zForDevelopers – Onboarding

MicrobeTrace Onboarding

Set up your system

MicrobeTrace is built with Angular and Node.js. Before you begin, install the following tools:

• [Git](https://git-scm.com/)
• [Node.js and npm](https://nodejs.org/) (v16 or later recommended)
• [Angular CLI](https://angular.io/cli) – npm install -g @angular/cli
• A text editor such as [VSCode](https://code.visualstudio.com/)
• A modern web browser. Development is tested primarily in Chrome/Chromium.

Optional but helpful tools:

• [nvm](https://github.com/nvm-sh/nvm) (or [nvm-windows](https://github.com/coreybutler/nvm-windows)) to manage Node versions.
• A Git GUI like [GitKraken](https://www.gitkraken.com/git-client).
• [Windows Terminal](https://github.com/microsoft/terminal) for a better command line on Windows

Get MicrobeTrace

Clone the repository and install dependencies:

git clone https://github.com/cdcgov/MicrobeTrace.git
cd MicrobeTrace
npm install

After installation you can start the development server with:

npm start

This runs ng serve under the hood and launches the app at http://localhost:4200/. The server reloads automatically when you change source files.

Building

To create a production build:

npm run build

The compiled files are written to the dist/ directory. You can deploy these static files with any web server or host them using services like GitHub Pages.

Development Tips

• Use the Angular CLI to generate new components and services.
• Most of the application's logic lives inside src/.
• Data remains client-side; no server is required beyond serving the static assets.

How we git

The angularUpdate branch reflects what is deployed in production.

Useful Documentation

• [MicrobeTrace Wiki](https://github.com/CDCgov/MicrobeTrace/wiki) – development notes and user guides.
• [Issue Tracker](https://github.com/CDCgov/MicrobeTrace/issues) – feature requests and bug reports.

Descendant Projects

MicrobeTrace depends on several companion libraries:

• TidyTree – D3-based phylogenetic tree rendering.
• Patristic – object model for phylogenetic branches.
• Physics Tree – experimental force‑directed tree layout.
• TN93.js – distance calculation algorithm.
• bioseq.js – sequence alignment utilities.
• AlignmentViewer – visualizes sequence alignments.
• Fileto – keeps file handles accessible after uploads.

Only TidyTree is user-facing; others support internal functionality.