# Download from github
git clone [email protected]:hfldai/scmattools.git
cd scmattools/

# Set up python requirements
pip install -r requirements.txt

# Install
pip install -e .

# Run test to check the installation is successful
python tests/test_main.py

usage: scmattools [-h] [-o OUTPUT] [-ort OUTPUT_RT] [-oct OUTPUT_CT]
                  [-omatt OUTPUT_MATT]
                  rq cq matq rt

positional arguments:
  rq                    path to query region intervals (make sure the file is
                        Tab separated)
  cq                    path to query cell names
  matq                  path to query rq x cq sparse count matrix (.mtx)
  rt                    path to target region intervals (make sure the file is
                        Tab separated)

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        path to output directory
  -ort OUTPUT_RT, --output_rt OUTPUT_RT
                        path to the output target region intervals
  -oct OUTPUT_CT, --output_ct OUTPUT_CT
                        path to the output target cell names
  -omatt OUTPUT_MATT, --output_matt OUTPUT_MATT
                        path to the output target region x cell sparse count
                        matrix (.mtx)

scmattools tests/test_data/test.query.regions \
           tests/test_data/test.query.cells \
           tests/test_data/test.query.mtx \
           tests/test_data/test.target.regions \
           -o tests/example_output