diff --git a/build.gradle b/build.gradle
index c303ed1fad..159f5c3178 100755
--- a/build.gradle
+++ b/build.gradle
@@ -219,122 +219,6 @@ def translateVariableSet = [
         'WEBHOST_FASTA_FILE_PATH',
 ]
 
-//These are the only files that need to be searched and replaced (<!--|KEY|-->)
-//Let's whittle this list down over time
-//Other
-
-def whitelistTemplateFiles = [
-    'cgi-bin/send_request.perl',
-    'cgi-bin/merge_markers.pl',
-    'server_apps/DB_maintenance/backupBlastDbsAndRsyncAlmostBlastDbs.sh',
-    'server_apps/DB_maintenance/checkVarcharOctetLength.pl',
-    'server_apps/DB_maintenance/check_undefined_environment.pl',
-    'server_apps/DB_maintenance/disable_updates.pl',
-    'server_apps/DB_maintenance/extentMonitoring/dailyExtentCheck.sh',
-    'server_apps/DB_maintenance/fx_permission_check.pl',
-    'server_apps/DB_maintenance/loadExternalNotes.pl',
-    'server_apps/DB_maintenance/loadExternalNotes.sql',
-    'server_apps/DB_maintenance/loadUp/README_loadUp',
-    'server_apps/DB_maintenance/loadUp/rsync.pl',
-    'server_apps/DB_maintenance/orphanChecks.pl',
-    'server_apps/DB_maintenance/postgres/compareTables.groovy',
-    'server_apps/DB_maintenance/pushDataToPublic.sh',
-    'server_apps/DB_maintenance/queryMonitoring/dailyQueryCostCheck.sh',
-    'server_apps/DB_maintenance/rotateInformixLog.sh',
-    'server_apps/DB_maintenance/set_unload_timestamp.sql',
-    'server_apps/DB_maintenance/warehouse/chromosomeMartPostgres/runChromosomeMart.sh',
-    'server_apps/DB_maintenance/warehouse/expressionMart/runExpressionMart.sh',
-    'server_apps/DB_maintenance/warehouse/phenotypeMart/runPhenotypeMart.sh',
-    'server_apps/DB_maintenance/warehouse/regenChromosomeMart.sh',
-    'server_apps/DB_maintenance/warehouse/regenExpressionMart.sh',
-    'server_apps/DB_maintenance/warehouse/regenPhenotypeMart.sh',
-    'server_apps/DB_maintenance/warehouse/switch.sh',
-    'server_apps/DB_maintenance/warehouse/who_is.sh',
-    'server_apps/DB_maintenance/warehouse/who_is_not.sh',
-    'server_apps/Reports/AnnualStats/runStats.sh',
-    'server_apps/Reports/BetterFish/betterFish.sql',
-    'server_apps/Reports/PubTracking/runAverageTimeInBinsCumulative.sh',
-    'server_apps/Reports/PubTracking/runLongestBinResidents.sh',
-    'server_apps/Reports/PubTracking/runMonthlyBinLengthReport.sh',
-    'server_apps/Reports/PubTracking/runPaperlessPubTrackingDailyIndexedMetrics.sh',
-    'server_apps/Reports/elsevier_report.pl',
-    'server_apps/Reports/reportPubsForGeneAndFeature.pl',
-    'server_apps/WebSiteTools/gen-jobs-rss.r',
-    'server_apps/WebSiteTools/gen-meetings-rss.r',
-    'server_apps/WebSiteTools/gen-news-rss.r',
-    'server_apps/WebSiteTools/signsoflife.sh',
-    'server_apps/apache/inc-redirect',
-    'server_apps/cron/crontab.production',
-    'server_apps/data_transfer/Downloads/GFF3/E_unload_ensembl_contig.sql',
-    'server_apps/data_transfer/Downloads/generateStagedAnatomy.pl',
-    'server_apps/data_transfer/Ensembl/fetch_ensdarT_dbacc.sh',
-    'server_apps/data_transfer/Ensembl/fetch_ensdarg.sh',
-    'server_apps/data_transfer/Ensembl/fetch_ensdargOttdargTable.sh',
-    'server_apps/data_transfer/Ensembl/fetch_ensembl_agp.sh',
-    'server_apps/data_transfer/Ensembl/fetch_sangerMutantInfo.sh',
-    'server_apps/data_transfer/Ensembl/notifyStaleIds.sh',
-    'server_apps/data_transfer/Ensembl/pullFromBioMart.pl',
-    'server_apps/data_transfer/Ensembl/reportEnsembleStatistics.sh',
-    'server_apps/data_transfer/ExternalSearch/CreateMarkerSearchPage.pl',
-    'server_apps/data_transfer/ExternalSearch/CreateMarkerSearchPage.sql',
-    'server_apps/data_transfer/GO/go.pl',
-    'server_apps/data_transfer/GO/gofile.sql',
-    'server_apps/data_transfer/GO/gofile2.sql',
-    'server_apps/data_transfer/GO/gofile2_all.sql',
-    'server_apps/data_transfer/GO/gp2protein.pl',
-    'server_apps/data_transfer/GO/gpad.pl',
-    'server_apps/data_transfer/GO/gpad2.0.sql',
-    'server_apps/data_transfer/GO/validateUniprotIDsZFIN.pl',
-    'server_apps/data_transfer/Genbank/gbaccession.pl',
-    'server_apps/data_transfer/Load/ReNo/Nomenclature/generate_special_Sanger_uniprot_nomenclature_run.sh',
-    'server_apps/data_transfer/Load/ReNo/load_run_report_hit.sh',
-    'server_apps/data_transfer/Load/blast_withdrawn.pl',
-    'server_apps/data_transfer/LoadOntology/parseHeader.pl',
-    'server_apps/data_transfer/LoadOntology/parseObo.pl',
-    'server_apps/data_transfer/MEOW/meow.pl',
-    'server_apps/data_transfer/NCBIStartEnd/NCBIStartEnd.pl',
-    'server_apps/data_transfer/OMIM/OMIM.pl',
-    'server_apps/data_transfer/OMIM/loadOMIM.sql',
-    'server_apps/data_transfer/ORTHO/downloadFiles.pl',
-    'server_apps/data_transfer/ORTHO/emailOrthologyReports.pl',
-    'server_apps/data_transfer/ORTHO/loadAndUpdateNCBIOrthologs.sql',
-    'server_apps/data_transfer/ORTHO/loadHumanSynonyms.sql',
-    'server_apps/data_transfer/ORTHO/parseHumanData.pl',
-    'server_apps/data_transfer/ORTHO/parseOrthoFile.pl',
-    'server_apps/data_transfer/ORTHO/reportOrthoNameChanges.pl',
-    'server_apps/data_transfer/ORTHO/runOrthology.pl',
-    'server_apps/data_transfer/ORTHO/updateZebrafishGeneNames.pl',
-    'server_apps/data_transfer/ORTHO/updateZebrafishGeneNames.sql',
-    'server_apps/data_transfer/PUBMED/Journal/checkAndUpdateJournals.sql',
-    'server_apps/data_transfer/PUBMED/Journal/insertJournalAlias.sql',
-    'server_apps/data_transfer/PUBMED/addMeshTermsToAllPubs.groovy',
-    'server_apps/data_transfer/PUBMED/addPMCidsToAllPubs.groovy',
-    'server_apps/data_transfer/PUBMED/loadNewPubs.sql',
-    'server_apps/data_transfer/PUBMED/load_complete_author_names.sql',
-    'server_apps/data_transfer/PUBMED/pubActivation.groovy',
-    'server_apps/data_transfer/PUBMED/updatePublicationDate.groovy',
-    'server_apps/data_transfer/RNACentral/loadTranscriptSequences.sql',
-    'server_apps/data_transfer/RNACentral/loadTscriptSeq.pl',
-    'server_apps/data_transfer/RNACentral/preLoadTranscriptSequence.sql',
-    'server_apps/data_transfer/RNACentral/runTscriptSequenceLoad.pl',
-    'server_apps/data_transfer/ResourceCenters/pullFromEZRC.pl',
-    'server_apps/data_transfer/ResourceCenters/pullFromZIRC.pl',
-    'server_apps/data_transfer/ResourceCenters/pushToZirc.pl',
-    'server_apps/data_transfer/ResourceCenters/pushToZirc.sql',
-    'server_apps/data_transfer/SNP/addNewClonesJSmith.pl',
-    'server_apps/data_transfer/SNP/addTalbotSNPAttr.sql',
-    'server_apps/data_transfer/SNP/dbSNP.pl',
-    'server_apps/data_transfer/SNP/loadNewSNPAttrs.sql',
-    'server_apps/data_transfer/SNP/loadNewSNPs.sql',
-    'server_apps/data_transfer/eco_go_mapping/insert_eco_go_map.sql',
-    'server_apps/data_transfer/maintainTermDisplay/checkRNAConsequenceTerm.groovy',
-    'server_apps/data_transfer/zfishbook/preprocess_zfishbook.pl',
-    'server_apps/data_transfer/zfishbook/zfishbook.pl',
-    'server_apps/data_transfer/zfishbook/zfishbook.sh',
-]
-
-project.ext.set("whitelistTemplateFiles", whitelistTemplateFiles)
-
 // load properties into gradle
 task setup {
     project.ext.ttNameMap = new Properties()
@@ -855,77 +739,91 @@ test {
     testLogging {
         //showStandardStreams = true
     }
+
+    def includeSmokeTests = project.hasProperty('smokeTests')
+    def includeNonSmokeTests = project.hasProperty('nonSmokeTests')
+    if (!includeSmokeTests && !includeNonSmokeTests) {
+        //if neither flag is set, run all tests
+        includeSmokeTests = true
+        includeNonSmokeTests = true
+    }
+
     filter {
-        includeTestsMatching "org.zfin.UnitTests"
-        //spock tests
 
-        includeTestsMatching "org.zfin.publication.MeshHeadingSpec"
+        if (includeNonSmokeTests) {
+            includeTestsMatching "org.zfin.UnitTests"
+            //spock tests
 
-        includeTestsMatching "org.zfin.publication.presentation.PublicationValidatorSpec"
-        includeTestsMatching "org.zfin.publication.repository.PublicationRepositorySpec"
-        includeTestsMatching "org.zfin.feature.service.MutationDetailsConversionServiceSpec"
-        includeTestsMatching "org.zfin.util.ReportGeneratorSpec"
-        includeTestsMatching "org.zfin.search.service.SolrServiceSpec"
-        includeTestsMatching "org.zfin.search.service.SolrQueryFacadeSpec"
-        includeTestsMatching "org.zfin.search.service.MarkerSearchServiceSpec"
-        includeTestsMatching "org.zfin.search.service.SearchSuggestionServiceSpec"
+            includeTestsMatching "org.zfin.publication.MeshHeadingSpec"
 
-        includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"
-        includeTestsMatching "org.zfin.uniquery.RelatedLinksSpec"
+            includeTestsMatching "org.zfin.publication.presentation.PublicationValidatorSpec"
+            includeTestsMatching "org.zfin.publication.repository.PublicationRepositorySpec"
+            includeTestsMatching "org.zfin.feature.service.MutationDetailsConversionServiceSpec"
+            includeTestsMatching "org.zfin.util.ReportGeneratorSpec"
+            includeTestsMatching "org.zfin.search.service.SolrServiceSpec"
+            includeTestsMatching "org.zfin.search.service.SolrQueryFacadeSpec"
+            includeTestsMatching "org.zfin.search.service.MarkerSearchServiceSpec"
+            includeTestsMatching "org.zfin.search.service.SearchSuggestionServiceSpec"
+
+            includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"
+            includeTestsMatching "org.zfin.uniquery.RelatedLinksSpec"
 
 //      Failing tests that we may want to bring back: (ZFIN-8271)
 //        includeTestsMatching "org.zfin.uniquery.CategoriesAndFacetsSpec"
 //        includeTestsMatching "org.zfin.uniquery.QuerySpec"
 //        includeTestsMatching "org.zfin.uniquery.ResultAttributesSpec"
-        
-        includeTestsMatching "org.zfin.sequence.repository.SequenceRepositorySpec"
-        includeTestsMatching "org.zfin.feature.FeatureServiceSpec"
-        includeTestsMatching "org.zfin.curation.service.CurationDTOConversionServiceSpec"
-        includeTestsMatching "org.zfin.expression.ExpressionSearchSpec"
-        includeTestsMatching "org.zfin.marker.presentation.GeneAddFormBeanValidatorSpec"
-        includeTestsMatching "org.zfin.marker.presentation.MarkerGoServiceIntegrationSpec"
-        includeTestsMatching "org.zfin.marker.presentation.SequenceTargetingReagentAddBeanValidatorSpec"
-        includeTestsMatching "org.zfin.figure.repository.FigureRepositorySpec"
-        includeTestsMatching "org.zfin.gbrowse.presentation.GBrowseImageSpec"
-        includeTestsMatching "org.zfin.figure.service.ImageServiceSpec"
-
-        /*need to figure out ..all tests fail here
+
+            includeTestsMatching "org.zfin.sequence.repository.SequenceRepositorySpec"
+            includeTestsMatching "org.zfin.feature.FeatureServiceSpec"
+            includeTestsMatching "org.zfin.curation.service.CurationDTOConversionServiceSpec"
+            includeTestsMatching "org.zfin.expression.ExpressionSearchSpec"
+            includeTestsMatching "org.zfin.marker.presentation.GeneAddFormBeanValidatorSpec"
+            includeTestsMatching "org.zfin.marker.presentation.MarkerGoServiceIntegrationSpec"
+            includeTestsMatching "org.zfin.marker.presentation.SequenceTargetingReagentAddBeanValidatorSpec"
+            includeTestsMatching "org.zfin.figure.repository.FigureRepositorySpec"
+            includeTestsMatching "org.zfin.gbrowse.presentation.GBrowseImageSpec"
+            includeTestsMatching "org.zfin.figure.service.ImageServiceSpec"
+
+            /*need to figure out ..all tests fail here
         includeTestsMatching "org.zfin.figure.service.FigureViewServiceSpec"*/
 
-        //includeTestsMatching "org.zfin.publication.PublicationServiceSpec"
-        // PublicationServiceSpec > #authorString should bring back #author FAILED
-        //org.spockframework.runtime.SpockAssertionError at UnrollIterationNameProvider.java:80
+            //includeTestsMatching "org.zfin.publication.PublicationServiceSpec"
+            // PublicationServiceSpec > #authorString should bring back #author FAILED
+            //org.spockframework.runtime.SpockAssertionError at UnrollIterationNameProvider.java:80
 
 
-        /*includeTestsMatching "org.zfin.figure.service.ImageServiceSpec" (needs fixing..null pointer here:  tempDir.newFolder(ZfinPropertiesEnum.IMAGE_LOAD.toString(), "medium"))
+            /*includeTestsMatching "org.zfin.figure.service.ImageServiceSpec" (needs fixing..null pointer here:  tempDir.newFolder(ZfinPropertiesEnum.IMAGE_LOAD.toString(), "medium"))
         includeTestsMatching "org.zfin.figure.service.VideoServiceSpec"*/
 
-        /*//following use geb..likely not to fix
+            /*//following use geb..likely not to fix
 
         includeTestsMatching "org.zfin.figure.presentation.FigureViewWebSpec" (geb test)
         includeTestsMatching "org.zfin.marker.MarkerselectWebSpec" (geb test)
         includeTestsMatching "org.zfin.framework.GroovyWebSpec"(geb test)
         includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"(geb test)*/
 
-        // db unit tests
-        includeTestsMatching "org.zfin.DbUnitTests"
-        includeTestsMatching "org.zfin.infrastructure.EnumValidationTest"
-        includeTestsMatching "org.zfin.DbControllerTests"
-        includeTestsMatching "org.zfin.ThirdPartyServiceTests"
-
-        includeTestsMatching "org.zfin.anatomy.AnatomySmokeTest"
-        includeTestsMatching "org.zfin.antibody.smoketest.AntibodySmokeTest"
-        includeTestsMatching "org.zfin.sequence.blast.smoketest.BlastSmokeTest"
-        includeTestsMatching "org.zfin.datatransfer.smoketests.DownloadSmokeTest"
-        includeTestsMatching "org.zfin.feature.presentation.FeatureDetailSmokeTest"
-        includeTestsMatching "org.zfin.feature.presentation.GenotypeDetailSmokeTest"
-        includeTestsMatching "org.zfin.expression.presentation.FigureSummarySmokeTest"
-        includeTestsMatching "org.zfin.fish.smoketest.FishSmokeTest"
-        includeTestsMatching "org.zfin.fish.smoketest.PhenotypeSummarySmokeTest"
-        includeTestsMatching "org.zfin.httpunittest.MarkerViewSmokeTest"
-        includeTestsMatching "org.zfin.sebservice.MarkerRestSmokeTest"
-        //include specific method in any of the tests
-//        includeTestsMatching "*ActiveDataTest"
+            // db unit tests
+            includeTestsMatching "org.zfin.DbUnitTests"
+            includeTestsMatching "org.zfin.infrastructure.EnumValidationTest"
+            includeTestsMatching "org.zfin.DbControllerTests"
+            includeTestsMatching "org.zfin.ThirdPartyServiceTests"
+        }
+
+        if (includeSmokeTests) {
+            includeTestsMatching "org.zfin.anatomy.AnatomySmokeTest"
+            includeTestsMatching "org.zfin.antibody.smoketest.AntibodySmokeTest"
+            includeTestsMatching "org.zfin.sequence.blast.smoketest.BlastSmokeTest"
+            includeTestsMatching "org.zfin.datatransfer.smoketests.DownloadSmokeTest"
+            includeTestsMatching "org.zfin.feature.presentation.FeatureDetailSmokeTest"
+            includeTestsMatching "org.zfin.feature.presentation.GenotypeDetailSmokeTest"
+            includeTestsMatching "org.zfin.expression.presentation.FigureSummarySmokeTest"
+            includeTestsMatching "org.zfin.fish.smoketest.FishSmokeTest"
+            includeTestsMatching "org.zfin.fish.smoketest.PhenotypeSummarySmokeTest"
+            includeTestsMatching "org.zfin.httpunittest.MarkerViewSmokeTest"
+            includeTestsMatching "org.zfin.sebservice.MarkerRestSmokeTest"
+            //include specific method in any of the tests
+    //        includeTestsMatching "*ActiveDataTest"
+        }
     }
 
     reports {
diff --git a/buildSrc/src/main/groovy/SimpleDirectoryCopyTask.groovy b/buildSrc/src/main/groovy/SimpleDirectoryCopyTask.groovy
index 962fe3a5a5..b830b35964 100644
--- a/buildSrc/src/main/groovy/SimpleDirectoryCopyTask.groovy
+++ b/buildSrc/src/main/groovy/SimpleDirectoryCopyTask.groovy
@@ -25,8 +25,115 @@ class SimpleDirectoryCopyTask extends DefaultTask {
     @Internal
     def ttNameMap = project.ext.ttNameMap
 
+//These are the only files that need to be searched and replaced (<!--|KEY|-->)
+//Let's whittle this list down over time
     @Internal
-    def whitelistTemplateFiles = project.ext.whitelistTemplateFiles
+    def whitelistTemplateFiles = [
+            'cgi-bin/send_request.perl',
+            'cgi-bin/merge_markers.pl',
+            'server_apps/DB_maintenance/backupBlastDbsAndRsyncAlmostBlastDbs.sh',
+            'server_apps/DB_maintenance/checkVarcharOctetLength.pl',
+            'server_apps/DB_maintenance/check_undefined_environment.pl',
+            'server_apps/DB_maintenance/disable_updates.pl',
+            'server_apps/DB_maintenance/extentMonitoring/dailyExtentCheck.sh',
+            'server_apps/DB_maintenance/fx_permission_check.pl',
+            'server_apps/DB_maintenance/loadExternalNotes.pl',
+            'server_apps/DB_maintenance/loadExternalNotes.sql',
+            'server_apps/DB_maintenance/loadUp/README_loadUp',
+            'server_apps/DB_maintenance/loadUp/rsync.pl',
+            'server_apps/DB_maintenance/orphanChecks.pl',
+            'server_apps/DB_maintenance/postgres/compareTables.groovy',
+            'server_apps/DB_maintenance/pushDataToPublic.sh',
+            'server_apps/DB_maintenance/queryMonitoring/dailyQueryCostCheck.sh',
+            'server_apps/DB_maintenance/rotateInformixLog.sh',
+            'server_apps/DB_maintenance/set_unload_timestamp.sql',
+            'server_apps/DB_maintenance/warehouse/chromosomeMartPostgres/runChromosomeMart.sh',
+            'server_apps/DB_maintenance/warehouse/expressionMart/runExpressionMart.sh',
+            'server_apps/DB_maintenance/warehouse/phenotypeMart/runPhenotypeMart.sh',
+            'server_apps/DB_maintenance/warehouse/regenChromosomeMart.sh',
+            'server_apps/DB_maintenance/warehouse/regenExpressionMart.sh',
+            'server_apps/DB_maintenance/warehouse/regenPhenotypeMart.sh',
+            'server_apps/DB_maintenance/warehouse/switch.sh',
+            'server_apps/DB_maintenance/warehouse/who_is.sh',
+            'server_apps/DB_maintenance/warehouse/who_is_not.sh',
+            'server_apps/Reports/AnnualStats/runStats.sh',
+            'server_apps/Reports/BetterFish/betterFish.sql',
+            'server_apps/Reports/PubTracking/runAverageTimeInBinsCumulative.sh',
+            'server_apps/Reports/PubTracking/runLongestBinResidents.sh',
+            'server_apps/Reports/PubTracking/runMonthlyBinLengthReport.sh',
+            'server_apps/Reports/PubTracking/runPaperlessPubTrackingDailyIndexedMetrics.sh',
+            'server_apps/Reports/elsevier_report.pl',
+            'server_apps/Reports/reportPubsForGeneAndFeature.pl',
+            'server_apps/WebSiteTools/signsoflife.sh',
+            'server_apps/apache/inc-redirect',
+            'server_apps/cron/crontab.production',
+            'server_apps/data_transfer/Downloads/GFF3/E_unload_ensembl_contig.sql',
+            'server_apps/data_transfer/Downloads/generateStagedAnatomy.pl',
+            'server_apps/data_transfer/Ensembl/fetch_ensdarT_dbacc.sh',
+            'server_apps/data_transfer/Ensembl/fetch_ensdarg.sh',
+            'server_apps/data_transfer/Ensembl/fetch_ensdargOttdargTable.sh',
+            'server_apps/data_transfer/Ensembl/fetch_ensembl_agp.sh',
+            'server_apps/data_transfer/Ensembl/fetch_sangerMutantInfo.sh',
+            'server_apps/data_transfer/Ensembl/notifyStaleIds.sh',
+            'server_apps/data_transfer/Ensembl/pullFromBioMart.pl',
+            'server_apps/data_transfer/Ensembl/reportEnsembleStatistics.sh',
+            'server_apps/data_transfer/ExternalSearch/CreateMarkerSearchPage.pl',
+            'server_apps/data_transfer/ExternalSearch/CreateMarkerSearchPage.sql',
+            'server_apps/data_transfer/GO/go.pl',
+            'server_apps/data_transfer/GO/gofile.sql',
+            'server_apps/data_transfer/GO/gofile2.sql',
+            'server_apps/data_transfer/GO/gofile2_all.sql',
+            'server_apps/data_transfer/GO/gp2protein.pl',
+            'server_apps/data_transfer/GO/gpad.pl',
+            'server_apps/data_transfer/GO/gpad2.0.sql',
+            'server_apps/data_transfer/GO/validateUniprotIDsZFIN.pl',
+            'server_apps/data_transfer/Genbank/gbaccession.pl',
+            'server_apps/data_transfer/Load/ReNo/Nomenclature/generate_special_Sanger_uniprot_nomenclature_run.sh',
+            'server_apps/data_transfer/Load/ReNo/load_run_report_hit.sh',
+            'server_apps/data_transfer/Load/blast_withdrawn.pl',
+            'server_apps/data_transfer/LoadOntology/parseHeader.pl',
+            'server_apps/data_transfer/LoadOntology/parseObo.pl',
+            'server_apps/data_transfer/MEOW/meow.pl',
+            'server_apps/data_transfer/NCBIStartEnd/NCBIStartEnd.pl',
+            'server_apps/data_transfer/OMIM/OMIM.pl',
+            'server_apps/data_transfer/OMIM/loadOMIM.sql',
+            'server_apps/data_transfer/ORTHO/downloadFiles.pl',
+            'server_apps/data_transfer/ORTHO/emailOrthologyReports.pl',
+            'server_apps/data_transfer/ORTHO/loadAndUpdateNCBIOrthologs.sql',
+            'server_apps/data_transfer/ORTHO/loadHumanSynonyms.sql',
+            'server_apps/data_transfer/ORTHO/parseHumanData.pl',
+            'server_apps/data_transfer/ORTHO/parseOrthoFile.pl',
+            'server_apps/data_transfer/ORTHO/reportOrthoNameChanges.pl',
+            'server_apps/data_transfer/ORTHO/runOrthology.pl',
+            'server_apps/data_transfer/ORTHO/updateZebrafishGeneNames.pl',
+            'server_apps/data_transfer/ORTHO/updateZebrafishGeneNames.sql',
+            'server_apps/data_transfer/PUBMED/Journal/checkAndUpdateJournals.sql',
+            'server_apps/data_transfer/PUBMED/Journal/insertJournalAlias.sql',
+            'server_apps/data_transfer/PUBMED/addMeshTermsToAllPubs.groovy',
+            'server_apps/data_transfer/PUBMED/addPMCidsToAllPubs.groovy',
+            'server_apps/data_transfer/PUBMED/loadNewPubs.sql',
+            'server_apps/data_transfer/PUBMED/load_complete_author_names.sql',
+            'server_apps/data_transfer/PUBMED/pubActivation.groovy',
+            'server_apps/data_transfer/PUBMED/updatePublicationDate.groovy',
+            'server_apps/data_transfer/RNACentral/loadTranscriptSequences.sql',
+            'server_apps/data_transfer/RNACentral/loadTscriptSeq.pl',
+            'server_apps/data_transfer/RNACentral/preLoadTranscriptSequence.sql',
+            'server_apps/data_transfer/RNACentral/runTscriptSequenceLoad.pl',
+            'server_apps/data_transfer/ResourceCenters/pullFromEZRC.pl',
+            'server_apps/data_transfer/ResourceCenters/pullFromZIRC.pl',
+            'server_apps/data_transfer/ResourceCenters/pushToZirc.pl',
+            'server_apps/data_transfer/ResourceCenters/pushToZirc.sql',
+            'server_apps/data_transfer/SNP/addNewClonesJSmith.pl',
+            'server_apps/data_transfer/SNP/addTalbotSNPAttr.sql',
+            'server_apps/data_transfer/SNP/dbSNP.pl',
+            'server_apps/data_transfer/SNP/loadNewSNPAttrs.sql',
+            'server_apps/data_transfer/SNP/loadNewSNPs.sql',
+            'server_apps/data_transfer/eco_go_mapping/insert_eco_go_map.sql',
+            'server_apps/data_transfer/maintainTermDisplay/checkRNAConsequenceTerm.groovy',
+            'server_apps/data_transfer/zfishbook/preprocess_zfishbook.pl',
+            'server_apps/data_transfer/zfishbook/zfishbook.pl',
+            'server_apps/data_transfer/zfishbook/zfishbook.sh',
+    ]
 
     @TaskAction
     void copyFiles() {