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Updating bwa Dockerfiles #147

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118 changes: 79 additions & 39 deletions bwa/Dockerfile_0.7.17
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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="0.7.17"
LABEL org.opencontainers.image.authors="[email protected]"
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="0.7.17" \
org.opencontainers.image.authors="[email protected]" \
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

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
118 changes: 79 additions & 39 deletions bwa/Dockerfile_latest
View file
Open in desktop
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="[email protected]"
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="[email protected]" \
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

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
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