diff --git a/batchmapper.sh b/batchmapper.sh
index ad177fdf7..e4fab9d7e 100755
--- a/batchmapper.sh
+++ b/batchmapper.sh
@@ -1,2 +1,6 @@
 #!/bin/sh
-java -jar dist/bridgedb-batchmapper.jar "$@"
+
+# change to directory of this script
+cd $(dirname $0)
+
+java -jar dist/org.bridgedb.tools.batchmapper.jar "$@"
diff --git a/org.bridgedb.tools.batchmapper/build.xml b/org.bridgedb.tools.batchmapper/build.xml
index 0fb0c411d..d7ba2a44d 100644
--- a/org.bridgedb.tools.batchmapper/build.xml
+++ b/org.bridgedb.tools.batchmapper/build.xml
@@ -34,8 +34,8 @@
 	<target name="jar" depends="compile">
 		<jar jarfile="${jar.file}">
 			<manifest>
-				<attribute name="Main-Class" value="org.bridgedb.tools.BatchMapper"/>
-				<attribute name="Class-Path" value="bridgedb.jar bridgedb-bio.jar"/>
+				<attribute name="Main-Class" value="org.bridgedb.tools.batchmapper.BatchMapper"/>
+				<attribute name="Class-Path" value="org.bridgedb.jar org.bridgedb.bio.jar org.bridgedb.rdb.jar"/>
 			</manifest>
 			<fileset dir="build" includes="**/*.class"/>
 		</jar>
diff --git a/start-server.sh b/start-server.sh
index 8df1f86db..8a65b25b8 100755
--- a/start-server.sh
+++ b/start-server.sh
@@ -1,3 +1,6 @@
 #!/bin/sh
 
+# change to directory of this script
+cd $(dirname $0)
+
 java -jar dist/org.bridgedb.server.jar "$@"