JHU BME Design Team 6 Data Analysis Pipeline and Clinical Study Packages
We advocate for micromamba as the package manager. To install micromamba, refer to the installation guide.
Alternatively, you can use the conda environment management package, which should be installed by default on most research computers and clusters. To verify that you have a conda installations, try conda help.
To install PedAccel:
git clone https://github.com/fyng/PedAccel.git
cd PedAccel
# if using micromamba
micromamba env create -f environment.yaml
# if using conda
conda env create -f environment.yaml
To run the data preprocessing:
cd data_analysis/PythonPipeline/preprocessing.py
# change the data folder path according to the code comments in the file
# if using micromamba
micromamba activate pedaccel
# if using conda
conda activate pedaccel
python preprocessing.py