Thanks Junjun, I'll try that. Isaac El 22/12/2011 19:56, "Junjun Zhang" <[email protected]> escribió:
> Dear Isaac, > > Yes, you need a lot of memory in order to open this registry, it's large. > > After compilation with ant, please edit the following file: > > dist/scripts/martconfigurator.sh > > So that the following line looks like: > > $JAVA -Xmx8g -Xms3g -cp $TMP_CLASSPATH > org.biomart.configurator.test.MartConfigurator $@ > > Hope this helps, > > Junjun > > > > From: Isaac cano <[email protected]> > Date: Thu, 22 Dec 2011 07:17:04 -0500 > To: jzhang <[email protected]>, Arek Kasprzyk < > [email protected]> > Cc: BioMart Users <[email protected]> > Subject: Re: [BioMart Users] BioMart Central Portal > > Dear JunJun, > > After a long long time trying martconfigurator to open the central portal > registry file I've got an out of memory error: GC overhead limit exceed. > > Is this really that I should increase the system's physical RAM memory of > maybe the Java heap??!! > > Thanks! > > Isaac > > 2011/12/22 Isaac cano <[email protected]> > >> Dear JunJun, >> >> I'm trying to open the CentralPortal.xml registry file but >> martconfigurator is not able to open it. I get no logs so just command line >> output that first says something regarding password encryption (see >> password.png screenshot attached) and then some other outputs (see >> martconfigurator_output.txt attached). >> >> I'm using proxy server so I've set it properly and I've tried to open the >> icgc7.xml registry file and it worked. Any idea why I cannot get opened the >> CentralPortal.xml registry file??! >> >> Thanks!! >> >> Isaac >> >> >> 2011/12/21 Junjun Zhang <[email protected]> >> >>> The CentralPortal registry file is at: >>> https://code.oicr.on.ca/svn/biomart/biomart-java/branches/release-0_8-candidate_7/registry/ >>> Junjun >>> >>> From: Isaac cano <[email protected]> >>> Date: Wed, 21 Dec 2011 13:08:16 -0500 >>> To: Arek Kasprzyk <[email protected]> >>> Cc: "[email protected]" <[email protected]>, jzhang < >>> [email protected]>, BioMart Users <[email protected]> >>> Subject: Re: [BioMart Users] BioMart Central Portal >>> >>> Thanks a lot Arek, I'll check the registry directory first. >>> I have to say that Nuria is now in another professional situation but I >>> think she continues being interested. >>> Thanks, >>> Isaac >>> El 21/12/2011 18:46, "Arek Kasprzyk" <[email protected]> escribió: >>> >>>> Hi Isaac, >>>> yes it is possible. The config should be available from the 'registry' >>>> directory in rc6 but if not Junjun Zhang (cc'ed on this email) will be able >>>> to make this configuraiton available to you. I believe that Nuria (cc'ed on >>>> this email) is also interested in this config. >>>> a >>>> >>>> On Wed, Dec 21, 2011 at 11:26 AM, Isaac cano <[email protected]> wrote: >>>> >>>>> Dear BioMart users, >>>>> >>>>> I've recently known about the BioMart Central Portal and I was >>>>> wondering if it is available as a mart so we can import the complete >>>>> central portal as a source into martconfigurator. Is this possible?! >>>>> >>>>> Thanks, >>>>> >>>>> -- >>>>> Isaac Cano >>>>> Bioinformatics >>>>> Linkcare Health Services SL >>>>> C/Villarroel 170 >>>>> 08036 - Barcelona >>>>> Tel.: (+34)932 275 400, ext. 4182\4523 >>>>> Mobile: (+34) 666 186 748 >>>>> Fax: (+34) 932 275 455 >>>>> [email protected] >>>>> >>>>> >>>>> _______________________________________________ >>>>> Users mailing list >>>>> [email protected] >>>>> https://lists.biomart.org/mailman/listinfo/users >>>>> >>>>> >>>> >> >> >> -- >> Isaac Cano >> Bioinformatics >> Linkcare Health Services SL >> C/Villarroel 170 >> 08036 - Barcelona >> Tel.: (+34)932 275 400, ext. 4182\4523 >> Mobile: (+34) 666 186 748 >> Fax: (+34) 932 275 455 >> [email protected] >> >> > > > -- > Isaac Cano > Bioinformatics > Linkcare Health Services SL > C/Villarroel 170 > 08036 - Barcelona > Tel.: (+34)932 275 400, ext. 4182\4523 > Mobile: (+34) 666 186 748 > Fax: (+34) 932 275 455 > [email protected] > >
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