Morning Paulo, On Fri Nov 16 10:44:56 2012, Paolo Di Tommaso wrote: > 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). I think this would be preferable in the long run - but it is a not insignificant amount of work to create new service archetypes in JABAWS.
> 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 ;) ah. ok. Then all that would be needed is to get JABAWS to use that version, which is a matter of changing the config file. > > You can find it at the following link > http://www.tcoffee.org/Packages/Stable/Latest/linux/ ok. Thanks for that - am cc-ing this to the jabaws discussion list, so it's on the record over there. > 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. exactly. > 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. A native T-COFFEE client would be a great addition. > I will try to join the Jalview hackathon to collaborate on on with this. I was going to suggest that ! I'll add it to the list of topics. Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
