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Updating bwa Dockerfiles to account for Docker Scout recommendations …
…and pull package versions automatically
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,41 +1,81 @@ | ||
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| # Using the Ubuntu base image | ||
| FROM ubuntu:noble-20241011 | ||
| # Use specific SHA for better reproducibility | ||
| FROM ubuntu:noble-20241011@sha256:e6173d4dc55e76b87c4af8db8821b1feae4146dd47341e4d431118c7dd060a74 | ||
|
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| # Adding labels for the GitHub Container Registry | ||
| LABEL org.opencontainers.image.title="bwa" | ||
| LABEL org.opencontainers.image.description="Docker image for the use of bwa in FH DaSL's WILDS" | ||
| LABEL org.opencontainers.image.version="0.7.17" | ||
| LABEL org.opencontainers.image.authors="wilds@fredhutch.org" | ||
| LABEL org.opencontainers.image.url=https://hutchdatascience.org/ | ||
| LABEL org.opencontainers.image.documentation=https://getwilds.org/ | ||
| LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library | ||
| LABEL org.opencontainers.image.licenses=MIT | ||
|
|
||
| # Installing prerequisites | ||
| RUN apt-get update \ | ||
| && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4.1 \ | ||
| zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \ | ||
| libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \ | ||
| libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 gnutls-bin=3.8.3-1.1ubuntu3.2 \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| # Pulling and extracting bwa source code | ||
| RUN wget -q --no-check-certificate https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 && tar -jxf bwa-0.7.17.tar.bz2 | ||
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| # Installing bwa | ||
| WORKDIR /bwa-0.7.17 | ||
| RUN make CC='gcc -fcommon' | ||
| WORKDIR / | ||
| ENV PATH="${PATH}:/bwa-0.7.17" | ||
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| # Pulling and extracting Samtools source code | ||
| RUN wget -q --no-check-certificate https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 && tar -jxf samtools-1.11.tar.bz2 | ||
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| # Installing Samtools | ||
| WORKDIR /samtools-1.11 | ||
| RUN ./configure && make && make install | ||
| WORKDIR / | ||
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| # Cleanup | ||
| RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2 | ||
| LABEL org.opencontainers.image.title="bwa" \ | ||
| org.opencontainers.image.description="Docker image for the use of bwa in FH DaSL's WILDS" \ | ||
| org.opencontainers.image.version="0.7.17" \ | ||
| org.opencontainers.image.authors="wilds@fredhutch.org" \ | ||
| org.opencontainers.image.url=https://hutchdatascience.org/ \ | ||
| org.opencontainers.image.documentation=https://getwilds.org/ \ | ||
| org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library \ | ||
| org.opencontainers.image.licenses=MIT | ||
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| # Set environment variables for versions | ||
| ENV BWA_VERSION=0.7.17 \ | ||
| SAMTOOLS_VERSION=1.11 | ||
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| # Set shell options | ||
| SHELL ["/bin/bash", "-o", "pipefail", "-c"] | ||
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| # Update system and install security patches | ||
| RUN apt-get update && \ | ||
| apt-get upgrade -y && \ | ||
| # Store current versions in variables | ||
| BUILD_ESSENTIAL_VERSION=$(apt-cache policy build-essential | grep Candidate | awk '{print $2}') && \ | ||
| WGET_VERSION=$(apt-cache policy wget | grep Candidate | awk '{print $2}') && \ | ||
| ZLIB_VERSION=$(apt-cache policy zlib1g-dev | grep Candidate | awk '{print $2}') && \ | ||
| AUTOCONF_VERSION=$(apt-cache policy autoconf | grep Candidate | awk '{print $2}') && \ | ||
| AUTOMAKE_VERSION=$(apt-cache policy automake | grep Candidate | awk '{print $2}') && \ | ||
| LIBNCURSES_VERSION=$(apt-cache policy libncurses-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBBZ2_VERSION=$(apt-cache policy libbz2-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBLZMA_VERSION=$(apt-cache policy liblzma-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBSSL_VERSION=$(apt-cache policy libssl-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBCURL_VERSION=$(apt-cache policy libcurl4-gnutls-dev | grep Candidate | awk '{print $2}') && \ | ||
| GNUTLS_VERSION=$(apt-cache policy gnutls-bin | grep Candidate | awk '{print $2}') && \ | ||
| CA_CERTS_VERSION=$(apt-cache policy ca-certificates | grep Candidate | awk '{print $2}') && \ | ||
| # Install packages with specific versions | ||
| apt-get install -y --no-install-recommends \ | ||
| build-essential="${BUILD_ESSENTIAL_VERSION}" \ | ||
| wget="${WGET_VERSION}" \ | ||
| zlib1g-dev="${ZLIB_VERSION}" \ | ||
| autoconf="${AUTOCONF_VERSION}" \ | ||
| automake="${AUTOMAKE_VERSION}" \ | ||
| libncurses-dev="${LIBNCURSES_VERSION}" \ | ||
| libbz2-dev="${LIBBZ2_VERSION}" \ | ||
| liblzma-dev="${LIBLZMA_VERSION}" \ | ||
| libssl-dev="${LIBSSL_VERSION}" \ | ||
| libcurl4-gnutls-dev="${LIBCURL_VERSION}" \ | ||
| gnutls-bin="${GNUTLS_VERSION}" \ | ||
| ca-certificates="${CA_CERTS_VERSION}" \ | ||
| && apt-get clean \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
|
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| # Install BWA | ||
| WORKDIR /tmp | ||
| RUN wget -q https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 && \ | ||
| tar -jxf bwa-${BWA_VERSION}.tar.bz2 && \ | ||
| rm bwa-${BWA_VERSION}.tar.bz2 | ||
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| WORKDIR /tmp/bwa-${BWA_VERSION} | ||
| RUN make CC='gcc -fcommon' && \ | ||
| mv bwa /usr/local/bin/ && \ | ||
| rm -rf /tmp/bwa-${BWA_VERSION} | ||
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| # Install Samtools | ||
| WORKDIR /tmp | ||
| RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| tar -jxf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| rm samtools-${SAMTOOLS_VERSION}.tar.bz2 | ||
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| WORKDIR /tmp/samtools-${SAMTOOLS_VERSION} | ||
| RUN ./configure && \ | ||
| make && \ | ||
| make install && \ | ||
| rm -rf /tmp/samtools-${SAMTOOLS_VERSION} | ||
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| # Set working directory to a more appropriate location for workflow execution | ||
| WORKDIR /data | ||
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| # Add healthcheck | ||
| HEALTHCHECK CMD bwa 2>&1 | grep -q "Program: bwa" || exit 1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,41 +1,81 @@ | ||
|
|
||
| # Using the Ubuntu base image | ||
| FROM ubuntu:noble-20241011 | ||
| # Use specific SHA for better reproducibility | ||
| FROM ubuntu:noble-20241011@sha256:e6173d4dc55e76b87c4af8db8821b1feae4146dd47341e4d431118c7dd060a74 | ||
|
|
||
| # Adding labels for the GitHub Container Registry | ||
| LABEL org.opencontainers.image.title="bwa" | ||
| LABEL org.opencontainers.image.description="Docker image for the use of bwa in FH DaSL's WILDS" | ||
| LABEL org.opencontainers.image.version="latest" | ||
| LABEL org.opencontainers.image.authors="wilds@fredhutch.org" | ||
| LABEL org.opencontainers.image.url=https://hutchdatascience.org/ | ||
| LABEL org.opencontainers.image.documentation=https://getwilds.org/ | ||
| LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library | ||
| LABEL org.opencontainers.image.licenses=MIT | ||
|
|
||
| # Installing prerequisites | ||
| RUN apt-get update \ | ||
| && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.21.4-1ubuntu4.1 \ | ||
| zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 autoconf=2.71-3 automake=1:1.16.5-1.3ubuntu1 \ | ||
| libncurses-dev=6.4+20240113-1ubuntu2 libbz2-dev=1.0.8-5.1build0.1 liblzma-dev=5.6.1+really5.4.5-1build0.1 \ | ||
| libssl-dev=3.0.13-0ubuntu3.4 libcurl4-gnutls-dev=8.5.0-2ubuntu10.4 gnutls-bin=3.8.3-1.1ubuntu3.2 \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # Pulling and extracting bwa source code | ||
| RUN wget -q --no-check-certificate https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 && tar -jxf bwa-0.7.17.tar.bz2 | ||
|
|
||
| # Installing bwa | ||
| WORKDIR /bwa-0.7.17 | ||
| RUN make CC='gcc -fcommon' | ||
| WORKDIR / | ||
| ENV PATH="${PATH}:/bwa-0.7.17" | ||
|
|
||
| # Pulling and extracting Samtools source code | ||
| RUN wget -q --no-check-certificate https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 && tar -jxf samtools-1.11.tar.bz2 | ||
|
|
||
| # Installing Samtools | ||
| WORKDIR /samtools-1.11 | ||
| RUN ./configure && make && make install | ||
| WORKDIR / | ||
|
|
||
| # Cleanup | ||
| RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2 | ||
| LABEL org.opencontainers.image.title="bwa" \ | ||
| org.opencontainers.image.description="Docker image for the use of bwa in FH DaSL's WILDS" \ | ||
| org.opencontainers.image.version="latest" \ | ||
| org.opencontainers.image.authors="wilds@fredhutch.org" \ | ||
| org.opencontainers.image.url=https://hutchdatascience.org/ \ | ||
| org.opencontainers.image.documentation=https://getwilds.org/ \ | ||
| org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library \ | ||
| org.opencontainers.image.licenses=MIT | ||
|
|
||
| # Set environment variables for versions | ||
| ENV BWA_VERSION=0.7.17 \ | ||
| SAMTOOLS_VERSION=1.11 | ||
|
|
||
| # Set shell options | ||
| SHELL ["/bin/bash", "-o", "pipefail", "-c"] | ||
|
|
||
| # Update system and install security patches | ||
| RUN apt-get update && \ | ||
| apt-get upgrade -y && \ | ||
| # Store current versions in variables | ||
| BUILD_ESSENTIAL_VERSION=$(apt-cache policy build-essential | grep Candidate | awk '{print $2}') && \ | ||
| WGET_VERSION=$(apt-cache policy wget | grep Candidate | awk '{print $2}') && \ | ||
| ZLIB_VERSION=$(apt-cache policy zlib1g-dev | grep Candidate | awk '{print $2}') && \ | ||
| AUTOCONF_VERSION=$(apt-cache policy autoconf | grep Candidate | awk '{print $2}') && \ | ||
| AUTOMAKE_VERSION=$(apt-cache policy automake | grep Candidate | awk '{print $2}') && \ | ||
| LIBNCURSES_VERSION=$(apt-cache policy libncurses-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBBZ2_VERSION=$(apt-cache policy libbz2-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBLZMA_VERSION=$(apt-cache policy liblzma-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBSSL_VERSION=$(apt-cache policy libssl-dev | grep Candidate | awk '{print $2}') && \ | ||
| LIBCURL_VERSION=$(apt-cache policy libcurl4-gnutls-dev | grep Candidate | awk '{print $2}') && \ | ||
| GNUTLS_VERSION=$(apt-cache policy gnutls-bin | grep Candidate | awk '{print $2}') && \ | ||
| CA_CERTS_VERSION=$(apt-cache policy ca-certificates | grep Candidate | awk '{print $2}') && \ | ||
| # Install packages with specific versions | ||
| apt-get install -y --no-install-recommends \ | ||
| build-essential="${BUILD_ESSENTIAL_VERSION}" \ | ||
| wget="${WGET_VERSION}" \ | ||
| zlib1g-dev="${ZLIB_VERSION}" \ | ||
| autoconf="${AUTOCONF_VERSION}" \ | ||
| automake="${AUTOMAKE_VERSION}" \ | ||
| libncurses-dev="${LIBNCURSES_VERSION}" \ | ||
| libbz2-dev="${LIBBZ2_VERSION}" \ | ||
| liblzma-dev="${LIBLZMA_VERSION}" \ | ||
| libssl-dev="${LIBSSL_VERSION}" \ | ||
| libcurl4-gnutls-dev="${LIBCURL_VERSION}" \ | ||
| gnutls-bin="${GNUTLS_VERSION}" \ | ||
| ca-certificates="${CA_CERTS_VERSION}" \ | ||
| && apt-get clean \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # Install BWA | ||
| WORKDIR /tmp | ||
| RUN wget -q https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 && \ | ||
| tar -jxf bwa-${BWA_VERSION}.tar.bz2 && \ | ||
| rm bwa-${BWA_VERSION}.tar.bz2 | ||
|
|
||
| WORKDIR /tmp/bwa-${BWA_VERSION} | ||
| RUN make CC='gcc -fcommon' && \ | ||
| mv bwa /usr/local/bin/ && \ | ||
| rm -rf /tmp/bwa-${BWA_VERSION} | ||
|
|
||
| # Install Samtools | ||
| WORKDIR /tmp | ||
| RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| tar -jxf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| rm samtools-${SAMTOOLS_VERSION}.tar.bz2 | ||
|
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||
| WORKDIR /tmp/samtools-${SAMTOOLS_VERSION} | ||
| RUN ./configure && \ | ||
| make && \ | ||
| make install && \ | ||
| rm -rf /tmp/samtools-${SAMTOOLS_VERSION} | ||
|
|
||
| # Set working directory to a more appropriate location for workflow execution | ||
| WORKDIR /data | ||
|
|
||
| # Add healthcheck | ||
| HEALTHCHECK CMD bwa 2>&1 | grep -q "Program: bwa" || exit 1 |