Re: [Condor-users] Java world and executable parameter...

[Jaime Frey <jfrey@xxxxxxxxxxx>]

On May 29, 2012, at 12:56 PM, john alexander sanabria ordonez wrote:

I'm trying to run a Java class which is found in a .jar file. I don't have access to the .class file thus the following .condor definition fails

Universe                = java
Executable              = net.sf.ngstools.main.SAMPairing
Arguments               = -M 2000 -d 5 ID47_TGACCA_L008_007_bowtie2.sam ID47_TGACCA_L008_007_bowtie2_d5.bam >& ID47_TGACCA_L008_007_bowtie2_pairing.log
Log                     = demo.log.$(cluster).$(process)
Output                  = demo.output.$(cluster).$(process)
Error                   = demo.error.$(cluster).$(process)
should_transfer_files   = YES
when_to_transfer_output = ON_EXIT_OR_EVICT
transfer_input_files    = ID47_TGACCA_L008_007_bowtie2.sam
jar_files               = sam-1.68.jar,NGSTools2.jar
Queue

I appreciate your suggestions.

For java universe, in your submit file, the executable is the name of the jar or class file. The name of the main class should be the first argument. So the first three lines of your submit file should look like this (assuming NGSTools2.jar contains net.sf.ngstools.main.SAMPairing):

Universe = java

Executable = NGSTools2.jar

Arguments = net.sf.ngstools.main.SAMPairing -M 2000 -d 5 ID47_TGACCA_L008_007_bowtie2.sam

The Condor manual has more details:

http://research.cs.wisc.edu/condor/manual/v7.8/2_8Java_Applications.html

Thanks and regards,

Jaime Frey

UW-Madison Condor Team