geWorkbench

Using geWorkbench

Q. I get a Java error when I try to start geWorkbench.

A. This is almost always caused by the Sun Java 1.5 JRE not being installed or not being found. Try reinstalling the Java 1.5 JRE and then reinstall geWorkbench. geWorkbench must be installed after the JRE.

Q. How do I increase the amount of memory available to Java to run geWorkbench?

A. It depends on how you are running geWorkbench.

1. If you are running a packaged distribution of geWorkbench (created using InstallAnywhere), there is a file in the geWorkbench root directory called UILauncher.lax. There is a line there which specifies the Java heap size:

lax.nl.java.option.java.heap.size.max=640678989

Here it is shown set to about 640 MB. You can experiment with increasing this, subject to the amount of memory in your machine and demands on it from other applications.

2. If you are running geWorkbench from the source distribution using Ant, you can edit the build.xml file found in the geWorkbench root directory to alter the memory requested using the variable jvmarg:

<target name="run" depends="init" description="Runs geWorkbench.">
    <java fork="true" classname="org.geworkbench.engine.config.UILauncher">
       <jvmarg value="-Xmx512M"/>
       <jvmarg value="-Djava.library.path=lib"/>
       <arg value="all_release.xml"/>
       <classpath refid="run.classpath"/>
    </java>
</target>

Here it is shown requesting 512 MB.

Q. ARACNE does not run in version 1.0.4 (Note that this version has been superseded).

A. There were two text files that were omitted from the distribution, you can download them from the ARACNE tutorial page and install them into the geWorkbench root directory.

Q. ARACNE is not included in geWorkbench 1.0.5 - 1.0.6. How can I run this algorithm?

A. A new, Java-based version of ARACNE has been implemented in the development version of geWorkbench. You can download the development version from the GForge site (http://gforge.nci.nih.gov/scm/?group_id=78). There are two methods by which this can be done

1. Use the "Nightly CVS Tree Snapshot" link, or
2. If you are familiar with CVS, you can obtain the source via an anonymous CVS download. You will need the following parameters for CVS.
   1. username: anonymous
   2. password: anonymous
   3. protocol: ext
   4. CVS server: cbiocvs2.nci.nih.gov:
   5. CVS directory: /cvsshare/content/cabigcvs/cvsroot

This is a source distribution which you will need to compile yourself (you must have the Java JDK 5 installed on your machine - see http://java.sun.com, look under "previous releases". Or try JDK 6, the current version, however we have not tested this).

If you have Ant installed on your machine, you can just type "ant run" in the geworkbench root directory and the program will be built and run.

If you do not have Ant, you can just execute one of the provided launch scripts, also found the in geworkbench root directory. They are:

• Windows: launch_geworkbench.bat
• Linux/Unix: launch_geworkbench.sh
• Mac: your guess is as good as mine...., perhaps "launch_geworkbench.sh" will work.

A standalone version of ARACNE is also availabe at http://amdec-bioinfo.cu-genome.org/html/ARACNE.htm