454

Roche 454 gene-sequencer software

An example job submission file is shown below, you will need to change the values shown in bold

#!/bin/bash
#
#PBS -N gs454_test
#PBS -o test.out
#PBS -e test.err
#PBS -l walltime=00:30:00
#PBS -l pvmem=5gb
#PBS -l nodes=1:ppn=2
#
#----------------------------------------------------------
# Run from job submission directory
#----------------------------------------------------------
cd $PBS_O_WORKDIR

#----------------------------------------------------------
# Set up standard environment using modulefiles
#----------------------------------------------------------
module load gs454/2.5.3 

#----------------------------------------------------------
# Set up run specific environment 
#----------------------------------------------------------
export GS_CACHEDIR=$TMPDIR
export GS_NUM_PROCESSORS=$((PBS_NUM_NODES*PBS_NUM_PPN))

#----------------------------------------------------------
# If you don't have tight-integration you may also need..
#----------------------------------------------------------
#export GS_MPIARGS="-n $GS_NUM_PROCESSORS -machinefile $PBS_NODEFILE"

#----------------------------------------------------------
# Run the processor 
#----------------------------------------------------------
startGsProcessor --verbose --pipe=signalProcessing D_2011_02_10_14_22_56_FLX11070276_imageProcessingOnly

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