BioUnix

Run bioinformatics commands, chat with an Agent, and browse skills and memories from BioUnix — directly inside Obsidian.

This plugin integrates BioUnix with Obsidian. It connects to the local BioUnix API Server (default http://127.0.0.1:17564) and exposes the following features:

Features

• Code blocks: Run BioUnix commands inline in any Markdown note using a biounix fenced code block.
• Sidebar chat: A dedicated Agent chat view with streaming responses over WebSocket.
• File menu: Right-click any file in the vault to send it to the BioUnix Agent for analysis.
• Vault report: Scan your vault for bioinformatics files and generate a report.
• Command palette: Quick actions to open the chat or send the current file to the Agent.

Prerequisites

1. Install and run the BioUnix desktop app.
2. The BioUnix API Server must be running locally (it starts automatically with the app).
3. An API token is auto-read from ~/.biounix/api-token; you can also set it manually in settings.

Installation

From Obsidian Community Plugins

1. Open Settings → Community plugins.
2. Search for "BioUnix" and install it.
3. Enable the plugin.

Manual installation

1. Download main.js, manifest.json, and styles.css from the latest release.
2. Create a folder named biounix inside your vault's .obsidian/plugins/ directory.
3. Copy the three files into that folder.
4. Enable the plugin in Settings → Community plugins.

Usage

Code blocks

```biounix
run: samtools view -h sample.bam | head
```

Sidebar chat

Click the flask icon in the left ribbon, or run the command Open BioUnix Agent chat.

Settings

• API port: The port the BioUnix API Server listens on (default 17564).
• API token: Authentication token; leave empty to auto-read from ~/.biounix/api-token.
• Auto-connect: Connect to the server on plugin load.
• Default mode: chat or agent mode for new sessions.

License

MIT