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Install This Plugin

Installing a NOMAD plugin has two parts: getting the Python package into the environment, and turning its entry points on in nomad.yaml. The general mechanics are covered by the NOMAD plugin documentation; below is where each part concretely lives for FAIRmat's two workspaces.

In nomad-distro-dev (local development)

  1. Add this repo as a git submodule under packages/:
git submodule add git@github.com:FAIRmat-NFDI/nomad-eosc-galaxy-actions.git packages/nomad-eosc-galaxy-actions

  1. Register it as a workspace package in the root pyproject.toml: add "nomad-eosc-galaxy-actions" to the plugin dependencies list, and nomad-eosc-galaxy-actions = { workspace = true } under [tool.uv.sources]. Then run uv sync.

  2. Add both entry points to the root nomad.yaml:

plugins:
  entry_points:
    include:
      - "nomad_eosc_galaxy_actions.actions.find_peaks:find_peaks_action"
      - "nomad_eosc_galaxy_actions.example_uploads:find_peaks_example_upload"
    options:
      nomad_eosc_galaxy_actions.actions.find_peaks:find_peaks_action:
        galaxy_workflow_id: "..."   # see below
        # galaxy_url: "https://usegalaxy.eu"  # default, override if needed

The example upload isn't strictly required. Leave it out if you don't want the XPS Peak Finding via Galaxy entry showing up under Uploads → Add example uploads; but it's the fastest way for anyone else to try this plugin, see Use This Plugin.

There's no separate schema package to enable: triggering happens through NOMAD's generic Actions page, not through a bespoke entry, see Use This Plugin and Explanation for why.

In a (production / Oasis deployment)

  • Once this plugin is published to PyPI: add it, with a pinned version, to pyproject.toml's [project.optional-dependencies].plugins list, alongside the other plugin packages there.
  • Until then: install it as a git dependency in that same list instead, e.g "nomad-eosc-galaxy-actions @ git+https://github.com/FAIRmat-NFDI/nomad-eosc-galaxy-actions.git@<tag>".
  • Ensure that both entry points are activated in your NOMAD configuration (e.g., your nomad.yaml).

Import the workflow

The Action calls an already-imported Galaxy workflow by ID; it never imports or looks one up itself. Import it once, into whichever Galaxy account the Action will run as:

echo "GALAXY_API_KEY=..." > .env
uv run --env-file .env scripts/import_workflow.py

Put the printed workflow_id into nomad.yaml's galaxy_workflow_id option above.

Temporal

This plugin needs the CPU action queue running. For local development, run docker compose up -d (brings up Temporal) and uv run poe cpuworker (the worker process), from the nomad-distro-dev repo root.