Pixi tools on HPC centers

Pixi
HPC
Secure Data Environment
Author

Pavlin

Published

November 13, 2025

Modified

December 11, 2025

Pixi

Pixi is a package management tool for developers. It allows the developer to install libraries and applications in a reproducible way. Use pixi cross-platform, on Windows, Mac and Linux.

On HPC centers, the default setup should be altered to reflect the particular storage allocation. The setup bellow is for personal use. Setting pixi for shared use in a project will be covered in a separate topic.

Install and configure pixi

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

# Redirect cache and globals in project folder
export PIXI_CACHE_DIR=/crex/proj/uppmax-xxx/user/nobackup/.PIXI_CACHE_DIR
export PIXI_HOME=/crex/proj/uppmax-xxx/user/nobackup/.PIXI_HOME
# make the folders
mkdir -p $PIXI_CACHE_DIR $PIXI_HOME

# add global bin to $PATH
export PATH=$PATH:$PIXI_HOME/bin

Install global tools

Pixi can install packages (usually tools) in a separate environment and expose them like any common command-line tool. Each tool will be isolated and independent from any other tool installation.

Install samtools as a global tool - example

pixi global install -c conda-forge -c bioconda samtools
Global environments as specified in '/crex/proj/uppmax-xxx/user/nobackup/.PIXI_HOME/manifests/pixi-global.toml'
└── samtools: 1.9 (installed)
    └─ exposes: ace2sam, blast2sam, bowtie2sam, export2sam, interpolate_sam, maq2sam-long, maq2sam-short, md5fa, md5sum-lite, novo2sam, plot-bamstats, psl2sam, sam2vcf, samtools, seq_cache_populate, soap2sam, wgsim, wgsim_eval, zoom2sam

List all globally installed tools

pixi global list
Global environments as specified in '/crex/proj/uppmax-xxx/user/nobackup/.PIXI_HOME/manifests/pixi-global.toml'
├── samtools: 1.9
│   └─ exposes: ace2sam, blast2sam, bowtie2sam, export2sam, interpolate_sam, maq2sam-long, maq2sam-short, md5fa, md5sum-lite, novo2sam, plot-bamstats, psl2sam, sam2vcf, samtools, seq_cache_populate, soap2sam, wgsim, wgsim_eval, zoom2sam
├── ipython: 9.6.0
│   └─ exposes: ipython, ipython3
├── julia: 1.10.4
│   └─ exposes: .julia-post-link, julia
├── lazydocker: 0.24.1
│   └─ exposes: lazydocker
...

Maintaining pixi

# Update pixi
pixi self-update

# Update single global tool
pixi global update samtools

# Update all tools
pixi global update

# clean cache
pixi clean cache

pixi-pack

There is a convenient way to pack whole environment/project (download all necessary packages and wrap them in a single file) and unpack it on another machine into a new environment (even without conda or pixi available on that machine).

Example - CellTrek

# Install pixi-pack as global tool
pixi global install pixi-pack pixi-unpack

# Init new project
pixi init --platform linux-64 -c conda-forge -c bioturing -c bioconda CellTrek

# Add packages
cd CellTrek
pixi add bioturing::r-celltrek "r-seurat<5.0" "r-seuratobject<5.0" bioconda::bioconductor-consensusclusterplus

# create executable that can unpack itself
pixi-pack --create-executable --use-cache ./cache

# on the other machine create folder and run to unpack
./environment.sh

# One can use conda to activate the environment as well
conda activate /full/path_to_env

Example - gsMap

pixi init --platform linux-64 -c conda-forge -c bioconda gsMap
cd gsMap
pixi add "python>=3.10" bioconda::gsmap

# Test the setup
pixi shell

(gsMap) gsmap -v
gsMap version 1.73.5

exit
# then pixi-pack ... and so on...