vsearch in R markdown issue

[js3110]

When I try to run vsearch in an R markdown file using bash I am getting the error vsearch: command not found

In the console if i run system('vsearch -version') i get: sh: vsearch: command not found Warning message: In system("vsearch -version") : error in running command

But in the terminal on R, vsearch -version gives: vsearch v2.5.1_macos_x86_64, 8.0GB RAM, 4 cores https://github.com/torognes/vsearch

Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) VSEARCH: a versatile open source tool for metagenomics PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584

I have installed it but it isn't working in the markdown file and I don't know how to fix it.

[frederic-mahe]

When I try to run vsearch in an R markdown file using bash

I don't think you can run a Rmarkdown file directly in a bash terminal. You would need to extract the bash chunks to a bash script first.

vsearch is not a R package, how did you install it?

You seem to be working on macOS, could you please try to run which vsearch in a Terminal? That would help to locate the vsearch binary on your system.

[js3110]

Sorry, when I said using bash I mean that the chunk uses {bash} not that its directly in a bash terminal.

I installed vsearch on my mac, not on R, using instructions from https://astrobiomike.github.io/bash/installing_tools Running which vsearch returns nothing in my Terminal

[frederic-mahe]

did you find a way to fix that issue?

Also, I suggest to install a more recent version of vsearch if you can. The latest is version 2.22.1.

[js3110]

Yes, I reinstalled vsearch and made sure that it was in the same path as my other installations and now its wokring. For some reason the first time I installed it something didnt work so it wasn't actually installed. Thanks!

[frederic-mahe]

good! thank you for trying vsearch