# ChatSpatial Installation
## Step 1: Create Virtual Environment
```bash
# Python 3.11+ required
python3 -m venv venv
source venv/bin/activate # macOS/Linux
# venv\Scripts\activate # Windows
# Or use conda
conda create -n chatspatial python=3.12
conda activate chatspatial
```
## Step 2: Install
```bash
pip install --upgrade pip
pip install chatspatial[full]
```
| Option | Command | Features | Time |
|--------|---------|----------|------|
| **Full** | `pip install chatspatial[full]` | All 60+ methods | ~13 min |
| Standard | `pip install chatspatial` | Core methods | ~6 min |
## Step 3: Configure MCP Client
```bash
# Get your Python path
which python # e.g., /Users/you/venv/bin/python
# Add to Claude Code (recommended)
claude mcp add chatspatial /path/to/venv/bin/python -- -m chatspatial server
```
**Other clients:** See [Configuration Guide](docs/advanced/configuration.md) for Codex, Claude Desktop, and advanced options.
## Step 4: Verify
```bash
python -c "import chatspatial; print('Ready')"
```
Restart your client, then see [Quick Start](docs/quickstart.md) to begin analyzing.
---
## Requirements
- **Python 3.11+** (3.12 recommended)
- **8GB+ RAM** (16GB+ for large datasets)
- **macOS, Linux, or Windows**
---
## Platform Notes
### Windows
**Not available:** SingleR, PETSc
**Use instead:** Tangram, scANVI, CellAssign for annotation; CellRank works without PETSc.
### Python Version Error
If you see `mcp>=1.17.0 not found`:
```bash
rm -rf venv
python3.12 -m venv venv
source venv/bin/activate
pip install chatspatial[full]
```
---
## Optional Dependencies
### R Methods
For RCTD, SPOTlight, CARD, scType, Numbat:
```bash
# Install R 4.4+ from https://cran.r-project.org/
Rscript install_r_dependencies.R
```
### STAGATE
```bash
git clone https://github.com/QIFEIDKN/STAGATE_pyG.git
cd STAGATE_pyG && python setup.py install
```
---
## Help
- [Configuration Guide](docs/advanced/configuration.md) — MCP client setup
- [Troubleshooting](docs/advanced/troubleshooting.md) — Common issues
- [GitHub Issues](https://github.com/cafferychen777/ChatSpatial/issues)
