在Ubuntu中执行python脚本默认为shell而不是bash

Question

I am running a python script in Ubuntu which relies on packages being installed. These are all installed as i can invoke them, but the script cannot.

I think this is because the script is using shell(sh) and not the bash version.i get this error message out:

sh: genomeCoverageBed: command not found

but can invoke genomeCoverageBed manually in Bash:

ubuntu@fat:~/jonathan/scripty$ genomeCoverageBed 


Tool:    bedtools genomecov (aka genomeCoverageBed)
Version: v2.26.0

Summary: Compute the coverage of a feature file among a genome.

This part of my Stackoverflow question is misleading and wrong!:

I have added this shebang to the start of my python script:

#!/bin/bash

But this has not affected the outcome,

Taking this out of my script still causes the same error messages Here is part of the script:

for filename in os.listdir(folder):
if filename.endswith(".sorted.bam"):
    namefile = filename.replace(".sorted.bam", "_ncoverage.txt")
    folder_name = filename.replace(".sorted.bam", "")
    os.system("mkdir " + folder_name)
    os.system("coverageBed -s -d -a bam " + folder + filename + " -b " + gff_file + " > " + folder_name + "/" + namefile)

Here is what happens when i run this script:

ubuntu@fat:~/jonathan/script$ sudo python2.7 script1.py ./Folder/ ./Folder/ref.fasta genbank.gff
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: coverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found
sh: genomeCoverageBed: command not found

Do you have any suggestions about what i can do, or even if i am on the right track? thanks for your help!

Answer 1

You are using the wrong shebang

#!/bin/bash

When a linux shell is asked to run a text file (eg, ./myprogram.py ), it looks at the shebang to figure out which program should be used to interpret the text. In your case you asked the shell to run /bin/bash - another shell and it tried to interpret the python script as a shell script.

You can write the shebang differently

#!/usr/bin/env python3

This tells the shell to run /usr/bin/env which will search the PATH for a thing called pythnon3 . Now, you run the python setup for your current environment. By default its the system python but if you run in a python virtual environment, it runs that python.

The shebang is only used on linuxy systems and is only used when you make a script executable and run it directly. If running on windows (outside of cygwin or other unix-like shell) or running python directly ( python /path/to/myscript.py ) then its not used.

Answer 2

Your shebang is calling a subshell, as @tdelaney mentioned in the comments. You need to use something like the following to use python as the program executing the file:

#! /usr/bin/env python

Answer 3

Ubuntu won't run the python file in python if you put #!/bin/bash , that will open in bash. Try putting #!/usr/bin/python or #!/usr/bin/env python

Answer 4

I followed this post:

https://unix.stackexchange.com/questions/83191/how-to-make-sudo-preserve-path

and added:

sudo env "PATH=$PATH"

to the start of my command and this solved my issue!

Thanks to all who helped!