name
input
err1
out1
1
40G
DET
sylamer
dir1
dir2
123456

#!/bin/bash
#
# Name: name
# Task: name
#
#$ -N name
#$ -e input/err1.log
#$ -o input/out1.log
#$ -pe threaded 1
#$ -l h_vmem=40G

LD_LIBRARY_PATH="/usr/lib64/"

export LD_LIBRARY_PATH

cd input

mkdir input/DET/

mkdir input/sylamer/

mkdir input/DET/dir1_vs_dir2

mkdir input/sylamer/dir1_vs_dir2

myprogram.sh -i 123456 -o input/DET/dir1_vs_dir2 -1 input/dir1 -2 input/dir2

cd input/sylamer/dir1_vs_dir2

R CMD BATCH --no-save --no-restore "--args ref=\"mmu\" DETDIR=\"input/DET/dir1_vs_dir2\" outName=\"dir1_vs_dir2\" UCSCLink=\"http://test.com?id=123456\"" myprogram2.sh