$NetBSD: patch-ai,v 1.1.1.1 2004/11/19 19:27:31 daprice Exp $

--- jemboss/runJemboss.sh.orig	2004-02-13 02:30:25.000000000 -0700
+++ jemboss/runJemboss.sh	2004-07-28 14:53:34.000000000 -0600
@@ -7,6 +7,13 @@
 LIB=$JEMBOSS_HOME/lib
 export LIB
 
+EMBOSS_INSTALL=@PREFIX@/share/EMBOSS/jemboss
+export EMBOSS_INSTALL
+
+LD_LIBRARY_PATH=@PREFIX@/lib
+export LD_LIBRARY_PATH
+
+CLASSPATH=:@JAVA_CLASSPATH@:
 CLASSPATH=${JEMBOSS_HOME}:$LIB/JembossPrintAlignment.jar:
 CLASSPATH=${CLASSPATH}:$LIB/jakarta-regexp-1.2.jar:
 CLASSPATH=${CLASSPATH}:$LIB/jalview.jar:
@@ -48,4 +55,4 @@
 #Add local to run as 'standalone':
 #java org.emboss.jemboss.Jemboss local &
 #
-java org.emboss.jemboss.Jemboss &
+@JAVA@/java org.emboss.jemboss.Jemboss local &