recipes

Configuration files for a Neurobagel deployment.

How to use

For detailed instructions on deploying Neurobagel for your use case, see the official Neurobagel documentation on setting up a local knowledge graph (node) and configuration options.

Using the full-stack Docker Compose file

1. Clone the repository

   git clone https://github.com/neurobagel/recipes.git

2. Copy and rename the required template configuration files

   cp template.env .env
   
   # if also setting up local federation
   cp local_nb_nodes.template.json local_nb_nodes.json

   Ensure to edit the configuration file(s) according to your deployment. We strongly recommend changing the default passwords for your GraphDB instance, which are set using NB_GRAPH_ADMIN_PASSWORD.txt and NB_GRAPH_PASSWORD.txt in the ./secrets subdirectory by default.

   ⚠️ Note: You must change the value of the NB_API_QUERY_URL variable in the .env file before you can launch any service stack that includes a query tool (i.e., full_stack, local_federation). See comments in the .env file for more information.

3. In the repository root, start the Docker Compose stack and specify your desired deployment profile

   To set up a local node along with a graphical query tool and optional federation:

   docker compose up -d

   or

   docker compose --profile full_stack up -d

   To set up only a local node (without a graphical query tool):

   docker compose --profile local_node up -d

   To set up federation only:

   You may want to do this if you already have local or remote node(s) set up that you now want to send federated queries to.

   docker compose --profile local_federation up -d

A log file DEPLOY.log will be automatically created under scripts/logs/ with a copy of the STDOUT from the automatic deployment process.