Is it possible to run WSL Ubuntu in RStudio?

[HimyNameIsKevin]

Hi,

I am analysing genomic sequencing data, currently. For the analyis I am using R studio for data visualisation and tools that run via the Windows Linux subsystem (WSL) for data pre-processing. Now, I want to embed all analysis steps into a R shiny app. An app for the data visualisation is easy to implement. An app for the pre-processing is less trivial for me.

One example tool I am using for the pre-processing is Overview – Salmon: Fast, accurate and bias-aware transcript quantification from RNA-seq data. Unfortunately, there is no salmon implementation as a R package. There are comparable packages, but for my downstream anlyses, I specifically need this tool.

In WSL, I installed this tool with conda. How can I pass commands from R Studio to WSL?

I already read into shell(), system() and system2(), but none of this seems to do the trick.

With shell.exec(file = "C:/Windows/System32/wsl.exe") I get a WSL shell and can manually type in my commands. But I would prefer a solution where WSL runs in the background and stdout is printed in the R console.

system("wsl /home/kevin/miniconda3/condabin/conda --help") also works. However when it comes to calling conda installed programs or activate environments, I either get no output or an error that conda has not initialised a shell.

Do you have an idea what I could try?

[olyerickson]

What are your ultimate plans for deploying this app? Do you actually plan to deploy it on a Windoze server?

It seems like a cleaner architectural solution would be to bypass Windoze entirely and go 100% Linux. Either dual-boot your development machine or just switch to Linux permanently.

[HimyNameIsKevin]

Thanks for your reply! For now, it would just suffice to have an app that runs locally and covers all analysis steps. Do you think the installation of a RStudio server on WSL could be a solution? Could this allow me to call the shiny app from there and have access to all programs installed via conda on WSL?

[craddm]

I've had good experiences running RStudio Server on WSL and accessing it using Chrome, and it sounds to me like it's well worth a try for your case.

[andresrcs]

@HimyNameIsKevin

In WSL, I installed this tool with conda. How can I pass commands from R Studio to WSL?

Do you mean that this is a python library? if so, You can install python packages natively on Windows and use them from R using the reticulate package.

WSL is almost like a virtual machine so I think there is no practical way of getting output from it into a shiny app running on Windows or at least is not the simplest approach.