Separate out system dependencies of Bioconductor.

.github/workflows/test-images.yaml

@@ -13,7 +13,7 @@ jobs:
   test-built-containers:
     strategy:
       matrix:
-        container-tag: [devel, RELEASE_3_13]
+        container-tag: [devel, RELEASE_3_14]
     runs-on: ubuntu-latest
     container: bioconductor/bioconductor_docker:${{ matrix.container-tag }}
 

Dockerfile

@@ -7,7 +7,8 @@ ARG BIOCONDUCTOR_VERSION=3.15
 ##### IMPORTANT ########
 ## The PATCH version number should be incremented each time
 ## there is a change in the Dockerfile.
-ARG BIOCONDUCTOR_PATCH=14
+ARG BIOCONDUCTOR_PATCH=15
+
 ARG BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_VERSION}.${BIOCONDUCTOR_PATCH}
 
 LABEL name="bioconductor/bioconductor_docker" \
@@ -18,147 +19,28 @@ LABEL name="bioconductor/bioconductor_docker" \
       description="Bioconductor docker image with system dependencies to install all packages." \
       license="Artistic-2.0"
 
-# nuke cache dirs before installing pkgs; tip from Dirk E fixes broken img
-RUN rm -f /var/lib/dpkg/available && rm -rf  /var/cache/apt/*
-
-# issues with '/var/lib/dpkg/available' not found
-# this will recreate
-RUN dpkg --clear-avail
-
-# This is to avoid the error
-# '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 \
-        ## python3 dev
-        python3-dev \
-	&& apt-get clean \
-	&& rm -rf /var/lib/apt/lists/*
-
-## Python installations
-RUN pip3 install sklearn \
-        pandas \
-        pyyaml
-
-## 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/*
+##  Add Bioconductor system dependencies
+ADD bioc_scripts/install_bioc_sysdeps.sh /tmp/
+RUN bash /tmp/install_bioc_sysdeps.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/
-
+## Install specific version of BiocManager
+ADD bioc_scripts/install.R /tmp/
 RUN R -f /tmp/install.R
 
 # DEVEL: Add sys env variables to DEVEL image
 # Variables in Renviron.site are made available inside of R.
 # Add libsbml CFLAGS
 RUN curl -O http://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc \
-	&& cat Renviron.bioc | grep -o '^[^#]*' | sed 's/export //g' >>/etc/environment \
-	&& cat Renviron.bioc >> /usr/local/lib/R/etc/Renviron.site \
-	&& echo BIOCONDUCTOR_VERSION=${BIOCONDUCTOR_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
-        && echo BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_DOCKER_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
-        && echo 'LIBSBML_CFLAGS="-I/usr/include"' >> /usr/local/lib/R/etc/Renviron.site \
-        && echo 'LIBSBML_LIBS="-lsbml"' >> /usr/local/lib/R/etc/Renviron.site \
-	&& rm -rf Renviron.bioc
+    && cat Renviron.bioc | grep -o '^[^#]*' | sed 's/export //g' >>/etc/environment \
+    && cat Renviron.bioc >> /usr/local/lib/R/etc/Renviron.site \
+    && echo BIOCONDUCTOR_VERSION=${BIOCONDUCTOR_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
+    && echo BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_DOCKER_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
+    && echo 'LIBSBML_CFLAGS="-I/usr/include"' >> /usr/local/lib/R/etc/Renviron.site \
+    && echo 'LIBSBML_LIBS="-lsbml"' >> /usr/local/lib/R/etc/Renviron.site \
+    && rm -rf Renviron.bioc
 
 ENV LIBSBML_CFLAGS="-I/usr/include"
 ENV LIBSBML_LIBS="-lsbml"

install.R → bioc_scripts/install.R

@@ -2,4 +2,4 @@ install.packages("BiocManager", repos="https://cran.rstudio.com")
 
 BiocManager::install(version="3.15", update=TRUE, ask=FALSE)
 
-BiocManager::install(c('devtools', 'AnVIL'))
+BiocManager::install('devtools')

bioc_scripts/install_bioc_sysdeps.sh

@@ -0,0 +1,140 @@
+#!/bin/bash
+set -e
+
+# This is to avoid the error
+# 'debconf: unable to initialize frontend: Dialog'
+export DEBIAN_FRONTEND=noninteractive
+
+## Update apt-get
+apt-get update
+
+apt-get install -y --no-install-recommends apt-utils
+
+## Basic Deps
+apt-get install -y --no-install-recommends \
+	gdb \
+	libxml2-dev \
+	python3-pip \
+	libz-dev \
+	liblzma-dev \
+	libbz2-dev \
+	libpng-dev \
+	libgit2-dev
+
+## sys deps from bioc_full
+apt-get install -y --no-install-recommends \
+	pkg-config \
+	fortran77-compiler \
+	byacc \
+	automake \
+	curl \
+	cmake
+
+## This section installs libraries
+apt-get install -y --no-install-recommends \
+	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 \
+	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
+
+## software - perl extentions and modules
+apt-get install -y --no-install-recommends \
+	libperl-dev \
+	libarchive-extract-perl \
+	libfile-copy-recursive-perl \
+	libcgi-pm-perl \
+	libdbi-perl \
+	libdbd-mysql-perl \
+	libxml-simple-perl
+
+## new libs
+apt-get install -y --no-install-recommends \
+	libglpk-dev \
+	libeigen3-dev
+
+## Databases and other software
+apt-get install -y --no-install-recommends \
+	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
+apt-get install -y --no-install-recommends \
+	xfonts-100dpi \
+	xfonts-75dpi \
+	biber \
+	libsbml5-dev \
+	libzmq3-dev \
+	python3-dev
+
+## More additional resources
+## libavfilter-dev - <infinityFlow, host of other packages>
+## mono-runtime - <rawrr, MsBackendRawFileReader>
+## libfuse-dev - <Travel>
+## ocl-icd-opencl-dev - <gpuMagic> - but machine needs to be a GPU--otherwise it's useless
+apt-get -y --no-install-recommends install \
+	libmariadb-dev-compat \
+	libjpeg-dev \
+	libjpeg-turbo8-dev \
+	libjpeg8-dev \
+	libavfilter-dev \
+	libfuse-dev \
+	mono-runtime \
+	ocl-icd-opencl-dev
+
+## Python installations
+pip3 install sklearn pandas pyyaml
+
+## libgdal is needed for sf
+apt-get install -y --no-install-recommends \
+	libgdal-dev \
+	default-libmysqlclient-dev \
+	libmysqlclient-dev
+
+## clean up
+apt-get clean
+apt-get autoremove -y
+apt-get autoclean -y
+rm -rf /var/lib/apt/lists/*