feat: Create working Dockerfile for ViQuas

modules/viquas/Dockerfile

@@ -0,0 +1,58 @@
+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
+
+# Install R basic dependencies
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y \
+        sed \
+        curl \
+        ca-certificates
+RUN curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${ROCKER_VERSION}.tar.gz" | tar xvz
+RUN ./rocker-versioned2-R${ROCKER_VERSION}/scripts/install_R.sh
+RUN rm -rf rocker-versioned2-R${ROCKER_VERSION}
+
+# Install BioPerl
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y \
+        curl \
+        perl \
+        cpanminus \
+        build-essential \
+        make \
+        libexpat1-dev \
+        libssl-dev \
+        zlib1g-dev
+RUN cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
+
+# Install R packages
+RUN install2.r --error --skipinstalled BiocManager
+RUN R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
+
+# Install samtools
+RUN apt-get update && \
+    apt-get install --no-install-recommends -y libncurses5-dev
+RUN curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
+RUN cd samtools-${SAMTOOLS_VERSION} && make && make install && cd ..
+RUN rm -rf samtools-${SAMTOOLS_VERSION}
+
+# Cleanup
+RUN apt-get remove -y \
+    build-essential \
+    make
+
+# Install Viquas
+RUN apt-get update && apt-get install --no-install-recommends -y curl
+RUN mkdir /viquas && curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
+RUN apt-get remove -y curl
+
+# Add wrapper script
+COPY viquas /usr/bin/viquas
+RUN chmod +x /usr/bin/viquas
+RUN mkdir /work
+
+ENTRYPOINT [ "viquas" ]

modules/viquas/viquas

@@ -0,0 +1,55 @@
+#!/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