[Condor-users] Java job

["Xiao-lin \"Nick\" Wu" <nick.wu@xxxxxxxxxxxxxx>]

I have several JAVA jobs. A typical command line is as follows:

java -Xmx1000m -jar beagle.jar \
                 unphased=Bgl_refgeno_chr5.dat \
                 unphased=Bgl_stugeno_chr5.dat \
     markers=Bgl_Markerfile_chr5.dat  \
     missing=? \
     out=Bgl_chr5

Anyone can guide me through to set up a Condor submit job file? I tried the following but it did not work.

Universe     = JAVA
Executable   = beagle.jar
jar_files    = beagle.jar
Log          = beagle.$(process).log
Output       = beagle.$(process).out
Error        = beagle.$(process).error
notification = NEVER
should_transfer_files   = YES
when_to_transfer_output = ON_EXIT
 
arguments = -Xmx1000m -jar beagle.jar unphased=Bgl_refgeno_chr5.dat unphased=Bgl_stugeno_chr5.dat markers=Bgl_Markerfile_chr5.dat missing=? out=Bgl_chr5
Initialdir   = angus_chr5
transfer_input_files = Bgl_chrom_5_snp.dat, Bgl_Markerfile_chr5.dat, Bgl_refgeno_chr5.dat, Bgl_stugeno_chr5.dat  
Queue
 
arguments    = -Xmx1000m -jar beagle.jar unphased=Bgl_refgeno_chr6.dat unphased=Bgl_stugeno_chr6.dat markers=Bgl_Markerfile_chr6.dat missing=? out=Bgl_chr6
Initialdir   = angus_chr6
transfer_input_files = Bgl_chrom_6_snp.dat, Bgl_Markerfile_chr6.dat, Bgl_refgeno_chr6.dat, Bgl_stugeno_chr6.dat
Queue

Thanks!

Nick