Calling perl script doesn't work in PHP APACHE

Question

I have server side code that call a perl script, in this way

exec("perl /home/horus/Instaladores/variant_effect_predictor/variant_effect_predictor.pl --everything --offline -i ../users/$username/$project/results/remove_duplicated_lines/BED_filtered/qual/StrandBalance/dbSNP/SnpEff/$vcf -o ../users/$username/$project/results/remove_duplicated_lines/BED_filtered/qual/StrandBalance/dbSNP/SnpEff/VEP/$vcf --stats_file ../users/$username/$project/results/remove_duplicated_lines/BED_filtered/qual/StrandBalance/dbSNP/SnpEff/VEP/$vcf.html",$output);

I try the same with exec, system and passthru without success.

If i made a echo right before the exec, all the variables are set acordingly

If i copy past the echo result in a Linux console,using the www-data from the folder where the php script is, everything works as expected

I have perl and the variant_effect_predictor.pl script in the sudoers file

www-data ALL=(ALL)NOPASSWD:/usr/bin/perl www-data ALL=(ALL)NOPASSWD:/home/horus/Instaladores/variant_effect_predictor/variant_effect_predictor.pl

any idea of what is going there? why php is not calling the script?

Miller · Accepted Answer · 2014-05-06 21:21:58Z

0

First step. See if you can run a hello world perl script from that location.

use strict;
use warnings;

print "Hello World\n";

If you can get that to work properly, then I suspect the problem are the relative paths you're sending as parameters. Try setting them to absolute paths and see if that helps.

answered May 6, 2014 at 21:21

Miller

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