Dockerfile

<<<<<<< HEAD
FROM mambaorg/micromamba:1.5.8 AS micromamba

FROM rocker/tidyverse:latest

# copy files from micromamba image
ARG MAMBA_USER=${DEFAULT_USER}
ARG MAMBA_USER_ID=1000
ARG MAMBA_USER_GID=1000
ENV MAMBA_USER=${MAMBA_USER}
=======
FROM mambaorg/micromamba:2.0.5 AS micromamba

FROM rocker/verse:latest AS rocker

FROM docker.io/library/ubuntu:latest

COPY docker/scripts/install_requirements.sh /opt/docker/bin/
RUN /opt/docker/bin/install_requirements.sh

# copy files from micromamba image
ARG MAMBA_USER="mambauser"
ARG MAMBA_USER_ID="57439"
ARG MAMBA_USER_GID="57439"
ENV MAMBA_USER=${MAMBA_USER}
ENV MAMBA_USER_ID=${MAMBA_USER_ID}
ENV MAMBA_USER_GID=${MAMBA_USER_GID}
>>>>>>> ef3d886 (init: populate docker file)
ENV MAMBA_ROOT_PREFIX="/opt/conda"
ENV MAMBA_EXE="/bin/micromamba"

COPY --from=micromamba "${MAMBA_EXE}" "${MAMBA_EXE}"
COPY --from=micromamba /usr/local/bin/_activate_current_env.sh \
    /usr/local/bin/_dockerfile_initialize_user_accounts.sh \
    /usr/local/bin/_dockerfile_setup_root_prefix.sh \
    /usr/local/bin/_dockerfile_shell.sh \
    /usr/local/bin/
<<<<<<< HEAD

# setup mamba user
RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
    /usr/local/bin/_dockerfile_setup_root_prefix.sh

# install micromamba env
SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
ENV MAMBA_ENV_DIR="/opt/conda/envs/py_basis"
COPY environment.yml /opt/environment.yml
COPY docker/scripts/micromamba_clean_env.sh docker/scripts/py_setup.sh /opt/docker/bin/
RUN /bin/micromamba create -f /opt/environment.yml && \
    /bin/micromamba clean -a -y && \
    chown -R "${DEFAULT_USER}":"${DEFAULT_USER}" "${MAMBA_ENV_DIR}" && \
    /opt/docker/bin/micromamba_clean_env.sh

# python setup
RUN /opt/docker/bin/py_setup.sh
=======
# setup mamba user
RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
    /usr/local/bin/_dockerfile_setup_root_prefix.sh
# install micromamba env
SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
COPY environment.yml /opt/environment.yml
COPY docker/scripts/micromamba_clean_env.sh /opt/docker/bin/
ENV MAMBA_ENV_DIR="/opt/conda/envs/igfl_python"
RUN /bin/micromamba create -f /opt/environment.yml && \
    /bin/micromamba clean -a -y && \
    chown -R "${MAMBA_USER}":"${MAMBA_USER}" "${MAMBA_ENV_DIR}" && \
    /opt/docker/bin/micromamba_clean_env.sh


# install pandoc (required for quarto)
COPY --from=rocker /rocker_scripts/install_pandoc.sh \
    /rocker_scripts/install_quarto.sh \
    /opt/docker/bin/
RUN /opt/docker/bin/install_pandoc.sh
# install latest version of quarto
RUN /opt/docker/bin/install_quarto.sh 1.6.40
>>>>>>> ef3d886 (init: populate docker file)