Permission denied to run shell script by subprocess.call

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I wrote a shell script using python and it successfully run by command bash download_R1.sh on my terminal.

I wanted to test if subprocess can do the same thing in python because I would like to integrate a pipeline in python script. Here is the subprocess part of my code:

downR1 = subprocess.call('./download_R1.sh')

It failed to run the script with following error message:

Error message:
PermissionError: [Errno 13] Permission denied: './download_R1.sh'

Someone suggested using chmod +x to obtain authenitification of that script. But bash down.sh is working. I don't know which part goes wrong.

Any advice?

subprocess python bash
1 Answers

That's the normal way the shell behaves.

You can not directly run a program or script if it not has execution privileges (+x)

But, you can instruct other program bash, python or whatever to run a file even if not has +x

foo.sh

#!/bin/bash

# If a parameter is received in the command $1, assign it to $NAME
# if not use the default "World"
NAME="${1:-World}"

echo "Hello ${NAME}"

foo.py

#!/usr/bin/env python
print "Hello World"

$ bash foo.sh
Hello World

$ bash foo.sh Person
Hello Person

$ ./foo.sh
bash: ./foo.sh: Permission denied

$ python foo.py
Hello World


$ ./foo.py
bash: ./foo.sh: Permission denied

$ chmod +x foo.sh foo.py

$ ./foo.sh
Hello World
$ ./foo.py
Hello World

In your case, if you want to run the program with subprocess but not giving execution privileges to the file you must use:

subprocess.run(["bash", "download_R1.sh"])

If you need to pass arguments to the script just add more items to the list:

subprocess.run(["bash", "download_R1.sh", "argument1"])

There are several questions about using subprocess an arguments like this one.

If you prefer write you command in only one string be advised that use shell=True is not recommended. But you can use something like:

subprocess.run("bash download_R1.sh argument1".split())
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