jbrowse-config-assistant-bot

A tool for querying your JBrowse configuration file.

Installation

Prerequisites

• Python v3.13.0^
• Poetry python dependency manager
• Node.js (optional -- only if you want to run the webapp)
• Yarn package manager

Installation steps

In /jb-bot:

poetry install

In /web-app:

yarn dev

Note that you must have keys configured for your language model of choice for the application to work. See Environment Variables for details.

Usage

Web Interface

In /jb-bot:

poetry run flask —-app jb-bot/util.py run

Note: It may take few minutes for the bot to spin up

Open another tab, in /web-app:

yarn dev

CLI

Interactively

poetry run python jb-bot/app.py

Non-interactively

poetry run python jb-bot/app.py -p "What tracks do you have that show epigenetic modifications?"

Options

-c -config : directory to your JBrowse configuration file.
-h -help   : print this help message and exit.
-m -model  : specify the model you want to use, "openai" or "gemini."
-p -prompt : prompt query regarding your JBrowse config.json.

Configuration

Environment variables

• GOOGLE_API_KEY: API key to interface with [Google Gemini]().
• OPENAI_API_KEY: API key to interface with [OpenAI]().
• CONFIG: Path to configuration file(s) (may be remote location)
• HOST: the host URL of your JBrowse instance (used for generating dynamic links)

At least one language model specification is required.

Configure your environment variables with the POETRY_ alias:

e.g.

export POETRY_GOOGLE_API_KEY=your_google_api_key

OR place the following in your .env file:

GOOGLE_API_KEY=your_google_api_key

and install the poetry plugin poetry-plugin-dotenv:

pipx inject poetry poetry-plugin-dotenv

Acknowledgements

The author(s) of this project recognize the assistance and inspiration from the authors of Reactome ChatBot.