CODEWITHSUNDEEP
linuxbashbioinformaticsslurm
bb8
bb8

Reputation: 190

Directly call system command from SLURM/SGE

I would like to call a system command (kat hist) straight from the sbatch (slurm/sge) command without the .sh script. Not sure something like this is possible?

This is what I am currently doing:

"sbatch -p %s -n %s -t %s ./kat_reads_call.sh %s %s %s %s/filter_10xReads.py %s %s" % arg_list

Where .kat_reads.sh just does this:

#!/bin/bash
kat hist -o $1 -m $2 -t $3 <($4 -1 $5 -2 $6)

The goal is something like this :

"sbatch -p %s -n %s -t %s kat hist -o %s -m %s -t %s <(%s -1 %s -2 %s)" % arg_list

This is the error I recieve:

sbatch: error: This does not look like a batch script.  The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh

Upvotes: 1

Views: 190

Answers (1)

Poshi
Poshi

Reputation: 5762

Check the --wrap parameter of sbatch. You will need something like:

"sbatch -p %s -n %s -t %s --wrap \"kat hist -o %s -m %s -t %s <(%s -1 %s -2 %s)\"" % arg_list

Apply the proper escape sequence, as I don't know hich language is it.

Upvotes: 1

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