From 049fafd86d96d07949a462725eb2068b3103f11e Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Fri, 16 Aug 2024 23:54:35 +1000 Subject: [PATCH] docker: use multi-stage build --- .dockerignore | 2 +- Dockerfile | 53 +- conda/env/lock/conda-lock.yml | 3532 --------------------------------- 3 files changed, 36 insertions(+), 3551 deletions(-) delete mode 100644 conda/env/lock/conda-lock.yml diff --git a/.dockerignore b/.dockerignore index 8bcf70f..c8e0367 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,3 +1,3 @@ * -!conda +!conda/env/lock/dracarys-linux-64.lock !.dockerignore diff --git a/Dockerfile b/Dockerfile index 2a15e14..50cc442 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,24 +1,41 @@ -FROM condaforge/mambaforge:22.9.0-2 as conda -LABEL maintainer="https://github.com/pdiakumis" +FROM ubuntu:20.04 +LABEL org.opencontainers.image.authors="peterdiakumis@gmail.com" \ + org.opencontainers.image.description="Dracarys Workflow Output Tidier" \ + org.opencontainers.image.source="https://github.com/umccr/dracarys" \ + org.opencontainers.image.url="https://github.com/umccr/dracarys" \ + org.opencontainers.image.documentation="https://umccr.github.io/dracarys" \ + org.opencontainers.image.licenses="MIT" -# install conda-lock -RUN mamba config \ - --set always_yes yes \ - --set always_copy yes && \ - mamba install \ - -c conda-forge \ - -c nodefaults \ - conda-lock && \ - mamba clean --all --force-pkgs-dirs +ARG MINIF="miniforge" +ARG MINIF_VERSION="24.3.0-0" +ARG MINIF_URL="https://github.com/conda-forge/${MINIF}/releases/download/${MINIF_VERSION}/Miniforge3-${MINIF_VERSION}-Linux-x86_64.sh" +# install core pkgs, miniforge +RUN apt-get update && \ + apt-get install --yes --no-install-recommends \ + bash bzip2 curl less wget zip ca-certificates && \ + apt-get clean && \ + curl --silent -L "${MINIF_URL}" -o "${MINIF}.sh" && \ + /bin/bash "${MINIF}.sh" -b -p "/opt/${MINIF}/" && \ + rm "${MINIF}.sh" + +# create conda env +ENV PATH="/opt/${MINIF}/bin:$PATH" +ARG CONDA_ENV_DIR="/home/conda_envs" ARG DRACARYS_LOCK="dracarys-linux-64.lock" -ARG ENV_NAME="dracarys_env" -COPY ./conda/env/lock/${DRACARYS_LOCK} . -RUN conda-lock install --name ${ENV_NAME} ${DRACARYS_LOCK} && \ - mamba clean --all --force-pkgs-dirs +COPY "./conda/env/lock/${DRACARYS_LOCK}" "${CONDA_ENV_DIR}/" +RUN conda create -n "dracarys_env" --file "${CONDA_ENV_DIR}/${DRACARYS_LOCK}" +RUN conda clean --all --force-pkgs-dirs --yes + +# Now copy env to smaller image +FROM quay.io/bioconda/base-glibc-debian-bash:3.1 + +COPY --from=0 "/opt/miniforge/envs/" "/opt/miniforge/envs/" -ARG MAMBA_PREFIX="/opt/conda" -ENV PATH="${MAMBA_PREFIX}/envs/${ENV_NAME}/bin:${PATH}" -ENV CONDA_PREFIX="${MAMBA_PREFIX}/envs/${ENV_NAME}" +# env is activated by default +ARG MINIF="miniforge" +ARG CONDA_ENV_NAME="dracarys_env" +ENV PATH="/opt/${MINIF}/envs/${CONDA_ENV_NAME}/bin:${PATH}" +ENV CONDA_PREFIX="/opt/${MINIF}/envs/${CONDA_ENV_NAME}" CMD [ "dracarys.R" ] diff --git a/conda/env/lock/conda-lock.yml b/conda/env/lock/conda-lock.yml deleted file mode 100644 index c1f0255..0000000 --- a/conda/env/lock/conda-lock.yml +++ /dev/null @@ -1,3532 +0,0 @@ -# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). 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