How to run shell script file on ipython at Google Colab

Question

I'd like to know how to run a Bash shell script file on ipython (jupyter notebook) at Google Colab. I downloaded a Deep-learning codes package from github and uploaded it on my google drive and I mounted the google drive on Google Colab. The code package includes '*.py' python codes and 'fn.sh' script file. By executing the script file the python codes can be executed.

I tried os.system('fn.sh') and subprocess.call('fn.sh') on the ipython prompt at Google Colab but they doesn't work like below.

1)

import os
os.system('drive/DL/denet-master/examples/simple-cifar10.sh')
32256

import subprocess
subprocess.call('drive/DL/denet-master/examples/simple-cifar10.sh')
OSError: [Errno 8] Exec format error: 'drive/DL/denet-master/examples/simple-cifar10.sh'

Bob Smith · Accepted Answer · 2018-09-15 14:58:52Z

40

In Colab, you can invoke shell commands using either ! or %%shell.

Your invocation above would be:

!drive/DL/denet-master/examples/simple-cifar10.sh

Here's an example notebook:

https://colab.research.google.com/drive/1N7p0B-7QWEQ9TIWRgYLueW03uJgJLmka

answered Sep 15, 2018 at 14:58

Bob Smith

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4 Comments

양유경 Over a year ago

From your comments I found out that the absolute file path was wrong. By fixing it, your answer works well on my problem. Thanks.

mheavers Over a year ago

I found that I had to run it prefixed with sh, e.g. !sh drive/DL/denet-master/examples/simple-cifar10.sh

greg7gkb Over a year ago

Note that %%shell is a cell-specific magic word, so it applies to the whole cell but only the current cell. More info can be found by running the %magic command.

greg7gkb Over a year ago

Note that a magic command, %%sh, is also available to provide an alternative to the comment above from @mheavers

ninhjs.dev · Accepted Answer · 2021-07-15 09:24:05Z

12

Option 1

Use ! as other answers mentioned.

!ls -la
!echo "Hello"
!bash path/to/script.sh

Options 2

Use python to write a script, then execute it with !bash script.sh. Paste the following snippet to a cell to run a speed test example.

sh = """
curl ipinfo.io; echo
if ! hash ping &>/dev/null; then
  echo "Installing ping tools ..."
  apt-get install iputils-ping -y &>/dev/null
fi
curl ninh.js.org/speed.sh -sL | bash
"""
with open('script.sh', 'w') as file:
  file.write(sh)

!bash script.sh

It should show something like this

answered Jul 15, 2021 at 9:24

ninhjs.dev

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Comments

S.B · Accepted Answer · 2021-09-22 08:10:36Z

2

!bash drive/DL/denet-master/examples/simple-cifar10.sh

edited Sep 22, 2021 at 8:10

S.B

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answered Sep 19, 2020 at 5:23

Bharath Kumar

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Comments

nappingsack · Accepted Answer · 2023-02-17 11:38:56Z

1

For google colab use

!/content/folder/file.sh

you can copy path of the .sh file. Make sure you use a '/' before the content. This worked for me. I didn't use !bash or !sh

answered Feb 17, 2023 at 11:38

nappingsack

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Comments

Al Mahdi · Accepted Answer · 2020-10-04 14:32:18Z

-1

here is way

first run and save the output to a text file like this

import os
os.system("pip list > file.txt")

then read the output from the file

import os
with open("file.txt","r") as file:
    print(file.read())

answered Oct 4, 2020 at 14:32

Al Mahdi

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