B_sedsetup

#!/bin/sh
#$ -N setup
#### Use this script to set the user variables in all scripts in the directory.  It is important you copy the origianl scripts into a new directory 
#### Update /AAA/PIInitials/ with the first part of your home directory i.e /user/\home\/nlp71\/WORKING_DATA\/NICR_RNAseq\/rna_seq\/test_data\/fastqs\/scripts/
for fn in `ls *.sh`;
do
        sed "s/user/\home\/nmz33\/WORKING_DATA\/RNAseq/\FASTQ/g" ${fn} > t${fn}
		mv t$fn $fn
        chmod 744 $fn
done