[Bioperl-l] Problems installing BioPerl & cpan

Merche Castillo merche at uni-bonn.de
Mon Apr 23 08:31:27 EDT 2012

I'm posting this message out of pure desperation, because I really don't 
know what else to try. I'm a beginner in bioperl and I'm working on a 
script to parse out some results I got from MolQuest fgenesh. Results 
are out in .txt format and I want to parse them to GFF and fasta file 
for mRNA and protein sequences to facilitate comparison with other 
results we have. I would like to use BioPerl for other purposes in the 
future so I'm very interested in getting it ready on my pc

I followed the instructions 
herehttp://www.bioperl.org/wiki/Installing_Bioperl_for_Unix. I managed 
to install CPAN in root mode (otherwise it wouldn't work) and BioPerl 
via CPAN. All tests were ok, but when I ran this script to test the 

|  use strict;
  use warnings;

  use Getopt::Long;
  use Bio::EnsEMBL::Registry;

  my $reg = "Bio::EnsEMBL::Registry";
               -host =>  "ensembldb.ensembl.org",
               -user =>  "anonymous"
  my $db_list=$reg->get_all_adaptors();
  my @line;

foreach my $db (@$db_list){
     @line = split ('=',$db);
     print $line[0]."\n";

I got the error:*"Can't locate Bio/EnsEMBL/Registry.pm in @INC"*

I tried to install BioPerl again via Build.PL, running as root, but 
still came to the same outcome.

Thanks for your help Merche

Mercedes Castillo
INRES, Dept. Molecular Phytomedicine
University of Bonn

Karlrobert-Kreiten-str 13
53115 Bonn
merche at uni-bonn.de

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