spring.jobs.jobSFLD-context.xml Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of jms-implementation Show documentation
Show all versions of jms-implementation Show documentation
InterProScan JMS Implementation Module
The newest version!
<?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: SFLD ############################ -->
<bean id="jobSFLD" class="uk.ac.ebi.interpro.scan.management.model.Job">
<property name="description" value="SFLDs are protein families based on Hidden Markov Models or HMMs"/>
<property name="analysis" value="true"/>
<property name="doRunLocally" value="true"/>
<property name="libraryRelease" ref="signatureLibraryReleaseSFLD"/>
</bean>
<bean id="abstractSFLDStep" abstract="true" class="uk.ac.ebi.interpro.scan.management.model.Step">
<property name="job" ref="jobSFLD"/>
<property name="maxProteins" value="${analysis.max.sequence.count.SFLD}"/>
<property name="createStepInstancesForNewProteins" value="true"/>
<property name="retries" value="0"/>
<property name="nfsDelayMilliseconds" value="${nfs.delay.milliseconds}"/>
</bean>
<!-- STEP 1 -->
<bean id="stepSFLDWriteFastaFile"
class="uk.ac.ebi.interpro.scan.management.model.implementations.WriteFastaFileStep"
parent="abstractSFLDStep">
<!-- This step has no dependencies, so will be scheduled first for its associated job. -->
<property name="stepDescription" value="Create fasta file."/>
<property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
<property name="proteinDAO" ref="proteinDAO"/>
</bean>
<!--TODO - The run binary step for HMMER should choose between search or scan, depending
TODO - upon the number of proteins being searched. True for both HMMER2 & 3.
TODO - PROBLEM - HMMER2 hmmsearch ONLY ACCEPTS ONE MODEL AT A TIME. -->
<!-- STEP 2 -->
<bean id="stepSFLDRunHmmer3"
class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer.RunHmmerBinaryStep"
parent="abstractSFLDStep">
<!-- In example command line below, replace _ with -
/ebi/production/interpro/binaries/64_bit_Linux/HMMER3.1b1/hmmsearch -Z 4023 _-cut_tc /ebi/production/interpro/data/members/SFLD/15.0/SFLDs_15.0_HMM.LIB -->
<property name="dependsUpon" ref="stepSFLDWriteFastaFile"/>
<property name="stepDescription" value="Run hmmer3 Binary for selected proteins"/>
<property name="forceHmmsearch" value="${sfld.hmmsearch.force}"/>
<property name="fullPathToHmmsearchBinary" value="${binary.hmmer3.hmmsearch.path}"/>
<property name="fullPathToHmmScanBinary" value="${binary.hmmer3.hmmscan.path}"/>
<property name="binarySwitches" value="${hmmer3.hmmsearch.switches.sfld} ${hmmer3.hmmsearch.cpu.switch.sfld}"/>
<property name="fullPathToHmmFile" value="${sfld.hmm.path}"/>
<property name="fastaFileNameTemplate" ref="fastaFileNameTemplate"/>
<property name="usesFileOutputSwitch" value="true"/>
<property name="outputFileNameTemplate" ref="rawAnalaysisOutputFileTemplate"/>
<property name="useTbloutFormat" value="false"/>
<property name="useDomTbloutFormat" value="true"/>
<property name="outputFileNameDomTbloutTemplate" ref="rawAnalaysisOutputDomTbloutFileTemplate"/>
<property name="outputAlignments" value="true"/>
<property name="outputFileNameAlignmentsTemplate" ref="rawAnalaysisOutputAlignmentsFileTemplate"/>
<property name="retries" value="3"/>
<property name="requiresDatabaseAccess" value="false"/>
</bean>
<!-- STEP 3 -->
<bean id="stepSFLDPostProcessorBinaryRun"
class="uk.ac.ebi.interpro.scan.management.model.implementations.sfld.RunSFLDBinaryStep"
parent="abstractSFLDStep">
<property name="dependsUpon" ref="stepSFLDRunHmmer3"/>
<property name="stepDescription" value="Run sfld postprocessing binary for selected proteins"/>
<property name="requiresDatabaseAccess" value="false"/>
<property name="outputFileNameTemplate" ref="rawAnalaysisOutputOneFileTemplate"/>
<property name="fullPathToBinary" value="${sfld.postprocess.command}"/>
<property name="usesFileOutputSwitch" value="true" />
<property name="inputFileNameRawOutTemplate" ref="rawAnalaysisOutputFileTemplate"/>
<property name="inputFileNameDomTbloutTemplate" ref="rawAnalaysisOutputDomTbloutFileTemplate"/>
<property name="inputFileNameAlignmentsTemplate" ref="rawAnalaysisOutputAlignmentsFileTemplate"/>
<property name="sitesAnnotationFileName" value="${sfld.sites.annotation.file.path}"/>
</bean>
<bean id="stepSFLDStoreRawMatches"
class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.SFLDHmmer3ParseStep"
parent="abstractSFLDStep">
<property name="dependsUpon" ref="stepSFLDPostProcessorBinaryRun"/>
<property name="stepDescription" value="Parse the SFLD binary output and store as Filtered matches."/>
<property name="serialGroup" value="PARSE_SFLD"/>
<property name="parser">
<bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.SFLDHmmer3MatchParser">
<constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="SFLD"/>
<constructor-arg type="java.lang.String" ref="sfldSignatureLibraryReleaseVersion"/>
<property name="parserSupport">
<bean class="uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.SFLDHmmer3ParserSupport">
<property name="signatureLibraryRelease" ref="sfldSignatureLibraryReleaseVersion"/>
<property name="hmmKey" value="ACCESSION"/>
</bean>
</property>
<property name="sfldHierarchyFilePath" value="${sfld.hierarchy.file.path}"/>
</bean>
</property>
<property name="outputFileTemplate" ref="rawAnalaysisOutputOneFileTemplate"/>
<property name="excludeSites" value="${exclude.sites.from.output}"/>
<property name="rawMatchDAO" ref="sfldRawMatchDAO"/>
<property name="rawSiteDAO" ref="sfldRawSiteDAO"/>
</bean>
<bean id="stepSFLDDeleteJobFiles"
class="uk.ac.ebi.interpro.scan.management.model.implementations.DeleteFileStep"
parent="abstractSFLDStep">
<property name="dependsUpon" ref="stepSFLDStoreRawMatches"/>
<property name="stepDescription"
value="Delete the fasta file and the raw output file following successful parsing and persistence"/>
<property name="fileNameTemplate">
<list>
<ref bean="fastaFileNameTemplate"/>
<ref bean="rawAnalaysisOutputFileTemplate"/>
</list>
</property>
<property name="deleteWorkingDirectoryOnCompletion" value="${delete.temporary.directory.on.completion}"/>
</bean>
<bean id="stepSFLDPostProcessing"
class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.SFLDHmmer3FilterStep"
parent="abstractSFLDStep">
<property name="dependsUpon" ref="stepSFLDStoreRawMatches"/>
<property name="serialGroup" value="HMMER3_POST_PROCESSING"/>
<property name="stepDescription" value="Store raw SFLD matches as filtered matches"/>
<property name="signatureLibraryRelease" ref="sfldSignatureLibraryReleaseVersion"/>
<!--<property name="postProcessor"/> No post processing required-->
<property name="filteredMatchAndSiteDAO">
<bean class="uk.ac.ebi.interpro.scan.persistence.SFLDHmmer3FilteredMatchDAOImpl"/>
</property>
<property name="excludeSites" value="${exclude.sites.from.output}"/>
<property name="rawMatchDAO" ref="sfldRawMatchDAO"/>
<property name="rawSiteDAO" ref="sfldRawSiteDAO"/>
</bean>
<!--<!– TODO - Check for changes - presumably now using different objects to store the results? –>-->
<!--<bean id="stepSFLDPostProcessing"-->
<!--class="uk.ac.ebi.interpro.scan.management.model.implementations.hmmer3.SFLDHmmer3FilterStep"-->
<!--parent="abstractSFLDStep">-->
<!--<property name="dependsUpon" ref="stepSFLDStoreRawMatches"/>-->
<!--<property name="signatureLibraryRelease" ref="sfldSignatureLibraryReleaseVersion"/>-->
<!--<property name="stepDescription" value="Stores raw matches as filtered matches."/>-->
<!--<property name="filteredMatchDAO">-->
<!--<bean class="uk.ac.ebi.interpro.scan.persistence.SFLDHmmer3FilteredMatchDAOImpl"/>-->
<!--</property>-->
<!--<property name="serialGroup" value="HMMER3_POST_PROCESSING"/>-->
<!--<property name="rawMatchDAO" ref="sfldRawMatchDAO"/>-->
<!--<property name="signatureLibrary" value="SFLD"/>-->
<!--<property name="filter">-->
<!--<bean class="uk.ac.ebi.interpro.scan.business.filter.AllPassRawMatchFilter"/>-->
<!--</property>-->
<!--</bean>-->
<!-- !!!!!!!!!!!!!!!!!!!!! JOB-END: SFLD !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
<!-- ######################## Dependencies ############################ -->
<bean id="sfldRawMatchDAO"
class="uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl">
<constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.SFLDHmmer3RawMatch"/>
</bean>
<bean id="sfldRawSiteDAO" class="uk.ac.ebi.interpro.scan.persistence.raw.RawSiteDAOImpl">
<constructor-arg value="uk.ac.ebi.interpro.scan.model.raw.SFLDHmmer3RawSite"/>
</bean>
<bean id="signatureLibraryReleaseSFLD" class="uk.ac.ebi.interpro.scan.model.SignatureLibraryRelease">
<constructor-arg type="uk.ac.ebi.interpro.scan.model.SignatureLibrary" value="SFLD"/>
<constructor-arg type="java.lang.String" ref="sfldSignatureLibraryReleaseVersion"/>
</bean>
<bean id="sfldSignatureLibraryReleaseVersion" class="java.lang.String">
<constructor-arg value="${sfld.signature.library.release}"/>
</bean>
<!-- !!!!!!!!!!!!!!!!!!!!! Dependencies-END !!!!!!!!!!!!!!!!!!!!!!!!!!!! -->
</beans>
© 2015 - 2025 Weber Informatics LLC | Privacy Policy