refactor: Switch to multi-stage build
This commit is contained in:
parent
58759e3314
commit
ebcbb53cb1
GPG key ID:
09335146883990B9
2 changed files with 285 additions and 106 deletions
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@ -1,116 +1,248 @@
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FROM ubuntu:bionic
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###
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### R base image
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### Based on r-ver
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###
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FROM debian:buster AS rver
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ENV R_VERSION=3.6.3
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ENV ROCKER_VERSION=4.1.1
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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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LABEL org.label-schema.license="GPL-2.0" \
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org.label-schema.vcs-url="https://github.com/rocker-org/rocker-versioned" \
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org.label-schema.vendor="Rocker Project" \
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maintainer="Carl Boettiger <cboettig@ropensci.org>"
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ARG R_VERSION
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ARG BUILD_DATE
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ARG CRAN
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ENV BUILD_DATE ${BUILD_DATE:-2020-04-24}
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ENV R_VERSION=${R_VERSION:-3.6.3} \
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CRAN=${CRAN:-https://cran.r-project.org} \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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TERM=xterm
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RUN <<END_RUN_CMD
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# Install R
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apt-get update
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apt-get install --no-install-recommends -y \
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curl \
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ca-certificates
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curl -L "https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${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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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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cpanminus \
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build-essential \
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DEBIAN_FRONTEND=noninteractive
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apt-get update && apt-get install -y --no-install-recommends \
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bash-completion \
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ca-certificates \
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file \
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fonts-texgyre \
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g++ \
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gfortran \
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gsfonts \
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libblas-dev \
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libbz2-1.0 \
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libcurl4 \
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libicu63 \
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libjpeg62-turbo \
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libopenblas-dev \
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libpangocairo-1.0-0 \
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libpcre3 \
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libpng16-16 \
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libreadline7 \
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libtiff5 \
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liblzma5 \
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locales \
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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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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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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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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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# 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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# 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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unzip \
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zip \
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zlib1g
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echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
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locale-gen en_US.utf8
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/usr/sbin/update-locale LANG=en_US.UTF-8
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BUILDDEPS="curl \
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default-jdk \
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libbz2-dev \
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libcairo2-dev \
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libcurl4-openssl-dev \
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libpango1.0-dev \
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libjpeg-dev \
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libicu-dev \
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libpcre3-dev \
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libpng-dev \
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libreadline-dev \
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libtiff5-dev \
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liblzma-dev \
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libx11-dev \
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libxt-dev \
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perl \
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tcl8.6-dev \
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tk8.6-dev \
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texinfo \
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texlive-extra-utils \
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texlive-fonts-recommended \
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texlive-fonts-extra \
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texlive-latex-recommended \
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x11proto-core-dev \
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xauth \
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xfonts-base \
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xvfb \
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zlib1g-dev"
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apt-get install -y --no-install-recommends $BUILDDEPS
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## Download source code
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curl -O https://cran.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz
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## Extract source code
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tar -xf R-${R_VERSION}.tar.gz
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cd R-${R_VERSION}
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## Set compiler flags
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R_PAPERSIZE=letter \
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R_BATCHSAVE="--no-save --no-restore"
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R_BROWSER=xdg-open
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PAGER=/usr/bin/pager
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PERL=/usr/bin/perl
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R_UNZIPCMD=/usr/bin/unzip
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R_ZIPCMD=/usr/bin/zip
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R_PRINTCMD=/usr/bin/lpr
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LIBnn=lib
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AWK=/usr/bin/awk
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CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"
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CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"
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## Configure options
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./configure --enable-R-shlib \
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--enable-memory-profiling \
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--with-readline \
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--with-blas \
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--with-tcltk \
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--disable-nls \
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--with-recommended-packages \
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--prefix /usr/local
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## Build and install
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make -j $(nproc) -O
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make install
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## Add a library directory (for user-installed packages)
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mkdir -p /usr/local/lib/R/site-library
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chown root:staff /usr/local/lib/R/site-library
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chmod g+ws /usr/local/lib/R/site-library
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## Fix library path
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sed -i '/^R_LIBS_USER=.*$/d' /usr/local/lib/R/etc/Renviron
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echo "R_LIBS_USER=\${R_LIBS_USER-'/usr/local/lib/R/site-library'}" >> /usr/local/lib/R/etc/Renviron
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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
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echo "options(repos = c(CRAN='$CRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site
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## Clean up from R source install
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apt-get remove --purge -y $BUILDDEPS
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apt-get autoremove -y
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apt-get autoclean -y
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rm -rf /var/lib/apt/lists/*
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END_RUN_CMD
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###
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### Added Bioconductor packages to r-ver
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###
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FROM rver as bioconductor
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RUN <<END_RUN_CMD
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apt-get update && apt-get install --no-install-recommends -y \
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zlib1g-dev
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R -e "install.packages('BiocManager', repos='https://cran.r-project.org')"
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R -e "BiocManager::install('Biostrings')"
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R -e "BiocManager::install('seqinr')"
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apt-get autoremove -y
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apt-get autoclean -y
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rm -rf /var/lib/apt/lists/*
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END_RUN_CMD
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###
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### Perl base image
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###
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FROM buildpack-deps:buster AS perl
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LABEL maintainer="Peter Martini <PeterCMartini@GMail.com>, Zak B. Elep <zakame@cpan.org>"
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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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chmod -R 777 /viquas
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curl -fL https://www.cpan.org/src/5.0/perl-5.34.1.tar.xz -o perl-5.34.1.tar.xz
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tar --strip-components=1 -xaf perl-5.34.1.tar.xz -C /usr/src/perl
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rm perl-5.34.1.tar.xz
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cat *.patch | patch -p1
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gnuArch="$(dpkg-architecture --query DEB_BUILD_GNU_TYPE)"
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archBits="$(dpkg-architecture --query DEB_BUILD_ARCH_BITS)"
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archFlag="$([ "$archBits" = '64' ] && echo '-Duse64bitall' || echo '-Duse64bitint')"
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./Configure -Darchname="$gnuArch" "$archFlag" -Dusethreads -Duseshrplib -Dvendorprefix=/usr/local -des
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make -j$(nproc)
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TEST_JOBS=$(nproc) make test_harness
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make install
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cd /usr/src
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curl -fLO https://www.cpan.org/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7047.tar.gz
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tar -xzf App-cpanminus-1.7047.tar.gz && cd App-cpanminus-1.7047 && perl bin/cpanm . && cd /root
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cpanm IO::Socket::SSL
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curl -fL https://raw.githubusercontent.com/skaji/cpm/0.997011/cpm -o /usr/local/bin/cpm
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chmod +x /usr/local/bin/cpm
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rm -fr /root/.cpanm /usr/src/perl /usr/src/App-cpanminus-1.7047*
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END_RUN_CMD
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###
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### Added bioperl packaged
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###
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FROM perl AS bioperl
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RUN <<END_RUN_CMD
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cpanm -n -v Bio::Seq Bio::SeqIO Perl4::CoreLibs
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END_RUN_CMD
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###
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### Samtools build
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###
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FROM buildpack-deps:buster AS samtools
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ARG SAMTOOLS_VERSION=1.2
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RUN <<END_RUN_CMD
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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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END_RUN_CMD
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###
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### Viquas extraction
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###
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FROM buildpack-deps:buster AS viquas
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RUN <<END_RUN_CMD
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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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END_RUN_CMD
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###
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### Final build
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###
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FROM debian:buster as final
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RUN <<END_RUN_CMD
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apt-get update && apt-get install -y --no-install-recommends \
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bash-completion \
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file \
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fonts-texgyre \
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gfortran \
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gsfonts \
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libblas-dev \
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libbz2-1.0 \
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libcurl4 \
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libicu63 \
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libjpeg62-turbo \
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libncurses5-dev \
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libopenblas-dev \
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libpangocairo-1.0-0 \
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libpcre3 \
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libpng16-16 \
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libreadline7 \
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libtiff5 \
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liblzma5 \
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locales \
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unzip \
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zip \
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zlib1g
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apt-get autoremove -y
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apt-get autoclean -y
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rm -rf /var/lib/apt/lists/*
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END_RUN_CMD
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COPY --from=bioconductor /usr/local/bin /usr/local/bin
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COPY --from=bioconductor /usr/local/lib /usr/local/lib
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COPY --from=bioconductor /usr/local/share /usr/local/share
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COPY --from=bioperl /usr/local/bin /usr/local/bin
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COPY --from=bioperl /usr/local/lib /usr/local/lib
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COPY --from=bioperl /usr/local/share /usr/local/share
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COPY --from=bioperl /usr/share/perl /usr/share/perl
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COPY --from=samtools /usr/local/bin /usr/local/bin
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COPY --from=samtools /usr/local/lib /usr/local/lib
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COPY --from=samtools /usr/local/share /usr/local/share
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COPY --from=viquas /viquas /viquas
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COPY --chmod=755 viquas /usr/local/bin/viquas
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ENTRYPOINT [ "viquas" ]
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47
modules/viquas/viquas
Normal file
47
modules/viquas/viquas
Normal file
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@ -0,0 +1,47 @@
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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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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 -r /viquas/{viquas_files,ViQuaS.R} .
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case $NUM_ARGS in
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2)
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Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
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;;
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6)
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Rscript ./ViQuaS.R "${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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rm -rf ./{viquas_files,ViQuaS.R}
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