#!/bin/csh -f

#
# This shell script can run several commands,
# given two sequence files (DNA or protein) as input
#

# The -f option tells the script to ignore your .cshrc file

# Check to make sure you get two arguments (sequence files)

if ($#argv != 2) then
	echo "Usage: $0 seq1 seq2"; exit 1
endif

# turn the arguments into better names
set seq1=$1
set seq2=$2

# check to make sure each sequence file really exists

if (! -e $seq1) then
	echo $seq1 doesn't appear to exist; exit 1
endif
if (! -e $seq2) then
	echo $seq2 doesn't appear to exist; exit 1
endif

####################  real commands start here  #######################

# Place command for global alignment ("needle") under here



# Place command for local alignment ("water") under here




echo All done!