kinome-tree

The app is borrowed from the Phanistel lab at UNC Running app - http://phanstiel-lab.med.unc.edu/CORAL/ Code repo - https://github.com/dphansti/CORAL

setup difference libraries for different users/apps - https://shiny.rstudio.com/articles/libraries.html

create .Rprofile in /home/username/ direcotry with .libPaths("/path/to/libs")

local({
    r <- getOption("repos")
    r["CRAN"] <- "https://cloud.r-project.org"
    options(repos = r)
})

currently now, another .Rprofile in the kinome-tree app directory that has .libPaths("/usr/lib/R/addn-lib") to point to the depdencies
this was originally setup in order to prevent conflicts in library installs for different R-Shiny apps

location of the app

/srv/shiny-server/kinome-tree

location of logs

/var/log/shiny-server

location of config file

/etc/shiny-server/shiny-server.conf

different library paths

add route and set run as user
doesn't seem to work; so the .Rprofile in the main directory of the app works

location /PK_plots {
      run_as shinykinome;
    }

At the moment shinykinome user is being used for both PK_plots and kinome-tree app. kinome-tree app has .Rprofile pointing to "/usr/lib/R/addn-lib" and PK_plots pointing to "/home/shinykinome/R/library"

install.packages("PACKAGE_NAME", lib = "/home/shinykinome/R/library") for any new packages

Docker container

To run in a docker container and use of renv package to manage all depedencies, ensure to ignore following packages:

renv::settings$ignored.packages(c("rJava", "renv", "DBI", "RJDBC"), persist = FALSE)
renv::snapshot()