QuantMS Docker Containers

A repository of production-ready Docker and Singularity containers for proteomics tools used in quantms pipelines, including DIA-NN, Relink, and OpenMS.

Overview

This repository provides containerized versions of popular proteomics tools:

• DIA-NN: A powerful software solution for analyzing DIA proteomics data
• Relink: Crosslinking mass spectrometry analysis pipeline (xiSEARCH, xiFDR, Scout)
• OpenMS: A versatile open-source software for mass spectrometry data analysis
• WiffConverter: SCIEX .wiff / .wiff.scan to indexed .mzML conversion via the bundled OneOmics.WiffConverter .NET assembly

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, DIA-NN containers are not publicly distributed. Users must build these containers locally or have access to the private ghcr.io/bigbio/diann registry.

Version	Directory	Key Features	Container Tag
1.8.1	diann-1.8.1/	Core DIA-NN, library-free analysis	ghcr.io/bigbio/diann:1.8.1
1.9.2	diann-1.9.2/	QuantUMS quantification, redesigned NN	ghcr.io/bigbio/diann:1.9.2
2.0.2	diann-2.0.2/	Parquet output, proteoform confidence	ghcr.io/bigbio/diann:2.0.2
2.1.0	diann-2.1.0/	Native .raw on Linux (bundles .NET SDK 8)	ghcr.io/bigbio/diann:2.1.0
2.2.0	diann-2.2.0/	Native .raw on Linux (bundles .NET SDK 8)	ghcr.io/bigbio/diann:2.2.0
2.3.2	diann-2.3.2/	Native .raw on Linux (bundles .NET SDK 8)	ghcr.io/bigbio/diann:2.3.2
2.5.0	diann-2.5.0/	Native .raw on Linux (bundles .NET SDK 8)	ghcr.io/bigbio/diann:2.5.0

Native Thermo .raw support (DIA-NN ≥ 2.1.0). Starting with 2.1.0, DIA-NN can read Thermo .raw files directly on Linux via bundled RawWrapper.dll / ThermoFisher.CommonCore.* libraries (targeting net8.0). At startup DIA-NN runs dotnet --list-sdks and, if no SDK is found, aborts with ERROR: cannot read .raw files, please download and install .NET Runtime 8.0.14 or later. The 2.1.0 / 2.2.0 / 2.3.2 / 2.5.0 images therefore install dotnet-sdk-8.0 (from Ubuntu 22.04 jammy-updates); no extra action is needed. DIA-NN ≤ 2.0.2 does not ship the Thermo reader on Linux and still requires external conversion (e.g. ThermoRawFileParser → .mzML).

# Build Docker container locally
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

Relink Container

The Relink container provides a complete crosslinking mass spectrometry analysis environment.

Component	Version	Description
xiSEARCH	1.8.11	Crosslink identification search engine
xiFDR	2.3.10	FDR estimation for crosslinked peptides
Scout	2.0.0	Crosslink analysis tool
pyOpenMS	latest	Python bindings for OpenMS
.NET Runtime	9.0	Required by Scout
Java JRE	21	Required by xiSEARCH and xiFDR

Container Type	Tag	URL
Docker	1.0.0	ghcr.io/bigbio/relink:1.0.0
Docker	latest	ghcr.io/bigbio/relink:latest
Singularity	1.0.0	oras://ghcr.io/bigbio/relink-sif:1.0.0

# Pull Relink Docker image
docker pull ghcr.io/bigbio/relink:latest

# Run xiSEARCH
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  java -jar /opt/xisearch/xiSEARCH.jar --help

# Run Scout
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  dotnet /opt/scout/Scout_Unix.dll --help

WiffConverter Container

The WiffConverter container wraps the upstream sciex/wiffconverter image (bundles Mono + OneOmics.WiffConverter.exe) and adds a small convert CLI on PATH. It is used by quantmsdiann to ingest AbSciex data natively (.wiff + companion .wiff.scan → indexed .mzML in one step, no separate indexing pass). The output is always an indexedmzML (the converter is invoked with --index).

Container Type	Tag	URL
Docker	0.10	ghcr.io/bigbio/wiffconverter:0.10
Singularity	0.10	oras://ghcr.io/bigbio/wiffconverter-sif:0.10

0.10 tracks the latest tag published by SCIEX on Docker Hub (2019-05-17).

# Convert a SCIEX .wiff (with its .wiff.scan next to it) to indexed mzML:
docker run --rm -v "$PWD:/data" ghcr.io/bigbio/wiffconverter:0.10 \
    convert --input /data/sample.wiff --output /data/sample.mzML --mode centroid

# Flags:
#   --input   SCIEX .wiff file (companion .wiff.scan must sit next to it).
#   --output  Destination indexed mzML file.
#   --mode    'centroid' (default) or 'profile'.
#   --log     Path to keep the converter log (default: only kept on failure).

On failure the wrapper prints a banner with the input/output/mode and the last 40 lines of the underlying SCIEX converter log, so most issues (missing .wiff.scan, locked output, unsupported acquisition) are diagnosable from the console without re-running.

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.

License Information

Please note the following license restrictions:

• DIA-NN: Custom academic license with restrictions. Please review the DIA-NN license before using. No commercial use or cloud deployment without collaboration agreement.
• Relink/xiSEARCH/xiFDR/Scout: Please review the individual tool licenses
• OpenMS: Available under the BSD 3-Clause License
• WiffConverter: Proprietary SCIEX redistributable (via the public sciex/wiffconverter Docker Hub image). Users are responsible for complying with SCIEX's terms of use.

Technical Specifications

DIA-NN Containers

• Base Image: ubuntu:22.04
• Available Versions: 1.8.1, 1.9.2, 2.0.2, 2.1.0, 2.2.0, 2.3.2, 2.5.0
• Architecture: amd64/x86_64
• .NET SDK 8 (dotnet-sdk-8.0) is installed in 2.1.0+ images to enable native Thermo .raw reading.

Relink Container

• Base Image: python:3.12-slim (multi-stage build)
• Version: 1.0.0
• Architecture: amd64/x86_64
• Includes: Java 21, .NET 9.0, Python 3.12, pyOpenMS, polars, pandas

OpenMS Containers

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

WiffConverter Container

• Base Image: sciex/wiffconverter:0.10
• Version: 0.10
• Architecture: amd64/x86_64
• Includes: Mono runtime, OneOmics.WiffConverter.exe, convert wrapper

Installation & Usage

Fork repository to get access to private quantms containers

The workflow in .github/workflows/quantms-containers.yml is configured to build and push DIA-NN containers to the private ghcr.io/{owner}/diann and ghcr.io/{owner}/diann-sif registries. To access these containers, which runs the action in your own GitHub organization. If this fails, you will need to configure the packages on ghcr.io to allow pushing from the GitHub Actions. This can be configured for the entire organization or for each package individually. Please refer to the GitHub documentation for more details. See also the gif for details on the biosustain fork (do it for both diann and diann-sif packages):

Below you then need to replace bigbio with your GitHub username or organization name in the container tags.

Using Pre-built Docker Images

# Pull DIA-NN Docker image (requires GHCR access)
docker pull ghcr.io/bigbio/diann:2.1.0

# Pull Relink Docker image
docker pull ghcr.io/bigbio/relink:latest

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

Building Images Locally

# Build DIA-NN (any version)
cd diann-2.1.0/ && docker build -t diann:2.1.0 .

# Build Relink
cd relink-1.0.0/ && docker build -t relink:1.0.0 .

Basic Usage

DIA-NN

docker run -v /path/to/data:/data ghcr.io/bigbio/diann:2.1.0 diann \
  --f /data/input.raw \
  --lib /data/library.tsv \
  --out /data/results.tsv

DIA-NN in quantmsdiann pipeline

After building your container, create a custom configuration file to override the DIA-NN container:

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

Please check quantmsdiann documentation for more information.

Relink

# Run xiSEARCH
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  java -jar /opt/xisearch/xiSEARCH.jar [options]

# Run Scout
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  dotnet /opt/scout/Scout_Unix.dll [options]

OpenMS

docker run -v /path/to/data:/data 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 <container> [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. Builds and pushes DIA-NN Docker and Singularity containers (all versions)
2. Builds and pushes Relink Docker and Singularity containers
3. Builds and pushes WiffConverter Docker and Singularity containers
4. Syncs OpenMS containers from the official repository to BigBio

The workflow is triggered by:

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

Troubleshooting

1. Permission Errors

   chown -R $(id -u):$(id -g) /path/to/output

2. Memory Issues: Increase Docker memory allocation in Docker Desktop settings

3. DIA-NN Container Issues: Must be built locally or with GHCR access due to licensing

4. Relink Java/Dotnet Issues: Ensure the container has sufficient memory (recommend >= 4GB)

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_containers,
  author = {Perez-Riverol, Yasset},
  title = {QuantMS Docker Containers},
  year = {2025},
  url = {https://github.com/bigbio/quantms-containers}
}