Clinical Genomics command center

85.11.1 verified Mon Apr 27 auth: no python

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.

pip install cg

Common errors

error ModuleNotFoundError: No module named 'cg' ↓

cause The package is not installed or not installed in the current environment.

fix

Run pip install cg to install the package.

error ImportError: cannot import name 'CGConfig' from 'cg' ↓

cause CGConfig is not exposed at the top-level; it's in a submodule.

fix

Use from cg.apps.cg_config import CGConfig instead.

error TypeError: Store() takes at least 1 argument (0 given) ↓

cause Store requires a config argument after version 80.

fix

Create a CGConfig instance and pass it: store = Store(config)

Warnings

breaking In version 80+, the store API was restructured: Store is now a class, and connections are managed via CGConfig. ↓

fix Use `from cg.store import Store` and pass a `CGConfig` instance.

deprecated Old CLI entry points like `cg orders` have been moved to `cg workflow ...` subcommands. ↓

fix Use `cg workflow orders` instead of `cg orders`.

gotcha The package requires Python <3.13,>=3.11. Installing with Python 3.13 may fail silently or produce runtime errors. ↓

fix Ensure Python version is between 3.11 and 3.12 (exclusive of 3.13).

Imports

CGConfig
wrong
```
from cg import CGConfig
```
correct
```
from cg.apps.cg_config import CGConfig
```
CGConfig is under cg.apps.cg_config, not top-level.

Store

wrong

from cg.store.api import Store

correct

from cg.store import Store

Store is directly in cg.store.

DemultiplexAPI

wrong

from cg.apps import DemultiplexAPI

correct

from cg.apps.demultiplex import DemultiplexAPI

DemultiplexAPI lives in cg.apps.demultiplex.

Quickstart

Initialize CGConfig and Store, then perform operations like listing orders.

from cg.apps.cg_config import CGConfig
from cg.store import Store

config = CGConfig()
store = Store(config)
# Example: list orders
orders = store.orders()
print(orders)