From 9e19e836d98c652c4fc42a865b20bb0cdd57e5b0 Mon Sep 17 00:00:00 2001
From: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: Fri, 29 May 2020 13:15:44 -0400
Subject: [PATCH] Add work-in-progress RStudio-pro-bioconductor image

- Add Dockerfile, with sys dependencies installed.

- NOTES: IMO, these sys dependencies should just be in the base
  image just like in terra-jupyter-r, because these sys dependencies
  allow installation and use of most CRAN and Bioconductor packages.

- R version in this image is out of date with version R.3.6.3. The base
  image needs to be built on a more recent version of R.

- Once R-4.0 is used, it's possible to remove installation of
  Bioconductor packages manually as binary package insallation will be
  available with the `AnVIL` package. There will be no need of a special
  Bioconductor image. It can just be `rstudio-pro-base:<version>`, which
  all users use across the board.

cc-ing @rtitle and @mtmorgan for a broader discussion.
---
 terra-rstudio-pro-bioconductor/CHANGELOG.md |   1 +
 terra-rstudio-pro-bioconductor/Dockerfile   | 130 ++++++++++++++++++++
 terra-rstudio-pro-bioconductor/README.md    |   5 +
 3 files changed, 136 insertions(+)
 create mode 100644 terra-rstudio-pro-bioconductor/CHANGELOG.md
 create mode 100644 terra-rstudio-pro-bioconductor/Dockerfile
 create mode 100644 terra-rstudio-pro-bioconductor/README.md

diff --git a/terra-rstudio-pro-bioconductor/CHANGELOG.md b/terra-rstudio-pro-bioconductor/CHANGELOG.md
new file mode 100644
index 00000000..8a6fb13f
--- /dev/null
+++ b/terra-rstudio-pro-bioconductor/CHANGELOG.md
@@ -0,0 +1 @@
+## todo
diff --git a/terra-rstudio-pro-bioconductor/Dockerfile b/terra-rstudio-pro-bioconductor/Dockerfile
new file mode 100644
index 00000000..52c6b323
--- /dev/null
+++ b/terra-rstudio-pro-bioconductor/Dockerfile
@@ -0,0 +1,130 @@
+FROM rstudio-pro-test:latest
+
+# This is to avoid the error
+# 'debconf: unable to initialize frontend: Dialog'
+ENV DEBIAN_FRONTEND noninteractive
+
+## Create env variables for detecting version
+RUN echo "TERRA_R_PLATFORM='terra-rstudio-pro-bioconductor'" >> /opt/R/3.6.3/lib/R/etc/Renviron.site \
+	&& echo "TERRA_R_PLATFORM_BINARY_VERSION='0.99.0'" >> /opt/R/3.6.3/lib/R/etc/Renviron.site
+
+# Update apt-get
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends apt-utils \
+	&& apt-get install -y dselect \
+	&& dselect update \
+	&& apt-get install -y --no-install-recommends \
+	pkg-config \
+	fortran77-compiler \
+	byacc \
+	automake \
+	## This section install libraries
+	libpng-dev \
+	libpcre2-dev \
+	libnetcdf-dev \
+	libhdf5-serial-dev \
+	libfftw3-dev \
+	libopenbabel-dev \
+	libopenmpi-dev \
+	libexempi3 \
+	libxt-dev \
+	libgdal-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 \
+	libv8-3.14-dev \
+	libgtkmm-2.4-dev \
+	libmpfr-dev \
+	libudunits2-dev \
+	libmodule-build-perl \
+	libapparmor-dev \
+	libgeos-dev \
+	libprotoc-dev \
+	librdf0-dev \
+	libmagick++-dev \
+	libpoppler-cpp-dev \
+	libprotobuf-dev \
+	libperl-dev \
+	libz-dev \
+	liblzma-dev \
+	## software - perl extentions and modules
+	libarchive-extract-perl \
+	libfile-copy-recursive-perl \
+	libcgi-pm-perl \
+	libdbi-perl \
+	libdbd-mysql-perl \
+	libxml-simple-perl \
+	## Databases and other software
+	sqlite \
+	openmpi-bin \
+	mpi-default-bin \
+	openmpi-common \
+	openmpi-doc \
+	tcl8.5-dev \
+	tk-dev \
+	openjdk-8-jdk \
+	imagemagick \
+	tabix \
+	ggobi \
+	graphviz \
+	protobuf-compiler \
+	jags \
+	## Additional resources
+	xfonts-100dpi \
+	xfonts-75dpi \
+	biber \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
+
+## These two libraries don't install in the above section--WHY?
+RUN apt-get update \
+	&& apt-get -y --no-install-recommends install \
+	default-jdk \
+	libjpeg-dev \
+	libjpeg-turbo8-dev \
+	libjpeg8-dev \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
+
+## Python installations
+RUN apt-get update \
+	&& apt-get -y --no-install-recommends install python-dev python-pip python-setuptools\
+	&& pip install wheel \
+	## Install sklearn and pandas on python
+	&& pip install sklearn \
+	pandas \
+	pyyaml \
+	cwltool \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
+
+# Install libsbml and xvfb
+RUN cd /tmp \
+	## libsbml
+	&& curl -O https://s3.amazonaws.com/linux-provisioning/libSBML-5.10.2-core-src.tar.gz \
+	&& tar zxf libSBML-5.10.2-core-src.tar.gz \
+	&& cd libsbml-5.10.2 \
+	&& ./configure --enable-layout \
+	&& make \
+	&& make install \
+	## Clean libsbml, and tar.gz files
+	&& rm -rf /tmp/libsbml-5.10.2 \
+	&& rm -rf /tmp/libSBML-5.10.2-core-src.tar.gz \
+	## apt-get clean and remove cache
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
+
+# Install Bioconductor packages
+RUN curl -O https://raw.githubusercontent.com/Bioconductor/anvil-docker/master/anvil-rstudio-bioconductor/install.R \
+	&& R -f install.R \
+	&& rm -rf install.R
diff --git a/terra-rstudio-pro-bioconductor/README.md b/terra-rstudio-pro-bioconductor/README.md
new file mode 100644
index 00000000..ad311424
--- /dev/null
+++ b/terra-rstudio-pro-bioconductor/README.md
@@ -0,0 +1,5 @@
+Run with 
+
+```
+docker-compose -f docker-compose.yml up -d
+```