Hi Allyson, Glad to hear that it works for you, please do drop a line or two if you notice any evident improvements. Also, would you be interested in ontology part of the implementation ???
Thanks Syed > Hi Richard, > > Thanks - a cvs update (I was indeed in the release 0.7 branch/tag) > followed > by re-running configure.pl, then finally stopping and starting apache > results in a working result for the martwsdl. > > Thanks! :) > > 2009/1/8 Richard Holland <[email protected]> > >> 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/ >> > > > > -- > 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 > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
