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.

Answer 1

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

Answer 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.