Source a conda environment on the GenOuest cluster and start Shortstack

Creation du script Shortstack

The script is called shortstack_sbatch_script.sh and contains the following lines:

#! /bin/bash
source /local/env/envconda.sh
source activate /groups/bipaa/env/shortstack_4.0.3 # ou source activate /groups/bipaa/env/shortstack

ShortStack --readfile [my sample] --outdir [my output directory] --threads N --dn_mirna --genome [my genome] 

Submit the script to SLURM

# Request resources from genouest
srun -c4 --mem=40G --pty bash  
bash shortstack_sbatch_script.sh

Written on March 15, 2024