Getting Started

Choose a JABAWS distribution

I want to use JABAWS for... Quick Guide
Running Muptiple Sequence Alignments through Jalview on my own computer JABAWS Virtual Appliance (VA)
Running JABAWS on the cloud, for one or many users JABAWS on the Amazon cloud
Running JABAWS for my group, lab, or organization on the local infrastructure JABAWS Web Application aRchive (WAR)
Accessing a JABAWS server from my own code JABAWS Java Client

Installing A JABAWS Server Web Application Archive (WAR) package

This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABA server to use the cluster or perform very large tasks.

  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 7.0) and at least Java 1.6 (i.e. JAVA 6).
  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, then you'll need to do this manually, it's just a zip archive in the end).
  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 ./ script to compile all binaries JABAWS depends on.


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/jaba-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:
    • Launch the desktop version of Jalview
    • Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the Webservices panel and press the New Service URL button.
    • Enter the URL for the tomcat server, including the context path for the JABAWS web app (e.g. http://localhost:8080/jabaws).