running shell script from php

Question

I have a shell script which works perfectly if I run it in the terminal (MAC OSX)

#!/bin/bash
cd /Applications/XAMPP/xamppfiles/htdocs/chemedit/

babel -imol  'a.mol' -oinchi 'outputfile.inchi'
babel -imol  'a.mol' -osmi 'a.smsi'
babel a.smi -O out.svg  -xC -xe
exit

I have this in a file called a.sh

I want to run this from PHP using:

$output = shell_exec("bash a.sh 2>&1");

This does not work and returns:

  Cannot write to outputfile.inchi
0 molecules converted
1 errors

for all files

I have given both files chmod 777.
I am pretty sure safe mode is off for PHP.

which shell and user is shell_exec using with your PHP configuration? Which shell and user are you using when you run it in your terminal? Do both configurations differ? If yes, in which points? — hakre
– hakre, Commented Mar 12, 2012 at 0:26

Umbrella · Accepted Answer · 2012-03-12 00:28:47Z

2

The babel command is likely not in the PATH environment variable for the user running PHP, and thus the script via PHP. The simplest solution is to edit your shell script to refer to babel by its full path.

answered Mar 12, 2012 at 0:28

Umbrella

4,8083 gold badges24 silver badges32 bronze badges

Sign up to request clarification or add additional context in comments.

1 Comment

TJF Over a year ago

thanks i seem to be getting somewhere now i get a Cannot write to a.smsi error im guessing this has somthing to do with permissions

bkconrad · Accepted Answer · 2012-03-12 00:27:34Z

1

Try calling babel with its absolute name. Use which babel to determine this, and replace 'babel' with it in your script.

answered Mar 12, 2012 at 0:27

bkconrad

2,6603 gold badges22 silver badges30 bronze badges

2 Comments

TJF Over a year ago

thanks i seem to be getting somewhere now i get a Cannot write to a.smsi error im guessing this has somthing to do with permissions

TJF Over a year ago

Thankyou so much you've helped me so much

Collectives™ on Stack Overflow

running shell script from php

2 Answers 2

1 Comment

2 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

1 Comment

2 Comments

Your Answer

Sign up or log in

Post as a guest

Related