CLAMP analyses

🔧 Dependencies

CLAMP uses three Conda environments to separate core package development, large-scale analyses, and GPU-accelerated workflows:

Environment	File	Purpose
clamp-analyses.yaml	envs/clamp-analyses.yaml	Default environment for CPU-based modeling, priors, projections, and vignettes.
gpu-kmeans.yaml	envs/gpu-kmeans.yaml	Optional environment for GPU-accelerated clustering and benchmarking.

This separation avoids dependency conflicts between R (Bioconductor) and GPU libraries (rapids, cupy, cuml).

🛠️ Install dependencies

Recommended steps to install the system-level and Conda tooling required to create the CLAMP environments.

1. Install a Conda distribution

• Install Miniconda or Mambaforge for your platform (Mambaforge is recommended for faster environment solves).

2. (Optional) Verify GPU drivers for RAPIDS/cuML workflows

• Ensure a compatible NVIDIA driver / CUDA version is installed before creating the GPU environment:

nvidia-smi

• Check RAPIDS compatibility matrix for the correct CUDA version (match driver/CUDA with RAPIDS/cuML requirements).

3. Create environments using conda

conda env create -f envs/clamp-analyses.yaml
conda activate clamp-analyses

# Clone CLAMP the repo into REPO_PATH (adjust path as needed)
export REPO_PATH=~/path/to/CLAMP
mkdir -p "$(dirname "$REPO_PATH")"
git clone https://github.com/chikinalab/CLAMP.git "$REPO_PATH"

# Install and check CLAMP using devtools
Rscript -e "devtools::install_local('$REPO_PATH', force=TRUE, dependencies=FALSE)"

conda env create -f envs/envs/gpu-kmeans.yaml
conda activate gpu-kmeans.yaml

# Clone CLAMP the repo into REPO_PATH (adjust path as needed)
export REPO_PATH=~/path/to/CLAMP
mkdir -p "$(dirname "$REPO_PATH")"
git clone https://github.com/chikinalab/CLAMP.git "$REPO_PATH"

# Install and check CLAMP using devtools
Rscript -e "devtools::install_local('$REPO_PATH', force=TRUE, dependencies=FALSE)"

📘 Notebook Headers

Each notebook explicitly states which environment to use in the first Markdown cell.

Citation

License

This project is licensed under the CC-BY 4.0 License.

Acknowledgments

Supported by the National Human Genome Research Institute,
The Eunice Kennedy Shriver National Institute of Child Health and Human Development,
the National Science Foundation, and the National Eye Institute.