natbutter / monai-contained

Container for moani that works on ubu 16.04

MonAI Label Container

Docker/Singularity image to run MonAI Label on a Centos 6.10 kernel

If you have used this work for a publication, you must acknowledge SIH, e.g: "The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney."

Quickstart for Artemis

Put this repo on Artemis e.g.

cd /project/<YOUR_PROJECT>
git clone https://github.com/Sydney-Informatics-Hub/monai-contained.git

Then cd monai-contained and modify the run_artemis.pbs script and launch with qsub run_artemis.pbs.

Otherwise here are the full instructions for getting there....

How to recreate

Build with docker

Check out this repo then build the Docker file.

sudo docker build . -t sydneyinformaticshub/monailabel

Run with docker.

To run this, mounting your current host directory in the container directory, at /project, map port 8000 (the default port monai server is hosted on) and execute an interactive shell:

sudo docker run -it -v `pwd`:/project -p 8000:8000 --gpus all sydneyinformaticshub/monailabel /bin/bash

Push to docker hub

sudo docker push sydneyinformaticshub/monai

See the repo at https://hub.docker.com/r/sydneyinformaticshub/monai

Build with singularity

export SINGULARITY_CACHEDIR=`pwd`
export SINGULARITY_TMPDIR=`pwd`

singularity build monai.img docker://sydneyinformaticshub/monai

Run with singularity

To run the singularity image (noting singularity mounts the current folder by default)

singularity run --bind /project:/project monai.img /bin/bash -c "cd "$PBS_O_WORKDIR" && monailabel start_server --app pathology/ --studies images/"