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Main.InstallationNotes History
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June 01, 2006, at 06:22 PM
by 157.99.164.30 -
Changed lines 70-72 from:
Alternativley you may want to specify where those libraries are in the java -Djava.ext.dirs= parameter. In this case edit the cytoscape.sh or cytoscape.bat file and add this parameter to the java instruction that runs Cytoscape.
to:
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.
June 01, 2006, at 06:21 PM
by 157.99.164.30 -
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June 01, 2006, at 06:20 PM
by 157.99.164.30 -
Changed lines 68-76 from:
On windows systems, copy all of them in:
On a Linux system, copy all of them in:
Alternativley copy all of them in a directory accessible to the system, then edit the cytoscape.sh file provided with the RDFScape distribution and replace the original cytoscape.sh file in the Cytsocape distribution.
You will need to specify where those libraries are in the java -Djava.ext.dirs= parameter.
You can do the same for the .bat file on windows.
to:
/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= parameter. In this case edit the cytoscape.sh or cytoscape.bat file and add this parameter to the java instruction that runs Cytoscape.
June 01, 2006, at 06:12 PM
by 157.99.164.30 -
Changed line 11 from:
4) Unpack the context of your Analysis Contyext in the Cytoscape directory. The result (of your Cytoscape directory) should be look like:
to:
4) Unpack the context of your Analysis Contyext in the Cytoscape directory. The result (the listing of your Cytoscape directory) should be look like:
Changed lines 47-48 from:
This is the complete list.
to:
This is the complete list:
(:table :)
(:cell :) antlr-2.7.5.jar
(:cell :) icu4j_3_4.jar
(:cell :) json.jar
(:cell :) wstx-asl-2.8.jar
(:cellnr :) arq.jar
(:cell :) iri.jar
(:cell :) junit.jar
(:cell :) xercesImpl.jar
(:cellnr :) commons-logging.jar
(:cell :) jena.jar
(:cell :) log4j-1.2.12.jar
(:cell :) xml-apis.jar
(:cellnr :) concurrent.jar
(:cell :) jenatest.jar
(:cell :) stax-api-1.0.jar
(:cellnr :)pellet.jar
(:tableend :)
June 01, 2006, at 06:02 PM
by 157.99.164.30 -
Changed lines 3-11 from:
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 Cuytoscape directory. The result should be look like:
to:
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 (of your Cytoscape directory) should be look like:
Changed line 43 from:
5) Make the Jena and Pellet libraries visible to the RDFScape plugin. This is the most complex part.
to:
5) Make the Jena and Pellet libraries visible to the RDFScape plugin. This is the most complex part.
Changed lines 59-60 from:
6) Start Cytoscape, go to edit->preferences then add plugin and then restart it.
to:
6) Start Cytoscape, go to edit->preferences then add plugin and then restart it.
June 01, 2006, at 05:50 PM
by 157.99.164.30 -
Changed lines 13-42 from:
cell annotation
cell Cytoscape-v2.2.lax
cell plugins
cellnr Cytoscape2_2Manual.pdf
cell INSTALL.txt
cell rdfscapecontexts
cellnr cytoscape.bat
cell jre
cell sampleData
cellnr cytoscape.jar
cell lax.jar
cell tax_report.txt
cellnr cytoscape.props
cell lib
cell Uninstall_Cytoscape-v2.2
cellnr cytoscape.sh
cell licenses
cell vizmap.props
cellnr Cytoscape-v2.2
cell LICENSE.txt
cell
tableend
to:
(:cell :) annotation
(:cell :) Cytoscape-v2.2.lax
(:cell :) plugins
(:cellnr :) Cytoscape2_2Manual.pdf
(:cell :) INSTALL.txt
(:cell :) rdfscapecontexts
(:cellnr :)cytoscape.bat
(:cell :) jre
(:cell :) sampleData
(:cellnr :) cytoscape.jar
(:cell :) lax.jar
(:cell :) tax_report.txt
(:cellnr :) cytoscape.props
(:cell :) lib
(:cell :) Uninstall_Cytoscape-v2.2
(:cellnr :) cytoscape.sh
(:cell :) licenses
(:cell :) vizmap.props
(:cellnr :) Cytoscape-v2.2
(:cell :) LICENSE.txt
(:cell :)
(:tableend :)
June 01, 2006, at 05:48 PM
by 157.99.164.30 -
Changed lines 12-20 from:
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
to:
(:table :)
(: cell :) annotation
(: cell :) Cytoscape-v2.2.lax
(: cell :) plugins
(: cellnr :) Cytoscape2_2Manual.pdf
(: cell :) INSTALL.txt
(: cell :) rdfscapecontexts
(: cellnr :)cytoscape.bat
(: cell :) jre
(: cell :) sampleData
(: cellnr :) cytoscape.jar
(: cell :) lax.jar
(: cell :) tax_report.txt
(: cellnr :) cytoscape.props
(: cell :) lib
(: cell :) Uninstall_Cytoscape-v2.2
(: cellnr :) cytoscape.sh
(: cell :) licenses
(: cell :) vizmap.props
(: cellnr :) Cytoscape-v2.2
(: cell :) LICENSE.txt
(: cell :)
(: tableend :)
May 30, 2006, at 05:42 PM
by 157.99.164.30 -
Changed lines 5-13 from:
1) First, you'll need Cytoscape here. See [[]] for details on compatibility and versions.
2) Second, you will need Jena and Pellet. Donwload them here and here. See [[]] 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 Cuytoscape directory. The result should be the following:
to:
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 Cuytoscape directory. The result 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
May 30, 2006, at 05:38 PM
by 157.99.164.30 -
Changed lines 7-8 from:
2) Second, you will need Jena and Pellet. Donwload them here and here. See [[]] for details on compatibility and versions.
to:
2) Second, you will need Jena and Pellet. Donwload them here and here. See [[]] for details on compatibility and versions.
May 30, 2006, at 12:04 PM
by 157.99.164.30 -
Added lines 1-32:
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 [[]] for details on compatibility and versions.
2) Second, you will need Jena and Pellet. Donwload them here and here. See [[]] 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 Cuytoscape directory. The result should be the following:
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.
Now, on macosx system, copy all of them in:
On windows systems, copy all of them in:
On a Linux system, copy all of them in:
Alternativley copy all of them in a directory accessible to the system, then edit the cytoscape.sh file provided with the RDFScape distribution and replace the original cytoscape.sh file in the Cytsocape distribution.
You will need to specify where those libraries are in the java -Djava.ext.dirs= parameter.
You can do the same for the .bat file on windows.
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.
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