condaToContainer

#!/bin/bash

USAGE="""
  Usage: condaToContainer <CONDA_ENV> <docker|singularity> <OUTPUT>
"""

read -r -d '' DOCKERFILE <<- EOM
FROM  continuumio/miniconda3:latest

ADD packed_environment.tar.gz /opt/conda/

RUN conda-unpack
EOM

read -r -d '' SINGULARITY_FILE <<- EOM
Bootstrap: docker

From: continuumio/miniconda3

%files
	packed_environment.tar.gz /packed_environment.tar.gz

%environment
    export NUMBA_CACHE_DIR=/tmp/numba_cache

%post
	tar xvzf /packed_environment.tar.gz -C /opt/conda
	conda-unpack
	rm /packed_environment.tar.gz
EOM

[[ "$#" -ne 3 ]] && echo "fatal: missing argument(s). " && echo $USAGE && exit 1

[[ ! "$2" =~ doc|sing ]] && echo "fatal: must specify docker or singularity build." && exit 1

CONDAENV=$1
CONTAINER=$(readlink -f $3)
TMPDIR=$(mktemp -d)

DIR=${TMPDIR}/$(echo $CONDAENV | md5sum | awk '{print $1}')

mkdir -p $DIR

echo ENV=$CONDAENV
echo CONTAINER=$CONTAINER
echo DIR=$DIR

echo "Packing conda environment.." > /dev/stderr
conda-pack -n $CONDAENV -o $DIR/packed_environment.tar.gz --ignore-missing-files --force

[[ $? -ne 0 ]] && exit 1

case "$2" in
  sing*)
    echo "Building singularity container.." > /dev/stderr
    echo "$SINGULARITY_FILE" > $DIR/Singularity && \
    cd $DIR && \
    singularity build --fakeroot --force $CONTAINER Singularity
    ;;
  doc*)
    echo "Building docker container.." > /dev/stderr
    echo "$DOCKERFILE" | docker build - --tag "$1:docker" --rm -o $CONTAINER
    ;;
  *)
    echo $USAGE
    ;;
esac