Java Bioinformatics Analyses Web Services (JABAWS) Server Web Aplication aRchive manual

JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, only Clustal and Muscle are currently available for MS Windows platform. +

JABAWS Web Application aRchive can run on any host operating system that supports Java 1.6. However JABAWS depends on a number of third party programs which are not available for all operating systems. In particular, not all web services are currently available for MS Windows platform.

JABAWS comes with pre-compiled MS Windows and Linux IA32 binaries, as well as the source code and build scripts necessary to recompile them.

JABAWS comes with pre-compiled MS Windows and Linux x86 binaries, as well as the source code and build scripts necessary to recompile them.

To run JABAWS on the cluster you must have shared disk space accessible from all cluster nodes.

Installing the JABAWS WAR file

JABAWS is distributed as a web application archive (WAR). To @@ -104,28 +111,13 @@ configuration files so these are used instead.

Using the pre-compiled i386 binaries on Linux

Before the binaries that are bundled with JABAWS can be used, -they must first be made executable using the provided 'setexecflag.sh' script:

cd to <webapplicationpath>/binaries/src
run sh setexecflag.sh
Make sure binaries supplied work under your OS.
- For this run each binary, without any command line options or +
JABAWS comes with pre-compiled x86 Linux binaries, thus on such systems JABAWS should work straight out of the box. If you are in any doubts or experience problems you may want to make sure that the binaries supplied work under your OS. To do this just execute each binary, without any command line options or input files. If you see an error message complaining about missing libraries or other problems, then you probably need to recompile the binaries.

Restart the Tomcat.

Note: You may want to enable logging, as described here

the Executable.properties

JABAWS Configuration chapter.

Obtaining alignment -programs for your operating system

Obtaining command line binaries for your operating system

You could search for pre-packaged compiled executable in your system package repository or alternately, download pre-compiled @@ -192,14 +183,22 @@ replace the executables supplied with the downloaded ones, or modify the paths in executable.properties as described above. Below are some suggestions on where you may be able to get the binaries for your system.

ClustalW
Clustal Omega
ClustalW
Mafft
Muscle
Tcoffee
Probcons (Linux x86 | x64)
Probcons (Linux x86 | x64 | Mac)
IUPred (Linux x86 | x64 | Mac)

Testing JABAWS Server

First of all make sure that Tomcat server is started successfully. If this was the case, then you should see JABAWS home page when you navigate to your Tomcat JABAWS context path e.g. http://myhost.compbio.ac.uk:8080/jabawsIf you see it, then it is time to make sure that web services are working too. Assuming that you have unpacked/deployed JABAWS from the server war file, you should be able to navigate to the test program which can be found in <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type: java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path>

Using JABAWS service status checker

If you see it, then it is time to make sure that web services are working too. The easiest way to do so is to access Services Status page available from the main JABAWS web page menu.

If you need to monitor web service health automatically when the best option is to use service checker that responds with the standard HTTP status code. To access this checker use the following URL: <jabaws_server>/HttpCodeResponseServiceStatus This page returns code 200, and no page context if all services are operational, 503 if one of the services have problems. You can also check each web service individually by providing the name of the web service to check at the end of the service checker URL like this: <jabaws_server>/HttpCodeResponseServiceStatus/ClustalWS

Upon request, the service status checker will examine the health of the ClustalWS web service only. If the service name is not valid, then the service checker will return code 400.

Using command line client

Alternatively, you should be able to use the test program which can be found in <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type: java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path>

For example to test all JABAWS web services on host myhost.compbio.ac.uk type:

java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws

You can choose a particular web server using -s option like this java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=ClustalWS This command line assumes that java executable is in your path and jabaws-client.jar is located in the current directory.

Restart the Tomcat, sometimes it will not since that the new war file is added without restart

If Tomcat still refuses to unpack the war file, unpack it manually into web application folder (the war file is just a zip archive). Restart the Tomcat.