haplotyper-battle-royale/modules/viquas/Dockerfile

FROM ubuntu:bionic

ENV R_VERSION=3.6.3
ENV ROCKER_VERSION=4.1.1
ENV R_HOME=/usr/local/lib/R
ENV TZ=Etc/UTC
ENV SAMTOOLS_VERSION=1.2

RUN <<END_RUN_CMD
    # Install R
    apt-get update
    apt-get install --no-install-recommends -y \
        curl \
        ca-certificates
    curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
    ./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
    rm -rf rocker-versioned2-R${ROCKER_VERSION}

    # Install BioPerl
    apt-get update
    apt-get install --no-install-recommends -y \
        curl \
        perl \
        cpanminus \
        build-essential \
        make \
        libexpat1-dev \
        libssl-dev \
        zlib1g-dev \
        libncurses5-dev
    cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs

    # Install R packages
    install2.r --error --skipinstalled BiocManager
    R -e "BiocManager::install(c('Biostrings', 'seqinr'))"

    # Install samtools
    curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
    cd samtools-${SAMTOOLS_VERSION} && make &&  make install && cd ..
    rm -rf samtools-${SAMTOOLS_VERSION}

    # Install viquas
    mkdir /viquas && \
    curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1

    # Cleanup
    apt-get remove -y \
        build-essential \
        make \
        curl
    rm -rf /var/lib/apt/lists
END_RUN_CMD

RUN <<END_RUN_CMD
cat << 'EOF' > /usr/bin/viquas
#!/bin/sh
USAGE="
  USAGE:
    viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
"

NUM_ARGS=$#
case $NUM_ARGS in
  2)
  ;;
  6)
  ;;
  *)
  echo "${USAGE}"
  echo "Incorrect number of arguments: expecting 2 or 6"
  exit 1
esac

PWD_BACKUP=$PWD

if [ ! -f "${1}" ]; then
  echo "Error: ${1} is not a file"
  exit 1
fi

if [ ! -f "${2}" ]; then
  echo "Error: ${2} is not a file"
  exit 1
fi

REFERENCE_FILE=$(basename "${1}")
BAM_FILE=$(basename "${2}")

cp "${1}" /viquas
cp "${2}" /viquas

cd /viquas || exit 1

case $NUM_ARGS in
  2)
    Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
  ;;
  6)
    Rscript /viquas/ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
  ;;
  *)
  echo "${USAGE}"
  echo "Incorrect number of arguments: expecting 2 or 6"
  exit 1
esac

mv /viquas/ViQuaS-Spectrum.fa "${PWD_BACKUP}"
mv /viquas/ViQuaS-Richness.txt "${PWD_BACKUP}" 2> /dev/null

cd "${PWD_BACKUP}" || exit 1
EOF
chmod +x /usr/bin/viquas
mkdir /work
END_RUN_CMD

ENTRYPOINT [ "viquas" ]