Working with environments

The different operating systems support different tools. In order to solve this issue, we can use environments, which wil help us make our bioinformatics work more reproducible. This environments specifiy the tools needed to perform the task and the managers inside the environment will make sure to install these tools with their dependencies so that you can run the analysis in your device.

There are different types of environments, like Conda, but in this course we are going to focus on Pixi.

Install Pixi

In order to install pixi just run the following command in your terminal:

curl -fsSL https://pixi.sh/install.sh | sh

You can find more infromation about pixi here

Create an environment

To create an environment for your project we will ask pixi to initialize a folder named pixi_training. We will also add conda-forge and bioconda channles with the -c flag.

pixi init pixi_training -c conda-forge -c bioconda

If you look in the new folder created you find a file called pixi.toml.

1. pixi.toml

[workspace]
channels = ["conda-forge", "bioconda"]
name = "amrei_pixi_training"
platforms = ["osx-arm64"]
version = "0.1.0"

[tasks]

[dependencies]

This is how the pixi.tomlfile would like like after creating it. This file gives you information about your project:

• Workspace: An overview of the environment: the channels that we added when we called pixi init -c, the name of the environment, the operating system and the version.
• Tasks (not covered)
• Dependencies: it will list the different tools that you install within the environment.

2. pixi.lock

Adding a tool or a dependency to the environemnt will generate another file called pixi.lock.

This file contains information about the channels added to you environment, where the packages were dowloaded from, liceses information and more.

DO NOT DELETE pixi.tomlor pixi.lock files, it will break your environment!

Adding dependencies

The comand pixi add will tell Pixi to install a specified program for you and it will be added to the dependencies list found in the pixi.toml file that we talked about in the previous section.

pwd
cd pixi_training
pixi add quarto

If we now check the dependencies in the pixi.toml file we would see the new program added quarto = ">=1.7.32,<2"(the versions might be different).

Running a package

In order to run a package we use the run command followed by the package.

pixi run quarto --help

You can substitute quarto with any other package followed by the pertinent commands.