[Bioperl-l] Problems installing BioPerl & cpan

Fields, Christopher J cjfields at illinois.edu
Mon Apr 23 10:20:59 EDT 2012


Not sure, but it may have something to do with the requirement for a very old bioperl (v1.2.3).

chris

On Apr 23, 2012, at 9:16 AM, Leon Timmermans wrote:

> Yeah, that's fairly useless. Does anyone know the reason for that? Is it just inertia, or is it more?
> 
> Leon
> 
> On Mon, Apr 23, 2012 at 3:51 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> 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
> >> *****************************************
> >>
> >> _______________________________________________
> >> 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
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




More information about the Bioperl-l mailing list