[EMBOSS] emma via perl/cgi system command

[小野塚 智美]

Dear friends

I have an trouble in executing emma command.
The situation is like following.

I'd like to perform multiple alignment using a protein
sequence fasta format as input via Perl/CGI web system.

I thought the best way to achieve this objective is to use
 system command like

#####
my $emma_com = "/usr/local/bin/emma /tmp/fasta /tmp/align
/tmp/dnd";

system("$emma_com");
#####

"/tmp/fasta" is the input fasta file. "/tmp/align" and
"/tmp/dnd" is supposed to be output files.

This $emma_com command works when I put the command from
xterm console, which means that I can get the output
files.But when I use the command from Perl/CGI web system,
only I can have is empty output files.

At first I thought that apache can't find clustalw which
is installed in /usr/local/bin but 
######
system("which clustalw")
######
returns "/usr/local/bin/clustalw"
This means apache detects clustalw I guess.

So. my question is 
(1)How to get the result output file in the Perl/CGI
apache web system?
(2)Is there any more smart way to get the clustalw result
file from command lile in Perl/CGI system?

Thank you in advance.