Conda Environment

For training UNet models We have created a Conda environment and export it through:

conda env export --from-history

It is possible to recreate conda env through

conda env create -f environment.yml

and run the code in that environment or use the containerized version.

Apptainer container

For creating an apptainer image of conda environment a docker definition file is defined as follows:

Bootstrap: docker

From: continuumio/miniconda3

%files
    environment_ubuntu.yml

%post
    conda env create -f environment_ubuntu.yml

%runscript
    exec conda/envs/$(head -n 1 environment.yml | cut -f 2 -d ' ')/bin/"$@"

The Windows Subsystem for Linux (WSL) tool were installed as well as Apptainer.

In ubuntu terminal the singulairity/apptainer image(.sif) file were built.

sudo apptainer build docker_def.def container_name.sif

and then activate the apptainer shell:

apptainer shell your-container-name.sif