R: docker: How to run your R scripts in a container manager on synology

R Docker: How to Run Your R Scripts in a Container Manager on Synology

Abstract We describing the how to deploy a Docker environment based on R running a specified script

Introduction

Docker is a popular open-source tool to create, distribute, deploy, and run software applications using containers. Here we will deploy an R Docker (shortly called Rocker) environment on a Synology NAS server.

Why should we run a R script in Docker on a Synology NAS server

There are several reason why you want to run R script on a Synology NAS server

  1. The operating system DSM on the Synology is not capable to run R and also when this was possible, it will pollute the DSM environment
  2. It is reproducible running an R script within a Docker environment
  3. A Synology NAS server you have the possibility to use a scheduled task to perform a certain activity.
  4. You can scale R applications, by running several containers

How to install Docker on Synology NAS server

  1. Install the Container Manager
  2. Create a Source location for storing Docker configuration file and Scripts
  3. Deploy the Docker Build script
  4. Schedule a Task to Run specified R-Docker

Install the Container Manager

Logon with an Adminstrator Account to the Synology NAS server

select the Package Center

Select the Container Manager from the ‘Open Source’

wait till the Container Manager is installed.

Now you’re ready to use Docker within DSM (Operating system from Synology NAS)

Create a Source location for your Docker configuration file and Scripts

Go to Configuration Screen/ Control Panel:

Select the ‘Shared Folder’

Select Create

Select Create Shared Folder

Specify as name: dockersource

Description: Source Files for Docker

And the select Next

Select Next

Select Next

Select Next

Confirm with Apply

Deploy the Docker Build script

  1. Create 2 files and copy store files.

  2. Create a scheduled Task on Synology or logon with ssh and Run it

Create 2 files and copy store files

Create a folder / directory where you are storing the next files

  • Dockerfile

  • dock_duck_script.r

(Remind the filenames are case sensitive)

The file named Dockerfile contains:

# Base R image} FROM rocker/r-ver

# Make a directory in the container

RUN mkdir /home/r-environment RUN mkdir /home/r-environment/data

# Install R dependencies

RUN R -e "install.packages(c('tidyverse','DBI', 'duckdb'))"

# Copy our R script to the container

COPY dock_duck_script.r /home/r-environment/dock_duck_script.r

# Run the R script

CMD R -e "source('/home/r-environment/dock_duck_script.r'

The file named dock_duck_script.r contains:

library(duckdb)

# Use the famous iris data

DBname       <- '/home/r-environment/data/dock_duck.db'

mydb         <- dbConnect(duckdb::duckdb(), DBname)

dbWriteTable(mydb,'table_iris',iris, overwrite = TRUE)

dbDisconnect(mydb, shutdown = TRUE)

Create a folder / directory on the Synology NAS server in the Shared Folder: dockersource

Called: rocker_test

Upload both files

  • Dockerfile

  • dock_duck_script.r

To specified folder ‘rocker-test’

Create a scheduled Task on Synology or logon with ssh and Run it

  • Scheduled task

Open the Control Panel on the Synology NAS server and select the Task Scheduler

Select Create

Create a Scheduled Task->User-defined script

Call the Task: Build Docker

User: root (modify this from the original value)

Enabled: off (modify this from the original value)

In the Tab: Task Settings specify the next in the User-defined script

cd /volume1/dockersource/rocker_test
docker build -t rocker_test .

Run the Task

This is a one-time action, (you could delete the Build Docker task)

Alternative

  • use ssh

In this case you’ve to activate the SSH (Could be found in the Control Panel)

logon with putty or ssh to Synology server (this is outside this scope)

Run the next commands

cd /volume1/dockersource/rocker_test
sudo docker build -t rocker_test .

This will run for several minutes

This is a ONE time activity (and should only run Once)

Scheduling a task to run specified R-Docker

Although the above describes how to run a Docker (based on R, or a Rocker), you can’t access the data from outside by default. We are going to connect a volume within the Rocker with an external volume on the NAS. On the NAS, the next volume is already present.

  • /export/data

Redefine a Task, but this but schedule it

The Task description will state:

docker run -d --name=rocker_test\ 
-v /volume1/export/data:/home/r-environment/data

When running now this Task a file with the name

  • dock_duck.db

will end up in the

  • /export/data

folder

This file is a ‘duckdb’ database containing the ‘iris’ table. I herewith refering to ‘www.duckdb.org’

Conclusion

A Docker on a Synology environment is very easy to create, and could be used for intergrations.

References

Bookmarks

Last modified: 28 December 2023