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Dependency management

Related pages: Workflow management

Note

This page is about the management of (software) dependencies, which involves ensuring the availability of the necessary libraries, environments, and system tools for programs to run properly.

Workflow dependencies, which means the ordering of tasks and the input/output relationships required for a workflow to function, are covered in Workflow management.

Introduction

Lockfiles

TBD

System package managers

Homebrew (macOS)

The default installation path is opt/homebrew

Chocolatey (Windows)

Language package managers

CRAN (R)

pip (Python)

npm (JavaScript)

Environment managers

renv (R)

venv (Python)

TBD

Conda (multi-language)

List all conda environments:

conda env list
conda info --envs

Create a new conda environment:

conda create --name <env_name>
conda create --name <env_name> python=3.10
conda create -h # documentation

Export an environment:

conda env export --from-history > environment.yml
conda env export --from-history | grep -v "^prefix:" > environment.yml

conda env export --no-builds | grep -v "^prefix:" > environment.yml

Install packages:

conda install -h

List packages:

conda list
conda list -h

Conda files

Pixi (multi-language)

Container managers

Docker

TBD

Podman

Singularity