If needed, add Java 8 to alternatives:

update-alternatives --install <link> <command> <real_path> <priority>

ex: update-alternatives --install /usr/bin/java java /usr/local/bin/java 80

Switch to Java 8:

sudo update-alternatives --config java

Select the correct number to switch versions, then confirm that you are using the correct version:

user@ubuntu:~/Desktop/kinc-nf-demo$ java -version
openjdk version "1.8.0_242"
OpenJDK Runtime Environment (build 1.8.0_242-8u242-b08-0ubuntu3~18.04-b08)
OpenJDK 64-Bit Server VM (build 25.242-b08, mixed mode)

It should be 1.8.XXX.

Go to the kinc-nf-demo folder:

cd <PATH>/kinc-nf-demo

Select one of the demoes in the demos folder to run:

• yeast-cpu: Running the Yeast GEM on CPU resources.
• cervix-gpu: Running the Cervix GEM on GPU resources.

Load the input data onto the PVC:

./kube-load.sh <PVC> <DEMO_FOLDER> <PATH_ON_PVC>

ex: ./kube-load.sh teach-compbio yeast-cpu user-cole

Deploy KINC using nextflow-kuberun:

nextflow kuberun systemsgenetics/kinc-nf -v <PVC> -c demos/<DEMO_FOLDER>/nextflow.config

Wait until the workflow is finished running.

Copy the output of KINC from the PVC to your VM:

./kube-save.sh <PVC> <DEMO_FOLDER>-output

Open Cytoscape. (Applications -> Other -> Cytoscape)

Go to your desktop and open a file browsing window, navigate to <PATH>/kinc-nf-demo/<DEMO_FOLDER>-output/<INPUT_GEM>.

Finally, drag the file <INPUT_GEM>.net from the file browser to Cytoscape!

The network should now be visualized!