Rhup

#!/bin/sh
# Rhup will prepare and submit an R job and email the user when it
# is finished

# Test usage; if incorrect, output correct usage
if [ "$#" -ne 1 ]; then
	echo "********************************************************************"
	echo "*                         Rhup version 2.0                         *"
	echo "********************************************************************"
	echo "The 'Rhup' script submits R batch jobs using nohup."
	echo ""
	echo "Usage is:"
	echo "	       Rhup <r_file.R>"
	echo ""
	echo "Spaces in the filename or directory name may cause failure."
	echo ""


else
	# Stem and extension of file
	filestem=`echo $1 | cut -f1 -d.`
	extension=`echo $1 | cut -f2 -d.`
    extension=`echo "$extension" | awk '{print tolower($0)}'`

	# Test if file exist
	if [[ ! -r $1 ]]; then
		echo ""
		echo "File does not exist"
		echo ""
	elif [[ $extension != r ]]; then
		echo ""
		echo "Invalid input file, must be an R-file"
		echo ""
	else
		# Direct output
		output=$filestem.Rout
		echo "R: directing output to $output"

		
		
		
		
		# Use user-defined 'TMPDIR' if possible; else, use /tmp
		if [[ -n $TMPDIR ]]; then
			pathy=$TMPDIR
		else
			pathy=/tmp
		fi
		
		# Tempfile to enable emailing content
		timer=`mktemp $pathy/timer.XXXXXX` || exit 1
		chmod 600 $timer
		
		# Tempfile for the script
		shell=`mktemp $pathy/shell.XXXXXX` || exit 1
		chmod 700 $shell
		
		# Create email body: path, filename, and start time
		starter=`date`
		echo "$PWD/$1 finished" >> $timer
		echo "$starter S"       >> $timer

		# Create script; add end time to email subject
		echo "#!/bin/sh"                                                                           >> $shell
		echo "time -p R CMD BATCH $1 "                                                             >> $shell
		echo "date >> $timer"                                                                      >> $shell
		echo "mutt -s \"$1 finished\" -a $output nohup.out -- $USER@duke.edu < $timer"             >> $shell
		nohup $shell &
		
		# Nohup takes a split second longer than other commands
		sleep 0.01s
	fi
fi