isub script for easy job submission

gistfile1.txt

#!/bin/bash
function usage
{
    echo ""
    echo "usage: isub -q <queue> -m <memory> -a <docker image> -h"
    echo ""
    echo "  -q | --queue     LSF Queue - default general-interactive"
    echo "  -g | --group     Compute group - default compute-griffith (other options: compute-mgriffit, compute-obigriffith, etc.)"
    echo "  -m | --mem       Memory to reserve (in Gb). Default 4"
    echo "  -n | --nthreads  number of processors to reserve"
    echo "  -i | --image     use this docker image"
    echo "                   Default: docker(chrisamiller/docker-genomic-analysis)"
    echo "                   expects a comparably formatted LSF docker string"
    echo "  -h | --help      show help/options"
    echo ""
    exit 1
}
while [[ "$1" != "" ]]; do
    case $1 in
         -q | --queue )         shift
                                queue=$1
                                ;;
        -g | --group )          shift
                                group=$1
                                ;;
        -m | --mem )            shift
                                mem=$1
                                ;;
        -n | --nthreads )       shift
                                nthreads=$1
                                ;;
        -i | --image )          shift
                                image=$1
                                                        ;;
        -h | --help )           usage
                                exit
                                ;;
        * )                     usage
                                exit 1
    esac
    shift
done
if [[ $queue == "" ]];then
    queue="general-interactive"
fi
if [[ $mem == "" ]];then
    mem=2;
fi
if [[ $ntheads == "" ]];then
    nthreads=1;
fi
if [[ $image = "" ]];then
    image="docker(chrisamiller/docker-genomic-analysis)";
fi
if [[ $group = "" ]];then
    group="compute-timley";
fi
#add "docker($image)" if necessary
regex='^docker\('
if [[ ! $image =~ $regex ]];then
    image="docker(${image})";
fi
selectString="select[mem>$(( mem * 1000 ))] rusage[mem=$(( mem * 1000 ))]";
echo "bsub command being run is:"
echo "bsub -Is -M $(( $mem * 1000000 )) -G $group -n $nthreads -R '$selectString' -q $queue -a '$image' /bin/bash"
bash -l -c "bsub -Is -M $(( $mem * 1000000 )) -G $group -n $nthreads -R '$selectString' -q $queue -a '$image' /bin/bash"