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Taverna command line tool 2.5.0
Released by myGrid
(c) Copyright 2005-2014 University of Manchester, UK
Taverna is licenced under the GNU Lesser General Public Licence. (LGPL) 2.1.
See the file LICENCE.txt or for
If the source code was not included in this download, you can download it from or
If you installed a OS-specific distribution of Taverna it may come
bundled with a distribution of OpenJDK. OpenJDK is distributed under the
GNU Public License (GPL) 2.0 w/Classpath exception. See jre/LICENSE.txt or
for details.
Taverna uses various third-party libraries that are included under compatible
open source licences such as the Apache Licence.
See for
documentation and tutorials on using Taverna.
In particular
will explain how to use the command line tool.
See for the
Taverna 2.5 user manual.
See the file "known-issues.txt" for known issues with this release, and the file
"release-notes.txt" for improvements since the previous version of Taverna.
In Windows, execute "executeworkflow.bat", while on OSX/Linux/UNIX,
execute "sh".
On Linux/OSX/UNIX you may set the executable bit using
"chmod 755", allowing you to execute ./
directly. You can make symlinks to this shell script from /usr/local/bin or
Run executeworkflow with parameter -help for detailed help, also see
usage: executeworkflow [options] [workflow]
-clientserver connects as a client to a derby
server instance.
-dbproperties <filename> loads a properties file to
configure the database
-embedded connects to an embedded Derby
database. This can prevent
mulitple invocations
-help displays comprehensive help
-inmemory runs the workflow with data
stored in-memory rather than in a
database. This can give
performance inprovements, at the
cost of overall memory usage
-inputdelimiter <inputname delimiter> causes an inputvalue or inputfile
to be split into a list according
to the delimiter. The associated
workflow input must be expected
to receive a list
-inputdoc <document> load inputs from a Baclava
-inputfile <inputname filename> load the named input from file or
-inputvalue <inputname value> directly use the value for the
named input
-logfile <filename> the logfile to which more verbose
logging will be written to
-outputdir <directory> save outputs as files in
directory, default is to make a
new directory workflowName_output
-outputdoc <document> save outputs to a new Baclava
-port <portnumber> the port that the database is
running on. If set requested to
start its own internal server,
this is the start port that will
be used.
-provenance generates provenance information
and stores it in the database.
-startdb automatically starts an internal
Derby database server.
For example:
$ taverna-commandline-2.5.0/ Retrieve_sequence_in_EMBL_format.t2flow
Outputs will be saved to the directory:
$ cat Retrieve_sequence_in_EMBL_format_output/sequence
ID X52524; SV 1; linear; genomic DNA; STD; INV; 4507 BP.
AC X52524;
DT 20-SEP-1990 (Rel. 25, Created)
DT 18-FEB-1991 (Rel. 27, Last updated, Version 6)
aggttagaaa aaataaataa aaataaaatt gagaagaatg taaattaaat atagaattcg 4500
agctcgg 4507
You can use full URLs to workflows and inputs, for instance:
Example Taverna 2.5 workflows can be found in the myExperiment starter pack at
TODO: Update
You can share and find other workflows at
See for contact details.
You may email for any questions on using Taverna
workbench. myGrid's support team should respond to your query within a
Mailing lists
We also encourage you to sign up to the public *taverna-users* mailing list,
where you may post about any problem or give us feedback on using Taverna.
myGrid developers are actively monitoring the list.
If you are a developer, writing plugins for Taverna, dealing with the code
behind Taverna or integrating Taverna with other software, you might find it
interesting to also sign up for the public *taverna-hackers* mailing list,
where you can also track the latest developments of Taverna.
Taverna requires the Java Runtime Environment (JRE) version 7.
Platform-specific builds of the command-line tool should include a build of
OpenJDK, if you are running the platform-independent distribution, you
may need to download and install Java, see
for more requirement details.
Secure web services
If you do not use the bundled OpenJDK (which has security enabled by default),
you may need to modify your Java installation to enable security.
If you need to invoke secure services or access secured data from your
workflows (e.g. if you need to provide username and password to gain access to
your service/data or your service's URL starts with HTTPS), then you need to
allow Taverna to communicate securely to such resources using the strongest
possible cryptography.
To do so, you have to install the 'Unlimited Strength Java Cryptography
Extension' policy instead of the default restrictive policy that is
shipped with Java; the default policy will for export reasons only
allows the use of "weak" cryptography (e.g. short passwords and keys).
Java by default only comes with limited-strength cryptography support
because of import control restrictions in some countries, where
unlimited-strength cryptography is classified as a "weapon technology".
Thus, you must determine whether your country's laws allow you to
install such software and you are responsible for doing so.
The policy files on your system are located in:
where <java-home> is the jre directory of the Java Development Kit (JDK) or the
top-level directory of the JRE (Java Runtime Environment) on your system.
If eligible, you may download the unlimited strength versions of the above
policy files and replace the ones that were installed by default. This will
effectively "turn on" the use of unlimited-strength security in Java on your
system. Not installing these files will most probably cause invoking of secure
services from Taverna to fail. Note that if you switch to another Java version
you will have to install the policy files again in the appropriate directory of
your new Java installation.
For Java 6, you can download the unlimited cryptography policy jar files from:
You will find detailed logs in Taverna's home directory. You can
view this directory from within Taverna by choosing
Advanced->Show Log Folder in the menu.
Windows XP: C:\Documents and settings\JohnDoe\
Application Data\taverna-cmd-2.4.0\logs
Vista/Windows 7: C:\Users\JohnDoe\AppData\Roaming\taverna-cmd-2.4.0\logs
OS X: /Users/JohnDoe/Library/Application support/taverna-cmd-2.4.0/logs
Linux: /home/johndoe/.taverna-cmd-2.4.0/logs
Note that "Application data" and "AppData" are hidden folders in Windows.
To modify the log levels, edit "conf/" in the Taverna
installation folder.
Memory usage
The Taverna command line tool will by default use a maximum of
300 MB.
If Taverna happens to run out of memory while running a workflow with
large data by using the option -embedded This will reduce execution speed
slightly, but should consume less memory.
If you need to increase the available memory, edit "" or
"executeworkflow.bat" and replace "-Xmx300m" with say "-Xmx600m" to use
600 MiB.