DIA-NN Docker Container

A production-ready Docker container for DIA-NN, a cutting-edge software tool for data-independent acquisition (DIA) proteomics data processing.

Overview

DIA-NN is a powerful software solution for analyzing DIA proteomics data. This containerized version offers:

• Simplified installation and deployment
• Consistent runtime environment across platforms
• Pre-configured dependencies and optimizations
• Support for both DIA-NN 1.9.2 and 2.0

⚠️ Important License Information

Please note the following license restrictions:

• DIA-NN 1.8.1 and earlier: License permits distribution of Docker/Singularity images
• DIA-NN 1.9.2 and 2.0: License does not permit distribution of pre-built images

Before using this container, ensure compliance with the version-specific license:

• DIA-NN 1.9.2 License
• DIA-NN 2.0 License

Technical Specifications

Container Details

• Base Image: ubuntu:22.04
• Available Versions:
  • DIA-NN 1.9.2
  • DIA-NN 2.0
• Architecture Support: amd64/x86_64

Included Dependencies

Category	Components
Build Tools	g++, build-essential, cmake
Compression	zlib1g-dev, libbz2-dev
Libraries	libboost-all-dev
Utilities	wget, locales, unzip

Installation & Usage

Building the Images

Standard Build (x86_64/amd64)

# Build DIA-NN 1.9.2
cd diann-1.9.2/
docker build -t diann:1.9.2 .

# Build DIA-NN 2.0
cd diann-2.0/
docker build -t diann:2.0 .

Platform-Specific Build (e.g., AMD Mac)

# Build DIA-NN 1.9.2
cd diann-1.9.2/
docker buildx build --platform linux/amd64 . --tag diann:1.9.2

# Build DIA-NN 2.0
cd diann-2.0/
docker buildx build --platform linux/amd64 . --tag diann:2.0

Basic Usage

# View DIA-NN help
docker run -it diann:1.9.2 diann --help
docker run -it diann:2.0 diann --help

# Process data (example)
docker run -v /path/to/data:/data -it diann:2.0 diann \
  --f /data/input.raw \
  --lib /data/library.tsv \
  --out /data/results.tsv

Data Mounting

When processing data, mount your local directories using Docker volumes:

docker run -v /local/path:/container/path -it diann:2.0 diann [commands]

Performance Tips

1. Memory Allocation: Ensure sufficient memory is allocated to Docker
2. Storage: Use fast storage (SSD recommended) for data directories
3. CPU: DIA-NN benefits from multiple cores; allocate accordingly
4. Temp Files: Consider mounting a temp directory for large analyses

Troubleshooting

Common issues and solutions:

1. Permission Errors

   # Fix file ownership issues
   chown -R $(id -u):$(id -g) /path/to/output

2. Memory Issues

   • Increase Docker memory allocation in Docker Desktop settings
   • Use --memory flag to specify container memory limit

Maintainers

• Yasset Perez-Riverol (@ypriverol) - [email protected]
• Ryan Smith - [email protected]

Contributing

We welcome contributions! Please:

1. Fork the repository
2. Create a feature branch
3. Submit a pull request

Citation

If you use this container in your research, please cite:

@software{diann_docker,
  author = {Perez-Riverol, Yasset and Smith, Ryan},
  title = {DIA-NN Docker Container},
  year = {2025},
  url = {https://github.com/ypriverol/diann-container}
}