Re: [galaxy-dev] How to set java heap size in Galaxy?

2011-06-27 Thread Roman Valls
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,

Re: [galaxy-dev] postgresql connection error: could not connect to server: No such file or directory...

2011-06-27 Thread Marco Moretto
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

Re: [galaxy-dev] How to set java heap size in Galaxy?

2011-06-27 Thread liu bo
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

Re: [galaxy-dev] input security validation

2011-06-27 Thread Roman Valls
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

Re: [galaxy-dev] input security validation

2011-06-27 Thread Roman Valls
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

[galaxy-dev] Launching a JAVA or external app

2011-06-27 Thread Bossers, Alex
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

Re: [galaxy-dev] How to set java heap size in Galaxy?

2011-06-27 Thread Marco Moretto
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

Re: [galaxy-dev] picard / srma index .loc

2011-06-27 Thread Holger Klein
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

[galaxy-dev] How to set java heap size in Galaxy?

2011-06-27 Thread liu bo
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