Kniting from command line: Rscript -e "library(knitr); knit('batch_analysis.Rmd')"
Running the shiny app from the command line:
Rscript -e 'library(methods); shiny::runApp("shinyapp/", launch.browser=TRUE)' or
R --slave --no-restore -e 'shiny::runApp("shinyapp/", launch.browser=TRUE)'