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?