Taverna 1.7.x Command Line Tool (previously known as the Workflow Launcher) enables stand-alone running of workflows from a terminal without popping up the GUI. It is useful for running data-intensive or long-running worklows on some server with lots of memory as you can detach and come back later to collect your results.
Unless you are tied to Taverna 1.7.x for some reason – we would advise you to switch to Taverna 2.x Command Line Tool.
executeworkflow script
executeworkflow script runs Taverna 1.7.x workflows from a terminal. Examples on how it can be invoked are shown below.
To get help and a full set of options:
executeworkflow -help
usage: executeworkflow <workflow> [..]
Execute workflow and save outputs. Inputs can
be specified by multiple -input options, or
loaded from an XML input document as saved from
Taverna. By default, a new directory is created
named workflow.xml_output unless the –output
or –outputdoc options are given. All files to
be read can be either a local file or an URL.
-help print this message
-input <name filename> load the named input from file or URL
-inputdoc <document> load inputs from XML document
-output <directory> save outputs as files in directory, default is
to make a new directory workflowName_output
-outputdoc <document> save outputs to a new XML document
-report <file> save progress report in file, default is
progressReport.xml in the output directory
Examples of invoking the script on Windows:
executeworkflow file:myworkflow.xml
executeworkflow -input swiss_in swiss_in.txt file:myworkflow.xml
executeworkflow -inputdoc file:inputdoc.xml file:myworkflow.xml
On Linux/UNIX:
sh ./executeworkflow.sh file:myworkflow.xml
sh ./executeworkflow.sh -input swiss_in swiss_in.txt file:myworkflow.xml
sh ./executeworkflow.sh -inputdoc file:inputdoc.xml file:myworkflow.xml
This would create a new directory myworkflow.xml_output containing files for the outputs. If you like, you can add -outputdoc outputs.xml and view outputs.xml using dataviewer. Similarly, you can save complex inputs (i.e. lists) by making them in Taverna Workbench 1.7.x, and saving the input document. This input document can be used as -inputdoc inputs.xml
WorkflowLauncher application
The WorkflowLauncher application shows how workflows can be executed programmatically outside of Taverna.
- Source for workflowlauncher using Taverna 1.7.1
- Using the Taverna API to programmatically execute a workflow from the Taverna 1.7 manual
