[Bioperl-l] Problems installing BioPerl & cpan

Fields, Christopher J cjfields at illinois.edu
Mon Apr 23 09:51:24 EDT 2012


Unfortunately the Ensembl code isn't on CPAN (wish it were, it might make things a little easier).  

chris
 
On Apr 23, 2012, at 8:44 AM, 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
>> *****************************************
>> 
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> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
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