The title is pretty much the question.

Is it possible to generate multiple conda/mamba environments in a single container using the recipe.

I’ve been trying using the code below but when I build the container, only the first environment is created.

%post
        mamba create --quiet --channel bioconda --name fastqc python=3.9 numpy fastqc multiqc
        mamba create --quiet --channel bioconda --channel conda-forge --name conda-env python=3.9 numpy
        conda config --add --yes channels defaults
        conda config --add --yes channels conda-forge
        conda config --add --yes channels bioconda
        conda config --set --yes channel_priority strict

This seems like a relatively simple and likely common desire but I can’t find any information in my searches.

Any help would be appreciated.

The code above is what I tried.

I’m expecting this.

$ singularity shell gge_container_v3.sif
Singularity> conda env list
# conda environments:
#
base                  *  /opt/mamba
fastqc                   /opt/mamba/envs/fastqc
conda-env                /opt/mamba/envs/conda-env

I’m getting this:

$ singularity shell gge_container_v3.sif
Singularity> conda env list
# conda environments:
#
base                  *  /opt/mamba
fastqc                   /opt/mamba/envs/fastqc