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| @@ -1,102 +1,92 @@ | ||
| # Create an argument to pull a particular version of micromamba image | ||
| ARG micromamba_version | ||
| ARG micromamba_version=${micromamba_version:-1.5.3} | ||
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| ############# base image ################## | ||
| FROM --platform=$BUILDPLATFORM ubuntu:focal as base | ||
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| # 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 | ||
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| ############# micromamba image ################## | ||
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| FROM --platform=$BUILDPLATFORM mambaorg/micromamba:${micromamba_version} as micromamba | ||
| RUN echo "Getting micromamba image" | ||
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| ############# Build Stage: Final ################## | ||
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| # Build the final image | ||
| FROM base as final | ||
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| # 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=$MAMBA_USER_GID | ||
| ENV MAMBA_ROOT_PREFIX="/opt/conda" | ||
| ENV MAMBA_EXE="/bin/micromamba" | ||
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| COPY --from=micromamba "$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 | ||
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| # Install system dependencies | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
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| # 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 \ | ||
| && apt clean autoclean \ | ||
| && apt autoremove --yes \ | ||
| && rm -rf /var/lib/{apt,dpkg,cache,log}/ | ||
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| # Create working directory | ||
| ENV WORKDIR=/data | ||
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| # Set up volume directory | ||
| VOLUME ${WORKDIR} | ||
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| # Set up working directory | ||
| WORKDIR ${WORKDIR} | ||
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| # Allow permission to read and write to working directory | ||
| RUN chmod -R a+rwx ${WORKDIR} | ||
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| # Create a program variable | ||
| ENV PROJECT_DIR=/seqsender | ||
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| # Set up a volume directory | ||
| VOLUME ${PROJECT_DIR} | ||
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| # Copy all files to project directory | ||
| COPY . ${PROJECT_DIR} | ||
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| ############ Set-up micromamba environment ################## | ||
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| # Copy requirement files to program directory | ||
| COPY env.yaml "${PROJECT_DIR}/env.yaml" | ||
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| # Set up environments | ||
| RUN micromamba install --yes --name base -f "${PROJECT_DIR}/env.yaml" \ | ||
| && micromamba clean --all --yes | ||
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| ############# Launch PROGRAM ################## | ||
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| # Copy bash script to run PROGRAM to docker image | ||
| COPY seqsender-kickoff "${PROJECT_DIR}/seqsender-kickoff" | ||
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| # Convert bash script from Windows style line endings to Unix-like control characters | ||
| RUN dos2unix "${PROJECT_DIR}/seqsender-kickoff" | ||
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| # Allow permission to excute the bash script | ||
| RUN chmod a+x "${PROJECT_DIR}/seqsender-kickoff" | ||
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| # Allow permission to read and write to program directory | ||
| RUN chmod a+rwx ${PROJECT_DIR} | ||
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| # Export bash script to path | ||
| ENV PATH="$PATH:${PROJECT_DIR}" | ||
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| # Activate conda environment | ||
| ENV PATH="$PATH:${MAMBA_ROOT_PREFIX}/bin" | ||
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| # Execute the pipeline | ||
| ENTRYPOINT ["tail", "-f", "/dev/null"] | ||
| # Create an argument to pull a particular version of micromamba image | ||
| ARG micromamba_version | ||
| ARG micromamba_version=${micromamba_version:-1.5.3} | ||
|
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||
| ############# micromamba image ################## | ||
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| FROM mambaorg/micromamba:${micromamba_version} as micromamba | ||
| RUN echo "Getting micromamba image" | ||
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| ############# base image ################## | ||
|
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| FROM ubuntu:focal as base | ||
|
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||
| # if image defaults to a non-root user, then we may want to make the | ||
| # next 3 ARG commands match the values in our image. | ||
| ENV MAMBA_USER=$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" | ||
|
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| 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 | ||
|
|
||
| # 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 \ | ||
| && apt-get install --no-install-recommends -y \ | ||
| dos2unix \ | ||
| ca-certificates \ | ||
| && apt clean autoclean \ | ||
| && apt autoremove --yes \ | ||
| && rm -rf /var/lib/{apt,dpkg,cache,log}/ | ||
|
|
||
| # Create working directory | ||
| ENV WORKDIR=/data | ||
|
|
||
| # Set up volume directory | ||
| VOLUME ${WORKDIR} | ||
|
|
||
| # Set up working directory | ||
| WORKDIR ${WORKDIR} | ||
|
|
||
| # Allow permission to read and write to working directory | ||
| RUN chmod -R a+rwx ${WORKDIR} | ||
|
|
||
| # Create a program variable | ||
| ENV PROJECT_DIR=/seqsender | ||
|
|
||
| # Set up a volume directory | ||
| VOLUME ${PROJECT_DIR} | ||
|
|
||
| # Copy all files to project directory | ||
| COPY . ${PROJECT_DIR} | ||
|
|
||
| ############ Set-up micromamba environment ################## | ||
|
|
||
| # Copy requirement files to program directory | ||
| COPY env.yaml "${PROJECT_DIR}/env.yaml" | ||
|
|
||
| # Set up environments | ||
| RUN micromamba install --yes --name base -f "${PROJECT_DIR}/env.yaml" \ | ||
| && micromamba clean --all --yes | ||
|
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||
| ############# Launch PROGRAM ################## | ||
|
|
||
| # Copy bash script to run PROGRAM to docker image | ||
| COPY seqsender-kickoff "${PROJECT_DIR}/seqsender-kickoff" | ||
|
|
||
| # Convert bash script from Windows style line endings to Unix-like control characters | ||
| RUN dos2unix "${PROJECT_DIR}/seqsender-kickoff" | ||
|
|
||
| # Allow permission to excute the bash script | ||
| RUN chmod a+x "${PROJECT_DIR}/seqsender-kickoff" | ||
|
|
||
| # Allow permission to read and write to program directory | ||
| RUN chmod a+rwx ${PROJECT_DIR} | ||
|
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| # Export bash script to path | ||
| ENV PATH="$PATH:${PROJECT_DIR}" | ||
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| # Activate conda environment | ||
| ENV PATH="$PATH:${MAMBA_ROOT_PREFIX}/bin" |