--- scripts/phredPhrap.orig	2007-09-26 04:02:20.000000000 +0900
+++ scripts/phredPhrap	2007-12-11 17:32:27.000000000 +0900
@@ -101,7 +101,7 @@
 
 
 # change this to reflect wherever you put the phredpar.dat file
-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
+$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
 #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
 #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
 
@@ -207,7 +207,7 @@
 $chromatDirPath = "../chromat_dir";
 $phdDirPath = "../phd_dir";
 
-$niceExe = "/bin/nice";
+$niceExe = "/usr/bin/nice";
 $mvExe = "/bin/mv";
 $lsExe = "/bin/ls";
 $pwdExe = "/bin/pwd";
@@ -568,11 +568,11 @@
 
 # only uncomment the following 4 lines when you have customized 
 # determineReadTypes.perl
-#print "\n\n--------------------------------------------------------\n";
-#print "Now running determineReadTypes.perl...\n";
-#print "--------------------------------------------------------\n\n\n";
+print "\n\n--------------------------------------------------------\n";
+print "Now running determineReadTypes.perl...\n";
+print "--------------------------------------------------------\n\n\n";
 
-#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
+!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
 
 
 print "\n\n--------------------------------------------------------\n";
