Yup, if you are in release 0.7 branch already, then cvs update will fix it, and you'll need to re-run bin/configure.pl afterwards to get it to compile the updated service scripts correctly.
You can check which branch you currently have checked out by running 'cvs status' from inside biomart-perl/cgi-bin. It should report the checked out branch in the output under the 'Existing Tags' sections. cheers, Richard Allyson Lister wrote: > Hi Richard, > > Thanks for the quick reply. I do have release 0.7 (sorry I forgot to > mention that in the original post), but I'm sure I checked out from the > head/trunk. Looking in the cgi-bin dir, it does seem that I don't have > the SOAP features. Here's the contents of that directory: > > dsn dsn.PLS features features.PLS martresults martresults.PLS > martservice martservice.PLS martview martview.PLS > > So does that mean that, without switching to a particular branch, I can > only use REST services? > > I'm not an expert on Biomart, so would it be relatively straightforward > for me to switch ? I thought I had expressly taken the 0.7 release, as I > just followed the user docs and they say to run the following command: > > cvs -d :pserver:[email protected]:/cvsroot/biomart \ > co -r release-0_7 biomart-perl > > Hmmm - it looks like the martsoap and wsdl / xsd files were only added > in December (looking here > http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/cgi-bin/Attic/martwsdl.PLS?rev=1.1.2.2&root=BioMart&only_with_tag=release-0_7&view=log > <http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/cgi-bin/Attic/martwsdl.PLS?rev=1.1.2.2&root=BioMart&only_with_tag=release-0_7&view=log>) > , and I think that I checked out 0.7 in November. Should I just run a > cvs update command, and then re-run the whole installation process? > > Thanks! :) > > 2009/1/8 Richard Holland <[email protected] > <mailto:[email protected]>> > > The BioMart SOAP scripts are only available on the release-0_7 branch of > /cvsroot/biomart/biomart-perl at cvs.sanger.ac.uk > <http://cvs.sanger.ac.uk>. They have not been > committed to the HEAD/TRUNK. To get them, you need to make sure you've > checked out the release-0_7 branch. > > If you look in the cgi-bin folder inside biomart-perl and don't see > martsoap.pl etc. present there, then you probably don't have the 0.7 > branch checked out. > > cheers, > Richard > > Allyson Lister wrote: > > Hi all, > > > > I've made a local biomart installation, and have started with just the > > default registry (accessing the msd and uniprot marts from the ebi), > > though of course the plan later is to have my own marts etc. > > > > I can use martview successfully on my local install, but I cannot seem > > to see the wsdl files that should be there according to the > > documentation (as I now want to programmatically query my local > biomart > > install using SOAP). > > > > My local martview: > > http://mygrid.ncl.ac.uk:9002/biomart/martview (nothing special > yet, but > > it is running and works) > > What *should* give me the wsdl: > > http://mygrid.ncl.ac.uk:9002/biomart/martwsdl > > > > Why am I not seeing anything here? Is there some extra step in the > > installation that I would need to do in order to "install" the web > > services aspect? Any help would be most appreciated. > > > > Thanks :) > > > > -- > > Thanks, > > Allyson :) > > > > Allyson Lister > > Research Associate > > Centre for Integrated Systems Biology for Ageing and Nutrition > > Newcastle University > > http://www.cisban.ac.uk > > School of Computing Science > > Newcastle University > > Newcastle upon Tyne, NE1 7RU > > -- > Richard Holland, BSc MBCS > Finance Director, Eagle Genomics Ltd > M: +44 7500 438846 | E: [email protected] > <mailto:[email protected]> > http://www.eaglegenomics.com/ > > > > > -- > Thanks, > Allyson :) > > Allyson Lister > Research Associate > Centre for Integrated Systems Biology for Ageing and Nutrition > Newcastle University > http://www.cisban.ac.uk > School of Computing Science > Newcastle University > Newcastle upon Tyne, NE1 7RU -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [email protected] http://www.eaglegenomics.com/
