on December 13, 2010 by in Tools, Comments (1)

Taverna command line

There are times when it becomes impractical to run workflows within the Taverna workbench. Examples of such scenarios are when running a workflow that is expected to take a long time to complete, or requires greater resources than that available on a typical desktop or laptop computer.

To assist in these types of scenarios, Taverna provides a command line utility, that allows an existing workflow to be run without the graphical user interface. Along with removing the additional overhead of the user interface, this also allows workflows to be executed remotely using a command line terminal (most likely using ssh).

The command line utility is provided with information about which workflow to execute, the input data to be fed into the workflow, and how to retrieve the results. There are also some more advanced configuration options for defining how the workflow is executed, such as which database to use, whether to gather provenance information, and how intermediate data is stored. The command line tool can use MySQL as the database for storing intermediate values and provenance.

Of course, the command line utility does not support creation or editing of workflows. The workflow should first be created, tested and refined using the Taverna workbench, and then stored either as a local file or online at myExperiment.

There follows an example of using the command line tool to execute a workflow that has been published on myExperiment. This Get Kegg Pathway information workflow, by Paul Fisher, gets a series of information relating to a list of KEGG pathways supplied to it.

$ sh ./executeworkflow.sh -inputvalue kegg_pathway_id_list "path:mmu04010 path:mmu05014" http://www.myexperiment.org/workflows/1099/download?version=1

The command line utility is available for Windows, Linux and Unix based platforms including Mac OS X. Full technical details about using the command line, and the available options, are described in the Taverna User Guide.

The command line utility can also be used as a simple solution to embedding Taverna within another application. However, if you are interested in using the command line tool in this way, you should also consider using the Taverna server and related libraries.

As a rule of thumb, if you are working alone, and want a quick simple solution to remote execution then the Taverna Command Line utility would most likely be the preferred option. If you are wanting to create a long term solution that is to be used collaboratively as part of a wider team then the Taverna Server is going to be more suitable.

1 Comment

  1. Taverna server | The Taverna Knowledge Blog

    December 13, 2010 @ 2:51 pm

    […] described for the Taverna command line utility, sometimes it may be impractical to run Taverna workflows within the Taverna workbench. […]

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