Thanks,
>Maybe try to run it as a "system" command.
>my $programtorun = 'ls';
>my @parameters = qw/. ../;
>my @cmdline = ( $programtorun, @parameters );
>system (@cmdline);
>It can be a bit tricky getting all the parameters to
your system >command
>to be quoted properly, try a little experimentation.
>For example:
>system ('water', 'water1.seq', 'water2.seq',
'-outfile water.out')
>may not work, while changing the outfile to
>system ('water', 'water1.seq', 'water2.seq',
'-outfile', >'water.out')
>will. Experiment if you have trouble.
I've tried all the above ways as:
my $programtorun = 'water';
my @parameters =
qw/\/var\/www\/cgi-bin\/emboss\/water1.seq
\/var\/www\/cgi-bin\/emboss\/water2.seq -gapopen 10
-gapextend 5 -outfile
\/var\/www\/cgi-bin\/emboss\/water.out/;
#my @parameters =
qw(/var/www/cgi-bin/emboss/water1.seq
/var/www/cgi-bin/emboss/water2.seq -gapopen 10
-gapextend 5 -outfile
/var/www/cgi-bin/emboss/water.out);
my @cmdline = ( $programtorun, @parameters );
system (@cmdline);
I tried to print the command as
my $out;
foreach my $line (@cmdline){
$out .= $line;
}
and then within html tag
print <<END;
<html>
<body>
END
print "<pre>$out</pre>";
What I could see is there is no gap in between the
parameters and program as:
water/var/www/cgi-bin/emboss/water1.seq/var/www/cgi-bin/
emboss/water2.seq-gapopen10-gapextend5-outfile/var/www/cgi-bin/emboss/water.out
I've also tried as
system ('water', 'water1.seq', 'water2.seq',
'-gapopen', '10', '-gapextend', '5', '-outfile',
'water.out');
#system ('./water', 'water1.seq', 'water2.seq',
'-gapopen 10', '-gapextend 5', '-outfile water.out');
#system ('water', 'water1.seq', 'water2.seq',
'-gapopen 10', '-gapextend 5', '-outfile water.out');
But none worked.
Is there is any permission problem.
with regards,
Soumyadeep
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