Installation#

Requirements#

  • Python 3.10 or newer

  • Linux or macOS (Windows via WSL2)

  • An HPC cluster running SLURM or SGE, or a local machine for testing

  • Apptainer / Singularity (only required for container-based pipelines)

For users — install from PyPI#

The simplest way to get launchcontainers is from PyPI:

pip install launchcontainers

Verify the install:

lc --help
checker --help

To upgrade to the latest release:

pip install --upgrade launchcontainers

For developers — install from source with Poetry#

If you want to contribute or run the latest development version, use Poetry to manage the virtual environment.

Step 1 — Install pipx and Poetry (once per machine):

pipx installs Poetry into its own isolated environment so it never conflicts with project dependencies.

pip install pipx
pipx install poetry
poetry --version   # verify

Step 2 — Clone the repository:

git clone https://github.com/garikoitz/launchcontainers.git
cd launchcontainers

Step 3 — Create the virtual environment and install:

poetry env use python3
poetry install

Step 4 — Activate the environment:

poetry shell

All subsequent lc and checker commands can be run directly inside the Poetry shell, or prefixed with poetry run without activating it:

poetry run lc --help

Entry points#

Both install paths register the same two command-line tools:

lc        # main pipeline launcher  (prepare / run / qc)
checker   # analysis integrity checker

Optional: build the documentation locally#

cd docs && make html
open _build/html/index.html

Requires sphinx and pydata-sphinx-theme, which are included in the Poetry dev dependencies. If you installed from PyPI, install them separately:

pip install sphinx pydata-sphinx-theme