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]<mailto:[email protected]>> Date: Thu, 22 Dec 2011 07:17:04 -0500 To: jzhang <[email protected]<mailto:[email protected]>>, Arek Kasprzyk <[email protected]<mailto:[email protected]>> Cc: BioMart Users <[email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Wed, 21 Dec 2011 13:08:16 -0500 To: Arek Kasprzyk <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, jzhang <[email protected]<mailto:[email protected]>>, BioMart Users <[email protected]<mailto:[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]<mailto:[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]<mailto:[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<tel:%28%2B34%29932%20275%20400%2C%20ext.%204182>\4523 Mobile: (+34) 666 186 748<tel:%28%2B34%29%20666%20186%20748> Fax: (+34) 932 275 455<tel:%28%2B34%29%20932%20275%20455> [email protected]<mailto:[email protected]> _______________________________________________ Users mailing list [email protected]<mailto:[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<tel:%28%2B34%29932%20275%20400%2C%20ext.%204182>\4523 Mobile: (+34) 666 186 748<tel:%28%2B34%29%20666%20186%20748> Fax: (+34) 932 275 455<tel:%28%2B34%29%20932%20275%20455> [email protected]<mailto:[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]<mailto:[email protected]>
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