From ebcbb53cb12db3c087a69fa5b68bfd2068d7e87e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 9 Aug 2023 23:21:33 -0500
Subject: [PATCH] refactor: Switch to multi-stage build

---
 modules/viquas/Dockerfile | 344 ++++++++++++++++++++++++++------------
 modules/viquas/viquas     |  47 ++++++
 2 files changed, 285 insertions(+), 106 deletions(-)
 create mode 100644 modules/viquas/viquas

diff --git a/modules/viquas/Dockerfile b/modules/viquas/Dockerfile
index 069c482..a152d91 100644
--- a/modules/viquas/Dockerfile
+++ b/modules/viquas/Dockerfile
@@ -1,116 +1,248 @@
-FROM ubuntu:bionic
+###
+### R base image
+### Based on r-ver
+###
+FROM debian:buster AS rver
 
-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
+LABEL org.label-schema.license="GPL-2.0" \
+      org.label-schema.vcs-url="https://github.com/rocker-org/rocker-versioned" \
+      org.label-schema.vendor="Rocker Project" \
+      maintainer="Carl Boettiger <cboettig@ropensci.org>"
+
+ARG R_VERSION
+ARG BUILD_DATE
+ARG CRAN
+ENV BUILD_DATE ${BUILD_DATE:-2020-04-24}
+ENV R_VERSION=${R_VERSION:-3.6.3} \
+    CRAN=${CRAN:-https://cran.r-project.org} \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    TERM=xterm
 
 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${ROCKER_VERSION}
-
-    # Install BioPerl
-    apt-get update
-    apt-get install --no-install-recommends -y \
-        curl \
-        perl \
-        cpanminus \
-        build-essential \
+DEBIAN_FRONTEND=noninteractive
+apt-get update && apt-get install -y --no-install-recommends \
+        bash-completion \
+        ca-certificates \
+        file \
+        fonts-texgyre \
+        g++ \
+        gfortran \
+        gsfonts \
+        libblas-dev \
+        libbz2-1.0 \
+        libcurl4 \
+        libicu63 \
+        libjpeg62-turbo \
+        libopenblas-dev \
+        libpangocairo-1.0-0 \
+        libpcre3 \
+        libpng16-16 \
+        libreadline7 \
+        libtiff5 \
+        liblzma5 \
+        locales \
         make \
-        libexpat1-dev \
-        libssl-dev \
-        zlib1g-dev \
-        libncurses5-dev
-    cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
-
-    # Install R packages
-    install2.r --error --skipinstalled BiocManager
-    R -e "BiocManager::install(c('Biostrings', 'seqinr'))"
-
-    # Install samtools
-    curl -L "https://github.com/samtools/samtools/releases/download/${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
+        unzip \
+        zip \
+        zlib1g
+echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
+locale-gen en_US.utf8
+/usr/sbin/update-locale LANG=en_US.UTF-8
+BUILDDEPS="curl \
+    default-jdk \
+    libbz2-dev \
+    libcairo2-dev \
+    libcurl4-openssl-dev \
+    libpango1.0-dev \
+    libjpeg-dev \
+    libicu-dev \
+    libpcre3-dev \
+    libpng-dev \
+    libreadline-dev \
+    libtiff5-dev \
+    liblzma-dev \
+    libx11-dev \
+    libxt-dev \
+    perl \
+    tcl8.6-dev \
+    tk8.6-dev \
+    texinfo \
+    texlive-extra-utils \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-latex-recommended \
+    x11proto-core-dev \
+    xauth \
+    xfonts-base \
+    xvfb \
+    zlib1g-dev"
+apt-get install -y --no-install-recommends $BUILDDEPS
+## Download source code
+curl -O https://cran.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz
+## Extract source code
+tar -xf R-${R_VERSION}.tar.gz
+cd R-${R_VERSION}
+## Set compiler flags
+R_PAPERSIZE=letter \
+R_BATCHSAVE="--no-save --no-restore"
+R_BROWSER=xdg-open
+PAGER=/usr/bin/pager
+PERL=/usr/bin/perl
+R_UNZIPCMD=/usr/bin/unzip
+R_ZIPCMD=/usr/bin/zip
+R_PRINTCMD=/usr/bin/lpr
+LIBnn=lib
+AWK=/usr/bin/awk
+CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"
+CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"
+## Configure options
+./configure --enable-R-shlib \
+            --enable-memory-profiling \
+            --with-readline \
+            --with-blas \
+            --with-tcltk \
+            --disable-nls \
+            --with-recommended-packages \
+            --prefix /usr/local
+## Build and install
+make -j $(nproc) -O
+make install
+## Add a library directory (for user-installed packages)
+mkdir -p /usr/local/lib/R/site-library
+chown root:staff /usr/local/lib/R/site-library
+chmod g+ws /usr/local/lib/R/site-library
+## Fix library path
+sed -i '/^R_LIBS_USER=.*$/d' /usr/local/lib/R/etc/Renviron
+echo "R_LIBS_USER=\${R_LIBS_USER-'/usr/local/lib/R/site-library'}" >> /usr/local/lib/R/etc/Renviron
+echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron
+echo "options(repos = c(CRAN='$CRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site
+## Clean up from R source install
+apt-get remove --purge -y $BUILDDEPS
+apt-get autoremove -y
+apt-get autoclean -y
+rm -rf /var/lib/apt/lists/*
 END_RUN_CMD
 
+###
+### Added Bioconductor packages to r-ver
+###
+FROM rver as bioconductor
+RUN <<END_RUN_CMD
+apt-get update && apt-get install --no-install-recommends -y \
+    zlib1g-dev
+
+R -e "install.packages('BiocManager', repos='https://cran.r-project.org')"
+R -e "BiocManager::install('Biostrings')"
+R -e "BiocManager::install('seqinr')"
+
+apt-get autoremove -y
+apt-get autoclean -y
+rm -rf /var/lib/apt/lists/*
+
+END_RUN_CMD
+
+###
+### Perl base image
+###
+FROM buildpack-deps:buster AS perl
+LABEL maintainer="Peter Martini <PeterCMartini@GMail.com>, Zak B. Elep <zakame@cpan.org>"
+
 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
-chmod -R 777 /viquas
+curl -fL https://www.cpan.org/src/5.0/perl-5.34.1.tar.xz -o perl-5.34.1.tar.xz
+tar --strip-components=1 -xaf perl-5.34.1.tar.xz -C /usr/src/perl
+rm perl-5.34.1.tar.xz
+cat *.patch | patch -p1
+gnuArch="$(dpkg-architecture --query DEB_BUILD_GNU_TYPE)"
+archBits="$(dpkg-architecture --query DEB_BUILD_ARCH_BITS)"
+archFlag="$([ "$archBits" = '64' ] && echo '-Duse64bitall' || echo '-Duse64bitint')"
+./Configure -Darchname="$gnuArch" "$archFlag" -Dusethreads -Duseshrplib -Dvendorprefix=/usr/local  -des
+make -j$(nproc)
+TEST_JOBS=$(nproc) make test_harness
+make install
+cd /usr/src
+curl -fLO https://www.cpan.org/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7047.tar.gz
+tar -xzf App-cpanminus-1.7047.tar.gz && cd App-cpanminus-1.7047 && perl bin/cpanm . && cd /root
+cpanm IO::Socket::SSL
+curl -fL https://raw.githubusercontent.com/skaji/cpm/0.997011/cpm -o /usr/local/bin/cpm
+chmod +x /usr/local/bin/cpm
+rm -fr /root/.cpanm /usr/src/perl /usr/src/App-cpanminus-1.7047*
 END_RUN_CMD
 
+###
+### Added bioperl packaged
+###
+FROM perl AS bioperl
+RUN <<END_RUN_CMD
+cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
+END_RUN_CMD
+
+###
+### Samtools build
+###
+FROM buildpack-deps:buster AS samtools
+ARG SAMTOOLS_VERSION=1.2
+RUN <<END_RUN_CMD
+curl -L "https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" | tar xvj
+cd samtools-${SAMTOOLS_VERSION} && make && make install && cd ..
+END_RUN_CMD
+
+###
+### Viquas extraction
+###
+FROM buildpack-deps:buster AS viquas
+RUN <<END_RUN_CMD
+mkdir /viquas
+curl -L "https://master.dl.sourceforge.net/project/viquas/ViQuaS1.3.tar.gz" | tar xvz -C /viquas --strip-components=1
+END_RUN_CMD
+
+
+###
+### Final build
+###
+FROM debian:buster as final
+RUN <<END_RUN_CMD
+apt-get update && apt-get install -y --no-install-recommends \
+        bash-completion \
+        file \
+        fonts-texgyre \
+        gfortran \
+        gsfonts \
+        libblas-dev \
+        libbz2-1.0 \
+        libcurl4 \
+        libicu63 \
+        libjpeg62-turbo \
+        libncurses5-dev \
+        libopenblas-dev \
+        libpangocairo-1.0-0 \
+        libpcre3 \
+        libpng16-16 \
+        libreadline7 \
+        libtiff5 \
+        liblzma5 \
+        locales \
+        unzip \
+        zip \
+        zlib1g
+
+apt-get autoremove -y
+apt-get autoclean -y
+rm -rf /var/lib/apt/lists/*
+
+
+END_RUN_CMD
+
+COPY --from=bioconductor /usr/local/bin /usr/local/bin
+COPY --from=bioconductor /usr/local/lib /usr/local/lib
+COPY --from=bioconductor /usr/local/share /usr/local/share
+COPY --from=bioperl /usr/local/bin /usr/local/bin
+COPY --from=bioperl /usr/local/lib /usr/local/lib
+COPY --from=bioperl /usr/local/share /usr/local/share
+COPY --from=bioperl /usr/share/perl /usr/share/perl
+COPY --from=samtools /usr/local/bin /usr/local/bin
+COPY --from=samtools /usr/local/lib /usr/local/lib
+COPY --from=samtools /usr/local/share /usr/local/share
+COPY --from=viquas /viquas /viquas
+COPY --chmod=755 viquas /usr/local/bin/viquas
 ENTRYPOINT [ "viquas" ]
diff --git a/modules/viquas/viquas b/modules/viquas/viquas
new file mode 100644
index 0000000..9b0f1d0
--- /dev/null
+++ b/modules/viquas/viquas
@@ -0,0 +1,47 @@
+#!/bin/sh
+USAGE="
+  USAGE:
+    viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
+"
+
+NUM_ARGS=$#
+case $NUM_ARGS in
+  2)
+  ;;
+  6)
+  ;;
+  *)
+  echo "${USAGE}"
+  echo "Incorrect number of arguments: expecting 2 or 6"
+  exit 1
+esac
+
+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 -r /viquas/{viquas_files,ViQuaS.R} .
+
+case $NUM_ARGS in
+  2)
+    Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
+  ;;
+  6)
+    Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
+  ;;
+  *)
+  echo "${USAGE}"
+  echo "Incorrect number of arguments: expecting 2 or 6"
+  exit 1
+esac
+
+rm -rf ./{viquas_files,ViQuaS.R}