Walter Jessen

In my scientific research, I use a Java program called GeneSpring GX, which provides statistical tools for fast visualization and analysis of gene expression data. Although the latest release is version 10, when we tested it earlier this year on OS X there were a number of issues, so I’ve continued to use an older release (version 7.3.1) on Leopard.

I upgraded to Snow Leopard on my MacBook two weeks ago (I did a format and install) and encountered some trouble with GeneSpring GX.

When I tried to install GeneSpring GX 7.3.1, I received an error that the JVM could not be found. I remembered having to switch Java versions from Java 5, version 1.5 to version 1.4 under Leopard in order to get the installation program to run. However, both Java 5, version 1.5 and version 1.4 don’t exist on Snow Leopard. Downloading either Java .dmg doesn’t work either, since the installation programs won’t let you install the package: “This volume does not contain a version of Java that needs updating.”

The problem is that Snow Leopard comes with Java 6, version 1.6 installed. The way around this is to manually install Java 1.4 — fire up Terminal and type the following:

cd /tmp/
curl -o java.1.4.2-leopard.tar.gz http://www.cs.washington.edu/homes/isdal/snow_leopard_workaround/java.1.4.2-leopard.tar.gz
tar -xvzf java.1.4.2-leopard.tar.gz
sudo mv 1.4.2 /System/Library/Frameworks/JavaVM.framework/Versions/1.4.2-leopard
cd /System/Library/Frameworks/JavaVM.framework/Versions/
sudo ln -s 1.4.2-leopard 1.4
sudo ln -s 1.4.2-leopard 1.4.2
open "/Applications/Utilities/Java Preferences.app"

When the Java Preferences window opens, drag “J2SE 1.4.2 32-bit” under Java Applications to the top of the list. You can now use the GeneSpring GX installation program.

One more trick: right click on the GeneSpring GX.app (in the GeneSpring GX data subfolder) and choose “Show Package Contents”. In the Contents folder, open Info.plist and look for JVMVersion.

Replace <string>1.4+</string> with <string>1.4*</string> (replace the + with an asterisk) and save.

This will force GeneSpring GX to always use Java 1.4. Any Java version greater than that and the GeneSpring graphics run much too slow.

You can then move the “J2SE 1.4.2 32-bit” entry under Java Applications in the Java Preferences window back to the bottom of the list.

UPDATE May 30, 2011: this appears to no longer work with OS X version 10.6.6 – the Java installation completes but the GeneSpring installer quits unexpectedly as soon as it is opened.