Hi Guys, Just to sum-up my experience
I couldn't get anything to run from martConfigurator & assumed I was missing having installed something crucial Turns out things were configured (mostly) right, but I couldn't start the server from within martConfigurator without the error: Invalid maximum heap size: -Xmx4096m Few edits to biomart-server.sh (bringing down heap size) sorted that out So I can't start from within martConfigurator, but can use biomart-server.sh instead Thanks again for your help Cheers Richard On Fri, 30 Sep 2011 15:22:56 +0100, Syed Haider <[email protected]> wrote: > Hi Christophe, > > Yes, it should be able to recover almost all of it if you connect it to > Type=RDBMS and say Yes to popup (documentation ref: 5.4 Adding a new > RDBMS Source) > > Best, > Syed > > On 30/09/2011 13:28, Christophe Klopp wrote: >> Hi Richard and Syed, >> >> To follow up with Richards' question about importing from 0.7 to 0.8, Is >> it possible to retrieve directly all the user interface done on mart0.7 >> in 0.8? >> For example by reading the compressed XML which is in the database? >> >> Cheers >> >> Christophe >> >> >> Le 30/09/2011 12:00, Syed Haider a écrit : >>> Hi Richard, >>> >>> On 30/09/2011 09:01, Richard Easty wrote: >>>> Hi Syed >>>> >>>> Thanks for your reply - you will have to excuse my ham-fisted >>>> attempts at >>>> getting to grips with biomart! >>>> >>>> As far as I can tell, 5.8 describes access points& how to modify >>>> filters >>>> and attributes which I am OK with so far >>>> >>>> Having loaded one of our marts, (and following 5.8) I inspected what >>>> was >>>> in 0.8's martConfigurator and it appeared to match what was in 0.7's >>>> martEditor >>>> >>>> My issue is with applying any changes to the mart using 0.8 such that >>>> they >>>> are reflected in the web interface >>>> >>>> In 0.7's ME I think Update was the menuitem I used, or Upload All to >>>> apply >>>> all the XML before restarting the server hence my false starts with >>>> Update >>>> & Materialize >>> >>> In v0.7, any configuration changes are saved to XML using 'Export' and >>> to have these reflected in the web interface, you would redo perl >>> bin/configure... followed by apache restart. In v0.8, just use the >>> File->save option and then restart jetty. >>> >>>> >>>> Is there a similar process in 0.8 or (very likely) am I missing >>>> something >>>> crucial? >>>> >>>> Regards >>>> >>>> Richard >>>> >>>> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[email protected]> >>>> wrote: >>>>> Hi Richard, >>>>> >>>>> >>>>> On 29/09/2011 18:09, Richard Easty wrote: >>>>>> Hi, >>>>>> >>>>>> This is just a quick question about moving existing marts from 0.7 to >>>> 0.8 >>>>>> >>>>>> Apologies in advance, but I'm new to biomart, and have been asked to >>>>>> check out what's involved in moving from 0.7 to 0.8 >>>>>> >>>>>> Could you tell me if there's some documentation that discusses this? >>>> I've >>>>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May, >>>>>> 2011' >>>>> >>>>> you are using the correct documentation. >>>>> >>>>>> >>>>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add >>>>>> source/RDBMS pointing at the existing marts& using existing >>>>>> config/add) but have not found a way to make changes and apply them. >>>>>> I tried to edit an attribute name, then call update, then restart the >>>>>> server with no change >>>>> >>>>> please see section 5.8. Dont use update for this, Update refers to >>>>> updating configuration based on underlying database changes. good you >>>>> brought this up, the terms are slightly confusing. >>>>> >>>>>> >>>>>> I tried Materialize to generate the SQL, but get an >>>>>> exception (IndexOutOfBounds) whether I aim it at file, text >>>>>> editor or martrunner >>>>> >>>>> Perhaps you do not need this. As i understand, your already have a >>>>> mart, >>>> >>>>> hence no point materialising it. Materialise is for converting a >>>>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run >>>>> this on >>>> >>>>> your mart. However, the exception definitely needs to be handled >>>>> gracefully. Its a release candidate after all :) >>>>> >>>>> HTH, >>>>> Syed >>>>> >>>>>> Any advice would be very welcome >>>>>> >>>>>> Regards >>>>>> >>>>>> Richard Easty >>>>>> Team87 WTSI >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Users mailing list >>> [email protected] >>> https://lists.biomart.org/mailman/listinfo/users >> > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
