GenePattern macOS Setup Guide

GenePattern macOS Setup Guide

The GenePattern team recommends using the (docker installation on modern Macs)[https://github.com/genepattern/genepattern-server/wiki/Running-GenePattern-in-a-Docker-Container]. However if you wish to continue using the This guide helps get the GenePattern mac app working for MacOS Sonoma and later builds.

Prerequisites

Install a Java 1.8 JVM. The recommended option is Zulu 8 (native arm64):

• Download from: https://www.azul.com/downloads/?version=java-8&os=macos&architecture=arm-64-bit&package=jdk
• Install the .dmg and verify with:

  /usr/libexec/java_home -V

  Confirm zulu-8.jdk appears in the list.

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Step 1: Bypass Gatekeeper

macOS will block GenePattern on first launch because it is not notarized.

1. Open System Settings → Privacy & Security
2. Scroll to the Security section
3. Click Open Anyway next to the GenePattern warning
4. Confirm when prompted

If "Open Anyway" doesn't appear, right-click the app in Finder → Open to force the dialog.

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Step 2: Fix the Java Launcher

GenePattern's launch script sets JAVA_HOME to Java 1.8 but then ignores it by finding the system java in PATH first. Edit the script to check JAVA_HOME first.

sudo nano /Applications/GenePattern.app/Contents/MacOS/GenePattern

Find this block:

if type -p java; then
    echo found java executable in PATH
    _java=java
elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then

Replace it with:

if [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]; then
    echo found java executable in JAVA_HOME
    _java="$JAVA_HOME/bin/java"
elif type -p java; then
    echo found java executable in PATH
    _java=java
elif

Save: Ctrl+O → Enter → Ctrl+X

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Step 3: Pin Tomcat to Java 1.8

Create a setenv.sh file that Tomcat automatically sources at startup, hardcoding the Zulu 8 JVM:

cat > /Applications/GenePattern.app/Contents/Resources/GenePatternServer/Tomcat/bin/setenv.sh << 'EOF'
#!/bin/bash
export JAVA_HOME=/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home
export JRE_HOME=/Library/Java/JavaVirtualMachines/zulu-8.jdk/Contents/Home
EOF

chmod +x /Applications/GenePattern.app/Contents/Resources/GenePatternServer/Tomcat/bin/setenv.sh

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Step 4: Launch GenePattern

Double-click GenePattern.app — it should now launch correctly, start Tomcat with Java 1.8, and open your browser to http://127.0.0.1:8080/gp.

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Troubleshooting

Still seeing the -Djava.endorsed.dirs error?
Verify Zulu 8 is installed and visible:

/usr/libexec/java_home -V

Confirm /Library/Java/JavaVirtualMachines/zulu-8.jdk appears. If not, reinstall Zulu 8.

GenePattern opens but browser doesn't load?
Wait a few extra seconds — Tomcat can take 10–15 seconds to start. Then manually open http://127.0.0.1:8080/gp.