Main»Installation Notes

Installation Notes

How to install and run RDFScape

0) You will need a standard Java environment set up. You will need it also for Cytoscape alone, so nothing to add here.

1) First, you'll need Cytoscape here. See Dependencies for details on compatibility and versions.

2) Second, you will need Jena and Pellet. Download them here and here. See Dependencies for details on compatibility and versions.

3) You will need an Analysis Context, download one here.

4) Unpack the context of your Analysis Contyext in the Cytoscape directory. The result (the listing of your Cytoscape directory) should be look like:

annotation Cytoscape-v2.2.lax plugins
Cytoscape2_2Manual.pdf INSTALL.txt rdfscapecontexts
cytoscape.bat jre sampleData
cytoscape.jar lax.jar tax_report.txt
cytoscape.props lib Uninstall_Cytoscape-v2.2 licenses vizmap.props
Cytoscape-v2.2 LICENSE.txt

5) Make the Jena and Pellet libraries visible to the RDFScape plugin. This is the most complex part. First, which libraries ? All the libraries in the /lib directory in Jena and and pellet-1.3.jar

This is the complete list:

antlr-2.7.5.jar icu4j_3_4.jar json.jar wstx-asl-2.8.jar
arq.jar iri.jar junit.jar xercesImpl.jar
commons-logging.jar jena.jar log4j-1.2.12.jar xml-apis.jar
concurrent.jar jenatest.jar stax-api-1.0.jar

Now, on macosx system, copy all of them in: /Library/Java/Extensions

On windows systems, copy all of them in (something like): C:\Program Files\Java\jreX.X.X\lib\ext

On a Linux system, copy all of them in (something like): j2sdk1.5/jre/lib/ext

Alternativley you may want to specify where those libraries are in the java -Djava.ext.dirs= directive. In this case edit the or cytoscape.bat file and add this parameter to the java instruction that runs Cytoscape.

6) Start Cytoscape, go to edit->preferences then add plugin and then restart it.

Your plugin is ready. More will be in the Instructions page.