Cytoscape and JAVA 11

I use Cytoscape for network analyses. It’s a JAVA program, that seems to quite picky about the version and flavour of JAVA. At the moment, Cytoscape 3.9.1 requires JAVA 11, specifically AdoptOpenJDK Hotspot. The project has recently moved to Adoptium, that offer prebuilt OpenJDK binaries.

I am using CRUX 3.6.1 at the moment, with jdk8-bin installed from opt. Most of my installed programs that require JAVA are happy with it, however I needed to install AdoptOpenJDK 11 Hotspot, just for Cytoscape. So, I used as a guide the openjdk11-jdk port .footprint (so I know where files should go), to make my own adoptium11-jdk port.

My port just repackages the tarball provided by upstream, placing its contents in:

/usr/lib/jdk/adoptium11-jdk/

So, when trying to install the program by running:

sh ./Cytoscape_3_9_1_unix.sh 

I get this error:

No suitable Java Virtual Machine could be found on your system.
The version of the JVM must be at least 11.0 and at most 12.
Please define INSTALL4J_JAVA_HOME to point to a suitable JVM.

Right… So, before installation, I needed to do the following:

export JAVA_HOME=/usr/lib/jdk/adoptium11-jdk/
export PATH="${JAVA_HOME}/bin/:${PATH}"

Now, installing Cytoscape works fine and it “remembers” the location of its JAVA.



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