Installation guide
The arborist package can be installed either via conda (recommended) or manually via pip. Both methods will automatically install dependencies
Installation via conda (recommended)
arborist is available on Bioconda. You can easily install it via conda/mamba with:
conda install -c bioconda arborist
Manual installation
Clone the repository and install the package using pip. Note: dependencies will be installed automatically
git clone https://github.com/VanLoo-lab/Arborist.git
cd Arborist
pip install .
Testing the installation
To test the installation of the CLI tool and Python package, run the following:
arborist -h
python -c "from arborist import arborist"
Dependencies
The arborist package requires the following dependencies:
python>=3.7numpy>=1.20scipy>=1.7pandas>=1.3pygraphviznumba>=0.61networkx>=3.6