Dear all,
I have added an application to Galaxy's Tools.
Now there occurs an error "java.lang.OutOfMemoryError: Java heap space".
Do you know how to set java heap size in Galaxy?
Thank you very much.
Best regards,
Bo
___
Please keep all repl
Hi Liu,
if you set up your application in the XML to run with Java, like java -jar
yourapplication.jar, it is sufficient to add the -Xmx parameter. Something
like
java -Xmx512m -jar yourapplication.jar
Greets
---
Marco
On 27 June 2011 12:15, liu bo wrote:
> Dear all,
>
> I have added an applic
Hi Marco,
Thanks for your kind reply.
My app is a python file, and there's not an explicit command to run java.
I just wonder whether there is a file to configure Galaxy, in order to
set the Java heap size.
Thank you.
Best wishes,
Bo
On Mon, Jun 27, 2011 at 7:51 PM, Marco Moretto wrote:
> Hi Li
Hi Liu,
Does your app execute Picard/GATK at some point ? In that case those
would be the ones triggering your Java OOM error, in that case Bo's
suggestion is the way to go. That's my best guess since Galaxy itself
doesn't use java either (only python AFAIK).
Regards,
Roman
On 2011-06-27 18:44,
Hello Liu,
I'm keeping our mail thread in the mailing list, as advised by its
guidelines on the footer of each mail.
Now, galaxy runs on top of paster, a minimal python webserver, but it
has nothing to do with Java, looks like your out of memory error comes
from your app then.
Have you tried the
Hi Roman,
Thanks for your explanation.
I'm sorry for this late reply.
I think the problem is on my app. I'll further check that.
Thanks,
Bo
Date: Thu, 30 Jun 2011 14:53:08 +0200
From: Roman Valls
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] How to set java heap size
