#!/usr/bin/perl -w
use strict;
use DBI;
use CGI;

my $query = new CGI;
print $query->header();
#my $my_database = "TrypSnoDB";
#my $localhost = "localhost";
#my $dsn = "DBI:mysql:$my_database:$localhost";
#my $db_user_name = "adrian";
#my $db_password = "temp_pass";
#my $dbh = DBI->connect("DBI:mysql:database=TrypSnoDB;host=localhost;m
+ysql_socket=/private/software/mysql/mysql.sock","adrian","temp_pass",
+ {'RaiseError' => 1});

if ($query->param('submit1')){
    my $family = $query->param('family');
    my $TB = $query->param('TB');
    my $LM = $query->param('LM');
    my $HS = $query->param('HS');
    my $SC = $query->param('SC');
    my $AT = $query->param('AT'); 
    my $db_query;
    print qq(TB: $TB<br>;
    print qq(LM: $LM)<br>;
    print qq(HS: $HS)<br>;
    print qq(SC: $SC)<br>;
    print qq(AT: $AT)<br>;
}
exit(0);
    if ($family eq "ALL") {
        $family = "'C/D' or ST.family='H/ACA'"
    }
    else {
        $family = "'$family'";
    }
    $db_query = "SELECT ST.sno_name,HT.homolog_name FROM sno_Table ST,
+Homolog_Table HT,sno_Homologs SH,Organism O 
WHERE ST.sno_id=SH.sno_id AND SH.homolog_id=HT.homolog_id AND HT.org_i
+d=O.org_id and (ST.family=$family) and
O.organism='$TB'";
    my $sth = $dbh->prepare($db_query);
    $sth->execute();
    my$total = $sth->rows;
    print "<table border=1>\n
    <tr>
        <th>snoRNA</th>\n
        <th>Homolog</th>\n
    </tr>\n";
    while (my@row = $sth->fetchrow_array()){
        my$sno_name = $row[0];
        my$homolog_name = $row[1];
        print "<tr>\n<td>$sno_name</d><td>$homolog_name</td></tr>\n";
    }
    print "<tr>
        <th>TOTAL</th>\n
        <th>$total</th>\n
    </tr>\n";
    print "</table>";        
}
[download]

OK, sorry I should have been clearer. You didn't copy the print statements correctly and you added a "}" right after them which caused errors. Another useful thing to do when you are debugging CGI scripts is to add the following line to the top of your script:

use CGI::Carp('fatalsToBrowser');
[download]

This will give you the reasons for the errors and where they occurred rather than the dreaded "Internal Server Error" message.

Just to get you past this, maybe it would be easier to just put the below lines before your whole script - click the 'download' link at the bottom and then copy and paste it right on the top line, forcing your original down. The '__END__' will exclude everything that comes after, as if you had commented it all out.

#!/usr/bin/perl -w
use strict;
use DBI;
use CGI;
use CGI::Carp('fatalsToBrowser');

my $query = new CGI;
print $query->header();
if ($query->param('submit1')){
    my $family = $query->param('family');
    my $TB = $query->param('TB');
    my $LM = $query->param('LM');
    my $HS = $query->param('HS');
    my $SC = $query->param('SC');
    my $AT = $query->param('AT'); 
    print "TB: $TB<br>";
    print "LM: $LM<br>";
    print "HS: $HS<br>";
    print "SC: $SC<br>";
    print "AT: $AT<br>";
}

__END__
[download]