diff --git a/SequenceAnalysis/test/configs/pipelineConfig.xml b/SequenceAnalysis/test/configs/pipelineConfig.xml
index 4279c2acb..febf454b1 100644
--- a/SequenceAnalysis/test/configs/pipelineConfig.xml
+++ b/SequenceAnalysis/test/configs/pipelineConfig.xml
@@ -4,11 +4,6 @@
        xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd">
 
     <bean id="pipelineJobService" class="org.labkey.pipeline.api.PipelineJobServiceImpl">
-        <property name="appProperties">
-            <bean class="org.labkey.pipeline.api.properties.ApplicationPropertiesImpl">
-                <property name="toolsDirectory" value="@@SEQUENCEANALYSIS_TOOLS@@" />
-            </bean>
-        </property>
         <property name="configProperties">
             <bean class="org.labkey.pipeline.api.properties.ConfigPropertiesImpl">
                 <property name="softwarePackages">