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Pixi- New conda era

· 3 min read
Thanh-Giang Tan Nguyen
Thanh-Giang Tan Nguyen
Founder at RIVER

Pixi is a fast, modern package management tool built on the conda ecosystem. Whether you're on a personal laptop or an HPC cluster, Pixi makes environment setup simple and reproducible. Here’s a primer on using Pixi. For a full workflow, see: Setting up single-cell RNA-seq analysis with Pixi as collaboration between RIVERXDATA and NGS101

Installing Pixi​

System Requirements​

  • OS: Any modern Unix (Ubuntu, Debian, CentOS, Fedora, Arch, MacOS, etc.)
  • Disk Space: 50–100 MB for Pixi, plus space for packages/cache
  • Privileges: No sudo/root needed—Pixi installs in user space

Ideal for shared environments without admin access.

One-Line Installation​

Run in your terminal:

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

This downloads Pixi, installs it to ~/.pixi/bin, and updates your shell config. After install, restart your terminal or run:

source ~/.bashrc  # or ~/.zshrc

Verify Installation​

Check Pixi is working:

pixi --version
pixi --help

HPC Configuration​

Custom Cache Location​

To avoid home directory quotas, set a custom cache:

export PIXI_CACHE_DIR=/scratch/$USER/pixi-cache

Add to your ~/.bashrc or ~/.bash_profile for persistence.

Proxy Settings​

If your cluster uses a proxy, edit $HOME/.pixi/config.toml:

[proxy-config]
http = "http://proxy.example.com:8080/"
https = "http://proxy.example.com:8080/"
non-proxy-hosts = [".cn", "localhost", "[::1]"]

See Pixi configuration docs for details.

Parallel Downloads​

Speed up downloads on fast networks:

[concurrency]
downloads = 5

Project Activation​

Pixi helps you create reproducible environments with lock files.

Initialize a Project​

pixi init
pixi workspace channel add conda-forge bioconda
pixi workspace platform add osx-arm64 linux-64

Example pixi.toml:

[workspace]
channels = ["bioconda", "conda-forge"]
name = "<your project>"
platforms = ["linux-64", "osx-arm64"]
version = "0.1.0"

[tasks]

[dependencies]

Add Tools​

pixi add fastqc multiqc

Updates dependencies in pixi.toml:

[dependencies]
fastqc = ">=0.12.1,<0.13"
multiqc = ">=1.17,<2"

A pixi.lock file is created for reproducibility, specifying exact package versions and checksums.

Run Tools​

Run tools directly:

pixi run fastqc --help

Or activate the environment shell:

pixi shell
fastqc --help

Recap​

  • Pixi is a user-space, conda-based package manager ideal for laptops and HPC clusters.
  • Easy one-line installation, no admin rights needed.
  • Supports custom cache and proxy settings for HPC environments.
  • Enables reproducible project environments with lock files.
  • Simple commands to add tools and run them in isolated environments.

Enjoy your Pixi-powered workflow!