expressed_variants.def

Bootstrap: docker
From: debian:stable-20211011-slim

%post

  apt update
  apt-get install -y dialog=1.3-20201126-1
  # Local related configuration
  apt-get install -y locales
  echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
  locale-gen
  update-locale "LANG=en_US.UTF-8"

  # Utilities needed during this build
  apt-get install -y wget=1.21-1+deb11u1
  apt-get install -y zip=3.0-12
  apt-get install -y perl=5.32.1-4+deb11u2

  #R
  apt-get install -y r-base=4.0.4-1
  apt-get install -y libcurl4-openssl-dev=7.74.0-1.3+deb11u1
  apt-get install -y libssl-dev=1.1.1k-1+deb11u1

  #BiocManger for R_4.0.4 (Bioconductor Version 3.12 (BiocManager 1.30.16), per BiocManager::version()):
  Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/BiocManager/BiocManager_1.30.15.tar.gz")'

  ##Pathway Enrichment: rWikiPathways
  apt-get install -y r-bioc-rwikipathways=1.10.0+dfsg-1

  #data.table
  Rscript -e 'BiocManager::install("data.table")'

  ##Tidyr
  Rscript -e 'BiocManager::install("tidyr")'

  ##ggplot2
  Rscript -e 'BiocManager::install("ggplot2")'

  ##gridExtra
  Rscript -e 'BiocManager::install("gridExtra")'

  ##ggradar
  Rscript -e 'devtools::install_github("ricardo-bion/ggradar", dependencies = TRUE)'

  ##ggpubr
  apt-get install -y r-cran-ggpubr=0.4.0-1


%runscript
    echo "The following expression variants analysis tools have been installed in this container: "

    echo
    #spit out software versions

    R --version | head -n 1
    #spit out R package versions
    echo -n "Bioconductor:"; Rscript -e 'BiocManager::version()' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g' ## Display the Bioconductor version (formatted)
    echo -n "ggplot2:"; Rscript -e 'packageVersion("ggplot2")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "gridExtra:"; Rscript -e 'packageVersion("gridExtra")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "dplyr:"; Rscript -e 'packageVersion("dplyr")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "tidyr:"; Rscript -e 'packageVersion("tidyr")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "magrittr:"; Rscript -e 'packageVersion("magrittr")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "rWikiPathways:"; Rscript -e 'packageVersion("rWikiPathways")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "ggradar:"; Rscript -e 'packageVersion("ggradar")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "ggpubr:"; Rscript -e 'packageVersion("ggpubr")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'
    echo -n "data.table:"; Rscript -e 'packageVersion("data.table")' | sed 's/\[1]//' | sed 's/‘//g' | sed 's/’//g'

%labels
    Author laitanawe@gmail.com
    Version 0.1
    Date 10mar2022

%help
    This definition file builds a singularity container for expression variants analysis.