[Bioperl-l] RE: Problem running clustalw.pl for the first time.

[Scott Cain]

Hi Lisa,

I think you need to shorten your use lib to:

use lib 
"/home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4";

Scott

On Thu, 2005-04-07 at 03:40 +0100, Lisa wrote:
> Hello,
> 
>  I am new to BioPerl and have had the modules installed by our system 
> admin (They appear to be installed correctly)
> and I have complied the clustalw and it works from cmd line. But I cant 
> run clustalw.pl it produces a typical perl error message below :
> 
> ------------------------------------------------------------
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: 
> /home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4/Bio/Tools/Run/Alignment/ 
> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 
> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi 
> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi 
> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi 
> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi 
> /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/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi 
> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi 
> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi 
> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi 
> /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 clustalw.pl line 39. BEGIN 
> failed--compilation aborted at clustalw.pl line 39.
> ------------------------------------------------------------
> 
> ------------------------------------------------------------
> This is the code  from clustalw.pl
> ------------------------------------------------------------
> #!/usr/bin/perl
> 
> # PROGRAM  :   
> # PURPOSE  : Demonstrate possible uses of 
> Bio::Tools::Run::Alignment::Clustalw.pm
> # AUTHOR   : Peter Schattner schattner at alum.mit.edu
> # CREATED  : Oct 06 2000
> # REVISION : $Id: clustalw.pl,v 1.1 2003/07/07 18:20:58 bosborne Exp $
> .
> 
> # Modify (and un-comment) the following line as required to point to 
> clustalw program directory on your system
> BEGIN {
>  $ENV{CLUSTALDIR} = 
> '/home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4/Bio/Tools/Run/Alignment/';
> }
> 
> use lib 
> "/home/httpd/vhosts/xxxx/cgi-bin/modules/bioperl-run-1.4/Bio/Tools/Run/Alignment/";
> use Getopt::Long;
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::SimpleAlign;
> use Bio::AlignIO;
> use Bio::SeqIO;
> use strict;
> 
> ------------------------------------------------------------
> 
> 
> I would like some information or suggestions for what I can do to get 
> this to work.
> 
> Cheers
> Lisa
> 
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> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory