---
author: Arun Seetharam
---

# Installing R packages
*Author: {{author}}*

On RCAC clusters, you can load any R modules (`r-scrnaseq`, `r-rnaseq`, etc.) and install packages using `BiocManager` or `install.packages`. However, Since you don't have write access to the system library, you will need to install the packages in your custom location. Here is how you can do it:

### 1.	Create directory

Create the required directory in your desired location. For home direcotry.

```bash
cd ~
mkdir -p local/r_packages
```

This is just an example, but you can project specific package directory if you prefer. 

```{note}
For major versions of R, you may have to create a new directory for the packages. For example, `local/r_packages/4.4.1` for `R 4.4.1`.
```

### 2.	 Install packages

Install the packages in your custom library:

```bash
ml purge
ml biocontainers
ml r-scrnaseq/4.4.1-rstudio
Rscript -e 'BiocManager::install("DESeq2", lib="~/local/r_packages")'
Rscript -e 'install.packages("data.table", lib="~/local/r_packages")'
```

You can also run this within an R session, if you prefer:

```r
BiocManager::install("DESeq2", lib="~/local/r_packages")
install.packages("data.table", lib="~/local/r_packages")
```


### 3.	Add the library path

To ensure R knows about your custom library, add the following line to your ~/.Renviron file:

```bash
echo 'R_LIBS_USER=${R_LIBS_USER}:'~/local/r_packages'' >> ~/.Renviron
```

### 4.	Testing

Test the installation:

```bash
ml purge
ml biocontainers
ml r-scrnaseq/4.4.1-rstudio
```

and in R session:

```r
library(DESeq2)
library(data.table)
.libPaths()
```

This should load your libraries and should show the path to your custom library.


## Using RStudio

Alternatively, if using RStudio, you can also set the environment variable in the RStudio configuration file. Add the following line to your ~/.Renviron file:

```r
usethis::edit_r_environ()
```

When the file opens, add the following line:

```r
R_LIBS_USER=~/local/r_packages
```

save and restart RStudio. You can test `.libPaths()` in RStudio to see if the path is set correctly.