Dockerfile

ARG micromamba_version=${micromamba_version:-1.5.3}

############# base image ##################
FROM --platform=$BUILDPLATFORM google/cloud-sdk:489.0.0-stable as base

# local apt mirror support
# start every stage with updated apt sources
ARG APT_MIRROR_NAME=
RUN if [ -n "$APT_MIRROR_NAME" ]; then sed -i.bak -E '/security/! s^https?://.+?/(debian|ubuntu)^http://'"$APT_MIRROR_NAME"'/\1^' /etc/apt/sources.list && grep '^deb' /etc/apt/sources.list; fi
RUN apt-get update --allow-releaseinfo-change --fix-missing

############# micromamba image ##################

FROM --platform=$BUILDPLATFORM mambaorg/micromamba:${micromamba_version} as micromamba
RUN echo "Getting micromamba image"

############# Build Stage: Final ##################

FROM base as final

# if image defaults to a non-root user, then we may want to make the
# next 3 ARG commands match the values in our image. 
ENV MAMBA_USER=$MAMBA_USER
ENV MAMBA_USER_ID=$MAMBA_USER_ID
ENV MAMBA_USER_GID=$MAMBA_USER_GID
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/_activate_current_env.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh

# Install system dependencies
ARG DEBIAN_FRONTEND=noninteractive

# Install system libraries of general use
RUN apt-get update --allow-releaseinfo-change --fix-missing \
  && apt-get install --no-install-recommends -y \
  dos2unix \
  ca-certificates \
  git \
  && apt clean autoclean \
  && apt autoremove --yes \
  && rm -rf /var/lib/{apt,dpkg,cache,log}/

ARG REPO_URL="https://github.com/erikwolfsohn/seqsender.git"
ARG REPO_BRANCH="seqsender-terra-submission"

RUN git clone --branch ${REPO_BRANCH} ${REPO_URL} /seqsender \
	&& chmod a+x /seqsender/*.py

RUN micromamba install --yes --name base -f "/seqsender/env.yaml" \
    && micromamba clean --all --yes \
	&& mkdir /data

RUN micromamba install --yes --name base --channel conda-forge --channel bioconda tqdm=4.66.5=pyhd8ed1ab_0 firecloud=0.16.37=pyhdfd78af_0

ENV PATH=${PATH}:/seqsender \
	LC_ALL=C

ENV PATH="$PATH:${MAMBA_ROOT_PREFIX}/bin"

WORKDIR /data

CMD cd /data && python /seqsender/seqsender.py --help