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增加多阶段构建，并在镜像中构建指定版本的vina 便于使用。

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hotwa
2025-10-15 21:52:49 +08:00
parent 7ac0e58599
commit 1248cd187d
4 changed files with 200 additions and 107 deletions
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198
docker/Dockerfile
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@@ -1,69 +1,167 @@
# 使用 Ubuntu 22.04 作为基础镜像（使用腾讯云镜像源） # ============ 构建阶段 ============
FROM ccr.ccs.tencentyun.com/library/ubuntu:22.04 FROM ubuntu:24.04 AS builder
# 设置环境变量
ENV DEBIAN_FRONTEND=noninteractive ENV DEBIAN_FRONTEND=noninteractive
ENV PATH="/root/.pixi/bin:$PATH"
# 配置 APT 镜像源（使用阿里云镜像） # 配置镜像源（使用阿里云镜像）
RUN sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list && \ RUN <<EOF
sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list sed -i 's@//.*archive.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
sed -i 's@//.*security.ubuntu.com@//mirrors.aliyun.com@g' /etc/apt/sources.list
EOF
# 安装系统依赖 # 安装构建依赖
RUN apt-get update && apt-get install -y \ RUN <<EOF
curl \ apt-get update
wget \ apt-get install -y \
git \ git \
build-essential \ build-essential \
ca-certificates \ libboost-all-dev \
gnupg \ swig \
lsb-release \ python3-dev \
&& rm -rf /var/lib/apt/lists/* python3-pip \
python3-venv
rm -rf /var/lib/apt/lists/*
EOF
# 创建构建虚拟环境并安装必要的 Python 包
RUN <<EOF
echo "创建构建虚拟环境..."
python3 -m venv /opt/build-venv
echo "配置 pip 镜像源..."
/opt/build-venv/bin/pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
echo "安装构建依赖包..."
/opt/build-venv/bin/pip install numpy packaging setuptools wheel
echo "构建环境准备完成"
EOF
# 克隆 AutoDock Vina 源码
ARG VINA_VERSION=1.2.7
RUN <<EOF
git clone https://github.com/ccsb-scripps/AutoDock-Vina.git /tmp/AutoDock-Vina
cd /tmp/AutoDock-Vina
git checkout v${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 # 配置 pip 镜像源
RUN mkdir -p /root/.pip && \ RUN pip3 config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
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
# 安装 pixi # 创建虚拟环境（解决 Python 3.12 PEP 668 保护问题）
RUN curl -fsSL https://pixi.sh/install.sh | bash 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:$PATH"
# 从构建阶段复制二进制文件
COPY --from=builder /binaries/* /usr/local/bin/
RUN chmod +x /usr/local/bin/vina*
# 设置工作目录 # 设置工作目录
WORKDIR /app WORKDIR /app
# 复制项目文件
COPY . .
# 创建 bin 目录
RUN mkdir -p bin
# 下载 AutoDock Vina 二进制文件
ARG VINA_VERSION=1.2.7
ARG VINA_PLATFORM=mac_aarch64
ARG DOWNLOAD_VINA=true
RUN if [ "$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:$PATH"
# 创建启动脚本 # 创建启动脚本
RUN echo '#!/bin/bash\n\ RUN <<EOF
source /root/.bashrc\n\ cat > /entrypoint.sh << 'SCRIPT_EOF'
exec "$@"' > /entrypoint.sh && \ #!/bin/bash
chmod +x /entrypoint.sh 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 # 设置入口点
ENTRYPOINT ["/entrypoint.sh"] ENTRYPOINT ["/entrypoint.sh"]
# 默认命令 # 默认命令
CMD ["/root/.pixi/bin/pixi", "shell"] CMD ["bash"]

32
docker/README.md
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@@ -30,14 +30,20 @@ docker build -f docker/Dockerfile -t vinatools:latest .
| 变量名 | 默认值 | 说明 | | 变量名 | 默认值 | 说明 |
|--------|--------|------| |--------|--------|------|
| `VINA_VERSION` | `1.2.7` | AutoDock Vina 版本 | | `VINA_VERSION` | `1.2.7` | AutoDock Vina 版本 |
| `VINA_PLATFORM` | `mac_aarch64` | 平台架构 | | `TARGETPLATFORM` | `linux/amd64` | 目标平台架构 |
| `DOWNLOAD_VINA` | `true` | 是否下载 AutoDock Vina |
**支持的平台：** **支持的平台：**
- `mac_aarch64` - Apple Silicon Mac - `linux/amd64` - Linux x86_64
- `mac_x86_64` - Intel Mac - `linux/arm64` - Linux aarch64
- `linux_x86_64` - Linux x86_64
- `windows_x86_64` - Windows x86_64 ### 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 ### 4. 运行容器
@@ -58,14 +64,13 @@ docker run -it --rm -v $(pwd):/app vinatools:latest bash
```bash ```bash
# Linux x86_64 平台 # Linux x86_64 平台
VINA_PLATFORM=linux_x86_64 docker-compose -f docker/docker-compose.yml build TARGETPLATFORM=linux/amd64 docker-compose -f docker/docker-compose.yml build
VINA_PLATFORM=linux_aarch64 docker-compose -f docker/docker-compose.yml build
# Intel Mac 平台 # Linux ARM64 平台
VINA_PLATFORM=mac_x86_64 docker-compose -f docker/docker-compose.yml build TARGETPLATFORM=linux/arm64 docker-compose -f docker/docker-compose.yml build
# 不下载 AutoDock Vina # 使用不同版本
DOWNLOAD_VINA=false docker-compose -f docker/docker-compose.yml build VINA_VERSION=1.2.6 TARGETPLATFORM=linux/amd64 docker-compose -f docker/docker-compose.yml build
``` ```
### 使用环境文件 ### 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 # 创建自定义环境文件
cat > docker/my.env << EOF cat > docker/my.env << EOF
VINA_VERSION=1.2.6 VINA_VERSION=1.2.6
VINA_PLATFORM=linux_x86_64 TARGETPLATFORM=linux/amd64
DOWNLOAD_VINA=true
EOF EOF
# 使用自定义环境文件构建 # 使用自定义环境文件构建

64
docker/docker-compose.yml
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@@ -7,8 +7,6 @@ services:
dockerfile: docker/Dockerfile dockerfile: docker/Dockerfile
args: args:
VINA_VERSION: ${VINA_VERSION:-1.2.7} VINA_VERSION: ${VINA_VERSION:-1.2.7}
VINA_PLATFORM: ${VINA_PLATFORM:-linux}
DOWNLOAD_VINA: ${DOWNLOAD_VINA:-true}
image: vinatools:latest image: vinatools:latest
container_name: vinatools-container container_name: vinatools-container
volumes: volumes:
@@ -19,8 +17,7 @@ services:
- ./results:/app/results - ./results:/app/results
working_dir: /app working_dir: /app
environment: environment:
- PIXI_ROOT=/root/.pixi - PATH=/opt/venv/bin:/usr/local/bin:$PATH
- PATH=/root/.pixi/bin:/app/bin:$PATH
# 保持容器运行 # 保持容器运行
tty: true tty: true
stdin_open: true stdin_open: true
@@ -28,6 +25,9 @@ services:
network_mode: host network_mode: host
# 重启策略 # 重启策略
restart: unless-stopped 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 # 资源限制
deploy: deploy:
resources: resources:
@@ -38,33 +38,29 @@ services:
memory: 2G memory: 2G
cpus: '1.0' cpus: '1.0'
# 可选：用于 Jupyter Notebook 服务 # # 可选：用于 Jupyter Notebook 服务
jupyter: # jupyter:
build: # build:
context: .. # context: ..
dockerfile: docker/Dockerfile # dockerfile: docker/Dockerfile
args: # args:
VINA_VERSION: ${VINA_VERSION:-1.2.7} # VINA_VERSION: ${VINA_VERSION:-1.2.7}
VINA_PLATFORM: ${VINA_PLATFORM:-linux_x86_64} # image: vinatools:latest
DOWNLOAD_VINA: ${DOWNLOAD_VINA:-true} # container_name: vinatools-jupyter
image: vinatools:latest # ports:
container_name: vinatools-jupyter # - "8888:8888"
ports: # volumes:
- "8888:8888" # - ..:/app
volumes: # - ./data:/app/data
- ..:/app # - ./results:/app/results
- ./data:/app/data # working_dir: /app
- ./results:/app/results # environment:
working_dir: /app # - PATH=/usr/local/bin:$PATH
environment: # command: >
- PIXI_ROOT=/root/.pixi # bash -c "
- PATH=/root/.pixi/bin:/app/bin:$PATH # pip3 install jupyter notebook &&
command: > # jupyter notebook --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' --NotebookApp.password=''
bash -c " # "
/root/.pixi/bin/pixi workspace platform add linux-aarch64 && # restart: unless-stopped
/root/.pixi/bin/pixi add jupyter notebook && # depends_on:
/root/.pixi/bin/pixi run jupyter notebook --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' --NotebookApp.password='' # - vinatools
"
restart: unless-stopped
depends_on:
- vinatools

13
docker/docker.env.example
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@@ -1,12 +1,7 @@
# AutoDock Vina 配置 # AutoDock Vina 配置
VINA_VERSION=1.2.7 VINA_VERSION=1.2.7
VINA_PLATFORM=mac_aarch64 TARGETPLATFORM=linux/amd64
DOWNLOAD_VINA=true
# 其他平台选项： # 支持的平台选项：
# VINA_PLATFORM=linux_x86_64 # TARGETPLATFORM=linux/amd64 # x86_64
# VINA_PLATFORM=mac_x86_64 # TARGETPLATFORM=linux/arm64 # aarch64
# VINA_PLATFORM=windows_x86_64
# 禁用 AutoDock Vina 下载
# DOWNLOAD_VINA=false