refactor: Minimize Dockerfile layers
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a1d0348697
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09335146883990B9
2 changed files with 89 additions and 86 deletions
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@ -6,18 +6,18 @@ ENV R_HOME=/usr/local/lib/R
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ENV TZ=Etc/UTC
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ENV SAMTOOLS_VERSION=1.2
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# Install R basic dependencies
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RUN apt-get update && \
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RUN <<END_RUN_CMD
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# Install R
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apt-get update
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apt-get install --no-install-recommends -y \
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sed \
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curl \
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ca-certificates
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RUN curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
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RUN ./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
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RUN rm -rf rocker-versioned2-R${ROCKER_VERSION}
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curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
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./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
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rm -rf rocker-versioned2-R${ROCKER_VERSION}
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# Install BioPerl
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RUN apt-get update && \
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# Install BioPerl
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apt-get update
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apt-get install --no-install-recommends -y \
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curl \
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perl \
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@ -26,33 +26,91 @@ RUN apt-get update && \
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make \
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libexpat1-dev \
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libssl-dev \
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zlib1g-dev
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RUN cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
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zlib1g-dev \
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libncurses5-dev
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cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
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# Install R packages
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RUN install2.r --error --skipinstalled BiocManager
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RUN R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
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# Install R packages
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install2.r --error --skipinstalled BiocManager
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R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
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# Install samtools
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RUN apt-get update && \
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apt-get install --no-install-recommends -y libncurses5-dev
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RUN curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
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RUN cd samtools-${SAMTOOLS_VERSION} && make && make install && cd ..
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RUN rm -rf samtools-${SAMTOOLS_VERSION}
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# Install samtools
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curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
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cd samtools-${SAMTOOLS_VERSION} && make && make install && cd ..
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rm -rf samtools-${SAMTOOLS_VERSION}
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# Cleanup
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RUN apt-get remove -y \
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build-essential \
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make
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# Install viquas
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mkdir /viquas && \
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curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
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# Install Viquas
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RUN apt-get update && apt-get install --no-install-recommends -y curl
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RUN mkdir /viquas && curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
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RUN apt-get remove -y curl
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# Cleanup
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apt-get remove -y \
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build-essential \
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make \
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curl
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rm -rf /var/lib/apt/lists
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END_RUN_CMD
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# Add wrapper script
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COPY viquas /usr/bin/viquas
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RUN chmod +x /usr/bin/viquas
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RUN mkdir /work
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RUN <<END_RUN_CMD
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cat << 'EOF' > /usr/bin/viquas
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#!/bin/sh
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USAGE="
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USAGE:
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viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
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"
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NUM_ARGS=$#
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case $NUM_ARGS in
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2)
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;;
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6)
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;;
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*)
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echo "${USAGE}"
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echo "Incorrect number of arguments: expecting 2 or 6"
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exit 1
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esac
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PWD_BACKUP=$PWD
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if [ ! -f "${1}" ]; then
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echo "Error: ${1} is not a file"
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exit 1
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fi
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if [ ! -f "${2}" ]; then
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echo "Error: ${2} is not a file"
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exit 1
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fi
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REFERENCE_FILE=$(basename "${1}")
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BAM_FILE=$(basename "${2}")
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cp "${1}" /viquas
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cp "${2}" /viquas
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cd /viquas || exit 1
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case $NUM_ARGS in
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2)
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Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
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;;
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6)
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Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
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;;
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*)
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echo "${USAGE}"
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echo "Incorrect number of arguments: expecting 2 or 6"
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exit 1
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esac
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mv /viquas/ViQuaS-Spectrum.fa "${PWD_BACKUP}"
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mv /viquas/ViQuaS-Richness.txt "${PWD_BACKUP}" 2> /dev/null
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cd "${PWD_BACKUP}" || exit 1
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EOF
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chmod +x /usr/bin/viquas
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mkdir /work
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END_RUN_CMD
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ENTRYPOINT [ "viquas" ]
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@ -1,55 +0,0 @@
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#!/bin/sh
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USAGE="
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USAGE:
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viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
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"
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NUM_ARGS=$#
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case $NUM_ARGS in
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2)
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;;
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6)
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;;
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*)
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echo "${USAGE}"
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echo "Incorrect number of arguments: expecting 2 or 6"
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exit 1
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esac
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PWD_BACKUP=$PWD
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if [ ! -f "${1}" ]; then
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echo "Error: ${1} is not a file"
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exit 1
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fi
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if [ ! -f "${2}" ]; then
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echo "Error: ${2} is not a file"
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exit 1
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fi
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REFERENCE_FILE=$(basename "${1}")
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BAM_FILE=$(basename "${2}")
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cp "${1}" /viquas
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cp "${2}" /viquas
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cd /viquas || exit 1
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case $NUM_ARGS in
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2)
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Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
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;;
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6)
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Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
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;;
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*)
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echo "${USAGE}"
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echo "Incorrect number of arguments: expecting 2 or 6"
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exit 1
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esac
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mv /viquas/ViQuaS-Spectrum.fa "${PWD_BACKUP}"
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mv /viquas/ViQuaS-Richness.txt "${PWD_BACKUP}" 2> /dev/null
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cd "${PWD_BACKUP}" || exit 1
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