conda.def

Bootstrap: library
From: ubuntu:20.04

%labels
	Author Antoine Prouvost
	Version v0.0.1

%help
	Singularity image used get dependencies from Conda.

%environment
	# Extremely lazy sourcing of the Conda activation script
	export PROMPT_COMMAND='source /opt/mamba/init.bash; unset PROMPT_COMMAND'

%files
	post.bash /opt/post.bash

%post
	# Minimum requirements for the image
	apt-get update
	apt-get install --yes --no-install-recommends wget git openssh-client tar gzip ca-certificates
	apt-get clean

	# Install Mamba (Conda alternative) through Mambaforge
	readonly mamba_installer="Mambaforge-$(uname)-$(uname -m).sh"
	readonly mamba_version="4.10.3-4"
	readonly mamba_prefix="/opt/mamba"
	wget "https://github.com/conda-forge/miniforge/releases/download/${mamba_version}/${mamba_installer}"
	bash "${mamba_installer}" -b -p "${mamba_prefix}"
	rm "${mamba_installer}"

	# Put the Conda initialization script in a file for lazy loading/
	# Singularity does all the environment sourcing as shell (only latter calls bash),
	# which conda does not support.
	# We put the content in a file, manually call bash, and source it.
	{
		echo 'eval "$(' "'${mamba_prefix}/bin/conda' 'shell.bash' 'hook' 2> /dev/null" ')"'
		echo 'if [ $? -eq 0 ]; then'
		echo '  eval "$__conda_setup"'
		echo 'else'
		echo '  if [ -f ' "'${mamba_prefix}/etc/profile.d/conda.sh'" ']; then'
		echo '    .' "'${mamba_prefix}/opt/mamba/etc/profile.d/conda.sh'"
		echo '  else'
		echo '    export PATH="/opt/mamba/bin:$PATH"'
		echo '  fi'
		echo 'fi'
		echo 'unset __conda_setup'
	} >> ${mamba_prefix}/init.bash


	# Execute the post.bash script.
	# Use bash to properly activate the conda environment and install packages.
	# Other command such as cmake, pip, etc are better run inside the post.bash file so that they can
	# Conda libraries.
	echo 'source' "'${mamba_prefix}/init.bash'" | cat - /opt/post.bash | bash