Install

Requirements

• Python ≥ 3.11
• git

Install from source (recommended during v0.1)

git clone https://github.com/CNNC-Lab/labflow.git ~/repos/labflow
cd ~/repos/labflow
pip install -e ".[dev,docs,snakemake]"

Verify:

labflow --version
# 0.1.0

Optional backends

• conda: install Miniforge or Miniconda and ensure conda is on PATH.
• uv: curl -LsSf https://astral.sh/uv/install.sh | sh
• apptainer: apt package or build from source; v1.3+ recommended.
• pixi: curl -fsSL https://pixi.sh/install.sh | bash

HPC systems registry

labflow reads ~/.claude/contexts/hpc-systems.yaml by default. On the workstation, this is a symlink to the vault-side file maintained by the hpc-engineer agent. See HPC systems registry.