Create an Anaconda environment

conda create --name umap_env python=3.8.0
conda activate umap_env

Load library path for libmkl_rt.so

export LD_LIBRARY_PATH=~/anaconda3/umap_env/lib/         # If loading from anaconda3

Install scanpy

pip install scanpy==1.8.1

Install pybind11

pip install pybind11

Install umap_extend and umap


pip uninstall umap-learn
cd umap_extend
python setup.py install             


cd ../umap
python setup.py install

Run Test

python test_umap_fast.py