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Commit c7ac762d authored by Christophe  BECAVIN's avatar Christophe BECAVIN
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Bash slurm

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#!/bin/bash
#SBATCH --job-name PDetect
#SBATCH --array=1-2
#SBATCH --output temp/PDetect.out
#SBATCH --error temp/PDetect.err
#SBATCH --mail-type FAIL
......
#!/bin/bash
#SBATCH --job-name SeqDep
#SBATCH --array=1-2
#SBATCH --output temp/SeqDep.out
#SBATCH --error temp/SeqDep.err
#SBATCH --qos=fast
#SBATCH --qos=hubbioit
#SBATCH --mail-type FAIL
#SBATCH --cpus-per-task 1
#SBATCH --mem=5GB
#SBATCH -p common
#SBATCH -p hubbioit
folder=/pasteur/projets/policy01/m6aAkker
scratch=/pasteur/scratch/cbecavin/m6aAkker/
......@@ -15,8 +14,11 @@ scriptFolder=/pasteur/projets/policy01/m6aAkker/MeRIPSeq/
line=$(head -n ${SLURM_ARRAY_TASK_ID} $1 | tail -n 1)
dataName=$(echo "$line" | awk '{print $2}')
rawData=$(echo "$line" | awk '{print $1}')
# prepare variables
mkdir $folder/temp/${SLURM_JOB_NAME}
if [ ! -d $folder/temp/${SLURM_JOB_NAME} ]; then
mkdir $folder/temp/${SLURM_JOB_NAME}
fi
shFile=$folder/temp/${SLURM_JOB_NAME}/${dataName}_${SLURM_JOB_NAME}_${SLURM_JOB_ID}.sh
logFile=$folder/temp/${SLURM_JOB_NAME}/${dataName}_${SLURM_JOB_NAME}_${SLURM_JOB_ID}.log
......
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