Running parallel jobs based on Rscript

IFB Core Cluster
,
11

Yes !

Voici un exemple de script :

#!/bin/bash

#SBATCH --array=0-11  # on démarre l'array à 0
#SBATCH --cpus=50
#SBATCH --mems=32GB
#SBATCH -o analysis-%j-%a_out.txt
#SBATCH -e analysis-%j-%a_err.txt

## Initiate the environment
module load conda
conda init bash
conda activate rnaseqmva

# liste des paramètres
RECOUNT_IDS=(SRP042620 SRP056295 SRP057196 SRP061240 SRP062966 SRP066834)
FEATURES=(gene transcript)

# calcul le recount et la feature en fonction de l'index courant du job
feature=$((SLURM_ARRAY_TASK_ID % 2))
recount_id=$((SLURM_ARRAY_TASK_ID / 2))

# lancement de l'analyse
srun Rscript --vanilla misc/main_processes.R ${RECOUNT_IDS[recount_id]} ${FEATURES[feature]}