How to install RDFScape
There are two distinct mode to install RDFScape, the simplified install and the step by step install procedure.
Note: Check to donwload the right binary for your environment, Java1.5 or 1.6.
Simplified install
1) If you have not done it yet, download and install Cytoscape.
2) Download a complete tarball here (JVM 1.6 JVM 1.5) .
note: While is binary is compiled for Java 1.5, we suggest the use of Java 1.6, as future versions will be built for this platform.
3) unpack (tar xvzf) the tarball in the Cytoscape directory.
Just copy the tarball in the Cytoscape main directory (cd Cytoscape_v2.5.2) and unpack it.
4) run cytordfscape.sh or cytordfscape.bat (depending on your system).
Under unix or macosx, run the .sh file. Under windows, run the .bat file. You may need to run them from a terminal. You may have to configure permissions accordingly.
Tested on unix, macosx (limited test on windows)
Step-by-Step install procedure
This will make you install each library and file individually.
1) download and install Cytoscape.
Available here. Check Dependencies for versions supported.
2) download and install Jena.
Available here. Install it, simply uncompress it.
3) download and install Pellet.
Available here. Install it, simply uncompress it.
4) download and install RDFScape.
RFScape is composed of:
- the plugin itself: RDFScape.jar
- a set of analysis contexts
Only the plugin is strictly required for functioning, but all the components toghether will enable all functionalities and present some ready to use examples.
You can download the above components from http://bioinformatics.org/project/filelist.php?group_id=601. Pick the last RDFSCape.jar plugin and one or more of the last analysis contexts.
From time to time all the files all released toghether with source code in a single tarball.
You can always access the svn repository for the latest version.
To install RDFScape:
- extract RDFSCape.jar from the file you downloaded and put it in Cytoscape_vy_x.z/plugins (x_y.z stands for your current version)
- unpack (tar xvzf) the analysis contexts in the Cytoscape_vy_x.< directory.
5) Make Cytoscape, RDFScape, Jena and Pellet work toghether.
You need to ensure the Pellet and Jena libraries are accessible by RDFScape while running as a Cytoscape plugin.
Copy all the libraries (.jar)in Jena-2.5.4/lib and in pellet-1.5.1 (the two files in pellet-1.5.1/lib/xsdlib/) in the Java extension directory: this is typically (for J2SE v1x.y.z):
- C:\Program Files\Java\j2rex.y.z\lib\ext on Windows
- /usr/java/j2rex.y.z/lib/ext on Linux
- /Library/Java/Extensions on Macosx
As an alternative, you may include required jars in your java execution command with the parameter: java -Djava.ext.dirs=your_dirs ... you will need to edit cytoscape.sh or cytoscape.bat for this.
You may also want to optimize this file to improve performances (memory allocated and virtual machine settings)
6) Start RDFScape
Start Cytoscape and select RDFScape from the plugin menu
7) You are ready to use or create an analysis context and use RDFScape, refer to Instructions for this.
Note: Whenever you update RDFScape, you will need only to replace RDFScape.jar !!!