Pass cmd commands via php script

Question

Here is my php code

$command = "C:\Program Files\ClustalW2>clustalw2 -INFILE=seq.txt -TYPE=Protein -OUTFILE=res.aln";
exec($command);

When i run the command using the cmd, it generates the desired file. However when i try passing the same command via my php code it generates no result. How do i fix this problem?

try using back tick operator ` try this php.net/manual/en/language.operators.execution.php — Khurram Ijaz
– Khurram Ijaz, Commented Mar 19, 2012 at 6:12
Probably you don't have permission to run this command from a PHP Script...... — MD Sayem Ahmed
– MD Sayem Ahmed, Commented Mar 19, 2012 at 6:12
@Mian_Khurram_Ijaz: i am new to php, so wud like to knw wats the differnce between the two? And wat may the problems in using exec()?? — Nikita
– Nikita, Commented Mar 19, 2012 at 6:15
@SayemAhmed: what do u mean by no permission to run this command?? — Nikita
– Nikita, Commented Mar 19, 2012 at 6:16
@Nikita: You want to run a command on the cmd. Doing so required user privileges from the operating systems. Are you sure you can run this command from your web app in the host machine? Does the web app have sufficient privileges granted to it? — MD Sayem Ahmed
– MD Sayem Ahmed, Commented Mar 19, 2012 at 6:19

galymzhan · Accepted Answer · 2012-03-20 07:10:14Z

2

Probably it's because of the > symbol before executable's filename? Also, try with single quotes:

$command = 'C:\Program Files\ClustalW2\clustalw2 -INFILE=seq.txt -TYPE=Protein -OUTFILE=res.aln';
exec($command, $output, $retval);
var_dump($output);
var_dump($retval);

edited Mar 20, 2012 at 7:10

answered Mar 19, 2012 at 9:13

galymzhan

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2 Comments

Nikita Over a year ago

I tried what u have suggested but it still doesnt work. Also the single quotes make no difference..

galymzhan Over a year ago

@Nikita Do you see any warnings/errors? Try running modified version of the code snippet

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