InterSubMod/Dockerfile.dev at main · liaoyoyo/InterSubMod · GitHub

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# =============================================================================
# InterSubMod Development Dockerfile
# =============================================================================
# Build: docker build -f Dockerfile.dev -t intersubmod:dev .
# Run:   docker run -it --rm -v $(pwd):/workspace intersubmod:dev
# =============================================================================

FROM ubuntu:22.04

LABEL maintainer="InterSubMod Team"
LABEL description="Development environment for InterSubMod bioinformatics tool"
LABEL version="1.0.0"

# Avoid interactive prompts during package installation
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ=Asia/Taipei

# =============================================================================
# System Dependencies
# =============================================================================
RUN apt-get update && apt-get install -y --no-install-recommends \
    # Build essentials
    build-essential \
    cmake \
    pkg-config \
    git \
    wget \
    curl \
    ca-certificates \
    # HTSlib dependencies (using gnutls for compatibility)
    libhts-dev \
    libz-dev \
    libbz2-dev \
    liblzma-dev \
    libcurl4-gnutls-dev \
    libssl-dev \
    # OpenMP support
    libomp-dev \
    # Jemalloc build dependencies
    autoconf \
    # Python 3.10
    python3.10 \
    python3.10-dev \
    python3-pip \
    # CJK fonts for matplotlib Chinese support
    fonts-noto-cjk \
    fonts-noto-cjk-extra \
    fontconfig \
    # Debugging tools
    gdb \
    valgrind \
    # Editor (optional, useful for debugging)
    vim \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# =============================================================================
# Python Dependencies
# =============================================================================
# Pin versions for reproducibility
RUN pip3 install --no-cache-dir \
    numpy==1.24.3 \
    pandas==2.0.3 \
    matplotlib==3.7.2 \
    seaborn==0.12.2 \
    scipy==1.11.2 \
    scikit-learn==1.3.0

# =============================================================================
# Matplotlib Font Configuration
# =============================================================================
# Clear matplotlib font cache and configure to use Noto CJK font
RUN fc-cache -fv && \
    mkdir -p /root/.config/matplotlib && \
    echo "font.family: Noto Sans CJK TC" > /root/.config/matplotlib/matplotlibrc && \
    echo "axes.unicode_minus: False" >> /root/.config/matplotlib/matplotlibrc && \
    rm -rf /root/.cache/matplotlib

# Set matplotlib backend to Agg for headless rendering
ENV MPLBACKEND=Agg

# =============================================================================
# Environment Setup
# =============================================================================
ENV LANG=C.UTF-8
ENV LC_ALL=C.UTF-8
ENV PYTHONUNBUFFERED=1

# Working directory
WORKDIR /workspace

# =============================================================================
# Default Command
# =============================================================================
CMD ["/bin/bash"]