Installation Guide

System Requirements

• Java 8
• Cytoscape 3.2.1 and later
  • Latest Cytoscape 3.3 nightly build

Installation

WARNING: App Manager Bug

There is a known bug in App Manager and you cannot install cyREST version 0.9.10+ from the menu. You need to use App Store's Install button instead to install latest version of cyREST.

From Cytoscape App Store

1. Start Cytoscape
2. Open cyREST page with your web browser
3. Click Install button

From JAR File

1. Download latest version as JAR file.
2. Apps → App Manager → and click Install from file...
3. Select the JAR file you just downloaded

From Source Code

Make sure you have:

• Oracle JDK 8+
• Apache Maven 3.3+

git clone https://github.com/idekerlab/cyREST.git
cd cyREST
mvn clean install

This creates new JAR file in target directory. Then, follow the instruction in From JAR File section of this document.

Test Your Installation

1. Make sure cyREST is up and running.

• Click Apps → AppManager

• Click Currently Installed tab

• Make sure you can see Installed in the status column

  

1. Open web browser
2. Type the following URL:

   http://localhost:1234/v1
   

3. If you get status message like the following, you are ready to use cyREST!

{
    apiVersion: "v1"
    numberOfCores: 8
    -memoryStatus: {
        usedMemory: 532
        freeMemory: 1430
        totalMemory: 1963
        maxMemory: 28217
    }
}

Change Port Number

By default, cyREST opens port 1234. This can be changed by editing Cytoscape Properties.

1. Click Edit → Preferences → Properties...
2. Click Add
3. Type rest.port and click OK
4. Type port number, like 8080, and click OK
5. Restart Cytoscape
6. Access the port (e.g. http://localhost:8080/v1) and make sure cyREST opens the specified port

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REST Clients

cyREST provides a platform-independent API to access Cytoscape. This means you can use any programming languages and tools to access its API. Here is a list of popular clients:

For Web Browsers

• Advanced REST client for Chrome
• Postman

Command Line Tools

• curl
• resty

For Python

• Requests: HTTP for Humans

For R

• RCurl: General network (HTTP/FTP/...) client interface for R

For Node.js

• node-rest-client