# configure.ac
AC_INIT([helloprog],[1.0],[abc@xyz.com])

AM_INIT_AUTOMAKE

MYVAR="1234abc"
AC_SUBST(MYVAR)
AC_CONFIG_FILES([Makefile])
AC_CONFIG_FILES([myscript.pl])
AC_OUTPUT

##</code><code>##

# Makefile.am
bin_SCRIPTS = myscript.pl

##</code><code>##

# myscript.pl.in
# all @MYVAR@ will be substituted by value in configure.ac file
my $var = "@MYVAR@";
print "var is : $var\n";