pipelineConfig.xml

<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       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="configProperties">
            <bean class="org.labkey.pipeline.api.properties.ConfigPropertiesImpl">
                <property name="softwarePackages">
                    <map>
                        <!--If the sequence tools are not in the standard pipeline tools dir, this is required.
                            These are the external binaries installed by sequence_tools_install.sh-->
                        <entry key="SEQUENCEANALYSIS_TOOLS" value="@@SEQUENCEANALYSIS_TOOLS@@"/>
                    </map>
                </property>
            </bean>
        </property>
    </bean>	
</beans>