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

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.

test client

deploying on Tomcat

test client

deploying on Tomcat

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

executable.properties

Clustal Omega
ClustalW
ClustalW
Mafft
Muscle
Tcoffee

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.

Connecting to service ProbconsWS on http://localhost:8080/ws ... OK
Testing alignment with default parameters:FAILED
Service ProbconsWS IS NOT FUNCTIONALIf the web server did not respond the message looks like following: Connecting to service TcoffeeWS on http://localhost:8080/ws ... FAILED

Running many JABAWS instances on the same server

JABAWS is supplied as a Web Application aRchive which can be dealt with as any other web applications. So it is perfectly possible to run two JABAWS instances from the same server. Just make two different contexts on your application server and unpack JABAWS in both of them. For example if your server name is http://www.align.ac.uk, and the context names are public and private. Than one group of users could be given a URL http://www.align.ac.uk/public and another http://www.align.ac.uk/private. These contexts will be served by two independent JABAWS instances, and could be configured differently. If you keep local engine enabled, make sure you reduce the number of threads local engine is allowed to use to avoid overloading the server. Alternatively two completely separate web application server instances (e.g. Apache-Tomcat) could be used. This will give you a better resilience and more flexibility in memory settings.

JABAWS on a single server

You can run JABAWS on a single server. Obviously the capacity will be limited, but may be sufficient for a small lab. Installed on a single server, JABAWS executes tasks in parallel, so the more cores the server has the more requests it will be able to handle.

@@ -241,17 +234,11 @@ modify the paths in 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.