Environment Setup

1. either do

conda create -n bmi500 python=3.12.4

or

python3 -m venv bmi500

2. activate environment

conda activate bmi500

or

source bmi500/bin/activate

3. Install required packages

pip install -r requirements.txt

It may be required to install g++ and cmake in order to install python louvain

4. run scanpy_pbmc.py

python scanpy_pbmc.py --data-dir {data_dir} --data-set {data_set} ---out-dir {output_dir} --num-threads {num_thread}

data_dir is the top level directory in which the data_set subdirectories resides. defaults to data

output_dir is where the output file is placed. defaults to data

data_set is one of 'pbmc3k', 'pbmc6k', and 'pbmc10k'.