Download and Install

Install PANKEGG

Installing Pankegg is simple. You can either download the repository as a zip file, or clone it using git.

Download via wget or curl

You can download the repository as a zip file with wget:

wget https://github.com/RVanDamme/PANKEGG/archive/refs/heads/master.zip
unzip master.zip
cd PANKEGG-master

Or with curl:

curl -L https://github.com/RVanDamme/PANKEGG/archive/refs/heads/master.zip -o master.zip
unzip master.zip
cd PANKEGG-master

Clone via git

Alternatively, you can clone the repository directly using git:

git clone https://github.com/RVanDamme/PANKEGG.git
cd PANKEGG

Install dependencies

You can install Pankegg and all necessary dependencies via conda, pip, or pixi.

Using conda

For a stable installation, use conda-lock to create and activate a stable conda environment using the provided conda-lock.yml file (found in the conda.recipe directory):

conda-lock install --name pankegg_env conda-lock.yml
conda activate pankegg_env

Alternatively, create and activate a new conda environment using the provided environment.yml file (found in the conda.recipe directory):

conda env create -f environment.yml
conda activate pankegg_env

Using pip

From within the repository folder, install all dependencies by running:

pip install .

Or, install dependencies only:

pip install flask pandas numpy scikit-learn scipy jinja2 click setuptools importlib-metadata

Using pixi

If you use pixi, you can use the pixi.lock and run all the Pankegg commands with:

pixi run <pankegg_command>

Substitube <pankegg_command> with the command you want to run.

Windows Subsystem for Linux

If you are using WSL, you should install Pankegg in the WSL itself and NOT on your Windows drive. This is required because of the disparity between the Linux FileSystem and the Windows FileSystem, which prevents the tools from running correctly through WSL when installed in the Windows FS.

We also recommend storing your database in the WSL rather than on your Windows drive. While this is not critical, it is a better practice and ensures that Pankegg will read the database properly.