# Installation Guide
Detailed setup for all platforms and configurations.
**Quick start?** See [Quick Start](../quickstart.md) for 5-minute setup.
---
## Install Options
```bash
# Standard (recommended for most users)
pip install chatspatial
# Full (all methods including deep learning)
pip install chatspatial[full]
```
| Option | Features | Install Time |
|--------|----------|--------------|
| Standard | Core analysis, basic deconvolution, cell communication | 3-5 min |
| Full | + Deep learning, Cell2location, CellRank, SpaGCN, STAGATE | 6-10 min |
---
## Requirements
- **Python 3.10+** (3.11-3.12 recommended)
- **8GB+ RAM** (16GB+ for large datasets)
- **macOS, Linux, or Windows**
```bash
python --version # Should be 3.10+
```
---
## Virtual Environment (Recommended)
```bash
# Create
python3 -m venv chatspatial_env
source chatspatial_env/bin/activate # macOS/Linux
# chatspatial_env\Scripts\activate # Windows
# Install
pip install chatspatial[full]
```
---
## Configure MCP
### Claude Desktop
Edit `~/Library/Application Support/Claude/claude_desktop_config.json` (macOS):
```json
{
"mcpServers": {
"chatspatial": {
"command": "python",
"args": ["-m", "chatspatial", "server"]
}
}
}
```
> Windows: `%APPDATA%\Claude\claude_desktop_config.json`
> Linux: `~/.config/Claude/claude_desktop_config.json`
### Claude Code
```bash
claude mcp add chatspatial python -- -m chatspatial server
```
**Restart Claude after configuration.**
---
## Platform Notes
### Windows
**Not available:** SingleR, PETSc acceleration
**Alternatives:**
- Cell type annotation: Tangram, scANVI, CellAssign, mLLMCelltype
- CellRank: Works without PETSc
### R-based Methods (RCTD, SPOTlight)
Optional. Requires R installation:
```bash
# Install R from https://cran.r-project.org/
# Then in R:
install.packages(c("spacexr", "SPOTlight"))
```
---
## Verify
```bash
python -m chatspatial server --help
python -c "import chatspatial; print('OK')"
```
---
## Troubleshooting
| Issue | Solution |
|-------|----------|
| Import errors | `pip install --upgrade pip chatspatial[full]` |
| Claude not seeing tools | Check Python path, restart Claude |
| R methods failing | Install R and required packages |
See [Troubleshooting Guide](troubleshooting.md) for more.
