Dockerfile

# Build stage
FROM rust:slim-bookworm AS builder

# Install build dependencies
RUN apt-get update && apt-get install -y \
    build-essential \
    clang \
    libclang-dev \
    libhts-dev \
    pkg-config \
    git \
    curl \
    wget \
    && rm -rf /var/lib/apt/lists/*

# Install Miniconda
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O /tmp/miniconda.sh && \
    bash /tmp/miniconda.sh -b -p /opt/conda && \
    rm /tmp/miniconda.sh

ENV PATH="/opt/conda/bin:$PATH"

WORKDIR /app
COPY . .

# Create conda environment
RUN conda env create -f environment.yaml

# Set build environment variables
ENV LIBCLANG_PATH="/usr/lib/aarch64-linux-gnu"
ENV C_INCLUDE_PATH="/usr/include"

# Build ConSTRain
WORKDIR /app/ConSTRain
RUN cargo build --release --bin ConSTRain

# Runtime stage
FROM debian:bookworm-slim

# Install only runtime dependencies
RUN apt-get update && apt-get install -y \
    libhts3 \
    python3 \
    python3-pip \
    && rm -rf /var/lib/apt/lists/*

# Copy the built binary
COPY --from=builder /app/ConSTRain/target/release/ConSTRain /usr/local/bin/ConSTRain

# Copy conda environment for Python dependencies
COPY --from=builder /opt/conda/envs/ConSTRain-analyses /opt/conda/envs/ConSTRain-analyses

# Set up environment
ENV PATH="/opt/conda/envs/ConSTRain-analyses/bin:/usr/local/bin:$PATH"
ENV CONDA_DEFAULT_ENV=ConSTRain-analyses

# Set working directory for Nextflow
WORKDIR /

# No entrypoint - let Nextflow control execution