Export env var that start with APP_ to RStudio session (#9)

* Export env var that start with APP_ to RStudio session

* Add example to .env.example

* Specify APP_* in comments of .env.example

* Update .env.example

Co-authored-by: Nicole Kauer <nicole.kauer@sagebase.org>

Co-authored-by: Nicole Kauer <nicole.kauer@sagebase.org>

.env.example

@@ -9,4 +9,8 @@ ROOT=FALSE
 SYNAPSE_TOKEN=yourtoken
 
 # Port on the host that connects to RStudio
-HOST_PORT=80
+HOST_PORT=80
+
+# User-specified settings (APP_*) made visible to RStudio
+APP_FOO=10
+APP_BAR=hello

README.md

@@ -102,6 +102,23 @@ Example projects that use this repository / image:
 
 - [Sage-Bionetworks-Challenges/challenge-analysis] (work in progress)
 
+## Configuration
+
+The configuration of the development environment is defined in the file `.env`.
+This file contains environment variables that are set when the environment
+starts.
+
+For security reason, a user session in RStudio does not see all the environment
+variables of the system. However, the variables defined in `.env` with a name
+that starts with `APP_` will be made visible to the user session via the
+creation of the file `.Renviron`.
+
+```r
+> variables <- names(s <- Sys.getenv())
+> variables[startsWith(variables, "APP_")]
+[1] "APP_BAR" "APP_FOO"
+```
+
 ## Manage R and Python dependencies
 
 ### R

root/etc/cont-init.d/30-configure-user

@@ -33,6 +33,12 @@ if [[ ! -z ${SYNAPSE_TOKEN} ]]; then
     fi
 fi
 
+# Create .Renviron
+> /home/${USER}/.Renviron
+for var in "${!APP_@}"; do
+    echo "$var=${!var}" >> /home/${USER}/.Renviron
+done
+
 # Fix sudo: setrlimit(RLIMIT_CORE): Operation not permitted
 # https://github.com/sudo-project/sudo/issues/42#issuecomment-659253293
 echo "Set disable_coredump false" >> /etc/sudo.conf