Comprehensive logging of all download operations
• 🚀 Progress: Visual progress bars for large sequencing data downloads
• ⚙️ Configurable: Simple configuration file format for BGI project settings
• 📊 Batch Processing: Efficiently handles multiple sequencing files and directories

Installation

From PyPI (Recommended)

pip install atlas-aws-autodownload

From Source

git clone https://github.com/yourusername/atlas-aws-autodownload.git
cd atlas-aws-autodownload
pip install -e .

Usage

Command Line Interface

After installation, you can use the atlas-aws-download command to download BGI sequencing data:

# Download to current directory
atlas-aws-download bgi_config.txt

# Download to specific directory
atlas-aws-download bgi_config.txt -o ./sequencing_data

# Download specific project data
atlas-aws-download project_config.txt -o ./projects/BGI_2024

Command Line Help

$ atlas-aws-download -h

Python API

from atlas_aws_autodownload import aws_download

# Download BGI sequencing data
aws_download("bgi_config.txt", "./sequencing_data")

# Download specific project
aws_download("project_config.txt", "./projects/BGI_Project_2024")

Configuration File Format

Create a configuration file with the following format for BGI sequencing data:

Project:***
Alias ID:***
S3 Bucket:***
Account:***
Password:***
Region:***
Aws_access_key_id:***
Aws_secret_access_key:***

Note:

• The tool also supports s3:// URI format in the configuration file
• For BGI projects, typically use ap-southeast-1 region (Singapore)
• Project names usually follow BGI naming conventions

Note: The tool also supports s3:// URI format in the configuration file.

Requirements

• Python 3.7+
• boto3 (for AWS S3 access)
• tqdm (for progress bars)

Typical Use Cases

• BGI Sequencing Data: Download raw sequencing data from BGI's AWS S3 storage
• Project Management: Organize downloads by project, sample, or experiment
• Batch Processing: Handle multiple sequencing runs and data types
• Data Transfer: Efficiently transfer large sequencing datasets to local storage

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Support

If you encounter any issues or have questions, please:

1. Check the Issues page
2. Create a new issue if your problem isn't already reported
3. Contact the maintainers at your.email@example.com

Changelog

Version 1.0.0

• Initial release
• Basic S3 download functionality
• Configuration file support
• Command line interface
• Progress bars and logging