Advanced Software Setup with Pixi

Purge Previous Installations (Optional)

If you are reinstalling from stratch on a system with existing other conda/mamba environments that may conflict, remove them first:

rm -rf ~/.mamba ~/.conda ~/.anaconda ~/.pixi ~/.jupyter ~/micromamba ~/.mambarc ~/.local/share/jupyter/

This step is optional but recommended for a clean installation.

Install a Bioinformatics Computing Environment

Run the following command to set up a complete bioinformatics environment with commonly used packages:

curl -fsSL https://raw.githubusercontent.com/StatFunGen/pixi-setup/refs/heads/main/pixi-setup.sh | bash

This command will install R, Python and command tools specified in these files.

Note: Full installation takes <10 minutes on your laptop. But it can take approximately 2 hours on CU Neurology AWS HPC if you install to $HOME where the disk performance is not optimized.

After installation, restart your shell or run:

source ~/.bashrc

Install Additional Software

Once pixi is configured, you can install additional software from conda channels.

Install Executables

Examples of applications available in conda channels:

# RStudio Server
pixi global install rstudio

# VS Code
pixi global install vscode

# Vim text editor
pixi global install vim

# Bioinformatics tools (e.g., STAR aligner)
pixi global install STAR

Verify installations:

which star
star --version

Note: Package names may differ between the install command and the executable name.

Install R Libraries

R and its libraries in this environment use precompiled conda packages. Install R libraries from conda whenever possible for best compatibility.

As an example, suppose we would like to install an R package (e.g., pacman). You can:

1. Verify it is available on anaconda.org
2. Install to the r-base environment configured by our pixi setup script:

pixi global install -c conda-forge --environment r-base r-pacman

For packages not on conda, you can use standard R installation methods (CRAN, Bioconductor, GitHub), but again, conda packages are strongly recommended to avoid compilation issues.

To update a specific package:

pixi global install --environment r-base <PACKAGE>=<VERSION>

To update all packages in the environment:

pixi global update r-base

Install Python Packages

To install a Python package, e.g., seaborn:

1. Verify it is available on anaconda.org
2. Install to the python environment:

pixi global install -c conda-forge --environment python seaborn

For packages not on conda, you can use pip install, but conda packages are preferred.

To update a specific package:

pixi global install --environment python <PACKAGE>=<VERSION>

To update all packages in the environment:

pixi global update python

File Permissions for Collaboration

For collaborative work where multiple users need to read/write shared files, add to ~/.bashrc:

umask 002

This sets default permissions so new files are group-writable (775 for directories, 664 for files).