https://github.com/bcbi/phylozoom-api

https://github.com/bcbi/phylozoom-api

Last synced: 7 months ago
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• Host: GitHub
• URL: https://github.com/bcbi/phylozoom-api
• Owner: bcbi
• License: mit
• Created: 2018-05-18T13:04:06.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2020-02-08T16:08:42.000Z (over 6 years ago)
• Last Synced: 2025-02-02T01:27:37.447Z (over 1 year ago)
• Language: Julia
• Homepage: https://bcbi.brown.edu
• Size: 160 KB
• Stars: 0
• Watchers: 7
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
## PhyloZoom API

[![Travis](https://img.shields.io/travis/bcbi/phylozoom-frontend.svg?style=flat-square)](https://travis-ci.org/bcbi/phylozoom-frontend)

[![License](https://img.shields.io/badge/license-MIT-orange.svg?style=flat-square)](https://github.com/bcbi/phylozoom-api/blob/master/LICENSE)

[![Docker](https://img.shields.io/badge/docker-latest-000fff.svg?style=flat-square)](https://hub.docker.com/r/fernandogelin/phylozoom-api/)

## Overview

Julia API to parse and access subtrees of a large tree in [newick format](https://en.wikipedia.org/wiki/Newick_format).

At the moment the parser is specific to the tree in `src/hd_consensus_tree.nwk`. Eventually we plan to generalize the application.

This API serves as the backend of PhytoKB Tree View, which is a visualization tool based on [D3.js](https://d3js.org/) and [Phylotree.js](https://github.com/veg/phylotree.js/wiki/phylotree.js-API).

## Requirements

- [Julia 0.6](https://julialang.org/downloads/)

- [HTTP.jl](https://github.com/JuliaWeb/HTTP.jl)

## Usage

To run:

```bash

julia api/server.jl

```

The API will be served to `0.0.0.0:8089`. You can use [Postman](https://www.getpostman.com/) to make API calls using the keys `id` and `levels` (how many levels up you want to navigate the tree from the taxon identified with ID).  

Ex.: `0.0.0.0:8089/?id=dr_1172206&levels=1`

## Using Docker

```bash

docker pull bcbi/phylozoom-api

docker run -p 8089:8089 bcbi/phylozoom-api

```

## Or to run the web application with the frontend:

```bash

docker-compose up

```

And navigate to `localhost:8080` on your browser.