Welcome to PanelSearch’s documentation!

Contents:

• Installation
• General Usage (for manual non-Docker use; not recommended)
  • Testing
• Application Programming Interface
• SQL Database
• Recommended usage: Running PanelSearch in a Docker container
  • Setting up using the setup.sh script
  • General Usage
• Alternative Usage
  • Alternative setups
  • Troubleshooting
  • References
• Jenkins Continuous Integration/Development
  • Command-line set-up
  • GUI set-up
  • Create credentials

Description

A tool to manage gene panels for NHS National Genomic Testing Directory tests in the laboratory. Allows user to search for gene panels and outputs BED file. Search history can be saved to a database and retrieved at a later date. Release 1.0 of PanelSearch currently uses v5.1 of the National Genomic Testing Directory.

Dependencies

Python 3.10 or greater is required to run this app. This app connects to the PanelApp API so requires an internet connection. Also, a MySQL database is created through this app so we recommend installing MySQLWorkBench https://www.mysql.com/products/workbench/ .

Features

• Returns gene panel information

• Returns BED file

• Saves gene panel information

Testing

To run tests make sure you are in the root directory before typing the following into the terminal:

pytest -vv

Contribute

• Issue Tracker: https://github.com/isabelrem/2023-Software-Development-Assessment/issues

• Source Code: https://github.com/isabelrem/2023-Software-Development-Assessment

• Trello: https://trello.com/b/gWEfG504/team-3-mie

Support

If you are having issues, please let us know.

License

This project is currently licensed under the MIT licence.

Authors

• Tom

• Isabel

• Egle

• Jess