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installation.md

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Installation

Step 1 Create and enter conda env (recommend)

conda create -y -n ONTraC python=3.11  # ONTraC supports Python 3.10, 3.11, and 3.12 for now
conda activate ONTraC

Add this kernel to jupyter (recommend)

pip install ipykernel
python -m ipykernel install --user --name ONTraC --display-name "Python 3.11 (ONTraC)"

Step2 Install ONTraC

using pip

pip install ONTraC
# Use this command if you want to visualise the results by `ONTraC_analysis`.
pip install "ONTraC[analysis]"

using conda

NOTE: For ARM-based macOS, we recommend installing via pip for now, as the dependency package, pytorh-geometric, does not have a conda build for it. NOTE: For x86-based macOS, conda install only support Python 3.10 and 3.11 for now. WARNING: Installing with conda can be very slow.

conda install -c gyuanlab -c pytorch -c pyg -c default -c nvidia -c conda-forge ontrac

install developmental version from GitHub

git clone [email protected]:gyuanlab/ONTraC.git .
cd ONTraC
pip install .
# Use this command if you want to visualise the results by `ONTraC_analysis`.
pip install ".[analysis]"