QuantMS Docker Containers

A repository of production-ready Docker and Singularity containers for proteomics tools, including DIA-NN and OpenMS.

Overview

This repository provides containerized versions of popular proteomics tools:

• DIA-NN: A powerful software solution for analyzing DIA proteomics data
• OpenMS: A versatile open-source software for mass spectrometry data analysis

These containerized versions offer:

• Simplified installation and deployment
• Consistent runtime environment across platforms
• Pre-configured dependencies and optimizations
• Automatic builds and releases via GitHub Actions
• Both Docker and Singularity container formats

Container Availability

DIA-NN Containers

Important: Due to licensing restrictions, DiaNN containers are not publicly distributed. Users must build these containers locally:

# Build Docker container
cd diann-2.1.0/
docker build -t diann:2.1.0 .

# Build Singularity container from Docker
singularity build diann-2.1.0.sif docker-daemon://diann:2.1.0

OpenMS Containers

OpenMS containers are publicly available and can be pulled directly:

Container Type	Version	URL
Docker	date-tagged	ghcr.io/bigbio/openms-tools-thirdparty:YYYY.MM.DD
Docker	latest	ghcr.io/bigbio/openms-tools-thirdparty:latest
Singularity	date-tagged	oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:YYYY.MM.DD
Singularity	latest	oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest

The date tag (YYYY.MM.DD) is manually set for each release to ensure version stability.

⚠️ Important License Information

Please note the following license restrictions:

• DIA-NN: Please review the DIA-NN 2.1.0 license before using
• OpenMS: OpenMS is available under the BSD 3-Clause License

Technical Specifications

DIA-NN Container Details

• Base Image: ubuntu:22.04
• Available Version: DIA-NN 2.1.0
• Architecture Support: amd64/x86_64

OpenMS Container Details

• Sourced from: ghcr.io/openms/openms-tools-thirdparty
• Architecture Support: amd64/x86_64

Installation & Usage

Using Pre-built Docker Images

# Pull DIA-NN Docker image
docker pull ghcr.io/bigbio/diann:latest

# Pull OpenMS Docker image
docker pull ghcr.io/bigbio/openms-tools-thirdparty:latest

Using Pre-built Singularity Images

# Pull OpenMS Singularity image
singularity pull openms.sif oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest

Building the Images Locally

DIA-NN Build

# Build DIA-NN 2.1.0
cd diann-2.1.0/
docker build -t diann:2.1.0 .

Basic Usage

DIA-NN Usage

# View DIA-NN help
docker run -it diann:2.1.0 diann --help

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

DIANN Usage in quantms pipeline

After you build your container, you chave to add a custom configuration file to resolve the diann container. You can do this by creating a file called diann_config.yml in the quantms directory. The content of the file should be:

process {
    withLabel: diann {
        container = '/path-singularity-file/diann-2.0.0.sif'
    }
}

Please check quantms documentation for more information about how to run the pipeline with custom configurations.

OpenMS Usage

# View OpenMS tools
docker run -it ghcr.io/bigbio/openms-tools-thirdparty:latest ls /usr/local/bin/

# Run an OpenMS tool (example)
docker run -v /path/to/data:/data -it ghcr.io/bigbio/openms-tools-thirdparty:latest \
  PeakPickerHiRes -in /data/input.mzML -out /data/output.mzML

Data Mounting

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

docker run -v /local/path:/container/path -it ghcr.io/bigbio/diann:latest diann [commands]

CI/CD Workflow

This repository includes a GitHub Actions workflow that builds and syncs all containers:

QuantMS Containers Build and Sync: A combined workflow that:

1. First builds and pushes DIA-NN Docker and Singularity containers
2. Then syncs OpenMS containers from the official repository to BigBio

The workflow is triggered by:

• Pushes to the main branch
• Pull requests (for DiaNN builds only)
• Release events (which also tag images as "latest")
• Manual dispatch with configurable options

This sequential approach ensures that all containers are built and pushed in a coordinated manner.

Performance Tips

1. Memory Allocation: Ensure sufficient memory is allocated to Docker
2. Storage: Use fast storage (SSD recommended) for data directories
3. CPU: These tools benefit 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

3. OpenMS Singularity Pull Issues

   If you encounter an error when pulling OpenMS Singularity images:

   FATAL: While pulling image from oci registry: error fetching image to cache: failed to get checksum for oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:YYYY.MM.DD: GET https://ghcr.io/v2/bigbio/openms-tools-thirdparty-sif/manifests/YYYY.MM.DD: DENIED: requested access to the resource is denied
   

   Try the following:

   • Verify you're using the correct date tag format (YYYY.MM.DD)
   • Check the workflow logs to confirm the exact version tag that was published
   • If using Nextflow, try increasing the pull timeout:

     nextflow run bigbio/quantms -r dev -profile test_lfq,singularity -with-singularity --singularity.pullTimeout '2h'
     

   • If the issue persists, please open an issue on the GitHub repository

4. DiaNN Container Issues

   Remember that DiaNN containers must be built locally due to licensing restrictions:

   • Follow the build instructions in the "DiaNN Containers" section
   • For quantms pipeline, specify your local DiaNN container path in a custom config file:

     process {
         withLabel: diann {
             container = '/path-to-your-singularity-file/diann-2.1.0.sif'
         }
     }

Maintainers

• Yasset Perez-Riverol (@ypriverol) - ypriverol@gmail.com

Contributing

We welcome contributions! Please:

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

Citation

If you use these containers in your research, please cite:

@software{quantms_docker,
  author = {Perez-Riverol, Yasset},
  title = {QuantMS Docker Containers},
  year = {2025},
  url = {https://github.com/ypriverol/quantms-docker}
}