Using linux PS to check if a tool is already running

[colindaven]

Hi community,

TL;DR - does ps -aux actually work with Nextflow or is it restricted/non-functional somehow ?

I've not been able to get a bash variable to update successfully to what I am getting on the command line (all running on one local machine for testing.

PASA_COUNT=\$(ps -aux | grep PASA | wc -l)

Maybe there is a more Nextflow-ish way to get running process counts, but my attempt in bash does not work. Artificially setting PASA_COUNT=10 does cause the process to pause (wait 1 minute).

Thanks,
Colin

/*
 *  check if PASA running and wait if it is - to avoid DB competition and corruption
 */

process pasa_check_wait {

    tag "$name"
    input:
    path transcripts

    output:
    path "done.txt", emit: done
    
    script:
    prefix = transcripts.baseName
    name = prefix
    
    """
    
        # Only start PASA if it is not already running (DB of other process will otherwise be overwritten)

        while true; do

            PASA_COUNT=\$(ps -aux | grep PASA | wc -l)
            ## fake high PASA_COUNT as the code never goes higher than 1, itself... why ... ?
            #PASA_COUNT=10
            echo "###### Number of PASA processed PASA_COUNT: \$PASA_COUNT ###########"

            # Check if the variable is greater than or equal to 2
            if [[ "\$PASA_COUNT" -ge 2 ]]; then
                echo "########### PASA already running, waiting for it to terminate. Waiting one minute ####### "
            else
                echo "########### Cannot find a running PASA - continue ####### "
                break
            fi

            # Wait for one minute
            sleep 60
        done

        touch done.txt
    """
}

[pditommaso]

Don't think there's nothing specific in nextflow in this regard. It just wrap the command in the Bash script and run it