Open sorenwacker opened 5 months ago
It seems the container does not execute the entrypoint script.
After banging my head against the wall for 2 days, I figured out a way to successfully activate the base environment for singularity exec
and singularity shell
.
Bootstrap: docker
From: mambaorg/micromamba:1.5.8
%files
# Import yml into /opt
./environment.yml /opt
%environment
export PATH="${MAMBA_ROOT_PREFIX}/bin:$PATH"
%post -c /bin/bash
# Install into base environment from input yml
micromamba install -y -n base -f /opt/environment.yml && \
micromamba clean --all --yes
%runscript
#!/bin/bash
# Activate base environment
source /usr/local/bin/_activate_current_env.sh
_activate_current_env.sh
is included within the micromamba-docker image (see here).
I have problems activating the environment by default within a container. Is micromamba using a different installation directory than conda?
Apptainer.def
Apptainer command
Error
Output