script to output SGE job array, which can then be submitted with qsub

jobarray.sh

#! /bin/bash
set -e
set -u

##
until [ -z "$1" ]
do
    # use a case statement to test vars. we always test $1 and shift at the end of the for block.
    case $1 in
    # parameters to qsub
    --scratch)
        shift
        scratch=$1;;
    --nhours)
        shift
        nhours=$1;;
    --ncores)
        shift
        ncores=$1;;
    --mem)
        shift
        vmem=$1;;
    --tc)
        shift
        tc=$1;;
    #log
    --qsub.out)
        shift
        out=$1;;
    --qsub.err)
        shift
        err=$1;;
    #
    --input.args)
        shift
        inputargs=$1;;
    --script)
        shift
        script=$1;;
    -* )
        echo "Unrecognized option: $1"
        usage
        exit 1;;
    esac
    shift
    if [ "$#" = "0" ]; then break; fi
done

#required input

njobs=`cat $inputargs | wc -l`

cat <<EOL
#!/bin/bash
#$ -S /bin/bash
#$ -o /dev/null
#$ -e /dev/null
#$ -cwd
#$ -V
#$ -R y
#$ -pe smp ${ncores-1}
#$ -l scr=${scratch-1}G
#$ -l tmem=${vmem-2}G,h_vmem=${vmem-1}G
#$ -l h_rt=${nhours-1}:0:0
#$ -t 1-${njobs}
#$ -tc ${tc-25}
set -u
set -x
let "SGE_TASK_ID=\$SGE_TASK_ID-1"
mkdir -p ${out-qsub.out} ${err-qsub.err}
exec >${out}/${script}_\${SGE_TASK_ID}_\${JOB_ID}.out 2>${err}/${script}_\${SGE_TASK_ID}_\${JOB_ID}.err
args=(\$(cat $inputargs))
./${script} \${args[\$SGE_TASK_ID]}
EOL