---
title: "Singularity"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Singularity-Image}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
A Singularity image is an essential part of creating a reproducible container and, eventually, reproducible research. This section explains the steps to create a singularity definition file, build an image, and run a container. The two primary sources for further discussion and details include:
- [Singularity Definition Files](https://docs.sylabs.io/guides/3.0/user-guide/definition_files.html)
- [Rocker Project (Singularity)](https://rocker-project.org/use/singularity/)
### Setting up the environment
In order to build a singularity image, you need to have singularity installed on your system, and you need to have a root privilege to build an image. There are sufficient instructions to do that (for example, [here](https://docs.sylabs.io/guides/3.7/user-guide/quick_start.html)). You can also use [Sylab Remote Builder](https://cloud.sylabs.io/builder/) services.
### Definition File
The Definition File (CausalGPS_rstudio.def) is the recipe for building the image. Please note that we build it upon [rocker/rstudio:4.0.4] image. For more details about generating a Definition File, please refer to [Singularity User Guide](https://docs.sylabs.io/guides/3.0/user-guide/definition_files.html).
### Building Singularity Image
To build the image, download the Definition File (CausalGPS_rstudio.def) and run the following:
```r
$ sudo singularity build CausalGPS_rstudio.sif CausalGPS_rstudio.def
```
Running the command will generate a Singularity image (CausalGPS_rstudio.sif). You can double-check the CausalGPS package version by running the image using the following command:
```r
singularity run CausalGPS_rstudio.sif
```
This will result in the following format:
```s
Container was created Thu 03 Feb 2022 07:54:45 PM UTC
CausalGPS package installed (ver: [1] ‘0.2.6.9000’)
```
### Run an R Session
If you want to use R in a console, you can follow these steps:
- Run shell command in the image
```r
singularity shell CausalGPS_rstudio.sif
```
and then run R.
```r
Singularity> R
```
This will provide the following results and will activate R.
```r
R version 4.0.4 (2021-02-15) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
```
Now, you can run an R command. For example:
```r
> utils::packageVersion("CausalGPS")
# [1] ‘0.2.6.9000’
```
### Run a Rstudio Session
You can also open an RStudio session in your browser by following these steps mentioned in [Rocker Project (Singularity)](https://rocker-project.org/use/singularity/).
```r
mkdir -p run var-lib-rstudio-server
printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf
singularity exec --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf CausalGPS_rstudio.sif rserver --www-address=127.0.0.1
```
Open your browser and enter this URL:
```r
127.0.0.1:8787
```