Make installation explicit

- Add comments to demystify package selection/removal

- Remove extraneous apt packages

Author: jwokaty

Dockerfile

@@ -7,7 +7,7 @@ ARG BIOCONDUCTOR_VERSION=3.14
 ##### IMPORTANT ########
 ## The PATCH version number should be incremented each time
 ## there is a change in the Dockerfile.
-ARG BIOCONDUCTOR_PATCH=5
+ARG BIOCONDUCTOR_PATCH=11
 ARG BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_VERSION}.${BIOCONDUCTOR_PATCH}
 
 LABEL name="bioconductor/bioconductor_docker" \
@@ -29,11 +29,11 @@ RUN dpkg --clear-avail
 # 'debconf: unable to initialize frontend: Dialog'
 ENV DEBIAN_FRONTEND noninteractive
 
-COPY bin /tmp
+COPY src /tmp
 COPY Ubuntu-files /tmp
 
 # Install dependencies
-RUN /bin/bash -C /tmp/install.sh
+RUN bash /tmp/install.sh
 
 ## Add host-site-library
 RUN echo "R_LIBS=/usr/local/lib/R/host-site-library:\${R_LIBS}" > /usr/local/lib/R/etc/Renviron.site

Ubuntu-files/20.04/apt_required.txt

@@ -1,44 +1,3 @@
 # APT required 
-byacc
 curl
-default-libmysqlclient-dev
-fortran77-compiler
-ggobi
-imagemagick
-libapparmor-dev
-libarchive-extract-perl
-libbz2-dev
-libcgi-pm-perl
-libdbd-mysql-perl
-libdbi-perl
-libfile-copy-recursive-perl
-libgl1-mesa-dev
-libgmp3-dev
-libgsl0-dev
-libgslcblas0
-libhdf5-dev
-libhdf5-serial-dev
-libjpeg8-dev
-libjpeg-turbo8-dev
-liblapack-dev
-#libmariadb-dev-compat          # Depends on libmariadb-dev, conflicts with libmysqlclient-dev
-libmodule-build-perl
-libncurses-dev
-libopenmpi-dev
-libperl-dev
-libprotoc-dev
-librdf0-dev
-libtiff5-dev
-libxml-simple-perl
-libxpm-dev
-libz-dev
 libzmq3-dev
-mpi-default-bin
-openmpi-bin
-openmpi-common
-openmpi-doc
-pkg-config
-software-properties-common
-sqlite
-tabix
-tcl8.6-dev

Ubuntu-files/20.04/apt_skip.txt

@@ -1,48 +1,11 @@
 # APT skip
-build-essential
-clustalo
-fuse
-gfortran
-git
-gobjc
-gsfonts-x11
-infernal
-kallisto
-libavfilter-dev
-libcurl4-openssl-dev
-libeigen3-dev
-libfribidi-dev
-libfuse-dev
-libgmp-dev                      # BD uses libgmp3-dev
-libgraphviz-dev
-libgsl-dev                      # BD uses libgsl0-dev
-libicu-dev
-librsvg2-dev
-libssl-dev
-libtiff-dev                     # BD uses libtiff5-dev
-libx11-dev
-manpages-dev
-mlocate
-mpi-default-dev                 # BD uses mpi-default-bin
-ocl-icd-opencl-dev
-pandoc
-pandoc-citeproc
-t1-xfree86-nonfree
-tcl-dev                         # BD uses tcl8.6-dev
-texi2html
-texinfo
-texlive
-texlive-bibtex-extra
-texlive-fonts-extra
-texlive-font-utils
-texlive-lang-european
-texlive-latex-extra
-texlive-luatex
-texlive-pstricks
-texlive-science
-tree
-ttf-xfree86-nonfree
-ttf-xfree86-nonfree-syriac
-xfonts-base                     # BD uses xfonts-100dpi and xfonts-75dpi
-xfonts-scalable
-zlib1g-dev
+gfortran            # Rocker
+libbz2-dev          # Rocker
+libcurl4            # Rocker
+libicui-dev         # Rocker
+libpcre2-dev        # Rocker
+libjpeg-dev         # Rocker uses libjpeg-turbo*
+libreadline-dev     # Rocker
+libtiff-dev         # Rocker
+liblzma-dev         # Rocker
+zlib1g-dev          # Rocker

bin/install.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+
+set -e
+
+# Set variables
+version="20.04"
+repo="https://github.com/Bioconductor/BBS"
+branch="master"
+bbs="/tmp/BBS/Ubuntu-files/$version"
+bioconductor_docker="/tmp/$version"
+bbs_apt_files="apt_bioc.txt apt_cran.txt apt_extra_fonts.txt apt_nice_to_have.txt apt_optional_compile_R.txt apt_required_build.txt"
+bbs_pip_files="pip_pkgs.txt pip_spb.txt"
+
+# Get repository with Ubuntu-files
+if [ ! -d "/tmp/BBS" ]; then
+  git clone -b $branch --depth 1 $repo /tmp/BBS
+fi
+
+cd $bbs
+
+# Write a sorted list of BBS apt packages, skipping any commented lines.
+cat $bbs_apt_files | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_apt_pkgs 
+# Write a sorted list of apt packages to remove from the install list,
+# excluding any commented lines.
+cat $bioconductor_docker/apt_skip.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_apt_pkgs
+# Write a file listing the apt packages to install, removing all packages
+# in skip_apt_pkgs.
+comm -23 /tmp/bbs_apt_pkgs /tmp/skip_apt_pkgs >> /tmp/install_apt_pkgs
+
+# Write a file with pip packages to install.
+cat $bbs_pip_files | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_pip_pkgs
+cat $bioconductor_docker/pip_skip.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_pip_pkgs
+comm -23 /tmp/bbs_pip_pkgs /tmp/skip_pip_pkgs >> /tmp/install_pip_pkgs
+
+cd ~
+
+# Packages always required by Bioconductor Docker
+cat $bioconductor_docker/apt_required.txt | awk '/^[^#]/ {print $1}' >> /tmp/install_apt_pkgs
+apt_pkgs=$(cat /tmp/install_apt_pkgs)
+pip_pkgs=$(cat /tmp/install_pip_pkgs)
+
+# Install dependencies
+
+# Install apt packages
+apt-get update \
+  && apt-get install -y --no-install-recommends apt-utils
+
+apt-get install -y --no-install-recommends $apt_pkgs \
+  && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install pip packages
+pip3 install $pip_pkgs
+rm -rf ~/.cache/pip
+
+# Remove files
+if test -n "$(find /tmp -maxdepth 1 -name '*_pkgs' -print -quit)"; then
+  rm /tmp/*_pkgs
+  rm -rf /tmp/BBS
+fi