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FragPipe Docker Containers for nf-core

⚠️ NO REDISTRIBUTION — READ THIS FIRST ⚠️

You MUST NOT redistribute FragPipe Docker images.

FragPipe tools are licensed software. Uploading built images to Docker Hub, GitHub Container Registry, Quay.io, or any other public registry is a violation of the FragPipe license agreement.

After building, store your image in:

  • A local Docker daemon (default after docker build)
  • A private container registry (e.g., AWS ECR, private Docker Hub repo, Artifactory)

Overview

nf-core/msproteomics supports two FragPipe Docker image variants:

  • Academic container — For academic and non-profit use (free license from NESViLab)
  • Commercial container — For industry use (paid license from Fragmatics)

Both containers use fcyucn/fragpipe:24.0 as their base image, which provides all open-source FragPipe tools pre-installed (Philosopher, Percolator, MSBooster, PTMShepherd, etc.). The academic container layers academic-licensed JARs (MSFragger, IonQuant, DiaTracer) on top. The commercial container replaces the base's lib/ and tools/ with the FragPipePlus distribution's (commercial JARs + DIA-NN), so no superseded public JAR (batmass-io 1.36.5, MSBooster 1.4.14) or tools/Skyline/ stays behind.

Both containers expose the same tool aliases in PATH, so pipeline modules work identically with either variant.

Academic Container (Step-by-Step)

Prerequisites

  • Docker installed and running
  • Internet access to download tools

Step 1: Download Licensed Tools

You need three tools from NESViLab (free for academic/non-profit use):

  1. MSFragger: https://msfragger-upgrader.nesvilab.org/upgrader/

    • Fill in your academic email and agree to the license
    • Download the zip (e.g., MSFragger-4.4.1.zip)

  2. IonQuant: https://msfragger-upgrader.nesvilab.org/ionquant/

    • Fill in your academic email and agree to the license
    • Download the zip (e.g., IonQuant-1.11.20.zip)

  3. DiaTracer: https://msfragger-upgrader.nesvilab.org/diatracer/

    • Fill in your academic email and agree to the license
    • Download the zip (e.g., diatracer-2.2.1.zip)

Step 2: Build the Container

cd docs/fragpipe-docker

export MSFRAGGER_ZIP=~/Downloads/MSFragger-4.4.1.zip
export IONQUANT_ZIP=~/Downloads/IonQuant-1.11.20.zip
export DIATRACER_ZIP=~/Downloads/diatracer-2.2.1.zip

./build_nfcore.sh academic

Step 3: Verify

docker run --rm fragpipe-nfcore:24.0 msfragger --version
docker run --rm fragpipe-nfcore:24.0 ionquant --version
docker run --rm fragpipe-nfcore:24.0 diatracer --version
docker run --rm fragpipe-nfcore:24.0 philosopher version
docker run --rm fragpipe-nfcore:24.0 percolator --help 2>&1 | head -1

Step 4: Save to Private Registry

# Tag for your private registry
docker tag fragpipe-nfcore:24.0 your-registry.example.com/fragpipe:24.0-academic

# Push to your private registry
docker push your-registry.example.com/fragpipe:24.0-academic

Step 5: Use with Pipeline

nextflow run main.nf \
  --mode fragpipe \
  --fragpipe_workflow /path/to/LFQ-MBR.workflow \
  --fragpipe_container your-registry.example.com/fragpipe:24.0-academic \
  --input samplesheet.csv \
  --database /path/to/database.fasta \
  --outdir results \
  -profile docker

Commercial Container (Step-by-Step)

Prerequisites

  • Docker installed and running
  • Commercial license from Fragmatics

Step 1: Obtain Commercial License

  1. Contact Fragmatics at info@fragmatics.com or visit https://www.fragmatics.com/
  2. Purchase a commercial license for FragPipePlus
  3. You will receive:
    • FragPipePlus-24.0-linux.zip — the complete distribution
    • license.dat — the license file (required at runtime by MSFragger, IonQuant, DiaTracer)

Step 2: Build the Container

cd docs/fragpipe-docker

export FRAGPIPEPLUS_ZIP=~/Downloads/FragPipePlus-24.0-linux.zip
export LICENSE_FILE=~/Downloads/license.dat

./build_nfcore.sh commercial

Step 3: Verify, Save & Use

Same as academic container (Steps 3-5 above). Replace academic with commercial in the tag.

Custom Image Tag

Override the default tag with the TAG environment variable:

TAG=my-fragpipe:latest ./build_nfcore.sh academic

Container Override

Every FragPipe module (licensed and open-source tools alike) runs from the one image given with --fragpipe_container, as FragPipe runs all tools from one distribution; there is no default image:

nextflow run main.nf \
  --mode fragpipe \
  --fragpipe_workflow /path/to/LFQ-MBR.workflow \
  --fragpipe_container your-registry.example.com/fragpipe:24.0-academic \
  --input samplesheet.csv \
  --database /path/to/database.fasta \
  --outdir results \
  -profile docker

All FragPipe-based workflows (DDA LFQ, TMT Label Check, generic FragPipe) use this container for commercial modules.

Tool Versions

Tool Version License
Java 17 (openjdk-17, from base image) GPL-2.0
MSFragger 4.4.1 Academic/Commercial
IonQuant 1.11.20 Academic/Commercial
DiaTracer 2.2.1 Academic/Commercial
Philosopher 5.1.3-RC9 GPL-3.0
Percolator 3.7.1 Apache-2.0
MSBooster 1.4.14 (academic) / 1.4.17 (commercial) LGPL-3.0
PTMShepherd 3.0.11 Open Source
TMT-Integrator 6.1.3 Open Source
Crystal-C 1.5.10 Open Source
DIA-Umpire 2.3.3 Open Source
MBG 0.3.6 Open Source
batmass-io 1.36.5 (academic) / 1.36.6 (commercial) Open Source
DIA-NN 1.8.1 Free (bundled in FragPipe container)

Architecture

Both containers are based on fcyucn/fragpipe:24.0, which installs the full FragPipe distribution at /fragpipe_bin/fragpipe-24.0/fragpipe-24.0/. Pipeline modules discover tools at runtime via the tools_dir path (default: /fragpipe_bin/fragpipe-24.0/fragpipe-24.0/tools).

/fragpipe_bin/fragpipe-24.0/fragpipe-24.0/
├── bin/                  (FragPipe CLI)
├── lib/                  (FragPipe Java libraries)
├── tools/
│   ├── MSFragger*.jar    (licensed, added by academic/commercial build)
│   ├── IonQuant*.jar     (licensed, added by academic/commercial build)
│   ├── DiaTracer*.jar    (licensed, added by academic/commercial build)
│   ├── MSBooster*.jar
│   ├── Philosopher/philosopher  (binary)
│   ├── percolator        (binary)
│   ├── PTMShepherd*.jar
│   ├── TMTIntegrator*.jar
│   ├── CrystalC*.jar
│   ├── DIAUmpire*.jar
│   ├── MBG*.jar
│   └── ...
└── ext/
    ├── bruker/           (Bruker native libs)
    └── thermo/           (Thermo native libs)

Troubleshooting

msfragger: command not found

Ensure the container was built correctly and the licensed JAR is in the tools directory. Check that the JAR exists:

docker run --rm <image> find /fragpipe_bin -name "MSFragger*.jar"

No MSFragger*.jar found

The licensed JAR was not properly extracted or copied into the tools directory. For academic builds, verify that your MSFRAGGER_ZIP points to a valid zip containing the JAR. Check that the zip structure matches (e.g., MSFragger-4.4.1/MSFragger-4.4.1.jar):

unzip -l $MSFRAGGER_ZIP | head -20

JAVA_HOME mismatch

Both containers inherit Java 17 (openjdk-17) from the fcyucn/fragpipe:24.0 base image.

If you see errors like UnsupportedClassVersionError or JAVA_HOME is not set, check which Java is active:

docker run --rm <image> java -version
docker run --rm <image> bash -c 'echo $JAVA_HOME'

FragPipe 24.0 tools are compatible with Java 17+. Do not downgrade to Java 11 or earlier, as MSFragger 4.x requires Java 17 at minimum.