Synteny Browser API

The JAX Synteny Browser http://syntenybrowser.jax.org/ is an interactive web-based conserved synteny browser application. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genomes based on the biological attributes of the features. The current implementation for the browser supports the reference genomes of the laboratory mouse, rat and human.

Note: This is the source code for the back-end API only! The source code of the front-end client and ETL (data loading) scripts can be found at this and this GitHub repositories respectively.

URL: https://syntenybrowser.jax.org/api

This application utilizes Flask-RESTPlus

This repository contains the source code for the Synteny Browser (v2) microservice API application. You can find the source for the first version of Synteny Browser here.

Installation and Setup

Prerequisites: Python (we're running 3.7 or higher)

Clone the API (back-end) code and navigate to the cloned project root

    git clone https://github.com/TheJacksonLaboratory/syntenybrowserv2-api.git

Create virtual environment:

    cd syntenybrowserv2-api
    python3 -m venv venv.sb

Activate Virtual environment:

    source venv.sb/bin/activate

Install dependencies in the virtual env:

    pip install -r requirements.txt
    pip freeze > requirements.txt

Setup DB (SQLite for development):

Once Virtualenv is installed, you'll need a database. Follow this guide to create a database and once created, copy the file to the project root.

Run tests:

    python manage.py test  (All test should be successful)

Run pylint for code quality check (optional - before committing new code)

    pylint app.main
    pylint app.test
    pylint app

Run the Flask app:

    python manage.py run

Swagger doc API will be available at http://localhost:5000/api/

Running the application with Docker

Clone the API (back-end) code and navigate to the cloned project root

    git clone https://github.com/TheJacksonLaboratory/syntenybrowserv2-api.git

Setup DB (SQLite for development):

You'll need a database. Follow this guide to create a database and once created, copy the file to the project root.

Build an image called synteny-api

    docker build . --tag=synteny-api

Start a container based on the created Docker image - synteny-api

    docker run -p 8000:8000 -d --rm synteny-api

Swagger doc API will be available at http://localhost:8000/api/

Further help

To get more help on the Flask-RESTPlus go check out the Flask-RESTPlus's documentation.

If you run into problems with Synteny Browser, specifically, feel free to email us at [email protected] or create an issue in the synteny-api repo on Github.

License

The JAX Synteny Browser is provided under the license found here