BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/

# This is an example of a custom-built singularity image to run Rstudio in Open OnDemand
# at https://www.umassrc.org:444/
#
# Bioconductor, leidenbase, monocle3, and DiffBind installs are commented out
# to serve as examples of different ways some packages may need to be installed

%help
  This will run RStudio Server

%environment
  export PATH=/usr/lib/rstudio-server/bin:${PATH}

%apprun rserver
  exec rserver "${@}"

%runscript
  exec rserver "${@}"

%post
    echo "Hello from inside the container"
    export DEBIAN_FRONTEND="noninteractive"
    sed -i 's/$/ universe/' /etc/apt/sources.list
    apt-get update

    # Install ubuntu system-level packages
    apt-get -y install pkg-config apt-transport-https zlib1g zlib1g-dbg zlib1g-dev libbz2-dev liblzma* *pcre* libcurl4-openssl-dev vim m4
 wget unzip autoconf automake dh-autoreconf curl tcl8.5 libx11-6 build-essential cmake libffi6 libffi-dev libssl* git wget software-prope
rties-common gcc fort77 aptitude gdebi-core libclang-3.8-dev libclang-common-3.8-dev libclang-dev libclang1-3.8 libobjc-5-dev libobjc4 ps
misc sudo libxml2-dev gdebi-core libudunits2-dev libgdal1-dev librsvg2* libv8-3.14.5 libv8-3.14-dev libv8-3.14-dbg
    # The aptitude command works better than apt-get for some packages
    aptitude -y install g++ xorg-dev libreadline-dev gfortran locales-all 

    # The installed version of GDAL is too old (or has a version issue) so this installs GDAL v2.
    add-apt-repository ppa:ubuntugis/ubuntugis-unstable
    apt-get update
    apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev 

    # install needed libgit2 library and dependency from non-default repository
    add-apt-repository ppa:cran/libgit2
    apt-get -y update
    apt-get -y install libssh2-1-dev libgit2-dev

    # Install Rstudio 4.0
    export PATH=/usr/lib/rstudio-server/bin:${PATH}
    # Add the R repository for version 4.0
    echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/" >> /etc/apt/sources.list
    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
    apt-get -y update
    apt-cache showpkg r-base
    aptitude -y install r-base-core r-base-dev r-recommended r-recommended r-cran-mgcv r-cran-nlme 

    # Install R packages
    echo "install.packages('Matrix')" | Rscript -
    echo "install.packages('codetools')" | Rscript -
    echo "install.packages(c('devtools','curl'))" | Rscript -

    # Download and install rstudio-server
    wget https://download2.rstudio.org/server/xenial/amd64/rstudio-server-1.3.1093-amd64.deb
    gdebi -n ./rstudio-server-1.3.1093-amd64.deb

    # Install bioconductor packages - there may be better ways to do this, but this is working currently.
    echo 'install.packages("BiocManager")
    BiocManager::install()' | Rscript -
    echo "BiocManager::install(c('DESeq2', 'ShortRead', 'Rsubread'))" | Rscript -    
    echo "BiocManager::install(c('systemPipeR', 'ChIPpeakAnno', 'EnsDb.Hsapiens.v75', 'regioneR', 'org.Hs.eg.db', 'clusterProfiler'))" | 
Rscript -

    # Install packages
    echo 'install.packages(c( "pwr", "reshape2", "ggpubr","ggdendro"),dependencies = TRUE)' | Rscript -
    echo 'install.packages(c("tidyverse", "extraDistr", "gplots", "GGally", "ggrepel", "RColorBrewer"),dependencies = TRUE)' | Rscript -
    echo 'install.packages(c( "knitr", "RCurl", "plotly", "rmarkdown"),dependencies = TRUE)' | Rscript -
    echo 'install.packages(c( "pheatmap", "stringr", "purr", "tibble"),dependencies = TRUE)' | Rscript -



    rm -rf /var/run && ln -s /tmp /var/run

%test
    # Uncommenting these tests would ensure that monocle3 and DiffBind load before finalizing the image
    #export PATH=/usr/lib/rstudio-server/bin:${PATH}
    #echo "library(monocle3)" | Rscript - && \
    #echo "library(DiffBind)" | Rscript - && echo "Successful test"