sharing a cytoscape installation with multiple terminals
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Entering edit mode
7 weeks ago

i am trying to implement cytoscape in my lab and have installed it on the centralized server which we access via ssh from own terminals (with x11 forwarding).

currently cytoscape 3.8.2 is installed (as root) in /opt/ and executing it as non-root users works. however, if a second user launches it while an instance is already running, it throws error:

karaf: There is a Root instance already running with name Cytoscape 3.8.2 and pid 121496. If you know what you are doing and want to force the run anyway, export CHECK_ROOT_INSTANCE_RUNNING=false and re run the command.

is there a way to have a centralised installation of cytoscape and have multiple users access it from their own terminals?

or is it safe to do:

CHECK_ROOT_INSTANCE_RUNNING=false

server hpc cytoscape • 251 views
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You could try doing this : https://stackoverflow.com/questions/37671889/apache-karaf-root-instance-already-running

Someone from cytoscape project stops by here periodically and may offer a solution.

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Entering edit mode
6 weeks ago
Scooter ▴ 50

Yes, it should be safe, although there are some caveats. Once you get past the "CHECK_ROOT_INSTANCE_RUNNING" you'll get an error about "port already open". This is because Cytoscape attempts to open a port for it's REST interface. You can easily wrap the Cytoscape launch in a python or shell script that randomizes the port to avoid that problem, but if you have users using RCy3 or py4cytoscape, they would have to know the port to connect to. The best solution, especially in an hpc environment, is to run Cytoscape in a docker or singularity container and map the REST port "1234" to something user-specific.

-- scooter

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