submit_str.pbs

#!/bin/bash
#PBS -N str_BOX_eastern_k3
#PBS -q qcondo
#PBS -j oe
#PBS -m abe
#PBS -M btm002@email.uark.edu
#PBS -o str_BOX_eastern_k3.$PBS_JOBID
#PBS -l nodes=1:ppn=8:m256gb
#PBS -l walltime=30:00:00:00
#PBS -V

cd $PBS_O_WORKDIR

infile=BOX_withPopmap_final.str
mparams=mainparams
eparams=extraparams
outdir=eastern

PATH=$PATH:/home/btm002/local/bin
export PATH;

cp $infile $mparams $eparams /scratch/$PBS_JOBID/

cd /scratch/$PBS_JOBID

mkdir ./$outdir
cd ./$outdir

/home/btm002/local/bin/parallel "/home/btm002/local/bin/structure -K 3 -D {}8825643 -m ../$mparams -e ../$eparams -i ../$infile -o k3_{}.out" :::: <(seq 1 8);

mkdir -p $PBS_O_WORKDIR/$outdir

rsync -vh /scratch/$PBS_JOBID/$outdir/*_f $PBS_O_WORKDIR/$outdir/
rsync -vh /scratch/$PBS_JOBID/$outdir/seed.txt $PBS_O_WORKDIR/$outdir/seeds_k3.txt