diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
index 2e3e84e2c..e9b0df727 100644
--- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
+++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java
@@ -204,6 +204,11 @@ private void setPath(ProcessBuilder pb)
         if (!StringUtils.isEmpty(toolDir))
         {
             String path = System.getenv("PATH");
+
+            getLogger().debug("Existing PATH: " + path);
+            getLogger().debug("toolDir: " + toolDir);
+
+
             if (path == null)
             {
                 path = toolDir;
diff --git a/SequenceAnalysis/test/configs/pipelineConfig.xml b/SequenceAnalysis/test/configs/pipelineConfig.xml
index febf454b1..4279c2acb 100644
--- a/SequenceAnalysis/test/configs/pipelineConfig.xml
+++ b/SequenceAnalysis/test/configs/pipelineConfig.xml
@@ -4,6 +4,11 @@
        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">