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Docker Guide

kreview is published as a Docker image to the GitHub Container Registry (GHCR) on every tagged release.

Pulling the Image

docker pull ghcr.io/msk-access/kreview:latest

Or pin to a specific version:

docker pull ghcr.io/msk-access/kreview:latest

Running with Docker

docker run --rm \
  -v /path/to/data:/app/data \
  -v /path/to/output:/app/results \
  ghcr.io/msk-access/kreview:latest \
  kreview run \
    --cancer-samplesheet /app/data/samplesheet.csv \
    --healthy-xs1-samplesheet /app/data/healthy_xs1.csv \
    --healthy-xs2-samplesheet /app/data/healthy_xs2.csv \
    --cbioportal-dir /app/data/cbioportal/ \
    --krewlyzer-dir /app/data/krewlyzer/ \
    --output /app/results/ \
    --workers 4

Volume Mounts

Mount your input data and output directories using -v. The container expects data at /app/data and writes results to /app/results by default.

Dockerfile Architecture

The image uses a multi-stage build for minimal size:

# Stage 1: Build the wheel
FROM python:3.12-slim as builder   # (1)!
WORKDIR /src
COPY . .
RUN pip install --upgrade pip build && python -m build --wheel

# Stage 2: Runtime (slim)
FROM python:3.12-slim              # (2)!
WORKDIR /app
COPY --from=builder /src/dist/*.whl /app/
RUN pip install --no-cache-dir /app/*.whl && rm /app/*.whl

# Install Quarto for dashboard rendering
RUN apt-get update && \            # (3)!
    wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.551/quarto-1.4.551-linux-amd64.deb && \
    dpkg -i quarto-*.deb && rm quarto-*.deb

RUN mkdir -p /app/data /app/results
CMD ["kreview", "--help"]
  1. Builder stage compiles the wheel but is discarded from the final image
  2. Runtime stage is a clean python:3.12-slim with only the installed package
  3. Quarto is required for generating the interactive HTML Plotly dashboards

GHCR Image Labels

Every image is annotated with OCI-standard metadata:

Label Value
org.opencontainers.image.title kreview
org.opencontainers.image.description Evaluate cfDNA fragmentomics features for ctDNA detection
org.opencontainers.image.vendor MSK-ACCESS
org.opencontainers.image.licenses AGPL-3.0