apptainer.def

Bootstrap: docker
From: mambaorg/micromamba:1.5
Stage: build

%files
./amplfi /opt/amplfi/amplfi
pyproject.toml /opt/amplfi/pyproject.toml
poetry.lock /opt/amplfi/poetry.lock
conda-lock.yml /opt/amplfi/conda-lock.yml

%post
mkdir -p /cvmfs /hdfs /gpfs /ceph /hadoop

# install git for pip installation from github
apt-get update
apt-get install -y --no-install-recommends git
apt-get clean

# activate micromamba and create environment from lockfile
/bin/bash /root/.bashrc
micromamba create -p /env -f /opt/amplfi/conda-lock.yml

cd /opt/amplfi
micromamba run -p /env python -m pip install -e .

# initialize our shell so that we can execute
# commands in our environment at run time
micromamba shell init --shell=bash --root-prefix=~/micromamba


# set path, and add it to /etc/profile
# so that it will be set if login shell
# is invoked
export PATH=/env/bin:$PATH
echo export PATH=$PATH >> /etc/profile

%environment
    export PATH=/env/bin:$PATH
    
%runscript
#!/bin/bash
eval "$(micromamba shell hook --shell bash)"
micromamba activate /env
exec "$@"