Hi Jim, About the M-Coffee web service integration in Jalview, I see two alternatives.
The first is the one you've described, modify the web service so that it will able to send back the T-Coffee score file (as well as other annotations if required). Regarding the problem of T-Coffee that automatically download and install the missing packages, this is true only if you use the source code based distribution package. But we are also distributing a pre-compiled installer which contains all the dependencies required by T-Coffee. Once you have installed this, T-Coffee has everything it needs to work and no magic installations happen ;) You can find it at the following link http://www.tcoffee.org/Packages/Stable/Latest/linux/ In any case, as far as I've understood having Jalview to support M-Coffee in this way, is more a problem to make JABAWS able to handle the extra annotation produced by T-Coffee, more than modify Jalview to support it. An alternative approach could be to have Jalview interacting with our T-Coffee server (http://tcoffee.crg.cat) which provides as REST based interface. It is a very easy API based on a GET request which return an XML response. It has already support for all the result files produced by T-Coffee (alignment, scores, etc). In this case the problem would be to make Jalview able to interact with it. I will try to join the Jalview hackathon to collaborate on on with this. Cheers, Paolo On Nov 15, 2012, at 4:49 PM, Jim Procter <[email protected]<mailto:[email protected]>> wrote: Hi Paolo. On 14/11/2012 20:21, Paolo Di Tommaso wrote: It's a think we could discuss. What would be the trickiest part to make Jalview able to run M-Coffee? Should it based on a web-service interaction? Ideally, Jalview should be able to run M-Coffee from the Web Service->Alignment submenu. This is nearly possible now, except that the alignment webservices don't include support to send back any annotation, only the alignment data. That means that a new type of service needs to be created that returns annotation on the alignment. One way might be to add a 'supplementary information' service to Jabaws that Jalview could call to discover any additional information provided by a service in addition to the standard data returned.. so for an M-COFFEE alignment, jalview gets the alignment as normal, but then queries the jabaws server for the score file. Such a service might also allow Jalview to recover the guide trees and any other data generated that aren't currently returned to the user. Apart from supporting this additional nuance, getting M-Coffee into JABAWS is also a little tricky. The way that M-COFFEE downloads all the additional tools is really amazing, but might alarm some sysadmins - who probably don't expect a web service to start downloading and compiling code after they've installed it. Ideally, the installation of the T-COFFEE suite shipped with JABAWS should be preconfigured to run M-COFFEE using the four other alignment methods available, and come with instructions for telling M-COFFEE about any other alignment tools available on the system. Is there a standard way of doing that when compiling the suite ? One more thing, I was trying to integrate the latest release in our web server to show the T-Coffee alignment score, but I'm unable to get it work. It shows the alignment as usual, but not the coloured scores. This is the applet code I'm using: <applet id="applet" code="jalview.bin.JalviewLite" width="800" height="600" archive="public/jalviewApplet.jar"> <param name="file" value="http://localhost:9000/data/7ce04b2b/result.fasta_aln";> <param name="scoreFile" value="http://localhost:9000/data/7ce04b2b/result.score_ascii"; > <param name="embedded" value="true"> <param name="showFeatureSettings" value="false"> <param name="widthScale" value="1.4"> <param name="heightScale" value="1.4"> <param name="nojmol" value="true" > hmm. not sure - is there anything shown on the java console ? The code is definitely in there still :) Add <param name="debug" value="true"> to the applet tag to make the applet more verbose. There should be some kind of message explaining why it didn't add the score file. Jim. _______________________________________________ Jalview-dev mailing list [email protected]<mailto:[email protected]> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
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