Bioclaw

开源生物科研环境一键安装包
Zero to Bio-Research Environment in 10 Minutes

English • 简体中文 • 快速开始 • 特性 • 截图

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🎯 What is Bioclaw?

Bioclaw is an open-source integration package that sets up a complete bio-research environment with one command.

In 10 minutes, you get:

• 🧬 RStudio Server - Professional statistical computing environment
• 🐍 JupyterLab - Interactive Python data science notebook
• 🤖 AI Assistant - Natural language bio-analysis via messaging apps
• 📦 Pre-installed Tools - 150+ curated bio-research skills

Perfect for:

• 🔬 Researchers who need a standardized analysis environment
• 🎓 Students learning bioinformatics
• 👥 Teams sharing reproducible workflows
• 🚀 Anyone who hates configuration hell

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✨ Features

🚀 One-Command Installation curl -fsSL https://.../install.sh | bash No Docker knowledge required. No complex configuration. Just works.	🐳 Fully Containerized Everything runs in Docker containers: Isolated from your system Reproducible across machines Easy to update/rollback
💬 AI-Powered Analysis Talk to your data: "Analyze this gene expression data" "Plot a volcano chart" "Search PubMed for CRISPR papers"	📊 Professional Tools Pre-configured with: R 4.3 + Bioconductor (DESeq2, Seurat) Python 3 + scanpy, biopython 150+ bio-research skills

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🚀 Quick Start

Prerequisites

• macOS 10.14+ or Linux (Ubuntu 20.04+)
• Docker Desktop (Install Guide)

Installation

# Download and install
curl -fsSL https://raw.githubusercontent.com/Rowtion/Bioclaw/main/install.sh | bash

# Start Bioclaw
bioclaw start

That's it!

After 5-10 minutes, access your research environment:

Service	URL	Password
RStudio	http://localhost:8787	bioclaw
JupyterLab	http://localhost:8888	bioclaw
AI Assistant (Opencode)	http://localhost:4096	-

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📸 Screenshots

  

RStudio Server and JupyterLab interfaces

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🎬 Demo

# Example 1: Start and analyze data
$ bioclaw start
🚀 启动 Bioclaw...
🤖 启动 Opencode...

✅ 已启动!

📊 访问地址:
   RStudio:    http://localhost:8787
   JupyterLab: http://localhost:8888
   Opencode:   http://localhost:4096
   密码: bioclaw

# Example 2: Use AI assistant (in Slack/Feishu)
User: "用opencode分析我的单细胞数据"
AI: "正在使用scanpy进行分析..."
[Generates UMAP plot, saves to ./outputs/]

# Example 3: Check status
$ bioclaw status
📊 服务状态:
   ✅ Opencode 正在运行 (http://localhost:4096)

# Example 4: Stop when done
$ bioclaw stop
✅ 已停止

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🏗️ Architecture

┌─────────────────────────────────────────────────────────────┐
│                     Your Computer                            │
│  ┌─────────────┐    ┌──────────────┐    ┌────────────────┐ │
│  │   Browser   │    │  Slack/飞书   │    │   Terminal     │ │
│  └──────┬──────┘    └───────┬──────┘    └───────┬────────┘ │
│         │                   │                    │          │
│         └───────────────────┼────────────────────┘          │
│                             │                               │
│                    ┌────────┴────────┐                      │
│                    │  OpenClaw       │                      │
│                    │  (AI Gateway)   │                      │
│                    └────────┬────────┘                      │
│                             │ HTTP                          │
│                    ┌────────┴────────┐                      │
│                    │  Opencode       │                      │
│                    │  (Port 4096)    │                      │
│                    └────────┬────────┘                      │
│                             │                               │
│         ┌───────────────────┴───────────────────┐          │
│         │           Docker Environment           │          │
│         │  ┌───────────────────────────────┐    │          │
│         │  │  RStudio (:8787)              │    │          │
│         │  │  • R + Bioconductor           │    │          │
│         │  └───────────────────────────────┘    │          │
│         │  ┌───────────────────────────────┐    │          │
│         │  │  JupyterLab (:8888)           │    │          │
│         │  │  • Python + scanpy            │    │          │
│         │  └───────────────────────────────┘    │          │
│         └───────────────────────────────────────┘          │
└─────────────────────────────────────────────────────────────┘

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🛠️ Installation Methods

Method 1: One-Line Install (Recommended)

curl -fsSL https://raw.githubusercontent.com/Rowtion/Bioclaw/main/install.sh | bash

Method 2: Manual Installation

# Clone repository
git clone https://github.com/Rowtion/Bioclaw.git ~/.bioclaw
cd ~/.bioclaw

# Run setup
bash install.sh

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📚 Usage Guide

Basic Commands

# Start Bioclaw
bioclaw start

# Check status
bioclaw status

# View logs
bioclaw logs

# Stop Bioclaw
bioclaw stop

# Update to latest version
bioclaw update

Working with Data

Upload data:

# Copy files to data directory
cp my_data.csv ~/.bioclaw/data/

# Access in RStudio/JupyterLab
# Path: /home/rstudio/data/

Save results:

# Results automatically saved to
~/.bioclaw/outputs/

AI Assistant Usage

Option 1: Feishu/Lark (飞书)

1. Create Feishu App:

   • Go to Feishu Developer Console
   • Create a new enterprise app
   • Enable "Bot" capability
   • Get App ID, App Secret, Encrypt Key, Verification Token

2. Configure OpenClaw:

   cd ~/.bioclaw
   cp openclaw-config/openclaw.json.example openclaw-config/openclaw.json
   # Edit and fill in your Feishu credentials
   nano openclaw-config/openclaw.json

3. Start all services:

   bioclaw start

4. Configure OpenClaw Gateway (使用 CLI):

   方法 A: 使用别名命令（推荐）

   # 配置 Gateway 模式
   bioclaw-openclaw config set gateway.mode local
   
   # 登录飞书通道
   bioclaw-openclaw channels login feishu
   
   # 检查状态
   bioclaw-openclaw doctor
   
   # 重启 Gateway 生效
   bioclaw restart

   方法 B: 使用 docker exec

   docker exec bioclaw-openclaw node /app/openclaw.mjs config set gateway.mode local
   docker exec -it bioclaw-openclaw node /app/openclaw.mjs channels login feishu
   docker exec bioclaw-openclaw node /app/openclaw.mjs doctor

   方法 C: Web UI 配置

   • 打开 http://localhost:18790
   • 点击 "Channels" → 添加飞书
   • 填入 App ID / App Secret / Encrypt Key / Verification Token

5. Add bot to Feishu group and chat:

   "帮我用DESeq2做差异表达分析"
   "Plot a heatmap of top 50 genes"
   "Search PubMed for COVID-19 vaccine papers"
   

Option 2: Direct Browser Access

Open http://localhost:4096 for direct Opencode interface.

OpenClaw CLI 命令参考

前提: 安装时已自动添加别名 bioclaw-openclaw，如果不可用请重新加载 shell 配置：source ~/.zshrc 或 source ~/.bashrc

常用命令:

# 诊断检查
bioclaw-openclaw doctor

# 查看/修改配置
bioclaw-openclaw config get                    # 查看所有配置
bioclaw-openclaw config set gateway.mode local # 设置本地模式

# 通道管理
bioclaw-openclaw channels status              # 查看通道状态
bioclaw-openclaw channels login feishu        # 登录飞书
bioclaw-openclaw channels logout feishu       # 退出飞书

# 查看日志
bioclaw-openclaw logs gateway                 # 查看 Gateway 日志

# 重启服务
bioclaw restart                               # 重启所有服务

如果别名不可用，使用完整命令:

docker exec bioclaw-openclaw node /app/openclaw.mjs <命令>

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🔧 Advanced Configuration

Change Default Password

Edit .env file:

cd ~/.bioclaw
nano .env

# Change these:
RSTUDIO_PASSWORD=your_secure_password
JUPYTER_TOKEN=your_secure_token

Restart:

docker-compose restart

Enable Remote Access

See docs/REMOTE_ACCESS.md

Add Custom Skills

Drop your skills into:

~/.bioclaw/scientific-skills/

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🐛 Troubleshooting

Installation Issues

Q: Docker not found

# macOS: Install Docker Desktop from https://docs.docker.com/desktop/install/mac-install/
# Ubuntu: sudo apt-get install docker.io

Q: Port already in use

# Check what's using port 8787
lsof -i :8787

# Kill process or change port in docker-compose.yml

Q: Build fails

# Check Docker daemon is running
docker info

# Retry build
cd ~/.bioclaw && docker-compose build --no-cache

Runtime Issues

Q: Cannot access localhost:8787

• Ensure Bioclaw is running: bioclaw status
• Check firewall settings
• Try http://127.0.0.1:8787

Q: Forgot password

• Default: bioclaw
• Change in ~/.bioclaw/.env

More issues? See FAQ.md

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🤝 Contributing

We welcome contributions!

Ways to Contribute

• 🐛 Report bugs
• 💡 Suggest features
• 📝 Improve documentation
• 🔧 Submit pull requests

Development Setup

# Fork and clone
git clone https://github.com/YOUR_USERNAME/Bioclaw.git
cd Bioclaw

# Test changes
bash install.sh

See CONTRIBUTING.md for guidelines.

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📄 License

This project is licensed under the MIT License.

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🙏 Acknowledgments

Bioclaw wouldn't be possible without:

• OpenClaw - AI conversation gateway
• Opencode - Code execution environment
• Docker - Container platform
• RStudio - Statistical computing IDE
• Project Jupyter - Interactive computing

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Made with ❤️ for the research community
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