The environment for Step 1 of this protocol require Singularity. The details of this installation can be found in the Section 1 notebook.
The environment for Sections 2 (Variant 1 and Variant 2) and 3 of this protocol can be installed through the included .yml with the following, which will also initialize a jupyter kernel:
conda env create -f qc_pipe_env.yml
python -m ipykernel install --user --name=qc_pipe
Otherwise, the requirements.txt file can be manually installed In a working Python virtual environment using pip:
pip install -r requirements.txt