How to set java heap size in Galaxy?
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
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 <liubo03@gmail.com> wrote:
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 replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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 <marco.moretto@gmail.com> wrote:
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 <liubo03@gmail.com> wrote:
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 replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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, liu bo wrote:
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 <marco.moretto@gmail.com> wrote:
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 <liubo03@gmail.com> wrote:
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 replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
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liu bo -
Marco Moretto -
Roman Valls