[Bioperl-l] Problems installing BioPerl & cpan

Jason Stajich jason.stajich at gmail.com
Mon Apr 23 09:54:54 EDT 2012


Then the next logical thing to do is go to the Ensembl page for info on how to install their modules. 
http://uswest.ensembl.org/info/docs/api/api_installation.html

On Apr 23, 2012, at 6:51 AM, Merche Castillo wrote:

> Hi
> 
> Thanks for your reply.  I'm working on some EnsEMBL scripts too, that's why I tried this script. I did look for the Bio::EnsEMBL::Registry on cpan but returns "no object found".
> 
> 
> 
> On 04/23/2012 03:44 PM, Jason Stajich wrote:
>> 
>> 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
>>> *****************************************
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
> 
> 
> -- 
> ************************************;)
> Mercedes Castillo
> INRES, Dept. Molecular Phytomedicine
> University of Bonn
> 
> Karlrobert-Kreiten-str 13 
> 53115 Bonn
> +49(0)22873-60143
> merche at uni-bonn.de
> *****************************************

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




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