[Bioperl-l] I can't access clustalw from my cgi perl program...

Wed May 21 18:41:00 UTC 2008

Hi,

My multiple alignment program works fine from command line but when i put
the
same piece of code in my cgi perl program, it gives me the same error, which
is,

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains:
/export/share/iNquiry/perl/lib/5.8.5/x86_64-linux-thread-multi
/export/share/iNquiry/perl/lib/5.8.5
/export/share/iNquiry/perl/lib/x86_64-linux-thread-multi
/export/share/iNquiry/perl/lib/5.8.4 /export/share/iNquiry/perl/lib/5.8.3
/export/share/iNquiry/perl/lib/5.8.2 /export/share/iNquiry/perl/lib/5.8.1
/export/share/iNquiry/perl/lib/5.8.0 /export/share/iNquiry/perl/lib
/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/5.8.5
/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.4/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.3/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.2/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.1/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.0/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4
/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
/usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.4/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.2/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.1/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.0/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4
/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2
/usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0
/usr/lib/perl5/vendor_perl .) at
/export/share/iNquiry/www/cgi-bin/bipod/nisa/snpfinder.cgi line 14.
BEGIN failed--compilation aborted at
/export/share/iNquiry/www/cgi-bin/bipod/nisa/snpfinder.cgi line 14.

Here is my cgi perl program

#!/usr/bin/perl -w

use strict;
use CGI qw(:standard);
use CGI::Carp qw/fatalsToBrowser/;
use Bio::SeqIO;
use Bio::Align::AlignI; 
use Bio::AlignIO;
use Bio::AlignIO::msf;
use Bio::SimpleAlign;
use Bio::PrimarySeq;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::PrimarySeqI;
use Bio::Root::IO;
use Bio::Seq;
use Bio::TreeIO;
use Bio::Root::Root Bio::Tools::Run::WrapperBase;
use Bio::LocatableSeq;

BEGIN {
	$ENV{CLUSTALDIR} = '/opt/Bio/bin/clustalw';
}
print"Content-type: text/html\n\n";

if (param()){ #condition if user supplied some data
	my $new_seq=param("sequence"); #to store sequence from text box of form
	my $selection=param("size");#to store drop down menu selection for
translation type
	my $file1=param("uploadfile");#variable for name of the file
	my $address=param("email");#variable to hold e.mail address

	if ($file1=~/.+/) {#test condition, if user supplied a file

		my $R_FH = upload("uploadfile");#get file handle

		my  $in  = Bio::AlignIO->new(-file   => $file1 ,
					-format => 'fasta');
		my $out = Bio::AlignIO->new(-file   => ">out.aln.pfam" ,
					-format => 'pfam');

		while ( my $aln1 = $in->next_aln() ) {
			$out->write_aln($aln1);
		}

		close $R_FH;
		open FH, "out.aln.pfam" || die "Alignment file doesn't exist\n";
		while(<FH>){

		print $_,"\n";
		}
		close FH;

		#To send results through e.mail
			$report=~s/<br \/>/\n/g;#change new line character
			$report=~s/(<.+?>)//g;#remove html tags
			$report=~s/(&nbsp;)/ /g;#change space character
			open(MAIL, "|/usr/sbin/sendmail -t") or die"can't compose an e.mail";
			print MAIL "To:$address\n";
			print MAIL "From: nisa\n";
			print MAIL "Subject: results of $file1\n";
			print MAIL  "\n$report\n";
			close(MAIL);#close mail

	}else{#error message if no file name is entered
		print "<html><head><h3>Error: </h3></head><body>You did not enter a file
name,please upload a file<br /></body></html>";

	}

}

Please let me know what should I do, because clustalw is there and my other
programs (non web-based) are working.

Thanks
Nisa
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