update PATH, add bin/ for custom programs

[rgallego]

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

[andy_kipp]

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

Adding to the PATH variable

I am trying to add the path of a package to the PATH environmental variable. following is the R command I am using: Sys.setenv(PATH=$PATH:/path to the package/) But I am getting the following error: Error: unexpected '$' in "Sys.setenv(PATH= Anyone knows how can I add the path of a package to the PATH variable in R using the system command?

[rgallego]

Thanks Andy - that worked!