Workflow1InputFiles11InputZipFiles11OutputFiles11MiraCommand11getFilesCommand11pathToSaveMiraResultsFromS300MiraOutputS3BucketName00getFilesJobIDrunMiraJobIDgetFilesFinalStaterunMiraFinalStateGetMiraOutputFilesReportRunMiraOnCloudOutputFiles1InputZipFiles1InputFiles1CommandLines1JobId00FinalState00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetFilesAndConvertOutputFiles1InputZipFiles1InputFiles1CommandLines1JobId00FinalState00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGetMiraOutputFromS3pathToSave0MiraOutputS3bucketName0report00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRunMiraOnCloudOutputFilesOutputFilesRunMiraOnCloudInputZipFilesInputZipFilesRunMiraOnCloudInputFilesInputFilesRunMiraOnCloudCommandLinesMiraCommandgetFilesAndConvertOutputFilesOutputFilesgetFilesAndConvertInputZipFilesInputZipFilesgetFilesAndConvertInputFilesInputFilesgetFilesAndConvertCommandLinesgetFilesCommandGetMiraOutputFromS3pathToSavepathToSaveMiraResultsFromS3GetMiraOutputFromS3MiraOutputS3bucketNameMiraOutputS3BucketNamegetFilesJobIDgetFilesAndConvertJobIdrunMiraJobIDRunMiraOnCloudJobIdgetFilesFinalStategetFilesAndConvertFinalStaterunMiraFinalStateRunMiraOnCloudFinalStateGetMiraOutputFilesReportGetMiraOutputFromS3report 61b61283-fbdb-4cee-a8a7-b33f5ad3c0b8 2012-05-03 17:03:19.440 BST 58237fac-b3c8-4280-b93c-55671b8f693f 2012-05-03 15:46:41.455 BST db1827fb-7306-4f88-9273-d92b361e2037 2012-05-02 20:18:00.734 BST b6e746a5-05fd-4147-8f70-804353efe6a8 2012-05-02 18:22:32.911 BST 3c9a4b11-b530-4ae4-994f-5b75302461b4 2012-05-02 20:15:00.529 BST ddb8253c-977a-406c-a1f5-6bae9dce7d5b 2012-05-03 11:46:32.126 BST 546b45ea-f3a4-4bc9-b626-164b30d13062 2012-05-02 18:14:35.943 BST c94f32a4-ced9-4290-ae1f-7053c368ef7b 2012-05-03 17:02:12.281 BST 8fa08c32-1c29-4277-915e-59fb37cb1e6a 2012-05-02 20:20:43.259 BST 281d06a3-c6fc-4c2e-9802-969036117de5 2012-05-03 11:47:21.983 BST Workflow4JobId00StategetJobState_inputmessageId0output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity messageId 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobState" name="parameters" qname="{http://ws.gcl.microbase.ncl.ac.uk/}getJobState"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="messageId" qname="{http://ws.gcl.microbase.ncl.ac.uk/}getJobState&gt;messageId" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobStateResponse" name="parameters" qname="{http://ws.gcl.microbase.ncl.ac.uk/}getJobStateResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="{http://ws.gcl.microbase.ncl.ac.uk/}getJobStateResponse&gt;return" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_2parameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://23.23.195.76:8080/TavernaMicrobaseGCLService/services/gcl?wsdl getJobState net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_inputmessageIdJobIdgetJobState_outputinputgetJobState_2parametersgetJobState_2parametersgetJobState_inputoutputStategetJobState_outputreturn 669b0d69-6e76-4483-a6d9-42e26382196e 2012-04-30 14:08:13.238 BST e2b0b8e3-5106-4c6d-ab83-6b1ef2ccd36d 2012-04-27 00:39:16.413 BST fea98a1b-10b8-46af-8530-377a32ede8fd 2012-05-01 13:46:08.20 BST 6f251d50-fc1e-4f73-811e-6663256268d7 2012-05-02 11:05:44.725 BST Workflow1CommandLines11OutputFiles11InputZipFiles11InputFiles11JobIdFinalStatesubmitGCLJob_inputcommandLine1outputFiles1inputZipFiles1inputFiles1output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity commandLine 1 l('text/plain') false inputFiles 1 l('text/plain') false inputZipFiles 1 l('text/plain') false outputFiles 1 l('text/plain') false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitGCLJob" name="parameters" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJob"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="commandLine" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJob&gt;commandLine"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="inputFiles" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJob&gt;inputFiles"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="inputZipFiles" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJob&gt;inputZipFiles"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="outputFiles" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJob&gt;outputFiles"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitGCLJob_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false return 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitGCLJobResponse" name="parameters" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJobResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="{http://ws.gcl.microbase.ncl.ac.uk/}submitGCLJobResponse&gt;return" /></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWorkflow4JobId0State00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop <activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns=""> <inputs> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <name>State</name> <depth>0</depth> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> </inputs> <outputs> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> <name>loop</name> <depth>0</depth> <granularDepth>0</granularDepth> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> </outputs> <classLoaderSharing>workflow</classLoaderSharing> <localDependencies /> <artifactDependencies /> <script>loop = "" + ! State.matches("FINISHED_SUCCEEDED|ERROR_FAILED"); if ("true".matches(loop)) { Thread.sleep(3000); }</script> <dependencies /> </net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity> true net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitGCLJob_2parameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity http://23.23.195.76:8080/TavernaMicrobaseGCLService/services/gcl?wsdl submitGCLJob net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitGCLJob_inputcommandLineCommandLinessubmitGCLJob_inputoutputFilesOutputFilessubmitGCLJob_inputinputZipFilesInputZipFilessubmitGCLJob_inputinputFilesInputFilessubmitGCLJob_outputinputsubmitGCLJob_2parametersWorkflow4JobIdsubmitGCLJob_outputreturnsubmitGCLJob_2parameterssubmitGCLJob_inputoutputJobIdsubmitGCLJob_outputreturnFinalStateWorkflow4State cbabbcbc-1b80-4c28-86a5-76d1f8f2cf9c 2012-05-02 15:18:36.847 BST b834e0b6-53bb-42e9-b9e1-ecadc3d96dda 2012-04-30 16:43:14.392 BST d0c4c2c8-cb56-41aa-8fb1-4216945aa80d 2012-04-30 18:00:01.418 BST 98dbff36-e7ac-48f1-9d2e-ed56ba21f91f 2012-04-26 23:37:15.717 BST 660482aa-8610-4fd5-b166-b35dc9ee90c9 2012-04-27 01:07:37.986 BST 3b23bc44-cd79-4fff-b1ae-e36c5cf7e395 2012-04-30 14:08:18.481 BST 83c71964-17cd-479b-ae88-00370327fbc5 2012-04-27 12:23:06.83 BST 19e5ce19-3338-492c-9bb9-bb7469ecce70 2012-05-01 13:14:58.55 BST afe247cc-c882-47ba-b4c0-72acf912bf5d 2012-04-30 16:55:11.598 BST 563a84e2-2476-437e-846e-ed1f98f7ec4d 2012-05-01 13:53:18.950 BST b0ac9b44-76f0-400e-8ccc-014a838cf87d 2012-05-01 13:46:37.535 BST 4a5f71bf-b5a3-40d0-ac09-b55c254c5e43 2012-04-30 16:54:14.804 BST 762424a9-b6aa-45e5-a987-d3c116979303 2012-04-30 18:03:43.653 BST 26dc953e-a006-41a2-a477-cb1c9a3b3758 2012-05-02 11:05:51.672 BST b0ac9b44-76f0-400e-8ccc-014a838cf87d 2012-05-01 13:54:27.383 BST Workflow26pathToSave00MiraOutputS3bucketName00reportGetMiraOutputFilesFromS3pathToSave0s3BucketName0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.3net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 977d9b40-ae97-4aa0-93e3-20d37bcec65a #Get mira oputput from S3 bucket (change "mira-out" to the name of your #mira output s3 bucket name s3cmd get -r -f s3://%%s3BucketName%%/ %%pathToSave%% 1200 1800 pathToSave s3BucketName s3BucketName s3BucketName false false false UTF-8 false false false pathToSave pathToSave false false false UTF-8 false false false false true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGetMiraOutputFilesFromS3pathToSavepathToSaveGetMiraOutputFilesFromS3s3BucketNameMiraOutputS3bucketNamereportGetMiraOutputFilesFromS3STDOUT 672697d8-dfa1-4082-a9e0-5f94bb19b05a 2012-05-03 11:33:39.776 BST 314cac3e-987e-4dd9-933d-17ff344cef4b 2012-05-03 11:47:14.515 BST 5378e87c-b44e-4a47-bfbb-0203493f6b90 2012-05-02 19:03:25.89 BST c17045f0-f3e2-4c65-8dbe-199c26ad232d 2012-05-03 17:03:12.423 BST 68b760fe-a96b-4bba-8a31-ea63d32b9c03 2012-05-02 19:10:12.713 BST 02923eb6-8a86-4e81-a968-587f0c437f60 2012-05-03 11:41:28.404 BST ae1be956-fbf3-4779-a2ea-ff59cdbff620 2012-05-03 15:48:23.403 BST fbf4a6be-75d5-49b3-890d-df09165da4b5 2012-05-03 15:45:58.12 BST 789523d9-c614-485a-97e6-b85f7c06a979 2012-05-02 18:54:18.752 BST 417dc3ed-c5a6-48a8-9be6-c901ebe78b52 2012-05-02 18:51:52.701 BST 3fa16cf6-d8b4-41de-939f-ebba907bd6e5 2012-05-02 19:09:30.681 BST 2ef9497a-7273-4811-91ba-96b05c8e7235 2012-05-03 11:43:03.898 BST c02934c6-715e-418f-bdb2-333dfbd8c38b 2012-05-02 19:04:02.147 BST fdb74a58-ade1-49e8-9272-3198023bb7c5 2012-05-03 11:46:27.314 BST 3fcc3b2e-d5b8-4f54-bacc-3685794a58b3 2012-05-02 18:47:24.613 BST