# Gens integration

[Gens][gens] is a interactive web-based tool to visualize copy number profiles using wgs data. It display the normalized read depth and alternative allele frequency in relation to transcripts, variants and previously annotated marker panels.

## Setup

To avoid dependency conflicts Gens should be installed in an environment separate from scout. Install Gens according to the instructions on the [tool homepage][gens].

### Config Parameters

* `GENS_HOST`: The IP or hostname of the server where Gens is hosted.
* `GENS_PORT`: Port number where gens is hosted (optional).
* `GENS_VERSION`: Gens major version (Optional int). If a host but no version is provided, Scout attempts to find the version via gens API call at first web interface use (after a user has authenticated).

### Configure Gens integration

In the scout config `config.py` provide the connection settings like:

```python
GENS_HOST = "127.0.0.1"
GENS_PORT = 5001
GENS_VERSION = 4
```

## Result
Now scout will display a button called "Gens" in the case view and in the variant view for structural variants.

[gens]: https://github.com/Clinical-Genomics-Lund/gens
