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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 management 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 environments by providing an environment recipe stored as .yaml file.

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

With the following command a new environment is created with the name stardist-cpu. The packages which are installed are defined in the file infrastructure/env-yamls/stardist-cpu-env.yaml.

mamba env create -f infrastructure/env-yamls/stardist-cpu-env.yaml

Activate environment

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

mamba activate stardist-cpu

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