Binary file not executed for web user - php

Question

I have a php script that creates a shell script file that finally executes as the www-data user, all of the commands are executed except for the last one which implies a binary file. If I run the command as root, it runs ok...
This is the last part of the script:
&& echo "Tokenizing the file........" >> Logs/table_of_contents.php \
&& perl ../common/Scripts/xmltokenize.pl --filename=xmlfiles/table_of_contents.xml >> Logs/table_of_contents.php \
&& perl ../common/Scripts/xmlrenumber.pl --filename=xmlfiles/table_of_contents.xml >> Logs/table_of_contents.php \
&& echo "Tagging the file........" >> Logs/table_of_contents.php \
# I have added this line to check if it helps but id doesn't
&& export HOME="/tmp/" \
# And this is the command that calls the binary file
&& perl tagfile.pl xmlfiles/table_of_contents.xml \
Here you have the content of the tagfile.pl
use File::Find;
$\ = "\n";
$fn = shift;
if ( $fn =~ /([^\/\.]+)\.xml/ ) { $fileid = $1; } else { exit;};
print $fileid;
$cmd = "perl tagfl2/makevrt.pl 'xmlfiles/$fileid.xml' > 'tagtmp/$fileid.vrt'";
print $cmd;
print `$cmd`;
#ALL OF THE PREVIOUS WORKS
#THIS IS THE ONE THAT GIVES PERMISSION ERRORS
# OF COURSE: "www-data:www-data tagtmp/" and "www-data:www-data $fileid.vrt = table_of_contents.vrt"
$cmd = "cut -f 1 tagtmp/'$fileid.vrt' | tagfl2/treetagger/bin/tree-tagger -no-unknown -token -lemma tagfl2/treetagger/lib/english.par > 'tagtmp/$fileid.tagged'";
print $cmd;
`$cmd`;
$cmd = "perl tagfl2/mrg.pl 'tagtmp/$fileid.vrt' 'tagtmp/$fileid.tagged' > 'tagtmp/$fileid.mrg'";
print $cmd;
`$cmd`;
$cmd = "perl tagfl2/tagxml.pl 'tagtmp/$fileid.mrg' 'xmlfiles/$fileid.xml'";
print $cmd;
`$cmd`;
Here is the error:
sh: 1: tagfl2/treetagger/bin/tree-tagger: Permission denied
Also, just in case:
chown -R www-data:www-data tagfl2/
chmod -R g+rwx tagfl2/

Answer 1

Try to define a full path to the script
$cmd = "perl /[full_path]/makevrt.pl 'xmlfiles/$fileid.xml' > 'tagtmp/$fileid.vrt'";

Answer 2

Why did you update user ownership?
Changing the group ownership should have been enough:
chgrp -R www-data tagfl2/
chmod -R g+rwX tagfl2/
And change the lowercase x by a greater one, to give access/execution permission, only if it is already the case for the user owner (no need to give otherwise).
You may then check the permission like this:
su -m -c 'ls -R tagfl2/' www-data
And see if you reproduce access issue; and then update permission accordingly.

Answer 3

Ok, all solved, one thing was giving the file system, actually the mounted unit, the exec attribution.
The second thing was moving treetagger directory to /usr/local/
Then, at /usr/local/bin/ I have created a soft link this way:
ln -s ../treetagger/bin/tree-tagger
Making the binary file globally executable. Actually, this last step was the ultimate solution.
Then at the tagfile.pl perl script, the line containing the tree-tagger command, I have changed it this way:
cut -f 1 'tagtmp/$fileid.vrt' | /usr/local/bin/tree-tagger -no-unknown -token -lemma tagfl2/treetagger/lib/english.par > 'tagtmp/$fileid.tagged'