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From within a Taverna workflow, you can call a tool (command) on the local machine, or on any machine to which Taverna can obtain an SSH connection. You can either obtain a tool description from a registry of descriptions, or you can create your own tool description.

Each call of a tool service works within its own specially created sub-directory of a directory specified by the location. When data is written to or read from a file, the file is within the sub-directory for that call.

In many cases the data used for calls of tools is kept where the tool was called. It will be deleted when the workflow run is deleted.

If a workflow run uses in-memory storage for data or does not capture provenance, then the data associated with calls of tool services will be deleted when the workflow run is deleted or when Taverna is next started. This can cause the Credential Manager to ask for password information.

Tutorial

Details on Tool service

Citation

The tool service was initially developed by Hajo Krabbenhöft and Steffen Möller as part of the KnowArc project.

Cite as:

H. Krabbenhöft, S. Möller, D. Bayer (2008) Integrating ARC Grid Middleware with Taverna Workflows.  Bioinformatics, 24(9):1221-1222.  doi:10.1093/bioinformatics/btn095

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