Project Setup

This page guides you through the setup of all necessary tools which are used for data processing and analysis in this project.

Mambaforge

Our recommended tool for environment managemt is Mambaforge. Please download the latest version and install it if you have not done so already.

Build environment

An environment is a collection of tools, packages and dependencies which are required to execute a script. With mambaforge we have an environment manager which we can use to build envrionments by providing an environment recipe stored as .yaml file.

Attention

Make sure that you are in the root-directory of your project.

With the following command a new envrionment is created with the name cohesin_residence_time. The packages which are installed are defined in the file infrastructure/env-yamls/cohesin_residence_time-env.yml.

mamba env create -f infrastructure/env-yamls/cohesin_residence_time-env.yml

Activate environment

Once an envrionment is created it must be activated such that we can use the installed packages.

mamba activate cohesin_residence_time

Once the environment is activate your CLI prompt will be prefixed with the environment name e.g.: (cohesin_residence_time)$