This image analysis project has been setup to take advantage of a technology known as Docker.

This means that you will need to:

1. Download and install the Docker Toolbox
2. Build a docker image

Before you can run the image analysis in a docker container.

Before you can run your analysis you need to build your docker image. Once you have built the docker image you should not need to do this step again.

A docker image is basically a binary blob that contains all the dependencies required for the analysis scripts. In other words the docker image has got no relation to the types of images that we want to analyse, it is simply a technology that we use to make it easier to run the analysis scripts.

$ cd docker
$ bash build_docker_image.sh
$ cd ..

The image analysis will be run in a Docker container. The script run_docker_container.sh will drop you into an interactive Docker session.

$ bash run_docker_container.sh
[root@048bd4bd961c /]#

Now you can run the image analysis.

[root@048bd4bd961c /]# python scripts/analysis.py --debug data/ output/

Create a singularity image from the docker image.

cd singularity
bash build_singularity_image.sh

Copy the singularity image file to the research group share.

Use the slurm_runner.py script and the slurm_analysis.yml to generate slurm scripts.

Copy the slurm scripts to the research group share.

Run the slurm scripts on the cluster.