Move dependencies out of Dockerfile

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=17
+ARG BIOCONDUCTOR_PATCH=19
 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 \
-        libeigen3-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 src /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 \
-	&& 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 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
 
-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 +1,4 @@
+# APT required 
+curl
+libzmq3-dev
+python3-pip

Ubuntu-files/20.04/apt_skip.txt

@@ -0,0 +1,20 @@
+# APT skip
+build-essential
+default-jdk                     # Rocker
+gfortran                        # Rocker
+git
+gobjc
+libbz2-dev                      # Rocker
+libcairo2-dev                   # Rocker
+libcurl4-openssl-dev            # Rocker
+libicu-dev                      # Rocker
+libjpeg-dev                     # Rocker
+liblzma-dev                     # Rocker
+libpcre2-dev                    # Rocker
+libpng-dev                      # Rocker
+libreadline-dev                 # Rocker
+libtiff-dev                     # Rocker
+libx11-dev
+libxt-dev                       # Rocker
+python3-minimal
+zlib1g-dev                      # Rocker

Ubuntu-files/20.04/pip_skip.txt

@@ -0,0 +1,5 @@
+pandas
+pyyaml
+sklearn
+tensorflow
+wheel

src/install.sh

@@ -0,0 +1,60 @@
+#!/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_required_compile_R.txt apt_required_build.txt apt_bioc.txt apt_cran.txt apt_optional_compile_R.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 $1}' >> /tmp/install_apt_pkgs
+
+# Packages to install
+apt_pkgs=$(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 -rf /tmp/BBS /tmp/*_pkgs /tmp/20.04
+fi