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1

listing permissions

rated 0 times [ 1] [ 0] / answers: 1 / hits: 521 / 3 Years ago, fri, august 13, 2021, 12:05:15

I'm a biomedical scientist and I'm having trouble running a custom data analysis pipeline written by one of our collaborators. His script crashes with

/bin/sh: 1: /usr/local/bin/FastQC/FastQC_v0.10.1: Permission denied

make[2]: *** [/home/kat/gentrap.git/gentrap_OUT/1_Bira_TAAGGCGAGAGTAG_R1.fastqc] Error 1

make[2]: Leaving directory `/home/kat'

Thing is, I've already made myself the owner of /usr/local/bin/FastQC (sudo chown -R user:user /usr/local/bin/FastQC) and given myself read/write/executable permissions (sudo chmod -R +rwx /usr/local/bin/FastQC). I tried listing permissions with ls -la and I'm a little confused by the output:

drwxr-xr-x 3 kat  kat  4096 mei  8 14:20 .

drwxr-xr-x 5 root root 4096 mei  8 14:20 ..

drwxr-xr-x 7 kat  kat  4096 mei  8 14:20 FastQC_v0.10.1

As I understand it, that means I'm the owner of the current directory and the subdirectory FastQC_v0.10.1, and I should have all the permissions. Root is the owner of the parent directory, which would be /usr/local/bin. Am I reading this output correctly? Why would the script be crashing due to insufficient permissions?

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confiorc

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4 Years ago

answered 3 Years ago rillrage · Accepted Answer

I got the same error. I end up putting FastQC to /usr/share, as many other packages are put there, and put a link to /usr/local/bin, as suggested by the installation guide. Then I changed the permissions to files under FastQC.

sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc

sudo chmod -R 755 /path/to/FastQC