Example_for_external_tools_with_gzip_and_gunzipOriginal_File Parameter file for GROMACS downloaded directly from http://md.chem.rug.nl/~mdcourse/minim.mdp Any file would do for this example. 2011-05-18 10:07:51.93 CEST Compressed_File A particular text file compressed with gzip. 2011-05-18 10:00:01.744 CEST Decompressed_File The compressed file is uncompressed again. 2011-05-18 10:01:18.7 CEST gunzip_STDERR Empty if executing normally. 2011-05-18 10:09:12.973 CEST gunzip_STDOUT Always empty. 2011-05-18 10:09:03.325 CEST gzip_STDERR Empty if executing normally. 2011-05-18 10:08:49.125 CEST gzip_STDOUT Always empty. 2011-05-18 10:08:55.373 CEST Read_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity fileurl 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 workflow net.sourceforge.taverna.scuflworkers.io.TextFileReader net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGROMACS_MDP_FILEvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity http://md.chem.rug.nl/~mdcourse/minim.mdp net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokegzipfile_to_compress0gzipped_file00STDOUT00STDERR00net.sf.taverna.t2.activitiesexternal-tool-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.externaltool.ExternalToolActivity default 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> http://taverna.nordugrid.org/sharedRepository/xml.php gzip gzip system Compressing single file to STDOUT gzip -c fred > fred.gz 1200 1800 file_to_compress fred true false true windows-1252 false false false gzipped_file fred.gz true false true true false net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokegunzipgzipped_file0STDOUT00STDERR00decompressed_file00net.sf.taverna.t2.activitiesexternal-tool-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.externaltool.ExternalToolActivity default 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> http://taverna.nordugrid.org/sharedRepository/xml.php gunzip gunzip system Uncompressing single file to STDOUT gunzip -c fred.gz > fred 1200 1800 gzipped_file fred.gz true false true windows-1252 false false false decompressed_file fred true false true true false net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlGROMACS_MDP_FILEvaluegzipfile_to_compressRead_Text_Filefilecontentsgunzipgzipped_filegzipgzipped_fileOriginal_FileRead_Text_FilefilecontentsCompressed_Filegzipgzipped_fileDecompressed_Filegunzipdecompressed_filegunzip_STDERRgunzipSTDERRgunzip_STDOUTgunzipSTDOUTgzip_STDERRgzipSTDERRgzip_STDOUTgzipSTDOUT 5def6db1-8ad5-4489-8fa7-13fb9d9b33d0 2011-05-11 17:17:16.379 CEST 5a9d9e4d-b39d-4adc-ac18-105edfa55da5 2011-05-10 14:28:41.282 CEST 5d81383a-33cb-42a3-a54a-0025c70e04d8 2011-05-18 09:59:20.533 CEST This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later. 2011-05-18 09:59:16.608 CEST 88042ede-d2fa-46bc-bb51-6f4365b377ea 2011-05-10 17:41:54.452 CEST 26c1c5da-94bc-4945-a579-9af8d8b8a1ed 2011-05-18 10:08:00.646 CEST Steffen Moeller Alan Williams 2011-05-18 09:56:32.351 CEST 1ca4833e-fd69-4a11-9249-de0a0fc49508 2011-05-10 16:23:08.670 CEST 9bd034c5-6356-4a02-8e46-339aaaba3900 2011-05-11 17:18:48.827 CEST 204626f2-fa91-4efe-a12b-ceea66ebbe39 2011-05-10 16:27:04.848 CEST cb0a2a1a-8f24-4a5e-862a-c51044d59d83 2011-05-18 09:55:28.652 CEST 2e3f8cd4-63db-4684-b10c-798aa671bbec 2011-05-18 10:09:16.597 CEST 96ac6bd6-084f-462b-8609-138c3fc02bef 2011-05-13 17:54:58.251 CEST aafe4651-f880-431b-a11b-0791f3d53939 2011-05-11 17:39:39.7 CEST Example for external tools with gzip and gunzip 2011-05-18 09:56:58.70 CEST 82bfd281-afe9-4136-b49b-90a9a0b3e9f1 2011-05-10 16:44:52.597 CEST 71961208-b9bc-4284-b163-b2c40eb4316b 2011-05-11 17:09:57.729 CEST 69681e3a-7113-492e-b6b2-0ed0a4aaab79 2011-05-10 18:31:13.719 CEST 05976c99-c066-4b43-a8dc-a9d096460071 2011-05-10 18:32:49.50 CEST f1f82722-871f-40b2-a143-9ec4b045e88d 2011-05-11 17:25:11.85 CEST ade60be2-6428-475c-9f67-f70563bc1859 2011-05-10 16:47:18.553 CEST 72fcee7c-a523-430e-84d6-545da6f20c10 2011-05-11 17:40:06.991 CEST 5e75b9da-695e-4867-8aa8-4bf75c20e603 2011-05-10 18:09:18.46 CEST ddf535eb-987c-441a-b807-42e48fd40c87 2011-05-13 17:57:36.108 CEST