18_compute_pvalue.bsub

#!/bin/bash
#BSUB -q long                                      #Set you submission
#BSUB -J computeGps_pvalue[1-225]                  #Name of the job
#BSUB -R "rusage[mem=20GB]"                        #Request memory
#BSUB -o /your/out/dir/computeGps_pvalue_%J_%I.out #Give path for the out file
#BSUB -e /your/out/dir/computeGps_pvalue_%J_%I.err #Give path for the out file

# Modules
module load R/4.3.0

# Set your dir
cd /your/dir/gps/gps_cpp/build/apps

# Main code
phenotypes=("Cell_B" "Cell_P" "CLL" "DLBCL" "Drug_G1" "FL" "HL" "LM" "LPL_WM" "MGUS" "MM_MGUS" "MM" "MZL" "Soma_G1" "Soma_G2")

# Calculate number of phenotypes
num_phenotypes=${#phenotypes[@]}
  
  # Calculate phenotype combination index
  combination_index=$((LSB_JOBINDEX - 1))
  
  # Calculate phenotype index pair from combination index
  pheno_index1=$((combination_index / num_phenotypes))
  pheno_index2=$((combination_index % num_phenotypes))
  
  # Get phenotype names
  pheno1=${phenotypes[$pheno_index1]}
  pheno2=${phenotypes[$pheno_index2]}
  

Rscript --vanilla 13_fit_gevd_compute_pvalue.R -g computeGpsCLI_${pheno1}_${pheno2}.txt -p 100_permuteTraitsCLI_${pheno1}_${pheno2}.txt -o gps_${pheno1}_${pheno2}_pvalue.txt

#collect all results together
cat gps_Cell_B_Cell_B_pvalue.txt | head -1 > gps_results.txt
find gps_*_pvalue.txt  -exec sh -c "cat {} | tail -n +2 -f " \; >> gps_results.txt