Tuesday, April 29, 2008

Running PaCE on BigRed

PaCE is software to cluster large collections of Expressed Sequence Tags(EST). BigRed provides PaCE package only for the internal use. Here are examples of job submission for the condorG to the BigRed for the PaCE package. Note: I set the "OutputFolder" parameter in the Phase.cfg as ".". This will let the gram job manager put all of the output files into the globus scratch directory.

executable = /N/u/leesangm/BigRed/bin/PaCE_v9
transfer_executable = false
should_transfer_files = true
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/EST/data/Brassica_rapa.mRNA.EST.fasta.PaCE, /home/leesangm/EST/data/Phase.cfg
universe = grid
grid_resource = gt2 gatekeeper.bigred.iu.teragrid.org/jobmanager-loadleveler
transfer_output_files = estClust.33316.3.PaCE
error = PaCE.err.$(Cluster)
err = PaCE.standardErr.$(Cluster)
log = PaCE.log.$(Cluster)
x509userproxy = /tmp/x509up_u500

globusrsl = (jobtype=mpi)(queue=DEBUG)(maxWallTime=00:15)\
(count = 4)\
(hostCount = 2)\
(arguments= 'Brassica_rapa.mRNA.EST.fasta.PaCE' '33316' 'Phase.cfg')


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