conda / mamba (software installation)

Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. Conda quickly installs, runs, and updates packages and their dependencies.

This is how the conda documentation puts it. One more major selling-point: you don't need administrator rights to install conda itself or the to install packages with it. And for our (bioinformatic) purposes, there are two more very useful aspects:

1. There is bioconda, a conda channel with pretty much any tool in bioinformatics pre-packaged for you.
2. conda seemlessly integrates with snakemake for automatic software installation in automated analysis workflows.

installing conda / mamba

We recommend using the mambaforge installation. mamba is a drop-in replacement command for most of conda (it can do exactly the same things), but it is much faster for solving package dependencies. This can mean a major speedup for creating and changing environments. Whenever a command does not actually work with mamba, you can simply use conda instead (it is also installed in the background and is used for any task that's not too slow).

creating and using environments

conda makes it easy to create and manage new (named) software environments. We recommend to create a new (and minimal) software environment whenever possible (for example, in a snakemake workflow, each rule will have its own software environment). You will then only activate that software environment whenever you need the software installed into it. By keeping environments minimal, you avoid clashes in the dependencies that software might have (for example, if software X needs python version 3, while software Y still requires python version 2, these cannot be installed into the same environment---but X and Y will happily install in separate environments, which will pull in the required python version).

But, long story short, here's the command to create an environment:

mamba create -n snakemake_env snakemake snakedeploy snakefmt

You can then activate that environment with:

mamba activate snakemake_env

And you will be able to call the installed tools, for example snakemake:

snakemake --version
snakemake --help

If you are done with your current session of using the software, the following gets you back to your original environment (the one you were in before activating snakemake_env):

mamba deactivate

If you no longer need the entire environment (and the software contained in it) and want to delete it, you can:

mamba env remove -n snakemake_env

And then, there are many other things you can do with environments---just look up the details whenever you need them.

installing specific versions of software

Sometimes, you want to install a specific version of a software, for example because something was proven to work with that version in the past. You can achieve this with:

mamba create -n snakemake_env_7_19_1 snakemake=7.19.1

And in case you ever need to dive into the details, there is of course documentation on how conda handles version number specifications.