--- runpsipred	2008-04-05 00:14:36.000000000 +0200
+++ runpsipred.new	2009-04-09 12:40:46.376203036 +0200
@@ -14,13 +14,13 @@
 set dbname = nr
 
 # Where the NCBI programs have been installed
-set ncbidir = /usr/local/bin
+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
 
 # Where the PSIPRED V2 programs have been installed
-set execdir = ./bin
+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
 
 # Where the PSIPRED V2 data files have been installed
-set datadir = ./data
+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
 
 set basename = $1:r
 set rootname = $basename:t
--- runpsipred_single	2008-04-05 00:14:38.000000000 +0200
+++ runpsipred_single.new	2009-04-09 12:41:10.086067082 +0200
@@ -10,10 +10,10 @@
 # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
 
 # Where the PSIPRED V2 programs have been installed
-set execdir = ./bin
+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
 
 # Where the PSIPRED V2 data files have been installed
-set datadir = ./data
+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
 
 set basename = $1:r
 set rootname = $basename:t