JABAWS MANUAL

Quick Start Guide

Choose JABAWS distribution

There are three main packages you could use

  1. A JABAWS Server Virtual Appliance (or Virtual Machine) - for anyone who wants to run JABAWS locally for themselves
  2. A JABAWS Server Web Application Archive (WAR) package - for anyone who wants to run JABAWS for their group, lab or organization. Wants to use the cluster or perform very large tasks
  3. A client package - for anyone who wants to use JABAWS from their own code, without Jalview, scripting against local or public version of JABAWS Server.

Virtual Appliance (VA) package (1) contains TurnKey Linux with JABAWS installed. JABAWS VA contains JABAWS WAR deployed on the Apache Tomcat 6 web application server. If you use MS Windows read no further - the VA is the way to go. You would need to install VMWare Player or Oracle VirtualBox (both are free) on your computer to use this package. More details about JABAWS virtual appliance is available from the Server VA section of the manual.

Option 2, Web Application Archive package contains JABAWS ready to be deployed on the Servlet 2.4 compatible web application server such as Apache Tomcat version 6. To make this version work you would need

  1. Install Apache-Tomcat or similar web application server.
  2. If you are not on Linux, you would have to make binaries for your system available to JABAWS.

Read more on JABAWS WAR in the manual.

A client only package (3) contains the JABAWS command line client. It functionality is equivalent to that of Jalview . This is the package for anyone who wants to connect to and to use JABAWS from their own software. Read more about how to use command line client in the CMD Client section of the manual. Also, JABA Web Services are fully WS-I compliant, so one could use any language to access them.

If you chose option 1

and you work on Windows or Linux or Unix

  • download and install VMWare Player
  • Download JABAWS Virtual Appliance
  • Unpack JABAWS virtual appliance and open it with VMware Player.

otherwise

  • download and install Virtual Box.
  • Download JABAWS Virtual Appliance
  • Unpack JABAWS virtual appliance, import it into VirtualBox and then start the appliance.

If you chose option 2

If you are on Linux or Windows

  1. Download JABAWS WAR
  2. Download and install Apache-Tomcat
  3. Drop the JABAWS war file into tomcat/webapps directory.
  4. If you are on Linux, cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script to set an executable flag for JABAWS binaries.
  5. Restart the Tomcat

otherwise

  • Complete steps 1-3 from the above.
  • cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on.
  • cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script.
  • Restart the Tomcat

Once you have JABAWS working you can point the Jalview to your local JABAWS.

  • Download and start the desktop version of Jalview
  • Go to Jalview->Tools->Preferences->Webservices->New Service URL and enter the JABAWS URL which you can see one your appliance is booted up.

if you chose option 3

You can use the client straight out of the box.