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InterProScan JMS Implementation Module
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<?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-4.2.xsd">
<import resource="../persistence/persistence-config-context.xml"/>
<!-- ######################## JOB: Gene 3D ############################ -->
<bean id="jobGene3d" class="uk.ac.ebi.interpro.scan.management.model.Job">
<property name="description"
value="Structural assignment for whole genes and genomes using the CATH domain structure database"/>
<property name="analysis" value="true"/>
<property name="active" value="true"/>
<property name="libraryRelease" ref="signatureLibraryReleaseGene3d"/>
</bean>
<bean id="abstractGene3dStep" abstract="true" class="uk.ac.ebi.interpro.scan.management.model.Step">
<property name="job" ref="jobGene3d"/>
<property name="maxProteins" value="${analysis.max.sequence.count.GENE3D}"/>
<property name="createStepInstancesForNewProteins" value="true"/>
<property name="retries" value="0"/>
<property name="nfsDelayMilliseconds" value="${nfs.delay.milliseconds}"/>
</bean>
<bean id="stepGene3dWriteFasta"
class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
parent="abstractGene3dStep">
<property name="stepDescription" value="Create FASTA file."/>
<property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
<property name="proteinDAO" ref="proteinDAO"/>
</bean>
<bean id="stepGene3dRunHmmer3"
class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer.RunHmmerBinaryStep"
parent="abstractGene3dStep">
<property name="dependsUpon" ref="stepGene3dWriteFasta"/>
<property name="stepDescription" value="Run HMMER3"/>
<property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
<property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
<property name="binarySwitches"
value="${hmmer3.hmmsearch.switches.gene3d} ${hmmer3.hmmsearch.cpu.switch.gene3d}"/>
<property name="fullPathToHmmFile" value="${gene3d.hmm.path}"/>
<property name="usesFileOutputSwitch" value="true"/>
<property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
<property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
<property name="useDomTbloutFormat" value="true"/>
<property name="outputFileNameDomTbloutTemplate" ref="rawAnalaysisOutputDomTbloutFileTemplate"/>
<property name="retries" value="3"/>
<property name="requiresDatabaseAccess" value="false"/>
<property name="forceHmmsearch" value="${gene3d.hmmsearch.force}"/>
</bean>
<bean id="stepRunCathResolveHitsStep"
class="uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.RunCathResolveHitsBinaryStep"
parent="abstractGene3dStep">
<property name="dependsUpon" ref="stepGene3dRunHmmer3"/>
<property name="stepDescription" value="Run CathResolveHits"/>
<property name="forceHmmsearch" value="${gene3d.hmmsearch.force}"/>
<property name="crhInputFileTemplate" ref="rawAnalaysisOutputFileTemplate"/>
<property name="fullPathToBinary" value="${cath.resolve.hits.path}"/>
<property name="binarySwitches" value="${cath.resolve.hits.switches.gene3d}"/>
<property name="crhOutputFileTemplate" ref="rawAnalaysisOutputOneFileTemplate"/>
<property name="requiresDatabaseAccess" value="false"/>
</bean>
<bean id="stepRunAssignCathFamiliesStep"
class="uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.RunAssignCathFamilyBinaryStep"
parent="abstractGene3dStep">
<property name="dependsUpon" ref="stepRunCathResolveHitsStep"/>
<property name="stepDescription" value="Run AssignCathFamilyStep"/>
<property name="forceHmmsearch" value="${gene3d.hmmsearch.force}"/>
<property name="inputFileTemplate" ref="rawAnalaysisOutputOneFileTemplate"/>
<property name="domainToFamilyMapFile" value="${gene3d.model2sf_map.path}"/>
<property name="discontinuousRegionsFile" value="${gene3d.discontinuous_regs.path}"/>
<property name="fullPathToPython" value="${python3.command}"/>
<property name="fullPathToBinary" value="${assign.cath.superfamilies.path}"/>
<property name="binarySwitches" value="${assign.cath.superfamilies.switches.gene3d}"/>
<property name="outputFileTemplate" ref="rawAnalaysisOutputTwoFileTemplate"/>
<property name="requiresDatabaseAccess" value="false"/>
</bean>
<bean id="stepGene3dParseOutputs"
class="uk.ac.ebi.interpro.scan.management.model.implementations.gene3d.Gene3DParseAndPersistOutputStep"
parent="abstractGene3dStep">
<property name="dependsUpon" >
<list>
<!--<ref bean="stepGene3dRunHmmer3"/>-->
<ref bean="stepRunAssignCathFamiliesStep"/>
</list>
</property>
<property name="stepDescription" value="Parse output from HMMER3 and CathResolveHits"/>
<property name="forceHmmsearch" value="${gene3d.hmmsearch.force}"/>
<property name="cathResolveHitsOutputFileNameTemplate" ref="rawAnalaysisOutputTwoFileTemplate"/>
<property name="outputFileNameDomTbloutTemplate" ref="rawAnalaysisOutputDomTbloutFileTemplate"/>
<property name="serialGroup" value="PARSE_GENE3D"/>
<property name="rawMatchDAO" ref="gene3dRawMatchDAO"/>
<property name="filteredMatchDAO">
<bean class="uk.ac.ebi.interpro.scan.persistence.Gene3dHmmer3FilteredMatchDAO"/>
</property>
<property name="hmmer3DomTblParser">
<bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3DomTblParser"/>
</property>
<property name="cathResolveHitsOutputParser">
<bean class="uk.ac.ebi.interpro.scan.io.gene3d.CathResolveHitsOutputParser"/>
</property>
<property name="signatureLibraryRelease" ref="latestGene3dSignatureLibraryRelease"/>
<property name="gene3dEvalueCutoff" value="${gene3d.evalue.cutoff}"/>
<!--<property name="parser">-->
<!--<bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3DomTblParser">-->
<!--<property name="parserSupport">-->
<!--<bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport">-->
<!--<!–TODO: We need to pass in or look up release number–>-->
<!--<property name="signatureLibraryRelease" ref="latestGene3dSignatureLibraryRelease"/>-->
<!--<property name="alignmentEncoder">-->
<!--<bean class="uk.ac.ebi.interpro.scan.model.raw.alignment.CigarAlignmentEncoder"/>-->
<!--</property>-->
<!--<property name="hmmKey" value="NAME"/>-->
<!--</bean>-->
<!--</property>-->
<!--</bean>-->
<!--</property>-->
<property name="retries" value="3"/>
</bean>
<bean id="stepGene3dRelatedTmpFiles"
class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
parent="abstractGene3dStep">
<property name="dependsUpon" ref="stepGene3dParseOutputs"/>
<property name="stepDescription" value="Delete output piped from SSF after post-processing has run"/>
<property name="fileNameTemplate">
<list>
<ref bean="fastaFileNameTemplate"/>
<ref bean="rawAnalaysisOutputFileTemplate"/>
<ref bean="rawAnalaysisOutputOneFileTemplate"/>
</list>
</property>
<property name="deleteWorkingDirectoryOnCompletion" value="false"/>
</bean>
<!-- ######################## Dependencies ############################ -->
<bean id="gene3dRawMatchDAO" class="uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl">
<constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.Gene3dHmmer3RawMatch"/>
</bean>
<bean id="signatureLibraryReleaseGene3d" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
<constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="GENE3D"/>
<constructor-arg type="java.lang.String" ref="latestGene3dSignatureLibraryRelease"/>
</bean>
<bean id="latestGene3dSignatureLibraryRelease" class="java.lang.String">
<constructor-arg value="${gene3d.signature.library.release}"/>
</bean>
<!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
</beans>
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