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,
Hi Gus,
it seems that your postgres is not configured to accept connection except
localhost (or the deamon is not running). Did you try to connect to postgres
from another PC in the network (no the localhost)?
Did you install postgres using apt-get install? Do you run postgres using
"/etc/init.d/po
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
Sorry for the cross-posting, but I guess that's also interesting to
Galaxy users...
I've been thinking about input validation too... only a bit more
generally, on a server/production basis. Nate, on your production
setup[1] (galaxy main), do you use any kind of filter or framework a la
modsecurity
Sorry for the cross-posting, but I guess that's also interesting to
Galaxy users...
I've been thinking about input validation too... only a bit more
generally, on a server/production basis. Nate, on your production
setup[1] (galaxy main), do you use any kind of filter or framework a la
modsecurity
Hello all,
would it be possible to launch for instance a JAVA app with preloaded
parameters and files from galaxy that needs interaction/display?
For instance a gui based annotation editor? It necessarily doesn't have to
support saving of files back to galaxy. Sort of end stage.
Any help or poin
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 Kelly,
On 06/24/2011 08:40 PM, Kelly Vincent wrote:
> That particular tool uses a different loc file--all_fasta.loc, which is
> simply a list of fasta files with full path/name. Are your other Picard
> tools working? Let us know if you run into further issues.
thank you. Now the indices show
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
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Please keep all repl
