CLI Installation Guide

CLI Installation Guide#

This section covers installation and verification for the command-line interface (CLI) of MEGqc.

1. Create a fresh environment#

# Optional once per machine: initialize your shell for conda
conda init zsh   # use bash/powershell as needed
# restart terminal after conda init

# Create dedicated environment with Python 3.10
conda create -n megqc-py310 python=3.10 pip -y

# Activate
conda activate megqc-py310

# Verify Python version
python --version
# Expected: Python 3.10.x

2. Install MEGqc#

python -m pip install --upgrade pip
pip install meg-qc

Dependencies

You do not need to install dependencies manually. Installing meg-qc from PyPI installs required dependencies automatically.

3. Verify CLI entry points#

run-megqc --help
run-megqc-plotting --help
globalqualityindex --help
get-megqc-config --help

If you also want to launch the GUI from the same environment:

megqc

4. Upgrade / uninstall#

# Upgrade MEGqc in the same environment
pip install --upgrade meg-qc

# Uninstall package only
pip uninstall meg-qc

# Remove whole environment (optional)
conda deactivate
conda env remove -n megqc-py310

Optional: export environment spec#

conda env export --from-history > megqc-py310.yml

Troubleshooting#

  • If python --version is not 3.10.x, recreate the environment with python=3.10.

  • If commands are not found, confirm the environment is active (conda activate megqc-py310).

  • If installation fails due to old pip metadata, run python -m pip install --upgrade pip setuptools wheel and retry.

Next section#

Continue to the tutorial section to run calculation, plotting, and GQI workflows: