[Bioperl-l] Problems installing BioPerl & cpan

Leon Timmermans l.m.timmermans at students.uu.nl
Mon Apr 23 10:16:04 EDT 2012


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
>
>
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