blastp_of_target_vs_source_databasetargetProteins00 Provide the name, and if not in your working directory, the location of the file of fasta sequence(s) that you wish to use to search the blast database created in this workflow. 2010-03-15 11:30:58.843 GMT text/plain 2010-03-15 11:30:58.843 GMT sourceProteins00 Filepath for source proteins 2010-03-19 03:06:10.216 GMT Provide the name, and if not in your working directory, the location of the file of fasta sequence(s) that you wish to use to create the blast database in this workflow. 2010-03-19 03:07:14.800 GMT dbSave00 name and filepath of created blast database 2010-03-19 03:08:10.445 GMT eValue00 e value used for the blast 2010-03-19 03:08:24.439 GMT blastFile00 filepath used to store the blast results in text format 2010-03-19 03:09:16.106 GMT Result blast results of target against a source database in xml format 2010-03-19 03:11:20.722 GMT create_blastall_cmdArgseValue0dbSave0inputFilePath0outputFilePath0cmdArgsList11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true inputFilePath 0 'text/plain' java.lang.String true eValue 0 text/plain java.lang.String true dbSave 0 text/plain java.lang.String true outputFilePath 0 text/plain 1 cmdArgsList 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_formatdb_cmdArgsseqFile10dbSave0cmdArgsList11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true seqFile1 0 text/plain java.lang.String true dbSave 0 text/plain 1 cmdArgsList 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerunBlastSearchargs1command0net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.LocalCommand workflow java.lang.String true command 0 'text/plain' java.lang.String true args 1 l('text/plain') 0 result 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelocal_create_blastdbargs1command0result00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.LocalCommand workflow java.lang.String true command 0 'text/plain' java.lang.String true args 1 l('text/plain') 0 result 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerunBlastSearch_command_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity C:\Users\RLWarrender-LT\Desktop\Jennifer\blast\bin\blastall.exe net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelocal_create_blastdb_command_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity C:\Users\RLWarrender-LT\Desktop\Jennifer\blast\bin\formatdb.exe net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_blastall_cmdArgseValueeValuecreate_blastall_cmdArgsdbSavedbSavecreate_blastall_cmdArgsinputFilePathtargetProteinscreate_blastall_cmdArgsoutputFilePathblastFilecreate_formatdb_cmdArgsseqFile1sourceProteinscreate_formatdb_cmdArgsdbSavedbSaverunBlastSearchargscreate_blastall_cmdArgscmdArgsListrunBlastSearchcommandrunBlastSearch_command_defaultValuevaluelocal_create_blastdbargscreate_formatdb_cmdArgscmdArgsListlocal_create_blastdbcommandlocal_create_blastdb_command_defaultValuevalueRead_Text_FilefileurlblastFileResultRead_Text_Filefilecontents This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created. All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use. 2010-03-15 11:30:59.109 GMT Bela Tiwari 2010-03-15 11:30:59.109 GMT "This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created. All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use." 2010-03-19 03:30:27.923 GMT blastp of target vs source database 2010-03-19 03:13:00.656 GMT nclteamc and Bela Tiwari - fetchEnsemblSeqsAndBlast 2010-03-19 03:12:03.981 GMT nclteamc and Bela Tiwari 2010-03-19 03:11:49.660 GMT fetchEnsemblSeqsAndBlast 2010-03-15 11:30:59.109 GMT