Checking for status of qsub jobs running within sh

I have been given a c shell script that launches 800 individual qsubs for a sample. I need to run this script on more than 500 samples (listed in samples.txt). To automate the process, I thought about running the script (named SrchDriver) using the following bash shell script:

#!/bin/sh

for item in $(cat samples.txt)
do
  (cd dir_"$item"/MAPGAPS && SrchDriver "$item"_Out 3)
done

This script would launch the SrchDriver script for all samples one right after another which would result in too many jobs on the server at one time. I would like to run only one sample at a time by waiting for all qsubs to finish for a particular sample.

What is the best way to put in a check for running/waiting jobs for a sample and holding the launch of the Srchdriver script for additional samples until all jobs are finished for the current sample?

I was thinking to first wait for 30 seconds and then check status of the qsubs (name of jobs is mapgaps). Next, I wanted to use a while loop to check the status every 30 seconds. Once the status is no longer 0, then proceed to the next sample. Would this be correct?

sleep 30
qstat | grep mapgaps &> /dev/null

while [ $? -eq 0 ]; 
do
    sleep 30
    qstat | grep mapgaps &> /dev/null
done;

If correct, how would I combine it with my for-loop? Would the following code below be correct?

#!/bin/sh

for item in $(cat samples.txt)
do
    (cd dir_"$item"/MAPGAPS && SrchDriver "$item"_Out 3)

    sleep 30
    qstat | grep mapgaps &> /dev/null
    status=$?

    while [ $status = 0 ]
    do
        sleep 30
        qstat | grep mapgaps &> /dev/null
        status=$?
    done

done

Thanks in advance for help. Please let me know if more information is needed.

Your script should work as is, indeed. The logic is sound and the syntax is correct.

A small improvement: the while statement can take the return status of a command directly, without using $?, so you could write your script like this:

#!/bin/sh

for item in $(cat samples.txt)
do
    (cd dir_"$item"/MAPGAPS && SrchDriver "$item"_Out 3)

    sleep 30
    while qstat | grep mapgaps &> /dev/null
    do
        sleep 30
    done
done