# How can I run the latest version of samtools on Slurm?

I am trying to run the following script on slurm to extract information from .sam files. While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. I have this error:

samtools: command not found


That means slurm cannot understand the module if I am not mistaken. What would be a solution here?

#!/bin/bash

#SBATCH --time=05:00:00
#SBATCH --account=def-myaccount
#SBATCH --mem=200000M
#SBATCH --mail-user=mymail@gmail.com
#SBATCH --mail-type=All

# module load samtools/1.11 # this is what I tried first
module spider samtools/1.11 # this does not help either...

for FILE in *.sam;

do

NUM=echo $FILE | sed -r 's/.sam//' | sed -r 's/nastya//' # echo "$FILE" ;

samtools flagstat -O tsv $$FILE > file$${NUM}.txt

done

• @OP, these kinds of specific questions should be discussed with your sysadmin as it is specific to the cluster you work on. Alternatively you can install a local version with package managers such as conda but. Feb 12 at 9:37

module avail


Then look to see (a) if there is a samtools module avilable and (b) exactly what it's called.

If it's called samtools/1.11 then:

module load samtools/1.11


• Great. Thanks for the tips. It worked. Didn't know about avail. Feb 12 at 17:20