Dear Mikołaj, > I'm not sure if I follow the calling methods of Java application part > - could you give me an code example? In short: my Java code wraps some commandline programs. When you create a Beanshell, you can add a dependency by putting the jar file in your Taverna home, lib directory ($HOME/.taverna-version/lib). The Beanshell editor (at least, in 2.x) allows you to select jar files in that directory. From there on my Beanshell code is simple: <code> import nl.umcg.medgen.ngspipeline.*; Util u = new Util(); bamName = u.samToBam ( samName ); </code> This creates a service with one input port: 'samName' and one output port: 'bamName'. After completing the workflow (input port with single value -> Beanshell service -> output port) I simply save it so I can use it as nested workflow. No more to it.
> How is .bsh file related with the workflow's XML file? (via 'source' > cmd/ inline / other?) It isn't. I save it for archiving purposes only. Or... for use outside Taverna alltogether. The .t2flow file contains a <processor> tag for each service in the workflow. The Beanshell code can be found in there. Hope this helps, despite my late response... Cheers, Wil 2010/9/1 Mikołaj Rybiński <[email protected]>: > Hi Wil, > > On Sat, Aug 14, 2010 at 11:39, Wil Koetsier <[email protected]> wrote: >> Hi Mikołaj and others, >> >> Sorry for the incredibly late reply, but Marco said: >> >>> Furthermore, I believe Morris Swertz and his group are working on general >>> solutions to use scripts and command line tools in other frameworks >>> including Taverna. >> >> for the record: I use very simple and short Beanshell scripts (a >> couple of lines of code at most) to call methods of a Java >> application. > > I'm not sure if I follow the calling methods of Java application part > - could you give me an code example? > >> Each Beanshell script has its own workflow (and is of >> course saved as a .bsh file) and I reuse them by nesting these >> workflows, like Marco described in a previous mail. As simple as that. > > How is .bsh file related with the workflow's XML file? (via 'source' > cmd/ inline / other?) > > Cheers, > Mikołaj > >> >>> Also check out their MolGenis tool. >> Please do. >> >>> The real experts may give you more details, but they might all be on holiday >>> ;-) >> Me: holiday, yes, expert, no :P >> >> Cheers, >> Wil >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by >> >> Make an app they can't live without >> Enter the BlackBerry Developer Challenge >> http://p.sf.net/sfu/RIM-dev2dev >> _______________________________________________ >> taverna-users mailing list >> [email protected] >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >> > > ------------------------------------------------------------------------------ > This SF.net Dev2Dev email is sponsored by: > > Show off your parallel programming skills. > Enter the Intel(R) Threading Challenge 2010. > http://p.sf.net/sfu/intel-thread-sfd > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ > ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
