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The workflows require the use of libsbml
version 3 in order to generate models in SBML format. The libsbml library has to be installed on your
computer and its location made known to Taverna in order for it to be used during workflow execution.
The use of libsbml 3 has been tested to work with the latest version of Taverna 2.1.2. To enact SBML workflows, Taverna
needs access to the Java binding of libSBML as well as to the underlying native library generated from the C and C++
source code for libsbml. Platform specific versions of libsbml 3 are available as zip files below.
Installation of the libsbml libraries and configuration of Taverna varies according to your PC platform.
Extract the zip file in the lib directory of your taverna.home folder in C:\Documents and Settings\username\Application
Data\taverna-2.1.2. This is followed by making the following changes highlighted in bold in the taverna-debug.bat file in
your Taverna installation directory:
@ECHO OFF
REM Taverna startup script
REM go to the distribution directory
pushd "%~dp0"
REM 300 MB memory, 140 MB for classes
set ARGS=-Xmx300m -XX:MaxPermSize=140m
REM Internal system properties
set ARGS=%ARGS% -Draven.profile=file:conf/current-profile.xml
set ARGS=%ARGS% -Djava.system.class.loader=net.sf.taverna.raven.prelauncher.BootstrapClassLoader
set ARGS=%ARGS% -Dsun.swing.enableImprovedDragGesture
set ARGS=%ARGS% -Dtaverna.startup=.
REM Required for dependencies on libsbml
set LIB_PATH=%APPDATA%\taverna-2.1.2\lib
set PATH=%PATH%;%LIB_PATH%
set ARGS=%ARGS% "-Djava.library.path=%LIB_PATH%"
java %ARGS% -jar lib\prelauncher-*.jar
pause
REM restore current directory
popd
For Linux, its zip file should be extracted into your $HOME/.taverna-2.1.2/lib folder. Your Taverna taverna.sh script
should then be edited with the text highlighted in bold as follows:
#!/bin/sh
## resolve links - $0 may be a symlink
PRG="$0"
progname=`basename "$0"`
saveddir=`pwd`
# need this to resolve relative symlinks
cd "`dirname "$PRG"`"
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG=`dirname "$PRG"`"/$link"
fi
done
# Required for dependencies on libsbml
LIB_PATH="$HOME/.taverna-2.1.2/lib"
export LIB_PATH
LD_LIBRARY_PATH="$LIB_PATH"
export LD_LIBRARY_PATH
TAVERNA_HOME="`dirname "$PRG"`"
cd $TAVERNA_HOME
# 300 MB memory, 140 MB for classes
exec java -Xmx300m -XX:MaxPermSize=140m \
-Djava.library.path=$LIB_PATH \
-Draven.profile=file:conf/current-profile.xml \
-Dtaverna.startup=. \
-Djava.system.class.loader=net.sf.taverna.raven.prelauncher.BootstrapClassLoader \
-Dapple.laf.useScreenMenuBar=true \
-Dapple.awt.graphics.UseQuartz=false \
-Dsun.swing.enableImprovedDragGesture \
-jar lib/prelauncher-*.jar
For the Mac OS X platform, the libsbml *.jni and *.dylib native libraries should be placed
within the Java folder in your Taverna application bundle . So, for
example, if Taverna was installed in the Applications folder then the jni and dylib libraries
should be moved into /Applications/Taverna 2.1.app/Contents/Resources/Java. In contrast, the *.jar files should be placed in
Taverna's lib folder which is located at /Users/peterli/Library/Application Support/taverna-2.1.2/lib.
Installers for semi-automated installation of the libsbml java and
native libraries for Windows, Linux and MacOS X are available below. These
installers will also make the necessary changes to the Taverna
startup script where required. To use these installers, download the file
relevant to your platform, and run the executable following its extraction if
required. You will need to inform the installer on where Taverna has been installed on your filesystem.
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Taverna 2.2.0
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Taverna 2.1.2
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Taverna 2.1.0
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