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slurm-submit-script-WITH-containers.sh
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R2915 eSCT pipeline interoperability
slurm-submit-script-WITH-containers.sh
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#!/bin/bash
#SBATCH --job-name=pipeline2-containers
#SBATCH --partition=sing
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=4
#SBATCH --mem=10G
#SBATCH --output=containers.log
#SBATCH --mail-user=alexander.kashev@math.unibe.ch
# define the number of cpus to use
# you can use env vars provided by your scheduler or hardcode the number of cpus to use
export
NUM_CPUS
=
${
SLURM_CPUS_PER_TASK
}
# Actual pipeline run+test
./pipeline.py
test
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