======================= | |
Taverna workbench 2.2.0 | |
======================= | |
http://www.taverna.org.uk/ | |
http://www.mygrid.org.uk/ | |
Released by myGrid, 2010-07-05 | |
(c) Copyright 2005-2010 University of Manchester, UK | |
Licence | |
======= | |
Taverna is licenced under the GNU Lesser General Public Licence. (LGPL) 2.1. | |
See the file LICENCE.txt for details. | |
If the source code was not included in this download, you can download it from | |
http://www.taverna.org.uk/download/source-code/ | |
Taverna uses various third-party libraries that are included under compatible | |
open source licences such as Apache Licence. | |
Running Taverna | |
=============== | |
For Windows, if you used the installer you should have | |
Taverna->Taverna workbench 2.2.0 in your Start menu. If you used the | |
self-extracting archive, double-click on "taverna.exe" in the extracted folder. | |
For OS X, copy the Taverna application bundle to /Applications or your | |
preference. Eject the disk image, and run Taverna from the installed location. | |
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. | |
Documentation | |
============= | |
See http://www.taverna.org.uk/documentation/taverna-2-x/ for | |
documentation and tutorials on using Taverna. | |
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 2.2 workflows can be found in the myExperiment starter pack at | |
http://www.myexperiment.org/packs/122 | |
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 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 at registration time. | |
For full terms and condition of our registration, see | |
http://www.taverna.org.uk/about/legal-stuff/terms/ | |
Requirements | |
============ | |
Taverna requires the Java Runtime Environment (JRE) version 5 or 6 from Sun. | |
No other versions of Java are officially tested with Taverna. | |
*Note that future versions of Taverna will require Java 6.* | |
Mac OS X 10.5 (Leopard) and later should come with Java 5 or newer. | |
Windows users might need to download Java from http://java.com/ | |
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. | |
To download Sun Java 6 for Ubuntu, start a Terminal, and type the following: | |
sudo aptitude 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 | |
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://tinyurl.com/java6sec -or- | |
https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jce_policy-6-oth-JPR@CDS-CDS_Developer | |
For Java 5, you can download the unlimited cryptography policy jar files from: | |
http://tinyurl.com/java5sec -or- | |
https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jce_policy-1.5.0-oth-JPR@CDS-CDS_Developer | |
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 XP: C:\Documents and settings\JohnDoe\ | |
Application Data\taverna-2.2.0\logs | |
Vista/Windows 7: C:\Users\JohnDoe\AppData\Roaming\taverna-2.2.0\logs | |
OS X: /Users/JohnDoe/Library/Application support/taverna-2.2.0/logs | |
Linux: /home/johndoe/.taverna-2.2.0/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 | |
400 MB or up to 50% of available memory when 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. | |
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. |