The following information is available for using libsbml in Taverna
workflows:
The use of libsbml 2.3.4 has been tested to work with the latest version of
taverna 1.6.2. 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 2.3.4
are available as zip files below. libSBML version 3.0 libraries will be made
available in November 2007.
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 Documents and Settings\username\Application Data\Taverna-1.6.2.
This is followed
by making the following changes highlighted in bold in the runme.bat file in
your Taverna installation directory:
@echo off
set ARGS=-Xmx300m
set ARGS=%ARGS%
-Djava.system.class.loader=net.sf.taverna.tools.BootstrapClassLoader
set ARGS=%ARGS% -Djava.protocol.handler.pkgs=uk.ac.rdg.resc.jstyx.client
set ARGS=%ARGS% "-Dtaverna.dotlocation=%~dp0\bin\win32i386\dot.exe"
REM NB: Proxy configuration settings have now been reverted to being in
conf/mygrid.properties
REM Required for dependencies on libsbml
set LIB_PATH=%APPDATA%\Taverna-1.6.2\lib
set PATH=%PATH%;%LIB_PATH%
set ARGS=%ARGS% "-Djava.library.path=%LIB_PATH%"
java %ARGS% -jar "%~dp0\taverna-bootstrap-1.6.2.0.jar" %*
For Linux, its zip file should be extracted into your
$HOME/.taverna-1.6.2/lib
folder. Your Taverna runme.sh script should then be edited with the text
highlighted in bold as follows:
(..)
# Load customised properties if they exist
if [ -f "$TAVERNA_HOME/custom.sh" ] ; then
source "$TAVERNA_HOME/custom.sh"
fi
# Set to $TAVERNA_HOME/lib for shared installation
LIB_PATH="$HOME/.taverna-1.6.2/lib"
LD_LIBRARY_PATH="$LIB_PATH"
export LD_LIBRARY_PATH
ARGS="-Djava.library.path=$LIB_PATH"
java $ARGS -jar "$TAVERNA_HOME/taverna-bootstrap-1.6.2.0.jar" $@
For those people using MacOS X, the libsbml native libraries should be placed
in the same directory where your Taverna application bundle resides. So for
example, if your Taverna application bundle is in
/Applications/Taverna-1.6.2/Taverna.app then the libxerces-c.27.dylib,
libsbml.dylib and libsbmlj.jnilib files should be placed
there. In constrast, the libsbml jar file should be placed in
Taverna's lib folder which is found at /Users/username/Library/Application
Support/Taverna-1.6.2/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 runme.* taverna
startup script where required. To use these installers, download the file
relevant to your
platform, and run the executable file following its extraction if
required. You will need to inform the installer where your Taverna
application has been installed on your filesystem.
-
Taverna 1.7.0
-
Taverna 1.6.2
The XML API configuration file for libsbml can be downloaded from the link
below. This file specifies those classes and methods from libsbml which can
be used for the construction of workflows. To import the API consumer
definition file into Taverna, right click on Available Processors in the
Scavenger panel. Select Add new API Consumer and select the above libsbml
definition file. A new branch labelled libsbml-2.3.4 will then be added to
the
scavenger panel, showing the libsbml class names and methods for use in SBML
workflows.
These libsbml methods can then be used as workflow processors by
right-clicking on them and adding them to your workflow model.
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