Installing Chanjo2 in a virtual environment

Installing the application on a local Conda environment

Given a conda environment containing Rust, Python >=3.8 with poetry installed, clone the repository from GitHub with the following command:

git clone https://github.com/Clinical-Genomics/chanjo2.git

The command will create a folder named chanjo2 in your current working directory. Move inside this directory:

cd chanjo2

And install the software with poetry:

poetry install

If you encounter any difficulties installing the pyd4 library due to its lack of support for PEP 517 builds, simply retry the aforementioned step using a version of poetry that is less than 1.8.

You can run a demo instance of the web server by typing:

uvicorn src.chanjo2.main:app --reload

The server will run on localhost and default port 8000 (http://0.0.0.0:8000)

Custom settings and the .env file

The demo server is connecting to a SQLite database whose temporary tables are destroyed and re-created every time the server is started. In order to connect to a permanent MYSQL database instance, you'd need to customise the settings present on the .env file:

MYSQL_USER=dbUser
MYSQL_PASSWORD=dbPassword
MYSQL_DATABASE_NAME=chanjo2_test
MYSQL_HOST_NAME=localhost
MYSQL_PORT=3306

The last line present on this file (DEMO=Y) should be removed or commented out.