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LalResearchGroup / CNV-clinviewer

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bedtoolsr installation fails due to "sh: 1: bedtools: not found" error #2

Open jordimaggi opened 2 years ago

jordimaggi commented 2 years ago

Hi,

I am trying to run CNV-ClinViewer locally through RStudio Server, installed on Ubuntu 20.04 LTS. During the installation of all dependencies, the installation of bedtoolsr fails because RStudio Server cannot find bedtools. However, bedtools v2.30.0 is installed on the system and on PATH.

I also tried to manually set the path to bedtools manually like so: options(bedtools.path = "/home/analyst/anaconda3/bin/").

I tried the same thing on Windows WSL, and faced the exact same problem.

That did not help either. Do you have any idea on how to overcome this problem?

jordimaggi commented 2 years ago

Hi,

I managed to fix this. As I matter of fact, I found out that the PATH variable within RStudio was different from the rest of my system. I then added the /home/analyst/anaconda3/bin/ to the PATH variable in RStudio and that solved it, at least for the current session.