Move dependencies out of Dockerfile

- Add bin/install.sh to install BBS dependencies

- Add Ubuntu-files to track docker-specific dependencies

- Move install.R to bin

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=2
+ARG BIOCONDUCTOR_PATCH=5
 ARG BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_VERSION}.${BIOCONDUCTOR_PATCH}
 
 LABEL name="bioconductor/bioconductor_docker" \
@@ -29,133 +29,15 @@ RUN dpkg --clear-avail
 # 'debconf: unable to initialize frontend: Dialog'
 ENV DEBIAN_FRONTEND noninteractive
 
-# Update apt-get
-RUN apt-get update \
-	&& apt-get install -y --no-install-recommends apt-utils \
-	&& apt-get install -y --no-install-recommends \
-	## Basic deps
-	gdb \
-	libxml2-dev \
-	python3-pip \
-	libz-dev \
-	liblzma-dev \
-	libbz2-dev \
-	libpng-dev \
-	libgit2-dev \
-	## sys deps from bioc_full
-	pkg-config \
-	fortran77-compiler \
-	byacc \
-	automake \
-	curl \
-	## This section installs libraries
-	libpcre2-dev \
-	libnetcdf-dev \
-	libhdf5-serial-dev \
-	libfftw3-dev \
-	libopenbabel-dev \
-	libopenmpi-dev \
-	libxt-dev \
-	libudunits2-dev \
-	libgeos-dev \
-	libproj-dev \
-	libcairo2-dev \
-	libtiff5-dev \
-	libreadline-dev \
-	libgsl0-dev \
-	libgslcblas0 \
-	libgtk2.0-dev \
-	libgl1-mesa-dev \
-	libglu1-mesa-dev \
-	libgmp3-dev \
-	libhdf5-dev \
-	libncurses-dev \
-	libbz2-dev \
-	libxpm-dev \
-	liblapack-dev \
-	libv8-dev \
-	libgtkmm-2.4-dev \
-	libmpfr-dev \
-	libmodule-build-perl \
-	libapparmor-dev \
-	libprotoc-dev \
-	librdf0-dev \
-	libmagick++-dev \
-	libsasl2-dev \
-	libpoppler-cpp-dev \
-	libprotobuf-dev \
-	libpq-dev \
-	libperl-dev \
-	## software - perl extentions and modules
-	libarchive-extract-perl \
-	libfile-copy-recursive-perl \
-	libcgi-pm-perl \
-	libdbi-perl \
-	libdbd-mysql-perl \
-	libxml-simple-perl \
-	libmysqlclient-dev \
-	default-libmysqlclient-dev \
-	libgdal-dev \
-	## new libs
-	libglpk-dev \
-	## Databases and other software
-	sqlite \
-	openmpi-bin \
-	mpi-default-bin \
-	openmpi-common \
-	openmpi-doc \
-	tcl8.6-dev \
-	tk-dev \
-	default-jdk \
-	imagemagick \
-	tabix \
-	ggobi \
-	graphviz \
-	protobuf-compiler \
-	jags \
-	## Additional resources
-	xfonts-100dpi \
-	xfonts-75dpi \
-	biber \
-        libsbml5-dev \
-        libzmq3-dev \
-	&& apt-get clean \
-	&& rm -rf /var/lib/apt/lists/*
+COPY bin /tmp
+COPY Ubuntu-files /tmp
 
-## Python installations
-RUN apt-get update \
-	&& apt-get install -y software-properties-common \
-	&& add-apt-repository universe \
-	&& apt-get update \
-	&& apt-get -y --no-install-recommends install python2 python-dev \
-	&& curl https://bootstrap.pypa.io/pip/2.7/get-pip.py --output get-pip.py \
-	&& python2 get-pip.py \
-	&& pip2 install wheel \
-	## Install sklearn and pandas on python
-	&& pip2 install sklearn \
-	pandas \
-	pyyaml \
-	cwltool \
-	&& apt-get clean \
-	&& rm -rf /var/lib/apt/lists/* \
-	&& rm -rf get-pip.py
-
-## FIXME
-## These two libraries don't install in the above section--WHY?
-RUN apt-get update \
-	&& apt-get -y --no-install-recommends install \
-	libmariadb-dev-compat \
-	libjpeg-dev \
-	libjpeg-turbo8-dev \
-	libjpeg8-dev \
-	&& apt-get clean \
-	&& rm -rf /var/lib/apt/lists/*
+# Install dependencies
+RUN /bin/bash -C /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
 
-ADD install.R /tmp/
-
 RUN R -f /tmp/install.R
 
 # DEVEL: Add sys env variables to DEVEL image

Ubuntu-files/20.04/apt_required.txt

@@ -0,0 +1,44 @@
+# 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

@@ -0,0 +1,48 @@
+# 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

Ubuntu-files/20.04/pip_skip.txt

@@ -0,0 +1,6 @@
+cwltool
+pandas
+pyyaml
+sklearn
+tensorflow
+wheel

bin/install.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+set -e
+
+# Set variables
+version="20.04"
+repo="https://github.com/Bioconductor/bbs"
+branch="master"
+bbs_files="/tmp/BBS/Ubuntu-files/$version"
+bd_files="/tmp/$version"
+
+# Get repository with Ubuntu-files
+if [ ! -d "/tmp/BBS" ]; then
+  git clone $repo /tmp/BBS 
+  cd /tmp/BBS
+  if [ $branch != "master" ]; then
+    git fetch origin $branch
+    git switch $branch
+  fi
+  cd ~
+fi
+
+# Constructing array of apt packages, removing unnecessary packages.
+cat $bbs_files/apt_*.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_apt_pkgs 
+cat $bd_files/apt_*.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_apt_pkgs
+apt_pkgs=$(comm -23 /tmp/bbs_apt_pkgs /tmp/skip_apt_pkgs)
+
+# Constructing array of pip packages, removing unnecessary packages.
+cat $bbs_files/pip_*.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_pip_pkgs
+cat $bd_files/pip_*.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_pip_pkgs
+pip_pkgs=$(comm -23 /tmp/bbs_pip_pkgs /tmp/skip_pip_pkgs)
+
+# Packages always required by Bioconductor Docker
+apt_required_pkgs=$(cat $bd_files/apt_required.txt | awk '/^[^#]/ {print $1}')
+
+# Install dependencies
+
+# Install apt packages
+apt-get update \
+  && apt-get install -y --no-install-recommends apt-utils
+
+apt-get update \
+  && apt-get install -y --no-install-recommends $apt_pkgs
+
+apt-get update \
+  && apt-get install -y --no-install-recommends $apt_required_pkgs \
+  && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install pip packages
+pip3 install $pip_pkgs
+
+# Remove files
+if test -n "$(find /tmp -maxdepth 1 -name '*_pkgs' -print -quit)"; then
+  rm /tmp/*_pkgs
+fi