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GraphViz dot location

Taverna Workbench uses the GraphViz program dot to draw the workflow diagrams.  If Taverna cannot find dot then the Workflow diagram will show a warning message in red.

The Windows distribution of Taverna Workbench contains a version of dot so no further installation should be required.

If you are running the developer editions of Taverna you might have to configure dot - you can find a copy of dot.exe (for Windows) within bin/win32i386 of an existing Taverna Workbench installation

Linux and Mac OS dot 

Details on how to install GraphViz (which includes dot) for Linux and for Mac OS can be found in the system requirements for Taverna. Once you have installed GraphViz, then the location of dot can be found by running

in a command line. Use the value returned to update the dot location.

Updating the dot location

After obtaining the path to dot, you can update Taverna as follows.

  1. Open the Preferences pop up window.
  2. Select Workbench.
  3. Under Path to Graphviz executable dot enter the command dot, or the full path to where the command was installed, e.g. /usr/bin/dot or /usr/local/bin/dot
  4. Click Apply.
  5. Close the Preferences pop up window.

Changing the dot location will not affect any workflows that are opened.  You need to save and close a workflow and then re-open it.

Make sure you enter the location of the dot program.

Do not use the location of GraphViz.

 

Changing the General Workbench configuration

The preferences for the General Workbench configuration can be changed by

  1. In Taverna, select Preferences from the Taverna or File menu.
  2. Select Workbench from the Preferences pop up window.
  3. Change the preferences as shown below - note there are other possibilites for the location of dot, see notes on various operating systems below.
  4. Click Apply.
  5. Close the Preferences pop up window.

Maximum number of entries in right-click menu

Taverna Workbench uses right-click menus, for example to show the input ports of a service that an output port can connect to.  If there are a large number of entries in the menu, then Taverna Workbench needs to split the menu into several sub-menus.

The number of entries in each sub-menu can be changed by:

  1. Open the Preferences pop up window.
  2. Select Workbench.
  3. Enter a new value in the Maximum number of services/ports in right-click menu field.
  4. Click Apply.
  5. Close the Preferences pop up window.

The default number of entries, twenty, is suitable for most display sizes.

Warn on internal errors

While running, Taverna Workbench might in exceptional circumstances generate internal errors. Normally the errors are written to a log file and not made visible to the user of the workbench. (See the menu Advanced->Show log folder). If you are developing an extension to Taverna Workbench, or want to investigate any problems, then it can be useful to see those errors when they occur.  If you tick the Warn on internal errors  box, Taverna Workbench will open a dialog showing details of any error when it occurs.

Warn on internal errors only affects errors caused by Taverna code.  Errors created by services called by a workflow will still be shown as error documents in the workflow run.

To make Taverna warn you about internal Taverna errors:

  1. Open the Preferences pop up window.
  2. Select Workbench.
  3. Tick the Warn on internal errors box.
  4. Click Apply.
  5. Close the Preferences pop up window.

To stop being warned of internal errors, follow the same procedure but untick the box.

Most users are not likely to want to be warned of internal errors. It is not necessary to tick this option unless you are developing or debugging Taverna.

Capture output on stdout/stderr to log file

Some services write information to the standard output and error streams.  This is sometimes done to produce debugging or progress information.  If the Capture output on stdout/stderr to log file box is ticked then Taverna Workbench copies the information written by the services into its log file.  If the box is not ticked then, depending upon how you run Taverna, that information is not saved or is written to the console where Taverna was started from.

To change the Capture output on stdout/stderr to log file option

  1. Open the Preferences pop up window.
  2. Select Workbench.
  3. Tick/untick the Capture output on stdout/stderr to log file box.
  4. Click Apply.
  5. Close the Preferences pop up window.

Writing the stdout/stderr to the log file is a good option for most users.

Buttons

If you click Help then you will obtain help on this dialog. Reset resets the values to the last applied values. Apply takes the shown values and applies them to Taverna.

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