gpu-uark/1-preprocess.sh at main · igorkf/gpu-uark · GitHub

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#!/bin/bash

#SBATCH --job-name=prep
#SBATCH --output=logs/prep_geno.out
#SBATCH --partition=cloud72
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --time=01:00:00

## configs
module purge
module load intel/21.2.0 mkl/21.3.0 gcc/11.2.1 R/4.3.0

## copy needed files to /scratch
cd /scratch/$SLURM_JOB_ID
mkdir -p data src logs output
mkdir -p data/Training_data
mkdir -p data/Testing_data
scp $SLURM_SUBMIT_DIR/data/Training_data/5_Genotype_Data_All_2014_2025_Hybrids_numerical.txt data/Training_data
scp $SLURM_SUBMIT_DIR/data/Training_data/1_Training_Trait_Data_2014_2023.csv data/Training_data
scp $SLURM_SUBMIT_DIR/data/Testing_data/1_Submission_Template_2024.csv data/Testing_data
scp $SLURM_SUBMIT_DIR/src/prep_geno.R src/

#####################################################
## run tasks
#####################################################
#
Rscript src/prep_geno.R > logs/prep_geno.log
#####################################################

## copy needed output files to /home
scp logs/prep_geno.log $SLURM_SUBMIT_DIR/logs/
scp output/geno_ok.csv $SLURM_SUBMIT_DIR/output/