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.