Conda 1: Introduction

Conda is a package and environment manager. As a package manager it enables you to install a wide range of software and tools using one simple command: conda install. As an environment manager it allows you to create and manage multiple different environments, each with their own set of packages. What are the benefits of using an environment manager? Some examples include the ability to easily run different versions of the same package, have different cross-package dependencies that are otherwise incompatible with each other and, last but not least, easy installation of all the software needed for an analysis.

Environments are of particular relevance when making bioinformatics projects reproducible. Full reproducibility requires the ability to recreate the system that was originally used to generate the results. This can, to a large extent, be accomplished by using Conda to make a project environment with specific versions of the packages that are needed in the project. You can read more about Conda here Links to an external site..

A Conda package is a compressed tarball (system-level libraries, Python or other modules, executable programs or other components). Conda keeps track of the dependencies between packages and platforms - this means that when installing a given package, all necessary dependencies will also be installed.

Conda packages are typically hosted and downloaded from remote so-called channels. Some widely used channels for general-purpose and bioinformatics packages are conda-forge Links to an external site. and Bioconda Links to an external site., respectively. Both of these are community-driven projects, so if you’re missing some package you can contribute to the channel by adding the package to it. When installing a Conda package you specify the package name, version (optional) and channel to download from.

A Conda environment is essentially a directory that is added to your PATH and that contains a specific collection of packages that you have installed. Packages are symlinked between environments to avoid unnecessary duplication.

This tutorial depends on files from the course GitHub repo. Take a look at the setup for instructions on how to set it up if, you haven’t done so already. Then open up a terminal and go to workshop-reproducible-research/tutorials/conda. Instructions below assume that you are standing in workshop-reproducible-research/tutorials/conda/ unless otherwise specified (e.g. if it says “create a file”, it means save it in workshop-reproducible-research/tutorials/conda/).