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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Cutadapt permission denied #1192

Closed ntromas closed 3 years ago

ntromas commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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'

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marwa38 commented 1 year ago

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 commented 1 year ago

@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.