How to use git repo in jupyter-notebook

Question

I created a conda envi and I cloned this repo https://github.com/bioinfo-ibms-pumc/SCSA from github.

I want this tool (SCSA) to work in my jupyter notebook. Inside the envi i installed pandas, numpy and scipy.

I tried this code in my jupyter notebook to use the repo:

%run SCSA.py
!python3 SCSA.py -h
%tb

I got the following error message:

usage: SCSA.py [-h] -i INPUT [-o OUTPUT] [-d DB] [-s SOURCE] [-c CLUSTER]
               [-M MARKERDB] [-f FOLDCHANGE] [-p PVALUE] [-w WEIGHT]
               [-g SPECIES] [-k TISSUE] [-m OUTFMT] [-T CELLTYPE] [-t TARGET]
               [-E] [-N] [-b] [-l]
SCSA.py: error: the following arguments are required: -i/--input

An exception has occurred, use %tb to see the full traceback.

SystemExit: 2


Traceback (most recent call last):
  File "SCSA.py", line 13, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'

I navigated to the cloned repo and tried the same in the terminal and it worked. But I really want to use it in the jupyter notebook.

Thanks for help