{"id":21032,"library":"cg","title":"Clinical Genomics command center","description":"Clinical Genomics command center (cg) is a Python-based tool for managing and automating clinical genomics workflows. Current version is 85.11.1, with a release cadence of several minor versions per month. Requires Python <3.13,>=3.11.","status":"active","version":"85.11.1","language":"python","source_language":"en","source_url":"https://github.com/Clinical-Genomics/cg","tags":["clinical genomics","bioinformatics","workflow","cli"],"install":[{"cmd":"pip install cg","lang":"bash","label":"Install from PyPI"}],"dependencies":[],"imports":[{"note":"CGConfig is under cg.apps.cg_config, not top-level.","wrong":"from cg import CGConfig","symbol":"CGConfig","correct":"from cg.apps.cg_config import CGConfig"},{"note":"Store is directly in cg.store.","wrong":"from cg.store.api import Store","symbol":"Store","correct":"from cg.store import Store"},{"note":"DemultiplexAPI lives in cg.apps.demultiplex.","wrong":"from cg.apps import DemultiplexAPI","symbol":"DemultiplexAPI","correct":"from cg.apps.demultiplex import DemultiplexAPI"}],"quickstart":{"code":"from cg.apps.cg_config import CGConfig\nfrom cg.store import Store\n\nconfig = CGConfig()\nstore = Store(config)\n# Example: list orders\norders = store.orders()\nprint(orders)","lang":"python","description":"Initialize CGConfig and Store, then perform operations like listing orders."},"warnings":[{"fix":"Use `from cg.store import Store` and pass a `CGConfig` instance.","message":"In version 80+, the store API was restructured: Store is now a class, and connections are managed via CGConfig.","severity":"breaking","affected_versions":">=80.0.0"},{"fix":"Use `cg workflow orders` instead of `cg orders`.","message":"Old CLI entry points like `cg orders` have been moved to `cg workflow ...` subcommands.","severity":"deprecated","affected_versions":">=85.0.0"},{"fix":"Ensure Python version is between 3.11 and 3.12 (exclusive of 3.13).","message":"The package requires Python <3.13,>=3.11. Installing with Python 3.13 may fail silently or produce runtime errors.","severity":"gotcha","affected_versions":">=85.0.0"}],"env_vars":null,"last_verified":"2026-04-27T00:00:00.000Z","next_check":"2026-07-26T00:00:00.000Z","problems":[{"fix":"Run `pip install cg` to install the package.","cause":"The package is not installed or not installed in the current environment.","error":"ModuleNotFoundError: No module named 'cg'"},{"fix":"Use `from cg.apps.cg_config import CGConfig` instead.","cause":"CGConfig is not exposed at the top-level; it's in a submodule.","error":"ImportError: cannot import name 'CGConfig' from 'cg'"},{"fix":"Create a CGConfig instance and pass it: `store = Store(config)`","cause":"Store requires a config argument after version 80.","error":"TypeError: Store() takes at least 1 argument (0 given)"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}