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* | ||
!conda | ||
!conda/env/lock/dracarys-linux-64.lock | ||
!.dockerignore |
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FROM condaforge/mambaforge:22.9.0-2 as conda | ||
LABEL maintainer="https://github.com/pdiakumis" | ||
FROM ubuntu:20.04 | ||
LABEL org.opencontainers.image.authors="[email protected]" \ | ||
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" | ||
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# 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-${MINIF_VERSION}-Linux-x86_64.sh" | ||
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# install core pkgs, miniforge | ||
RUN apt-get update && \ | ||
apt-get install --yes --no-install-recommends \ | ||
bash bzip2 curl less wget zip ca-certificates && \ | ||
apt-get clean && \ | ||
curl --silent -L "${MINIF_URL}" -o "${MINIF}.sh" && \ | ||
/bin/bash "${MINIF}.sh" -b -p "/opt/${MINIF}/" && \ | ||
rm "${MINIF}.sh" | ||
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# 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}/${DRACARYS_LOCK}" | ||
RUN conda clean --all --force-pkgs-dirs --yes | ||
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# Now copy env to smaller image | ||
FROM quay.io/bioconda/base-glibc-debian-bash:3.1 | ||
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COPY --from=0 "/opt/miniforge/envs/" "/opt/miniforge/envs/" | ||
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ARG MAMBA_PREFIX="/opt/conda" | ||
ENV PATH="${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}" | ||
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CMD [ "dracarys.R" ] |
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