Request deployment CellProfiler

[vemonet]

Describe the application

Profiling Cells, with a desktop UI, but the code can be exported to be run on the DSRI

Options:

• The users use the CellProfiler UI locally, then export the pipeline as a script. And the user will have a way to easily send this pipeline to be run on the DSRI (+ access and visualization of the logs and output)
• We deploy the CellProfiler UI directly on the DSRI. Is there a way to expose the CellProfiler UI as a web UI? Ideally packaged in a Docker container

Application Git repository URL

https://cellprofiler.org/ https://github.com/CellProfiler/CellProfiler

Docker image of the application

Official Docker image: https://hub.docker.com/r/cellprofiler/cellprofiler Best to build: https://github.com/CellProfiler/distribution/tree/master/docker

Docs: https://github.com/CellProfiler/distribution/blob/master/docker/README.md

On a Linux host machine, running CellProfiler's GUI from the container:

xhost +local:root
VERSION=4.0.0 docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix:ro cellprofiler:${VERSION} ""

Another image available: https://github.com/pharmbio/cellprofiler-docker

[vemonet]

https://github.com/CellProfiler/Distributed-CellProfiler : how it runs on AWS

Check Wiki for headless run infos: https://github.com/CellProfiler/CellProfiler/wiki

1 headless = 1 core. we need to start as many container as we want to use cores

Help: Github issues and https://forum.image.sc

If we want to publish scripts to deploy on Kubernetes: to https://github.com/CellProfiler/distribution

Plan

1. Use CellProfiler on DataHub to build the pipeline
2. Export pipeline
3. Use oc cp from DataHub to copy images and pipeline files to the DSRI
4. Use oc exec to run the pipeline file

What might be a bit tricky to do properly: dispatching the jobs. To allow deploying the number of workers we want (but kubernets should give good tools for that)

Next steps

I have no idea what the CellProfiler look like on DataHub and how I can install the oc tool and communicate with the DSRI cluster (we might need to ask for opening some things to the networking)

[vemonet]

Documentation to deploy the CellProfiler on the DSRI: https://maastrichtu-ids.github.io/dsri-documentation/docs/catalog-imaging