增加多阶段构建，并在镜像中构建指定版本的vina 便于使用。

2025-10-15 21:52:49 +08:00
parent 7ac0e58599
commit 1248cd187d
4 changed files with 200 additions and 107 deletions
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,69 +1,167 @@
-# 使用 Ubuntu 22.04 作为基础镜像（使用腾讯云镜像源）
-FROM ccr.ccs.tencentyun.com/library/ubuntu:22.04
+# ============ 构建阶段 ============
+FROM ubuntu:24.04 AS builder

-# 设置环境变量
 ENV DEBIAN_FRONTEND=noninteractive
-ENV PATH="/root/.pixi/bin:$PATH"

-# 配置 APT 镜像源（使用阿里云镜像）
-RUN sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list && \
-    sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+# 配置镜像源（使用阿里云镜像）
+RUN <<EOF
+sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+EOF

-# 安装系统依赖
-RUN apt-get update && apt-get install -y \
-    curl \
-    wget \
+# 安装构建依赖
+RUN <<EOF
+apt-get update
+apt-get install -y \
    git \
    build-essential \
-    ca-certificates \
-    gnupg \
-    lsb-release \
-    && rm -rf /var/lib/apt/lists/*
+    libboost-all-dev \
+    swig \
+    python3-dev \
+    python3-pip \
+    python3-venv
+rm -rf /var/lib/apt/lists/*
+EOF
+
+# 创建构建虚拟环境并安装必要的 Python 包
+RUN <<EOF
+echo "创建构建虚拟环境..."
+python3 -m venv /opt/build-venv
+echo "配置 pip 镜像源..."
+/opt/build-venv/bin/pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
+echo "安装构建依赖包..."
+/opt/build-venv/bin/pip install numpy packaging setuptools wheel
+echo "构建环境准备完成"
+EOF
+
+# 克隆 AutoDock Vina 源码
+ARG VINA_VERSION=1.2.7
+RUN <<EOF
+git clone https://github.com/ccsb-scripps/AutoDock-Vina.git /tmp/AutoDock-Vina
+cd /tmp/AutoDock-Vina
+git checkout v${VINA_VERSION}
+EOF
+
+# 编译 Python wheel 包
+RUN <<EOF
+cd /tmp/AutoDock-Vina
+echo "AutoDock Vina 源码结构:"
+find . -name "setup.py" -type f
+echo "检查 build/python 目录:"
+ls -la build/python/ 2>/dev/null || echo "build/python 目录不存在"
+echo "检查根目录的 setup.py:"
+ls -la setup.py 2>/dev/null || echo "根目录没有 setup.py"
+
+# 尝试在根目录构建
+if [ -f "setup.py" ]; then
+    echo "在根目录构建 wheel 包..."
+    /opt/build-venv/bin/python setup.py bdist_wheel
+else
+    echo "在 build/python 目录构建 wheel 包..."
+    cd build/python
+    /opt/build-venv/bin/python setup.py bdist_wheel
+fi
+
+echo "构建完成，查找所有 wheel 文件:"
+find /tmp/AutoDock-Vina -name "*.whl" -type f
+mkdir -p /wheels
+find /tmp/AutoDock-Vina -name "*.whl" -type f -exec cp {} /wheels/ \;
+echo "复制的 wheel 文件:"
+ls -la /wheels/
+EOF
+
+# 编译二进制可执行文件
+RUN <<EOF
+cd /tmp/AutoDock-Vina/build/linux/release
+make
+mkdir -p /binaries
+cp vina /binaries/
+cp vina_split /binaries/
+EOF
+
+# ============ 运行阶段 ============
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# 配置镜像源（使用阿里云镜像）
+RUN <<EOF
+sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
+EOF
+
+# 安装运行时依赖
+RUN <<EOF
+apt-get update
+apt-get install -y \
+    python3 \
+    python3-pip \
+    python3-venv \
+    libboost-system1.83.0 \
+    libboost-thread1.83.0 \
+    libboost-serialization1.83.0 \
+    libboost-filesystem1.83.0 \
+    libboost-program-options1.83.0
+rm -rf /var/lib/apt/lists/*
+EOF

 # 配置 pip 镜像源
-RUN mkdir -p /root/.pip && \
-    echo "[global]" > /root/.pip/pip.conf && \
-    echo "index-url = https://pypi.tuna.tsinghua.edu.cn/simple" >> /root/.pip/pip.conf && \
-    echo "trusted-host = pypi.tuna.tsinghua.edu.cn" >> /root/.pip/pip.conf
+RUN pip3 config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

-# 安装 pixi
-RUN curl -fsSL https://pixi.sh/install.sh | bash
+# 创建虚拟环境（解决 Python 3.12 PEP 668 保护问题）
+RUN <<EOF
+echo "创建虚拟环境..."
+python3 -m venv /opt/venv
+echo "虚拟环境创建完成，检查路径:"
+ls -la /opt/venv/bin/
+echo "升级 pip..."
+/opt/venv/bin/pip install --upgrade pip
+echo "虚拟环境准备完成"
+EOF
+
+# 从构建阶段复制 wheel 包并安装到虚拟环境
+COPY --from=builder /wheels/*.whl /tmp/
+RUN <<EOF
+/opt/venv/bin/pip install /tmp/*.whl
+rm -rf /tmp/*.whl
+EOF
+
+# 设置虚拟环境路径
+ENV PATH="/opt/venv/bin:$PATH"
+
+# 从构建阶段复制二进制文件
+COPY --from=builder /binaries/* /usr/local/bin/
+RUN chmod +x /usr/local/bin/vina*

 # 设置工作目录
 WORKDIR /app

-# 复制项目文件
-COPY . .
-
-# 创建 bin 目录
-RUN mkdir -p bin
-
-# 下载 AutoDock Vina 二进制文件
-ARG VINA_VERSION=1.2.7
-ARG VINA_PLATFORM=mac_aarch64
-ARG DOWNLOAD_VINA=true
-
-RUN if [ "$DOWNLOAD_VINA" = "true" ]; then \
-        curl -L -o ./bin/vina_${VINA_VERSION}_${VINA_PLATFORM} https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v${VINA_VERSION}/vina_${VINA_VERSION}_${VINA_PLATFORM} && \
-        curl -L -o ./bin/vina_split_${VINA_VERSION}_${VINA_PLATFORM} https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v${VINA_VERSION}/vina_split_${VINA_VERSION}_${VINA_PLATFORM} && \
-        chmod +x ./bin/vina_*; \
-    fi
-
-# 添加平台支持并安装 pixi 包
-RUN /root/.pixi/bin/pixi workspace platform add linux-aarch64 && \
-    /root/.pixi/bin/pixi add rdkit openbabel meeko
-
-# 设置环境变量
-ENV PATH="/root/.pixi/bin:/app/bin:$PATH"
-
 # 创建启动脚本
-RUN echo '#!/bin/bash\n\
-source /root/.bashrc\n\
-exec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
+RUN <<EOF
+cat > /entrypoint.sh << 'SCRIPT_EOF'
+#!/bin/bash
+echo "AutoDock Vina 环境已准备就绪 (Ubuntu 24.04 + Python 3.12 + Boost 1.83.0)"
+echo "虚拟环境: \$(which python)"
+echo "Python 版本: \$(python --version 2>&1)"
+echo "Python 绑定测试:"
+python -c "from vina import Vina; print('Vina Python 绑定可用')" 2>/dev/null || echo "Python 绑定不可用"
+echo "命令行工具: vina --version"
+vina --version 2>/dev/null || echo "vina 命令不可用"
+echo "Boost 库信息:"
+ldd /usr/local/bin/vina | grep boost || echo "无法获取 Boost 信息"
+if [ "\$#" -eq 0 ]; then
+    echo "进入交互模式..."
+    exec /bin/bash
+else
+    echo "执行命令: \$@"
+    exec "\$@"
+fi
+SCRIPT_EOF
+chmod +x /entrypoint.sh
+EOF

 # 设置入口点
 ENTRYPOINT ["/entrypoint.sh"]

 # 默认命令
-CMD ["/root/.pixi/bin/pixi", "shell"]
+CMD ["bash"]
--- a/docker/README.md
+++ b/docker/README.md
@@ -30,14 +30,20 @@ docker build -f docker/Dockerfile -t vinatools:latest .
 | 变量名 | 默认值 | 说明 |
 |--------|--------|------|
 | `VINA_VERSION` | `1.2.7` | AutoDock Vina 版本 |
-| `VINA_PLATFORM` | `mac_aarch64` | 平台架构 |
-| `DOWNLOAD_VINA` | `true` | 是否下载 AutoDock Vina |
+| `TARGETPLATFORM` | `linux/amd64` | 目标平台架构 |

 **支持的平台：**
- `mac_aarch64` - Apple Silicon Mac
- `mac_x86_64` - Intel Mac  
- `linux_x86_64` - Linux x86_64
- `windows_x86_64` - Windows x86_64
+- `linux/amd64` - Linux x86_64
+- `linux/arm64` - Linux aarch64
+
+### 4. 从源码编译
+
+Dockerfile 现在支持从源码编译 AutoDock Vina：
+
+- **Python 环境**: Python 3.12
+- **依赖包**: numpy (最新版本)、boost-cpp 1.82.0、swig 4.0.2
+- **编译方式**: 使用 pixi 管理环境，从源码编译
+- **版本控制**: 通过 VINA_VERSION 参数控制，默认 1.2.7

 ### 4. 运行容器

@@ -58,14 +64,13 @@ docker run -it --rm -v $(pwd):/app vinatools:latest bash

 ```bash
 # Linux x86_64 平台
-VINA_PLATFORM=linux_x86_64 docker-compose -f docker/docker-compose.yml build
-VINA_PLATFORM=linux_aarch64 docker-compose -f docker/docker-compose.yml build
+TARGETPLATFORM=linux/amd64 docker-compose -f docker/docker-compose.yml build

-# Intel Mac 平台
-VINA_PLATFORM=mac_x86_64 docker-compose -f docker/docker-compose.yml build
+# Linux ARM64 平台
+TARGETPLATFORM=linux/arm64 docker-compose -f docker/docker-compose.yml build

-# 不下载 AutoDock Vina
-DOWNLOAD_VINA=false docker-compose -f docker/docker-compose.yml build
+# 使用不同版本
+VINA_VERSION=1.2.6 TARGETPLATFORM=linux/amd64 docker-compose -f docker/docker-compose.yml build
 ```

 ### 使用环境文件
@@ -74,8 +79,7 @@ DOWNLOAD_VINA=false docker-compose -f docker/docker-compose.yml build
 # 创建自定义环境文件
 cat > docker/my.env << EOF
 VINA_VERSION=1.2.6
-VINA_PLATFORM=linux_x86_64
-DOWNLOAD_VINA=true
+TARGETPLATFORM=linux/amd64
 EOF

 # 使用自定义环境文件构建
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -7,8 +7,6 @@ services:
      dockerfile: docker/Dockerfile
      args:
        VINA_VERSION: ${VINA_VERSION:-1.2.7}
-        VINA_PLATFORM: ${VINA_PLATFORM:-linux}
-        DOWNLOAD_VINA: ${DOWNLOAD_VINA:-true}
    image: vinatools:latest
    container_name: vinatools-container
    volumes:
@@ -19,8 +17,7 @@ services:
      - ./results:/app/results
    working_dir: /app
    environment:
-      - PIXI_ROOT=/root/.pixi
-      - PATH=/root/.pixi/bin:/app/bin:$PATH
+      - PATH=/opt/venv/bin:/usr/local/bin:$PATH
    # 保持容器运行
    tty: true
    stdin_open: true
@@ -28,6 +25,9 @@ services:
    network_mode: host
    # 重启策略
    restart: unless-stopped
+    # 覆盖 ENTRYPOINT 用于交互式测试
+    entrypoint: ["/bin/bash"]
+    command: ["-c", "while true; do sleep 30; done"]
    # 资源限制
    deploy:
      resources:
@@ -38,33 +38,29 @@ services:
          memory: 2G
          cpus: '1.0'

-  # 可选：用于 Jupyter Notebook 服务
-  jupyter:
-    build:
-      context: ..
-      dockerfile: docker/Dockerfile
-      args:
-        VINA_VERSION: ${VINA_VERSION:-1.2.7}
-        VINA_PLATFORM: ${VINA_PLATFORM:-linux_x86_64}
-        DOWNLOAD_VINA: ${DOWNLOAD_VINA:-true}
-    image: vinatools:latest
-    container_name: vinatools-jupyter
-    ports:
-      - "8888:8888"
-    volumes:
-      - ..:/app
-      - ./data:/app/data
-      - ./results:/app/results
-    working_dir: /app
-    environment:
-      - PIXI_ROOT=/root/.pixi
-      - PATH=/root/.pixi/bin:/app/bin:$PATH
-    command: >
-      bash -c "
-        /root/.pixi/bin/pixi workspace platform add linux-aarch64 &&
-        /root/.pixi/bin/pixi add jupyter notebook &&
-        /root/.pixi/bin/pixi run jupyter notebook --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' --NotebookApp.password=''
-      "
-    restart: unless-stopped
-    depends_on:
-      - vinatools
+  # # 可选：用于 Jupyter Notebook 服务
+  # jupyter:
+  #   build:
+  #     context: ..
+  #     dockerfile: docker/Dockerfile
+  #     args:
+  #       VINA_VERSION: ${VINA_VERSION:-1.2.7}
+  #   image: vinatools:latest
+  #   container_name: vinatools-jupyter
+  #   ports:
+  #     - "8888:8888"
+  #   volumes:
+  #     - ..:/app
+  #     - ./data:/app/data
+  #     - ./results:/app/results
+  #   working_dir: /app
+  #   environment:
+  #     - PATH=/usr/local/bin:$PATH
+  #   command: >
+  #     bash -c "
+  #       pip3 install jupyter notebook &&
+  #       jupyter notebook --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' --NotebookApp.password=''
+  #     "
+  #   restart: unless-stopped
+  #   depends_on:
+  #     - vinatools
--- a/docker/docker.env.example
+++ b/docker/docker.env.example
@@ -1,12 +1,7 @@
 # AutoDock Vina 配置
 VINA_VERSION=1.2.7
-VINA_PLATFORM=mac_aarch64
-DOWNLOAD_VINA=true
+TARGETPLATFORM=linux/amd64

-# 其他平台选项：
-# VINA_PLATFORM=linux_x86_64
-# VINA_PLATFORM=mac_x86_64
-# VINA_PLATFORM=windows_x86_64
-
-# 禁用 AutoDock Vina 下载
-# DOWNLOAD_VINA=false
+# 支持的平台选项：
+# TARGETPLATFORM=linux/amd64    # x86_64
+# TARGETPLATFORM=linux/arm64    # aarch64