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`
2.5.1	`diann-2.5.1/`	Native `.raw` on Linux (bundles .NET SDK 8)	`ghcr.io/bigbio/diann:2.5.1`
2.5.1 Enterprise	`diann-enterprise-2.5.1/`	Knowledge Base (`--kb`), extra report QC metrics. Per-user license; built locally only (no CI / registry push).	`ghcr.io/bigbio/diann-enterprise:2.5.1`

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 / 2.5.1 (incl. Enterprise) 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

DIA-NN Enterprise (local-only)

The Enterprise image (diann-enterprise-2.5.1/) is built from a local enterprise zip plus a per-licensee diann-license-key.txt. Neither artefact is committed (both are .gitignored) and the image is never pushed to a registry — it has no CI entry. The license key is a per-user secret: do not redistribute it or bake it into a shared image.

# ENTERPRISE_SRC must point at the directory holding the zip + license key
ENTERPRISE_SRC=/path/to/enterprise ./build-diann-enterprise-singularity.sh

This produces ghcr.io/bigbio/diann-enterprise:2.5.1 locally and the matching Singularity .img. In quantmsdiann, select it with -profile diann_v2_5_1_enterprise; the Knowledge Base is enabled via --enable_kb and boosts identifications (primarily on human data).

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	2.1.0	Crosslink analysis tool
xi-mzidentml-converter	latest	mzIdentML parsing package (CLI: `process_dataset`)
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	1.1.0	`ghcr.io/bigbio/relink:1.1.0`
Docker	latest	`ghcr.io/bigbio/relink:latest`
Singularity	1.1.0	`oras://ghcr.io/bigbio/relink-sif:1.1.0`

All bundled tools are exposed directly on PATH:

Command	Tool
`scout`	Scout (cleavable XL-MS search)
`xisearch`	xiSEARCH
`xifdr`	xiFDR
`process_dataset`	xi-mzidentml-converter (already on PATH from the pip package)

The scout wrapper handles Scout's startup quirks transparently (Python detection, LD_LIBRARY_PATH for MPFR/GMP, CSMSL user-data dir).

Passing JVM options to xiSEARCH / xiFDR

Use --java-options "..." (GATK convention) to pass JVM flags such as -Xmx, -Xms, -XX:..., or -D.... All flags go inside a single space-separated quoted string. This survives the layered quoting in Nextflow / Singularity / Docker pipelines without escape pain. The flag may be repeated to append.

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

# Scout end-to-end (mount data + params under /data)
docker run --rm -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  scout -search -no_filter /data/search_params.json /data/filter_params.json

# xiSEARCH with a 16 GB heap
docker run --rm -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  xisearch --java-options "-Xmx16g" \
           --config=/data/config --peaks=/data/peaks.mgf \
           --fasta=/data/db.fasta --output=/data/results.csv

# xiFDR with custom heap and G1 GC
docker run --rm -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  xifdr --java-options "-Xmx8g -XX:+UseG1GC" --psmfdr=0.05 /data/results.csv

# xi-mzidentml-converter
docker run --rm -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  process_dataset --help

Nextflow

--java-options keeps everything on one line — no extra escaping inside the script block:

process XISEARCH {
    container 'ghcr.io/bigbio/relink:1.1.0'
    cpus 4
    memory '16 GB'
    script:
    """
    xisearch --java-options "-Xmx${task.memory.toGiga()}g" \\
             --config=${config} --peaks=${peaks} --fasta=${fasta} \\
             --output=xisearch_results.csv
    """
}

For Scout's CLI flags and params-file structure, see https://github.com/diogobor/Scout#26-automation.

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.
DIA-NN Enterprise: Separate per-user license issued by the DIA-NN authors. The key and the Enterprise binary are not redistributable — never commit them or publish the Enterprise image. Build locally only.
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, 2.5.1, plus 2.5.1 Enterprise (local-only)
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: 1.1.0
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-1.1.0/ && docker build -t relink:1.1.0 .

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

Tools are exposed directly on PATH (scout, xisearch, xifdr, process_dataset). For the Java-based tools, pass JVM flags via --java-options "..." (GATK convention):

# Scout
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  scout -search -no_filter /data/search_params.json /data/filter_params.json

# xiSEARCH with custom heap
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  xisearch --java-options "-Xmx16g" --config=/data/config [options]

# xiFDR with custom heap
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  xifdr --java-options "-Xmx8g" [options]

# xi-mzidentml-converter
docker run -v /path/to/data:/data ghcr.io/bigbio/relink:latest \
  process_dataset [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:

Builds and pushes DIA-NN Docker and Singularity containers (all versions)
Builds and pushes Relink Docker and Singularity containers
Builds and pushes WiffConverter Docker and Singularity containers
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

Permission Errors

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

Memory Issues: Increase Docker memory allocation in Docker Desktop settings
DIA-NN Container Issues: Must be built locally or with GHCR access due to licensing
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:

Fork the repository
Create a feature branch
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}
}

Name		Name	Last commit message	Last commit date
Latest commit History 139 Commits
.github/workflows		.github/workflows
assets		assets
diann-1.8.1		diann-1.8.1
diann-1.9.2		diann-1.9.2
diann-2.0.2		diann-2.0.2
diann-2.1.0		diann-2.1.0
diann-2.2.0		diann-2.2.0
diann-2.3.2		diann-2.3.2
diann-2.5.0		diann-2.5.0
diann-2.5.1		diann-2.5.1
diann-enterprise-2.5.1		diann-enterprise-2.5.1
relink-1.1.0		relink-1.1.0
wiffconverter-0.10		wiffconverter-0.10
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
build-diann-enterprise-singularity.sh		build-diann-enterprise-singularity.sh

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QuantMS Docker Containers

Overview

Container Availability

DIA-NN Containers

DIA-NN Enterprise (local-only)

Relink Container

Passing JVM options to xiSEARCH / xiFDR

Nextflow

WiffConverter Container

OpenMS Containers

License Information

Technical Specifications

DIA-NN Containers

Relink Container

OpenMS Containers

WiffConverter Container

Installation & Usage

Fork repository to get access to private quantms containers

Using Pre-built Docker Images

Building Images Locally

Basic Usage

DIA-NN

DIA-NN in quantmsdiann pipeline

Relink

OpenMS

Data Mounting

CI/CD Workflow

Troubleshooting

Maintainers

Contributing

Citation

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