viral-ngs/docker/Dockerfile.mega at 44c3d2fbc3a9a95c427585911d47a3681f9e87e3 · broadinstitute/viral-ngs · GitHub

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# viral-ngs mega image
# Builds on core, adds ALL tools (assembly, classification, phylogenetics)
#
# This provides:
# - All core bioinformatics tools (from core image)
# - All assembly tools (SPAdes, MUMmer, MAFFT, skani, etc.)
# - All classification tools (Kraken2, BLAST, BMTagger, KMC, etc.)
# - All phylogenetics tools (LoFreq, SnpEff, MUSCLE, V-Phaser2, etc.)
#
# Usage:
#   docker build --build-arg BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core -t viral-ngs:mega -f docker/Dockerfile.mega .

ARG BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core
FROM ${BASEIMAGE}

LABEL maintainer="viral-ngs@broadinstitute.org"
LABEL org.opencontainers.image.source="https://github.com/broadinstitute/viral-ngs"

# Enable conda environment activation for RUN commands
ARG MAMBA_DOCKERFILE_ACTIVATE=1

# Copy requirements and dependency installation script
COPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/assemble.txt docker/requirements/assemble-x86.txt docker/requirements/classify.txt docker/requirements/classify-x86.txt docker/requirements/phylo.txt docker/requirements/phylo-x86.txt /tmp/requirements/
COPY docker/install-conda-deps.sh /tmp/

# Install ALL conda dependencies in single resolver call for proper dependency resolution
# All files resolved together; x86-only files skipped on ARM
# Post-install fixups (inline so vulnerable files never appear in a committed layer):
#   - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
#   - Ruby json gem: mummer4 → yaggo → Ruby, whose bundled json gem has CVE-2026-33210;
#     remove the old default gem and install patched version (>=2.19.2)
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt /tmp/requirements/classify.txt /tmp/requirements/phylo.txt \
    --x86-only:/tmp/requirements/assemble-x86.txt \
    --x86-only:/tmp/requirements/classify-x86.txt \
    --x86-only:/tmp/requirements/phylo-x86.txt && \
    rm -f /opt/conda/libexec/mafft/dash_client && \
    find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
    rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
    gem install json --version '>=2.19.2' --no-document

# Copy source code (includes all modules)
COPY src/ /opt/viral-ngs/source/src/
COPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/

# Install viral-ngs package
# VERSION is passed from GitHub Actions via git describe
WORKDIR /opt/viral-ngs/source
ARG VERSION
ENV SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION}
RUN pip install --no-cache-dir . && \
    echo "${VERSION}" > /opt/viral-ngs/source/VERSION

# Verify installation - all modules
RUN python -c "from viral_ngs import read_utils, illumina; print('Core command modules OK')" && \
    python -c "from viral_ngs import assembly; print('Assembly command modules OK')" && \
    python -c "from viral_ngs import metagenomics, taxon_filter, kmer_utils; print('Classify command modules OK')" && \
    python -c "from viral_ngs import interhost, intrahost, ncbi; print('Phylo command modules OK')" && \
    python -c "from viral_ngs.core import samtools, picard, bwa; print('Core tools OK')" && \
    python -c "from viral_ngs.assemble import spades, mummer, mafft; print('Assemble tools OK')" && \
    python -c "from viral_ngs.classify import kraken2, blast, bmtagger; print('Classify tools OK')" && \
    python -c "from viral_ngs.phylo import mafft, muscle, snpeff; print('Phylo tools OK')"

# Clean up
RUN rm -rf /tmp/requirements /tmp/install-conda-deps.sh

CMD ["/bin/bash"]