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
|
cytoscape.sh
| 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
|
pellet.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 cytoscape.sh 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.