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Installation

This page is the docs-site version of the installation guide. It is the canonical installation page for the documentation site.

Requirements

  • Python 3.11-3.13 (3.12 recommended)
  • 8GB+ RAM (16GB+ for large datasets)
  • macOS, Linux, or Windows

Step 1: Create an Environment

# venv
python3 -m venv venv
source venv/bin/activate  # macOS/Linux
# venv\Scripts\activate   # Windows

# or conda
conda create -n chatspatial python=3.12
conda activate chatspatial

Step 2: Install ChatSpatial

Recommended: use uv for dependency resolution

# Install uv if needed
curl -LsSf https://astral.sh/uv/install.sh | sh

# Install all major methods
uv pip install chatspatial[full]

Why uv? ChatSpatial depends on a large scientific Python stack. Standard pip can fail on deep dependency resolution; uv is more reliable for this environment.

Install options

Option Command Use when
Full uv pip install chatspatial[full] You want the broadest method coverage
Standard uv pip install chatspatial You only need core functionality
Alternative: pip 
pip install --upgrade pip
pip install chatspatial[full]

If you hit resolution-too-deep, switch to uv.

Step 3: Register ChatSpatial in Your MCP Client

  1. Activate your environment.
  2. Get the absolute Python path:
which python
  1. Register ChatSpatial using this command shape:
/absolute/path/to/python -m chatspatial server
  1. Restart your client after configuration changes.

For exact client-specific syntax, use the Configuration Guide.

Step 4: Verify the Installation

python -c "import chatspatial; print(f'ChatSpatial {chatspatial.__version__} ready')"
python -m chatspatial server --help

If both commands work, continue to Quick Start.

Platform Notes

Windows

Not available: SingleR, PETSc

Use instead: Tangram, scANVI, CellAssign for annotation; CellRank works without PETSc.

If Python or MCP dependencies fail to resolve

rm -rf venv
python3.12 -m venv venv
source venv/bin/activate
uv pip install chatspatial[full]

Optional Dependencies

R-based methods

For RCTD, SPOTlight, CARD, CellChat, SPARK-X, scType, Numbat, and SCTransform:

# Install R 4.4+
Rscript install_r_dependencies.R

STAGATE

git clone https://github.com/QIFEIDKN/STAGATE_pyG.git
cd STAGATE_pyG && python setup.py install

Next Steps