Revision as of 15:29, 12 June 2009

Using geWorkbench

Q. How can I run geWorkbench on a 64-bit Windows system (or other system for which no installer currently is distributed)?

A. We have created a Zip file version of the geWorkbench distribution. It can be used on any operating system supporting Java, including 64 bit systems. Instructions are found on the geWorkbench releases notes at the GForge distribution site: https://gforge.nci.nih.gov/frs/?group_id=78

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. Where can I obtain the latest annotation files for my microarray platform?

A. Affymetrix annotation files can be downloaded from their support site, at www.affymetrix.com: Support->Technical Documentation->Annotation Files ([1])

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. How can I run ARACNE?

A. A new, Java-based version of ARACNE has been implemented and was released in geWorkbench v1.5.0.

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

Q. How can I download the geWorkbench source?

A. 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. Use anonymous CVS.

Using the Nightly CVS Tree:

1. Click on the SCM tab.
2. Click on the link titled "Download The Nightly CVS Tree Snapshot" to download the whole code tree (warning: this is a big zip file).
3. Unzip and go to the top directory of the distribution.
4. Execute the script launch_geworkbench.sh or launch_geworkbench.bat (Windows).

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. CVSROOT directory: /cvsshare/content/gforge/geworkbench
6. CVS module name: geworkbench

Whichever method is used, this is a source distribution which you will need to compile yourself:

• you must have the Java JDK 5 (or higher) installed on your machine - see http://java.sun.com, under the "Java SE" link.
• you must make sure that the value of the environment variable JAVA_HOME is the directory where the JDK is installed.

Note that Sun recommends adding the Java JDK bin directory to your machine's PATH variable. Under Windows, "Typically this full path looks something like C:\Program Files\Java\jdk1.5.0_<version>\bin." Full instructions can be found on the Java site.

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. Ant can be downloaded from http://ant.apache.org/. Note that installing Ant involves manually adding the Ant bin directory to the PATH variable, setting the ANT_HOME directory, and optionally setting the JAVA_HOME directory.

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/Mac: launch_geworkbench.sh

Q. How can I reference geWorkbench in a publication?

A. You can use the following statement:

"Analysis was carried out using geWorkbench (http://www.geworkbench.org), a free open source genomic analysis platform developed at Columbia University with funding from the NIH Roadmap Initiative (1U54CA121852-01A1) and the National Cancer Institute".

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.