How To add a new executable 1) Add executable to the binaries folder. If it has source code and can be recompiled for different platforms include it under binaries/src Edit binaries/src setexecutableflag.sh and compilebin.sh scripts accordingly. 2) Make sure all the dependencies of the software being installed are satisfied. If there are other binaries they should be included as well. Keep the dependant binaries in subfolder for the main executable. Update compile and setexecflag scripts accordingly. 3) Make sure executable - Does not have any hard links to its dependencies, e.g. is able to run from any installation folder and does not contain any hard coded paths. (TODO examples...) 4) Describe executable in conf/Exectuable.properties. The lowercase name of the wrapper should be included in the name of the property for example Clustal properties all include clustal as a part of the name e.g. local.clustalw.bin The same property for Mafft will be called local.mafft.bin. 5) Add Limit.xml, Parameters.xml and Presets.xml. All are optional (should be at least). If the executable does not support parameters you do not have to refer to the XXXParameter.xml file into the Executable.properties file. The same is true for Presets and Limits. 6) Create a Java wrapper class for your executable. Create it within runner source directory. Examples of other wrappers can be found in compbio.runner.msa or compbio.runner.disorder packages. Wrapper should extend SkeletalExecutable implements PipedExecutable if you need to pass the input or collect the results from the standard in/out. Please see Mafft code as example. Wrapper should expend SkeletalExecutable if input/output can be set as a parameter for an executable. Please see ClustalW code as example. 7) Create a testcase suit for your wrapper and run the test cases. 8) Create parser for the output files of your executable. Suggested location compbio.data.sequence.SequenceUtil 9) Test the parser 10) Decide which web services interface your executable is going to match. For example if the executable output can be represented as SequenceAnnotation then SequenceAnnotation interface might be appropriate. For multiple sequence alignment an Msa interface should be used. 11) If you find a web interface that matches your returning data type, then implement a web service which confirms to it within a webservices source folder 12) Register web service in WEB-INF/ web.xml and sun-jaxws.xml 13) Add generated wsdl to wsbuild.xml ant script to generate the stubs 14) Run build-server task in wsbuild file. Watch for errors. If the task fails that means that JAXB cannot serialize some of the data structures. Add appropriate annotations to your data types. Also check that - you do not have interfaces to serialize. JAXB cannot serialize them. - you have a default no args constructor (can be private if you do not need it) - JAXB cannot serialize a Map, use custom data structure instead! - Enum cannot be serialized as its abstract class (do not confuse with enum which is fine) - Fields serialization leave a little more space for manoeuvre, so use it. If you do then you can accept and return interfaces, e.g. List, Map; abstract classes etc, from your methods. If you have the data on the server side, but nothing is coming through to the client, this is a JAXB serialization problem. They tend to be very silent and thus hard to debug. Check your data structure can be serialized! 13) Modify the client to work with your new web service. Update Services enumeration to include new service and ensure that all the methods of this enumeration take into account the new service. In particular add the service to the compbio.ws.client.Services enumeration. Modify the getServiceImpl() and getServiceType() methods. Update the client help text (client_help.txt) and insert it into the Constraints class. 14) Test the web service with the client. 15) Make sure the statistics collector works fine with a new web service. 16) Test on the cluster...