Singularity container from conda environment

Question

I want to build a container from my conda environment following this post. However, I get the following error: '/bin/sh: 1: cannot create ~/.bashrc: Directory nonexistent'. I am using a vagrant VM to build my image and would be grateful for any help.

Answer 1

Editing the .bashrc, aside from failing, will not be helpful as the shell loaded by singularity is explicitly --norc. You want to use the $SINGULARITY_ENVIRONMENT variable in %post to have the values available.

Something along these lines:

%post
    # You may need to install some pre-reqs your host system has installed outside of conda, e.g.
    # apt update && apt install -y build-essential make zlib

    ENV_NAME=$(head -1 environment.yml | cut -d' ' -f2)
    echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
    echo "conda activate $ENV_NAME" >> $SINGULARITY_ENVIRONMENT

    . /opt/conda/etc/profile.d/conda.sh
    conda env create -f environment.yml -p /opt/conda/envs/$ENV_NAME

I listed a few libraries that you probably have installed in your current machine that might not be installed in the slim docker image. You can install them via apt or conda, depending on your preference. If it does happen though, it'll be specific to your environment.yml and host OS, so you'll have to iterate through until the build succeeds.