Elizabeth Skippington Notes: Difference between revisions
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= Useful links = | |||
Cytoscape with Power Plugin (via Java WebStart) [http://www.biotec.tu-dresden.de/schroeder/group/powergraphs/cytoscape_webstart/cy1_powergraphsonly.jnlp] | |||
Revision as of 09:10, 10 August 2008
Liz's Notes
Add some notes here.
Useful links
Cytoscape with Power Plugin (via Java WebStart) [1]
Running Java Apps
Currently it appears that only version 1.4.2 of the JRE (Java Runtime Environment) is installed, which is not suitable for all applications. To use the newer version of JRE, you need to specify the full path to the java executable that is installed in the home directory e.g. instead of
java app.jar
use
/home/e.skippington/Programs/java/jre1.6.0_07/bin/java app.jar
This has been temporarily fixed by creating a symlink in ~/bin/ of java pointing to the new version of java.
Running Java WebApps
The latest JRE has been installed, but only the 32 bit version, so a separate 32 bit version of firefox has been installed to use the latest 32 bit version of the JRE. The 32 bit, new JRE firefox is at:
/usr/lib/firefox-3.0.1/firefox
and a symlink called firefox32 has been created to point to it.
Running power graph Program
Run the power graph program by something like:
java -Xmx1024M -jar Oog.jar -convert -inputfiles=edg -output=bbl -v -writeLog=0 -sortbyfilesize -checkequality -minsim=0.0 -min_max=1 -useGlobalClustering=1 -useGreedyClustering=1
Use the following line for help:
java -Xmx1024M -jar Oog.jar -?