JABAWS distributions

Choose the JABAWS distribution that better suits your needs and read the Getting Started guides below. Detailed information is available in the documentation pages.


Quick Guide I want to use JABAWS for...
Jalview and the JABAWS Public Server Running JABAWS services through Jalview on the JABAWS public server
Command Line Interface (CLI) Accessing a public or private JABAWS server from my own software
Web Application aRchive (WAR) Running JABAWS for my group, lab, or organization on the local infrastructure
Virtual Appliance (VA) Running JABAWS services through Jalview on my computer with a private server

Jalview and the JABAWS Public Server

This is the easiest way to run JABAWS web-services. Simply launch Jalview and run any of the methods provided under the 'Web Service' menu. Jalview uses the public JABAWS server by default. If you are concerned about privacy or want to run sensitive analysis on your own hardware, you can either setup a local JABAWS Virtual Appliance (VA) or configue the JABAWS Web Application aRchive (WAR) in your infrastructure.

Command Line Interface (CLI)

This is a single Java archive which contains the JABAWS command line interface (CLI) client. It allows anyone who wants to connect to the JABAWS web-services running at the University of Dundee's Public Server, or to run a local private JABAWS server from their own software. You can read more about how to use JABAWS command line (CLI) client given in the documentation pages, but a brief instructions are given below:

  1. Download the Client Jar file
  2. Download and install Java (version 1.7)
  3. Provided that you have the Java ready to run, you can get command line help by changing to the directory where you downloaded the client jar, and typing:
    java -jar jabaws-full-client-2.2.0.jar

The JABA Web Services are WS-I compliant. This means that you can access them from any language that has libraries or functions for consuming interoperable SOAP web services. More information on how to develop software that access JABAWS services is provided in the documentation pages.

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Web Application aRchive (WAR)

The JABAWS Web Application aRchive (WAR) is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABAWS server to use the cluster or perform very large tasks. Complete documentation is provided in the documentation pages, but brief instructions are given below:

  1. Download the JABAWS WAR file
  2. Download and install Apache-Tomcat
    You will need at least Tomcat version 5.5 of (we would recommend version 8.5) and at least Java 1.7 (i.e. JAVA 7).
  3. Drop the JABAWS WAR file into tomcat/webapps directory.
  4. (Re)start the Tomcat.
  5. Once the tomcat has started, it should automatically unpack the WAR into the webapps directory (if it doesn't, simply unpack the WAR archive).
  6. If you are on Mac or other unix-like architecture with GNU compilers available or you'd like to get a maximum performance
    cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on.

Testing

You can test that your JABAWS server is working in several ways.

  1. Visit Services Status page available from the JABAWS main page using your web browser.
  2. If you are working on the command line, then use the command line client shipped with the JABAWS war to test it by running:
    java -jar <Path to tomcat WebApp directory>/jabaws/WEB-INF/lib/jabaws-client.jar -h=http://localhost:8080/jabaws
    In this example we assumed that your JABAWS server URL is http://localhost:8080 and JABAWS context path is jabaws
  3. Alternately, you can point Jalview at your new server:
    1. Launch the desktop version of Jalview
    2. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), elect the Webservices panel and press the New Service URL button.
    3. Enter the URL for the tomcat server, including the context path for the JABAWS web app (e.g. http://localhost:8080/jabaws).

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Virtual Appliance (VA)

The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a virtual machine on your laptop or desktop computer. A complete guide to the JABAWS VA is given in the documentation pages, but for the impatient, brief instructions are given below:

If you work on Windows, Linux or Unix:

  1. Download JABAWS Virtual Appliance
  2. Download and install VMWare Player
  3. Unpack the JABAWS virtual appliance and open it with VMware Player

If you work on Mac do the same using VMware Fusion.

Testing

To check that your JABAWS virtual appliance is working visit the Services Status page available from the main JABAWS menu. For this enter the JABAWS URL for your new server into a web browser. This is shown once the appliance is booted up.

Alternatively you can use Jalview to complete the testing.

  1. Launch the desktop version of Jalview
  2. Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the Webservices panel and press the New Service URL button.
  3. Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.


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