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Merge pull request #40 from Bioconductor/install_bioc_deps
Separate out system dependencies of Bioconductor into a folder `bioc_scripts` --> with `install_bioc_sysdeps.sh` as the place for all sys deps.
2 parents ea5985e + 723ca91 commit b92c946

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Lines changed: 156 additions & 134 deletions

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‎.github/workflows/test-images.yaml‎

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

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@@ -7,7 +7,8 @@ ARG BIOCONDUCTOR_VERSION=3.15
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##### IMPORTANT ########
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## The PATCH version number should be incremented each time
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## there is a change in the Dockerfile.
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ARG BIOCONDUCTOR_PATCH=14
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ARG BIOCONDUCTOR_PATCH=15
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ARG BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_VERSION}.${BIOCONDUCTOR_PATCH}
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LABEL name="bioconductor/bioconductor_docker" \
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description="Bioconductor docker image with system dependencies to install all packages." \
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license="Artistic-2.0"
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# nuke cache dirs before installing pkgs; tip from Dirk E fixes broken img
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RUN rm -f /var/lib/dpkg/available && rm -rf /var/cache/apt/*
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# issues with '/var/lib/dpkg/available' not found
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# this will recreate
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RUN dpkg --clear-avail
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# This is to avoid the error
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# 'debconf: unable to initialize frontend: Dialog'
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ENV DEBIAN_FRONTEND noninteractive
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# Update apt-get
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends apt-utils \
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&& apt-get install -y --no-install-recommends \
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## Basic deps
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gdb \
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libxml2-dev \
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python3-pip \
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libz-dev \
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liblzma-dev \
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libbz2-dev \
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libpng-dev \
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libgit2-dev \
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## sys deps from bioc_full
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pkg-config \
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fortran77-compiler \
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byacc \
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automake \
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curl \
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## This section installs libraries
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libpcre2-dev \
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libnetcdf-dev \
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libhdf5-serial-dev \
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libfftw3-dev \
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libopenbabel-dev \
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libopenmpi-dev \
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libxt-dev \
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libudunits2-dev \
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libgeos-dev \
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libproj-dev \
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libcairo2-dev \
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libtiff5-dev \
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libreadline-dev \
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libgsl0-dev \
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libgslcblas0 \
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libgtk2.0-dev \
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libgl1-mesa-dev \
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libglu1-mesa-dev \
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libgmp3-dev \
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libhdf5-dev \
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libncurses-dev \
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libbz2-dev \
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libxpm-dev \
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liblapack-dev \
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libv8-dev \
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libgtkmm-2.4-dev \
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libmpfr-dev \
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libmodule-build-perl \
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libapparmor-dev \
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libprotoc-dev \
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librdf0-dev \
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libmagick++-dev \
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libsasl2-dev \
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libpoppler-cpp-dev \
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libprotobuf-dev \
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libpq-dev \
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libperl-dev \
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## software - perl extentions and modules
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libarchive-extract-perl \
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libfile-copy-recursive-perl \
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libcgi-pm-perl \
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libdbi-perl \
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libdbd-mysql-perl \
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libxml-simple-perl \
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libmysqlclient-dev \
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default-libmysqlclient-dev \
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libgdal-dev \
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## new libs
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libglpk-dev \
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libeigen3-dev \
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## Databases and other software
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sqlite \
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openmpi-bin \
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mpi-default-bin \
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openmpi-common \
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openmpi-doc \
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tcl8.6-dev \
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tk-dev \
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default-jdk \
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imagemagick \
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tabix \
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ggobi \
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graphviz \
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protobuf-compiler \
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jags \
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## Additional resources
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xfonts-100dpi \
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xfonts-75dpi \
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biber \
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libsbml5-dev \
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libzmq3-dev \
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## python3 dev
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python3-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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## Python installations
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RUN pip3 install sklearn \
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pandas \
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pyyaml
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## FIXME
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## These two libraries don't install in the above section--WHY?
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RUN apt-get update \
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&& apt-get -y --no-install-recommends install \
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libmariadb-dev-compat \
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libjpeg-dev \
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libjpeg-turbo8-dev \
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libjpeg8-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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## Add Bioconductor system dependencies
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ADD bioc_scripts/install_bioc_sysdeps.sh /tmp/
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RUN bash /tmp/install_bioc_sysdeps.sh
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## Add host-site-library
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RUN echo "R_LIBS=/usr/local/lib/R/host-site-library:\${R_LIBS}" > /usr/local/lib/R/etc/Renviron.site
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ADD install.R /tmp/
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## Install specific version of BiocManager
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ADD bioc_scripts/install.R /tmp/
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RUN R -f /tmp/install.R
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# DEVEL: Add sys env variables to DEVEL image
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# Variables in Renviron.site are made available inside of R.
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# Add libsbml CFLAGS
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RUN curl -O http://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc \
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&& cat Renviron.bioc | grep -o '^[^#]*' | sed 's/export //g' >>/etc/environment \
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&& cat Renviron.bioc >> /usr/local/lib/R/etc/Renviron.site \
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&& echo BIOCONDUCTOR_VERSION=${BIOCONDUCTOR_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
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&& echo BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_DOCKER_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
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&& echo 'LIBSBML_CFLAGS="-I/usr/include"' >> /usr/local/lib/R/etc/Renviron.site \
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&& echo 'LIBSBML_LIBS="-lsbml"' >> /usr/local/lib/R/etc/Renviron.site \
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&& rm -rf Renviron.bioc
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&& cat Renviron.bioc | grep -o '^[^#]*' | sed 's/export //g' >>/etc/environment \
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&& cat Renviron.bioc >> /usr/local/lib/R/etc/Renviron.site \
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&& echo BIOCONDUCTOR_VERSION=${BIOCONDUCTOR_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
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&& echo BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_DOCKER_VERSION} >> /usr/local/lib/R/etc/Renviron.site \
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&& echo 'LIBSBML_CFLAGS="-I/usr/include"' >> /usr/local/lib/R/etc/Renviron.site \
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&& echo 'LIBSBML_LIBS="-lsbml"' >> /usr/local/lib/R/etc/Renviron.site \
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&& rm -rf Renviron.bioc
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ENV LIBSBML_CFLAGS="-I/usr/include"
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ENV LIBSBML_LIBS="-lsbml"

install.R renamed to bioc_scripts/install.R

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

‎bioc_scripts/install_bioc_sysdeps.sh‎

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#!/bin/bash
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set -e
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# This is to avoid the error
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# 'debconf: unable to initialize frontend: Dialog'
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export DEBIAN_FRONTEND=noninteractive
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8+
## Update apt-get
9+
apt-get update
10+
11+
apt-get install -y --no-install-recommends apt-utils
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13+
## Basic Deps
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apt-get install -y --no-install-recommends \
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gdb \
16+
libxml2-dev \
17+
python3-pip \
18+
libz-dev \
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liblzma-dev \
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libbz2-dev \
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libpng-dev \
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libgit2-dev
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24+
## sys deps from bioc_full
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apt-get install -y --no-install-recommends \
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pkg-config \
27+
fortran77-compiler \
28+
byacc \
29+
automake \
30+
curl \
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cmake
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33+
## This section installs libraries
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apt-get install -y --no-install-recommends \
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libpcre2-dev \
36+
libnetcdf-dev \
37+
libhdf5-serial-dev \
38+
libfftw3-dev \
39+
libopenbabel-dev \
40+
libopenmpi-dev \
41+
libxt-dev \
42+
libudunits2-dev \
43+
libgeos-dev \
44+
libproj-dev \
45+
libcairo2-dev \
46+
libtiff5-dev \
47+
libreadline-dev \
48+
libgsl0-dev \
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libgslcblas0 \
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libgtk2.0-dev \
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libgl1-mesa-dev \
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libglu1-mesa-dev \
53+
libgmp3-dev \
54+
libhdf5-dev \
55+
libncurses-dev \
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libxpm-dev \
57+
liblapack-dev \
58+
libv8-dev \
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libgtkmm-2.4-dev \
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libmpfr-dev \
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libmodule-build-perl \
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libapparmor-dev \
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libprotoc-dev \
64+
librdf0-dev \
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libmagick++-dev \
66+
libsasl2-dev \
67+
libpoppler-cpp-dev \
68+
libprotobuf-dev \
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libpq-dev
70+
71+
## software - perl extentions and modules
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apt-get install -y --no-install-recommends \
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libperl-dev \
74+
libarchive-extract-perl \
75+
libfile-copy-recursive-perl \
76+
libcgi-pm-perl \
77+
libdbi-perl \
78+
libdbd-mysql-perl \
79+
libxml-simple-perl
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81+
## new libs
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apt-get install -y --no-install-recommends \
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libglpk-dev \
84+
libeigen3-dev
85+
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## Databases and other software
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apt-get install -y --no-install-recommends \
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sqlite \
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openmpi-bin \
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mpi-default-bin \
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openmpi-common \
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openmpi-doc \
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tcl8.6-dev \
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tk-dev \
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default-jdk \
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imagemagick \
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tabix \
98+
ggobi \
99+
graphviz \
100+
protobuf-compiler \
101+
jags
102+
103+
## Additional resources
104+
apt-get install -y --no-install-recommends \
105+
xfonts-100dpi \
106+
xfonts-75dpi \
107+
biber \
108+
libsbml5-dev \
109+
libzmq3-dev \
110+
python3-dev
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## More additional resources
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## libavfilter-dev - <infinityFlow, host of other packages>
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## mono-runtime - <rawrr, MsBackendRawFileReader>
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## libfuse-dev - <Travel>
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## ocl-icd-opencl-dev - <gpuMagic> - but machine needs to be a GPU--otherwise it's useless
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apt-get -y --no-install-recommends install \
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libmariadb-dev-compat \
119+
libjpeg-dev \
120+
libjpeg-turbo8-dev \
121+
libjpeg8-dev \
122+
libavfilter-dev \
123+
libfuse-dev \
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mono-runtime \
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ocl-icd-opencl-dev
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127+
## Python installations
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pip3 install sklearn pandas pyyaml
129+
130+
## libgdal is needed for sf
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apt-get install -y --no-install-recommends \
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libgdal-dev \
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default-libmysqlclient-dev \
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libmysqlclient-dev
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## clean up
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apt-get clean
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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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