Dockerfile

FROM mambaorg/micromamba:2.5.0-debian12-slim

LABEL org.opencontainers.image.source="https://github.com/broadinstitute/qprimer_designer"
LABEL org.opencontainers.image.description="ML-guided qPCR primer design with off-target minimization"
LABEL org.opencontainers.image.licenses="MIT"

# Layer 1: Conda environment (cached unless environment.yml changes)
COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
RUN micromamba install -y -n base -f /tmp/environment.yml && \
    micromamba clean --all --yes

ARG MAMBA_DOCKERFILE_ACTIVATE=1
ENV PATH="/opt/conda/bin:$PATH"

# Layer 2: Install package (cached unless pyproject.toml, README.md, or src/ changes)
COPY --chown=$MAMBA_USER:$MAMBA_USER pyproject.toml README.md /app/
COPY --chown=$MAMBA_USER:$MAMBA_USER src/ /app/src/
WORKDIR /app
RUN pip install --no-cache-dir .

# Layer 3: Copy remaining files (workflows, training, CLAUDE.md, LICENSE, etc.)
COPY --chown=$MAMBA_USER:$MAMBA_USER . /app

# Verify installation
RUN qprimer --help && \
    qprimer generate --help && \
    RNAduplex --version && \
    bowtie2 --version | head -1

WORKDIR /data

CMD ["/bin/bash"]