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slurm_TCGAblRun
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slurm_TCGAblRun
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#!/bin/bash
#SBATCH --partition=general-compute --qos general-compute
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --array=0-32%6
#SBATCH --cpus-per-task=1
#SBATCH --tasks-per-node=8
#SBATCH --mem=48000
#SBATCH --output=slurm-%A_%a.out
##SBATCH [email protected]
##SBATCH --mail-type=ALL
##SBATCH --requeue
#Specifies that the job will be requeued after a node failure.
echo "SLURM_JOBID="$SLURM_JOBID
echo "SLURM_JOB_NODELIST"=$SLURM_JOB_NODELIST
echo "SLURM_NNODES"=$SLURM_NNODES
echo "SLURMTMPDIR="$SLURMTMPDIR
cd $SLURM_SUBMIT_DIR
echo "working directory = "$SLURM_SUBMIT_DIR
ulimit -s unlimited
# Modules:
module load R/4.0.2-horae
TCGA_Projects=($(cat ./data_sets/reference/tcga_projects))
cur_proj=${TCGA_Projects[${SLURM_ARRAY_TASK_ID}]}
Rscript ./TCGAbl_gather_data.R ${cur_proj}
echo "Processed ${cur_proj} and saved to data_sets"
echo "All done!"