[Bioperl-l] Problems installing BioPerl & cpan

Jason Stajich jason.stajich at gmail.com
Mon Apr 23 09:44:51 EDT 2012

That module really has nothing to do with Fgenesh parsing so I don't think this is a particularly good test script - try one of the scripts that comes in bioperl scripts directory like scripts/utilities/bp_sreformat.pl

However, you should know that module is part of EnsEMBL not BioPerl - it requires an additional package of modules be installed.  

if you use CPAN to install things you can do
cpan> install Bio::EnsEMBL::Registry

On Apr 23, 2012, at 5:31 AM, Merche Castillo wrote:

> 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 installation
> |  use strict;
> use warnings;
> use Getopt::Long;
> use Bio::EnsEMBL::Registry;
> my $reg = "Bio::EnsEMBL::Registry";
> $reg->load_registry_from_db(
>              -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
> +49(0)22873-60143
> merche at uni-bonn.de
> *****************************************
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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