Installation

Stable version

To use Garfield, first install it:

Recommended: install Garfield in a new virtual environment:

conda create -n env_garfield python=3.9
conda activate env_garfield

Additional Libraries

To use Garfield, you need to install some external libraries. These include:

• PyTorch

• PyTorch Scatter

• PyTorch Sparse

• bedtools

We recommend to install the PyTorch libraries with GPU support. If you have CUDA, this can be done as:

pip install torch==${TORCH}
pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html

where ${TORCH} and ${CUDA} should be replaced by the specific PyTorch and CUDA versions, respectively.

For example, for PyTorch 2.0.0 and CUDA 11.7, type:

pip install torch==2.0.0
pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-2.0.0+cu117.html

To install bedtools, you can use conda:

conda install bedtools=2.29.0 -c bioconda

Finally, to install Garfield with pip, run:

pip install Garfield

Dev version

To install the development version on GitHub, first install torch:

pip install torch torchvision torchaudio

then run:

git clone https://github.com/zhou-1314/Garfield.git
cd Garfield
python setup.py install

or:

pip install git+https://github.com/zhou-1314/Garfield.git

After a correct installation, you should be able to import the module without errors:

import Garfield as gf