is it possible to qsub a command instead of a script?

Question

For example from this page: https://bioinformatics.mdc-berlin.de/intro2UnixandSGE/sun_grid_engine_for_beginners/how_to_submit_a_job_using_qsub.html

The site save the following to this: runBowtie.sh

#!/bin/bash
                    #$ -N run_bowtie2
                    #$ -cwd
                    #$ -pe smp 6
                    #$ -l h_vmem=6G
                    
                    
                    infile=/data/bioinfo/READS2/R1_001.fastq.gz
                    outfile=/data/bioinfo/READS2/aln/R1_001.sam
                    btindex=/data/bioinfo/genome_data/Caenorhabditis_elegans/UCSC/ce10/Sequence/BowtieIndex/genome

gzip -dc $infile | bowtie  --chunkmbs 300 --best -m 1 -p 6 --phred33 -q $btindex   -  -S $outfile

and then do

qsub -runBowtie.sh

I am wondering if it's possible to just

qsub -pe smp 33 gzip -dc /data/bioinfo/READS2/R1_001.fastq.gz | bowtie  --chunkmbs 300 --best -m 1 -p 6 --phred33 -q $/data/bioinfo/genome_data/Caenorhabditis_elegans/UCSC/ce10/Sequence/BowtieIndex/genome   -  -S $/data/bioinfo/READS2/aln/R1_001.sam

thank you

Answer 1

The flag you are looking for is -b y. This will tell the scheduler you are submitting a binary rather than a script.

From the man page:

-b y[es]|n[o]
          Available for qsub, qrsh only. Qalter  does  not  allow
          changing this option. This option cannot be embedded in
          the script file itself.

          Gives the user the possibility to  indicate  explicitly
          whether  command should be treated as binary or script.
          If the value of -b is  'y',  then  command   may  be  a
          binary  or script.  The command might not be accessible
          from the submission host.  Nothing except the  path  of
          the  command  will  be  transferred from the submission
          host to the  execution  host.  Path  aliasing  will  be
          applied  to  the path of command before command will be
          executed.