#!/bin/bash -l
# Tisha Melia
# June 23 2015
# Bash file to loop over mapping all samples

#checking the command line arg
if [ $# -lt 1 ] ; then
      echo "Need at least one command line argument for a tab-delimited file for listing of samples to run"
      exit 0
fi
SAMPLE_FILE=$1
IFS=$'\t'

while read SAMPLE_NAME STRANDEDNESS INPUT_FILE OUTPUT_FOLDER; do

	if [[ "$SAMPLE_NAME" =~ \#.* ]];then
		echo "skipped comment line"
	else
		
		echo $SAMPLE_NAME
        	echo $STRANDEDNESS
		echo $INPUT_FILE
		echo $OUTPUT_FOLDER
		echo "qsub -N cuff${SAMPLE_NAME} -P waxmanlab -pe single_node 4-8 -l h_rt=72:00:00 cufflinks.qsub $SAMPLE_NAME $STRANDEDNESS $INPUT_FILE $OUTPUT_FOLDER"
		qsub -N cuff${SAMPLE_NAME} -P waxmanlab -pe single_node 4-8 -l h_rt=72:00:00 cufflinks.qsub $SAMPLE_NAME $STRANDEDNESS $INPUT_FILE $OUTPUT_FOLDER
       fi
        
done < $SAMPLE_FILE