genelastic 0.8.0

Generate and store genetic data into an Elasticsearch database.

genelastic

Storing of genetics data into an Elasticsearch database.

Prerequisites

• python >= 3.11
• make

Installation

To install dependencies, run the following command:

python -m venv .venv
source .venv/bin/activate
make install.deps

Configuration

To start the API server, the following environment variables should be defined:

• GENAPI_ES_URL: URL of the Elasticsearch server,
• GENAPI_ES_ENCODED_API_KEY: Encoded API key,
• GENAPI_ES_INDEX_PREFIX: Prefix to identify indices of interest,
• GENAPI_ES_CERT_FP: Certificate fingerprint of the Elasticsearch server.

Then, run the following command:

make start-api

To start the UI server, the following environment variables should be defined:

• GENUI_API_URL: URL of the API server.

Then, run the following command:

make start-ui

Developers

This project uses pre-commit to manage Git hooks scripts. To install project hooks, run:

pre-commit install

After that, each commit will succeed only if all hooks (defined in .pre-commit-config.yaml) pass.

If necessary (though not recommended), you can skip these hooks by using the --no-verify / -n option when committing:

git commit -m "My commit message" --no-verify # This commit will not run installed hooks.