2.2. Configuration

2.2.1. Artefact repository location

When Taverna starts up it downloads all the dependencies it needs in order to run, together with any updates if requested, and optional plugins. By default, this location is on Windows <Drive>:/Documents and Settings/<You>/Application Data/Taverna/repository, on Linux $HOME/.taverna-1.7.1/repository and on the Mac $HOME/Library/Application Support/Taverna-1.7.1/repository. This location can be changed by setting the property taverna.repository in the startup script. Be careful not to overwrite the existing other settings for ARGS by making sure you are appending your new setting. For windows this is the runme.bat and would be changed to end with:

set ARGS=%ARGS% -Dtaverna.repository=<new location> 

java %ARGS% -jar "%~dp0\taverna-bootstrap-1.7.1.jar" %*

Note that spaces in the path name should be replaced with %20, e.g. Documents%20and%20Settings.

In Linux, the runme.sh would be changed to end with:

ARGS="$ARGS –Dtaverna.repository=<new location>" 

java $ARGS -jar $TAVERNA_HOME/taverna-bootstrap-1.7.1.jar $@

In Taverna 1.5.0 and 1.5.1 the location of the repository was <Drive>:/Documents and Settings/<You>/Application Data/Taverna/repository,$HOME/.taverna, or $HOME/Library/Application Support/Taverna/repository. If this repository exists when running Taverna 1.5.2, or later versions, then this and later version repositories are shared to prevent duplication of artifacts eating up disk space. Artifacts unique to the version of Taverna being run are still stored in its specific repository described previously.

2.2.2. Proxy configuration

If you are behind an HTTP proxy, and there's a reasonable chance that you are, you'll need to modify the mygrid.properties. The properties http.proxyHost and http.proxyPort need to be set to the hostname, or IP address, and port. There is also the additional property http.nonProxyHosts which if set lists hosts for which the proxy is not used, separated by a ‘|’. If the proxy server also requires authentication you should also assign values to http.proxyUser and http.proxyPassword. By default these properties are commented out, to make them active uncomment them and assign them to an appropriate value, for example:


http.proxyUser = elvis
http.proxyPassword = theking

2.2.3. The mygrid.properties file

Many setttings can be modifed by editing the mygrid.properties file. Generally this file is found in the conf directory of the unpacked Taverna download. Optionally, you can override this file with the presence of a user specific mygrid.properties. In windows this would be Documents and Setttings\<user>\Application Data\Taverna-1.7.1\, in Linux $HOME/.taverna-1.7.1/, and on the Mac $HOME/Library/Application Support/Taverna-1.7.1/. This is useful when Taverna is deployed within a multi-user environment, allowing each user to customise their individual settings.

2.2.4. Default services

Taverna can be configured to automatically load libraries of components into the service selection panel when it starts up. This is configured in the mygrid.properties. This is worth looking into if you are, for example, running a course which involves Taverna and you want your students to see your sample services when the workbench starts up. For now I suggest leaving the values as specified, although as they contact the network to find additional information on startup commenting out these sections might speed up the load times.

# DEFAULT SERVICES (user editable)
# The service selection panel component can be populated with extra
# web services and soaplab installations using this configuration
# section. In order to enable this, uncomment and edit the two
# properties to suit.
# Note that the default services load in a new thread, so may not
# appear immediately within the service panel. If any errors occur
# during the load, the stack trace is displayed in the system
# console. This is not ideal, we'll have better reporting in the
# next release.
# Multiple instances of each (soaplab or wsdl) may be specified by
# including all endpoints, separated with the ',' character as shown
# below.
# Trailing whitespace is not allowed in these URLs! If you're having
# problems getting this to work then check there isn't a space at the
# end of the line.
   taverna.defaultsoaplab = \
   taverna.defaultwsdl = \
   taverna.defaultbiomoby = \
   taverna.defaultweb = \

2.2.5. Image types and the mysterious 'Error 4'

There are reports of some linux installations showing a mysterious error '4'. This is, as far as we can tell, a problem with java handling PNG format images - we use this for the workflow diagram. If you are having this problem you might like to try uncommenting one of the 'taverna.scufldiagram.imagetype' lines to use GIF or JPEG coding instead. This seems to be a problem particularly on Linux but this is worth trying on any installation showing this error. Note - as of version 1.1 and higher this problem should never appear, Taverna will detect the issue the first time and fix it behind the scenes without any further intervention. If this is not the case please let us know!

# By default the workflow diagram uses an internal image in PNG
# format. Some platforms (win2000 and linux) have exhibited problems
# with this which seem to be rectified by changing the format to one
# of 'gif' or 'jpg'
# If you're seeing messages with the extremely helpful text of '4' or
# similar and no diagram appearing in the workbench you might like to
# try uncommenting one of the options below
# taverna.scufldiagram.imagetype = gif
# taverna.scufldiagram.imagetype = jpg

2.2.6. Setting an alternative location for the 'dot' tool

If you are running Taverna without administrative privileges on a unix style system you may be unable to install Graphviz as described above. You may, however, be able to install it into an alternative location. If this is the case you can define the property 'taverna.dotlocation' to the full path of the dot executable, Taverna will pick it up from this location rather than attempting to search the $PATH environment variable. This is only required if the diagrams don't work - Windows users should never need this option.

# By default Taverna will look for the 'dot' executable used to draw
# the workflow diagram on the standard PATH (whatever that concept is
# on your architecture of choice). To override this and explicitly
# supply a path to the executable you should edit and uncomment the
# following property
# taverna.dotlocation = /bin/foo/mystuff/dot