IPMNPDACpaperArchive / PACA_PCAWG_BBDPCtiming / bbDPCtiming.sh
bbDPCtiming.sh
Raw
#!/bin/bash --login
#SBATCH -J bbtmtest
#SBATCH -p multicore
#SBATCH -n 2
#SBATCH -t 2-0
#SBATCH -a 1-2
#SBATCH -o /yourFolder/logs/%A_%a.out
#SBATCH -e /yourFolder/logs/%A_%a.err

set -euo pipefail

module purge
conda activate xtpy311

# Get the Nth line from a file based on array task ID
sampleID=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"] {print $1}' samplelist.txt)
ssDPCIfolderpath='/Data/dpcInputs'
dpcoutfolderpath='/Data/dpcOutputs/'
outpath4in='/Data/timingOutputs/'

python3 bbdpctiming.py "$sampleID" "$ssDPCIfolderpath" "$dpcoutfolderpath" "$outpath4in"