Dockerfile

FROM mambaorg/micromamba
LABEL org.opencontainers.image.authors="Johannes Köster <johannes.koester@tu-dortmund.de>"
ADD . /tmp/repo
WORKDIR /tmp/repo
ENV LANG C.UTF-8
ENV SHELL /bin/bash
USER root 

ENV APT_PKGS bzip2 ca-certificates curl wget gnupg2 squashfs-tools git

RUN apt-get update \
    && apt-get install -y --no-install-recommends ${APT_PKGS} \
    && apt-get clean \
    && rm -rf /var/lib/apt /var/lib/dpkg /var/lib/cache /var/lib/log

RUN micromamba create -q -y -c conda-forge -n apptainer apptainer

RUN micromamba create -q -y -c bioconda -c conda-forge -n snakemake \
    snakemake-minimal --only-deps && \
    eval "$(micromamba shell hook --shell bash)" && \
    micromamba activate /opt/conda/envs/snakemake && \
    micromamba install -c conda-forge mamba && \
    micromamba clean --all -y

ENV PATH /opt/conda/envs/snakemake/bin:/opt/conda/envs/apptainer/bin:${PATH}
RUN pip install .[reports,messaging,pep]