Generalising Grid Engine qsub job file for multiple programs and input file names

Question

I am using Grid Engine on a Linux cluster. I am running many jobs with different programs and different input files. I don't want to create multiple specific job scripts for each pair of program and input file. Instead I want to be able to specify the program name and the input file on the qsub line.

Therefore I can use qsub job.sh <programNameAndLocation> <inputFileName>

Where job.sh takes two arguments. This works fine. But there is another twist: my programs are located in a very very long directory which I don't want to type every time I submit a job - so aliases are an obvious choice.

So I want to do something like qsub job.sh <programNameAndLocationAlias> <inputFileName>

I initially set the alias in my .bashrc but was getting the error: <programNameAndLocationAlias>: command not found

So I set the alias in submit.sh. But I am getting the same error.

Thoughts on how can I can get the command qsub job.sh $1 $2 to accept aliases also?

Answer 1

A hash and a lookup function might look something like

#!/usr/bin/env bash

declare -A proggies

# "aliases" and then the path said should expand to
proggies[foo]=/some/big/long/stupid/path/foo
proggies[bar]=/some/big/long/stupid/path/bar

function qrunner {
    local exe
    exe=${proggies[$1]}
    if [[ -z "$exe" ]]; then
        echo >&2 "no mapping for '$1'"
        return 1
    fi
    # echo here is for debugging, remove when ready to
    # really break things
    echo qsub job.sh "$exe" "$2"
}

# positive test
qrunner bar filename
echo $?

# and also a negative one
qrunner nope filename
echo $?