Cutadapt permission denied

[ntromas]

Hi Ben,

I wonder if you have already met this issue with Rstudio.
When I added the path to cutadapt, system2(cutadapt, args= "--version") gave me:
sh:1: path cutadapt: permission denied

I guess I need to give privileges to RStudio but not sure how. Any idea?

Cheers,

Nico

[benjjneb]

Do you have control over the filestystem that cutadapat is on?
If it's a unix-like, you can use chmod to change the permissions to allow anyone to execute cutadapt. `chmod 777 path/to/cutadapt-binary'

[ntromas]

It works now. The issue was that I installed cutadapt during an open session of RStudio. When I reload RStudio it worked...
Thanks for your quick advice!

Cheers

[ntromas]

Hi Ben, Sorry for my delayed answer. I had troubles with RStudio but now it works fine... Thanks Cheers Le jeu. 5 nov. 2020 à 11:42, Benjamin Callahan <notifications@github.com> a écrit :

…

Do you have control over the filestystem that cutadapat is on? If it's a unix-like, you can use chmod to change the permissions to allow anyone to execute cutadapt. `chmod 777 path/to/cutadapt-binary' — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1192 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6ESBJIE4PSXBLXK3KTSOLIY7ANCNFSM4TLR6KZQ> .

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[marwa38]

Hi @benjjneb

Anyway to use cutadapt in rstudio that I am using in UNIX?
I installed via bioconda in unix but couldn't use in r when I tried library().
Any way to compile the source code in unix and then use in R? give me more details please so that I could try
I tried to use .exe but got the error: sh: 1: ./cutadapt.exe: Exec format error in r and in Unix I got bash: ./cutadapt.exe: cannot execute binary file: Exec format error which makes sense I know I can't use this .exe in UNIX

thank you
M

[benjjneb]

@marwa38

cutadapt is a command line program, it is not run in R. You can use system calls in R to run command line functions, see the ITS tutorial for an example of that.

In order to use cutadapt in unix, you will need to install it there. See: https://cutadapt.readthedocs.io/en/stable/installation.html

I'm not sure how you did this before, but there shouldn't be an .exe files involved, as those are executable files on Windows, and won't run on unix.