update PATH, add bin/ for custom programs

Hi there,

We have just created a new project , and to run the scripts included we have to access a program called cutadapt, which I succesfully installed (but it does so in the folder /home/rstudio-user/.local/bin/) so I have to add it to the $PATH

I can open a terminal window and run cutadapt --version and I can get the expected output 2.10; but if I try R to find this piece of software it does not manage to do it. So either with the console
system2('cutadapt', args = "--version")
it returns
sh: 1: cutadapt: not found
Warning message:
In system2("cutadapt", args = "--version") : error in running command

or with a Rmarkdown opening a bash chunk and running
cutadapt --version

it returns
/tmp/RtmpMzcC2h/chunk-code-b6f61eae772.txt: line 1: cutadapt: command not found.

I think the $PATH I set up in the console and the one R is using are different? How can I either:

  • Add a local folder to the PATH variable that R is using; or
  • copy a binary file to a place where the PATH variable can see it.

Ideally I want this only to be done once (by me) and not by every student that will eventually create a copy of this project.

Many, many thanks

I found a couple of suggestions for updating $PATH in this thread:

Thanks Andy - that worked!

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