Setup#

1. Clone this repository#

Warning

This project uses type-unions introduced in python 3.10. Make sure you are using at least python version 3.10. This can be done by running python --version

git clone https://gitlab.renkulab.io/expectmine/processing-pipeline
cd processing-pipeline

2. Setup environment#

Windows

Note

As this step relies on Make, which is only available as default through linux-based systems. To still use the following guide either install make through choco or use the linux sub system and follow the linux guide.

python -m venv env
.\env\Scripts\activate
make deps
make env-vars

macOS

python -m venv env
source env/bin/activate
make deps
make env-vars

Linux

python -m venv env
source env/bin/activate
make deps
make env-vars

3. Install required libraries#

Note

You only need to install the libraries which are used by the steps you are using.

You can go to the steps section to see which libraries are required by the steps you want to use.