======================= Taverna workbench 2.4.0 ======================= http://www.taverna.org.uk/ http://www.mygrid.org.

uk/ Released by myGrid, 2011-07-12 (c) Copyright 2005-2011 University of Manchester, UK Licence ======= Taverna is licenced under the GNU Lesser General Public Licence. (LGPL) 2.1. See the file LICENCE.txt or http://www.gnu.org/licenses/lgpl-2.1.html for details. If the source code was not included in this download, you can download it from http://www.taverna.org.uk/download/workbench/2-3/#download-source or http://www.taverna.org.uk/download/source-code/ Taverna uses various third-party libraries that are included under compatible open source licences such as the Apache Licence. Running Taverna =============== Windows ------If you used the installer you should have Taverna->Taverna workbench 2.4.0 in your Start menu. If you used the self-extracting archive, double-click on "taverna.exe" in the extracted folder. If you used the installer, it should have checked that you have a recent version of Java installed. See "Requirements" below. Mac OS X -------Running Taverna on a Mac requires Mac OS X 10.5 or later with the latest updates installed for Java 6. 32-bit machines will need 10.6 or later. Copy the "Taverna" application bundle to /Applications or a folder of your preference. Eject the disk image, and run Taverna from the installed location. You might also need to install Graphviz as it is no longer bundled with Taverna. See "Requirements" below. Linux ----For Linux, either double-click on "taverna.sh", or start a Terminal and execute "./taverna.sh" or "sh taverna.sh" from the folder where you extracted Taverna. You will need to have Graphviz and Oracle's Java runtime installed. See "Requirements" below. Documentation

============= See http://www.taverna.org.uk/documentation/taverna-2-x/ for documentation and tutorials on using Taverna. See http://www.mygrid.org.uk/dev/wiki/display/taverna24/User+Manual for the Taverna 2.4 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. Examples ======== Example Taverna 2.4 workflows can be found in the myExperiment starter pack at http://www.myexperiment.org/packs/254 You can also access these as the tab 'Starter pack' under the *myExperiment* view inside Taverna. You can share and find other workflows at http://www.myexperiment.org/ You can find and describe web services in life sciences at http://www.biocatalogue.org/ Support ======= See http://www.taverna.org.uk/about/contact-us/ for contact details. You may email <support@mygrid.org.uk> for any questions on using Taverna workbench. myGrid's support team should respond to your query within a week. 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. * http://lists.sourceforge.net/lists/listinfo/taverna-users * http://taverna-users.markmail.org/search/?q= 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. * http://lists.sourceforge.net/lists/listinfo/taverna-hackers * http://taverna-hackers.markmail.org/search/?q= Registration ============ Taverna might ask if you would like to register as a Taverna user. The myGrid team would appreciate if you do, as it would:

* Allow us to support you better; future plans will be directed towards solutions Taverna users require * Help sustain Taverna development By registering, you will *not* be giving us access to your data or service usage. We will *not* be monitoring your usage of Taverna, we will only record the information you provide in the registration form. For full terms and condition of our registration, see http://www.taverna.org.uk/about/legal-stuff/terms/ Requirements ============ Graphviz -------The external tool Graphviz ( http://www.graphviz.org/ ) is used for generating the workflow diagram in Taverna. A version of Graphviz is bundled in the Windows install, while Linux and Mac OS X users will need to install Graphviz separately. For OS X, see http://www.graphviz.org/Download_macos.php where you can download the *current stable release* for your operating system. For Linux, most distributions have a way to install Graphviz. For Ubuntu, try: sudo apt-get install graphviz For other distributions, see http://www.graphviz.org/Download.php for instructions. Please note that you do *not* need the Grappa java library. In most cases Taverna should be able to pick up the location of the Graphviz binary "dot" from the PATH, if this is not the case, see http://www.mygrid.org.uk/dev/wiki/display/taverna/Workbench+preferences on how to configure the location of "dot". Java ----Taverna requires the Java Runtime Environment (JRE) version 6 or later from Oracle. No other versions of Java are officially tested with Taverna. Windows users might need to download Java from http://java.com/ - but in most cases the Taverna installer would already have checked if Java is installed. Linux users have different options to install Java depending on their Linux distribution. Some distributions, such as Ubuntu, might come with alternative open source implementations of Java, like Gnu GCJ and OpenJDK. We've identified some issues with these implementations, and recommend using the official Java implementation from Sun/Oracle. To download Oracle Java 6 for Ubuntu, start a Terminal, and type the following: sudo apt-get install sun-java6-jre and follow the instructions. You might also need to change the default Java implementation by running: sudo update-alternatives --config java To check your version of Java on the command line, try:

$ java -version java version "1.6.0_22" Java(TM) SE Runtime Environment (build 1.6.0_22-b04) Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode) Read http://www.taverna.org.uk/download/workbench/system-requirements/ for more requirement details. Secure web services ------------------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: <java-home>/lib/security/local_policy.jar <java-home>/lib/security/US_export_policy.jar 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: http://www.oracle.com/technetwork/java/javase/downloads/jce-6-download-429243.ht ml For Java 7, you can download the unlimited cryptography policy jar files from: http://www.oracle.com/technetwork/java/javase/downloads/jce-7-download-432124.ht ml Advanced ======== Logging -------

If you are using a Windows operating system and want to see Taverna's logging information, then run "taverna-debug.bat" from the installed Taverna folder. In OS X, start "/Applications/Utillities/Console". In Linux run "taverna.sh" from a Terminal. You can also 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. See: Windows 7/Vista: C:\Users\JohnDoe\AppData\Roaming\taverna-2.4.0\logs Windows XP: C:\Documents and settings\JohnDoe\ Application Data\taverna-2.4.0\logs OS X: /Users/JohnDoe/Library/Application support/taverna-2.4.0/logs Linux: /home/johndoe/.taverna-2.4.0/logs Note that "Application data" and "AppData" are hidden folders in Windows. To modify the log levels, edit "conf/log4j.properties" in the Taverna installation folder. Default services and plugins ---------------------------You can edit the default service list for the Taverna installation by editing "conf/default_service_providers.xml". You can generate this service list from within Taverna by right-clicking on "Available Services" and selecting "Export Services To File". Similarly you can replace the installation "plugins/plugins.xml" with "plugins.xml" from the Taverna home directory to force installation of a plugin by default. Note that in this case it is also recommended to copy the full content of "repository" from the Taverna home directory to append the installation directory's "repository". Memory usage -----------For OS X and Linux, Taverna will use a maximum of 400 MB. In Windows, "taverna-debug.bat" will also use 400 MB, while "taverna.exe" will use up to 400 MB or, if higher, 15% of available memory at the point of launching Taverna. If Taverna happens to run out of memory while running a workflow with large data (or large number of data), you can set Taverna to store data in a database by going to Preferences->Data and Provenance and remove the tick for "In-memory storage". This will reduce execution speed slightly, but should consume less memory. Also remember to click 'Remove' on old runs you are no longer interested in. http://www.mygrid.org.uk/dev/wiki/display/taverna/Data+and+provenance+preference

s has more details on the data settings. If you need to increase the available memory, edit "taverna.sh" or "taverna-debug.bat" and replace "-Xmx400m" with say "-Xmx600m" to use 600 MiB. For OS X you would need to right click on "Taverna.app" and go inside the application bundle to edit Contents/Info.plist and change the same parameter using the Property List Editor. http://www.mygrid.org.uk/dev/wiki/display/taverna/Increase+memory+allocation has more details on memory allocation.