[Bioperl-l] Help with dependencies of Bioperl

[Alberto Davila]

Dear all,

I can run the script listed at the bottom without any problems in my
laptop using FC1 and kernel 2.4 with the following perl RPM's installed:

perl-URI-1.21-7
perl-XML-Parser-2.34-0_1.rhfc1.at
perl-HTML-Tagset-3.03-28
perl-XML-Encoding-1.01-23
perl-DateManip-5.42a-0_10.rhfc1.at
perl-libxml-enno-1.02-29
perl-SGMLSpm-1.03ii-12
perl-DBD-Pg-1.22-1
mod_perl-1.99_12-2
perl-Glib-1.040-1.rhfc1.dag
perl-5.8.3-16
perl-HTTP-GHTTP-1.07-2.rhfc1.at
perl-Filter-1.29-8
perl-Parse-Yapp-1.05-30
perl-libxml-perl-0.07-28
perl-Gtk-HandyCList-0.02-0.rhfc1.dag
perl-HTML-Parser-3.34-0_1.rhfc1.at
perl-libwww-perl-5.79-0_3.rhfc1.at
perl-DBI-1.37-1
perl-XML-Dumper-0.4-25
perl-GD-2.12-8.rhfc1.at
perl-DBD-MySQL-2.9002-1
perl-HTTP-Lite-2.1.6-8

however, it does not work when I try to run the same script in another
machine (FC2 and kernel 2.6), with the same version of bioperl installed
like in mine, and the following perl RPM's:

perl-libxml-perl-0.07-29
perl-HTML-Parser-3.36-8
perl-5.8.3-18
mod_perl-1.99_12-2.1
perl-HTML-Tagset-3.03-29
perl-Parse-Yapp-1.05-31
perl-libxml-enno-1.02-30
perl-XML-Parser-2.34-8
perl-DBI-1.40-4
perl-DBD-MySQL-2.9003-4
perl-SGMLSpm-1.03ii-13
perl-IO-String-1.05-8
perl-GD-2.12-8.rhfc2.at
perl-Filter-1.30-8
perl-URI-1.31-8
perl-XML-Encoding-1.01-25
perl-DateManip-5.42a-8
perl-XML-Dumper-0.71-8
perl-libwww-perl-5.79-1


Curiously I dont get any error msg to help to debug it... would you
offer any tip that could help to solve this, please ?

Thanks in advance, Alberto

******

#!/usr/local/bin/perl -w
 
use lib "/usr/local/bioperl14";
use strict;
use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use Bio::DB::GenBank;
 
my $organismname = $ARGV[0];
my $contaminantfile = "contaminant."."$organismname";
 
my $query_string = $organismname."[Organism] AND (ribosomal gene[title]
OR mitochondrial gene[title] OR rDNA [title] OR rRNA gene[title]";
my $query = new Bio::DB::Query::GenBank(-db=>'nucleotide',
                                        -query=>$query_string,
                                        -mindate => '1985',
                                        -maxdate => '2004');
my $count = $query->count;
my $seqio=new Bio::DB::GenBank->get_Stream_by_query($query);
 
#open a seqio handle for writing the outputfile in fasta
my $outfile = new Bio::SeqIO(-format=>'fasta',
                             -file=>">$contaminantfile");
                                   
 while (my $s = $seqio->next_seq) {
 
 print $query_string, "\n";
 print $count, "\n";
  
 
#write the fasta
   $outfile->write_seq($s);
    
        }
                                   
           
          exit;