Bootstrap: docker
From: rocker/r-ver:4.4.1 
Stage: build

%files
  GAPIT_3.4.0.tar.gz /app/GAPIT_3.4.0.tar.gz
  multtest_2.8.0.tar.gz /app/multtest_2.8.0.tar.gz

%environment

%post
    apt-get update
    # dependencies for GAPIT
    Rscript -e 'install.packages("ape")'
    Rscript -e 'install.packages("bigmemory")' 
    Rscript -e 'install.packages("EMMREML")' 
    Rscript -e 'install.packages("genetics")' 
    Rscript -e 'install.packages("gplots")' 
    Rscript -e 'install.packages("lme4")' 
    # multtest is no longer on cran
    Rscript -e 'install.packages("BiocManager")'
    Rscript -e 'BiocManager::install("Biobase")'
    R CMD INSTALL /app/multtest_2.8.0.tar.gz
    Rscript -e 'install.packages("plotly")' 
    Rscript -e 'install.packages("RcppArmadillo")' 
    Rscript -e 'install.packages("rgl")' 
    Rscript -e 'install.packages("scatterplot3d")' 
    Rscript -e 'install.packages("snowfall")' 
    R CMD INSTALL /app/GAPIT_3.4.0.tar.gz 

    Rscript -e 'install.packages("devtools")'
    Rscript -e 'install.packages("arrow")'
    #Rscript -e 'devtools::install_github("jiabowang/GAPIT", force=TRUE)'
    Rscript -e 'install.packages("tidyverse")'

%runscript

%startscript

%labels
    # adds metadata 
    Author Daniel.Kick@usda.go
    Version v0.0.1

%help
   This is a container to run gapit_cli.R .  
