Pass values from bash script to python script

Question

I'm working with an HPC where I write a bash script which executes my python_script.py job like so:

#!/bin/bash -l
#$ -l h_rt=0:00:10
#$ -l mem=1G
#$ -cwd

module load python3/3.8
python3 python_script.py

In my python_script.py I define the variables repeat, and directory like so:

repeat = 10
directory = r'User/somedir/'

I would like to be able to set these variables in my bash script, so that they overwrite these values within python_script.py and are used instead.

Pass the variables as arguments to your script. Or set them as environment variables in your bash script, then use `os.environ` in your Python script. — 9769953, Mar 16 '22 at 12:43
From the limited information in your question, I'd go with my first suggestion: pass the necessary variables as arguments to your script. Dive into the `argparse` module to make this easy (and safer) for your script. — 9769953, Mar 16 '22 at 12:44
Pendatic nitpick: your user name is missing an auxiliary verb. — 9769953, Mar 16 '22 at 12:47
Two ways: 1. Command line argument. 2. Environment variable. — Medo Paw, Mar 16 '22 at 13:02
Does this answer your question? [How to read/process command line arguments?](https://stackoverflow.com/questions/1009860/how-to-read-process-command-line-arguments) — MisterMiyagi, Mar 16 '22 at 13:07
@9769953, max character limits alas, will consider the feedback. — TheyTakingTheHobbitsToIsengard, Mar 16 '22 at 13:29
I guess they should have taken the hobbits to Bree, that would have fit. — 9769953, Mar 16 '22 at 14:26

score 0 · Accepted Answer · answered Mar 16 '22 at 12:58

0

The easier way is to use in your python script :

import sys
repeat = sys.argv[1]
directory = sys.argv[2]

and in your bash script

repeat="10"
directory="User/somedir/"
python3 python_script.py $repeat $directory

answered Mar 16 '22 at 12:58

Alexll7

For anyone else trying this: I found everything comes through as a string (even if using repeat=10 instead of repeat='10'), so just had to fix with repeat_int = int(repeat) in the python script and then use repeat_int from there on – TheyTakingTheHobbitsToIsengard Mar 17 '22 at 11:16

1 Answers1