[Bioperl-l] problems installing bioperl

Scott Cain cain.cshl at gmail.com
Thu Dec 21 15:03:48 EST 2006


Hi Stephan,

About your bioperl mail: did you cancel it, or did it just disappear?
If the latter, I might have accidentally deleted it, sorry :-/

So 'GBrowse is running' means that you can see the sample yeast chr1
database, browse around, etc, right?  I still don't know what is up with
the warning but my guess is that everything is working there.

As for your question about writing a callback, the reason it's not
working is that the attributes method returns a list (typically but not
always with only one element), so what you are really doing in your test
is this "number of elements in the list > 1200", which is almost always
going to be false.  You should change it to this:

  my $feature = shift;
  my ($score) = $feature->attributes('score');
  if ($score > 1200) {
  ...etc...

Finally, if you really want to test that you are using the correct
bioperl, you can put this simple cgi in your cgi-bin directory as
test_biographics.pl, set it as world executable and go to
http://localhost/cgi-bin/test_biographics.pl (and, yes, I use strict and
warnings even when the script is only 10 lines long :-)  :

#!/usr/bin/perl
use strict;
use warnings;
use Bio::Graphics::Panel;
use CGI qw/:standard/;

print header(),
      start_html,
      p("Bio::Graphics::Panel api_version is ".Bio::Graphics::Panel->api_version),
      p("It should be 1.654 for BioPerl 1.5.2"),
      end_html;

Scott


On Fri, 2006-12-22 at 08:27 +1300, Stephan Roessner wrote:
> Hi Scott,
> 
> responded to group but did get through.
> So I reply back to you.
> 
> I installed Class-Base-0.03 using CPAN.
> 
> Reinstalling GBrowse gives me still a warning like:
> Warning: prerequisite Bio::Perl 1.52 not found. We have 1.0050021.
> Writing Makefile for Bio::Graphocs::Browser::CAlign
> Writing Makefile for Generic-Genome-Browser.
> 
> GBrowse is running but I cannot access attributes and/or the score column
> of .gff files. Is this related to the warning?
> 
> To get an attribute I use
> 
> my $feature = shift;
>                 if ($feature->attributes('score') > 1200) {
>                   return 'blue';
>                 } else {
>                   return 'pink';
>                 }
> But I retrieve not data using $feature->
> 
> Can I somehaow verify what bioperl version GBrowse is using?
> 
> Stephan,
> 
> 
> 
> Quoting Scott Cain <cain.cshl at gmail.com>:
> 
> > Stephan,
> >
> > Yes, it is in cpan:
> >
> > http://search.cpan.org/~abw/Class-Base-0.03/lib/Class/Base.pm
> >
> > The cpan shell should be able to install it.
> >
> > Whether or not that works, please respond to the mailing list so that
> > the rest of the conversation can be archived.
> >
> > Scott
> >
> >
> > On Thu, 2006-12-21 at 08:24 +1300, Stephan Roessner wrote:
> > > Hi Scott,
> > >
> > > No I didn't.
> > > I had a look and couldn't find it.
> > > It is not part of CPAN?
> > >
> > > Stephan
> > >
> > >
> > > Quoting Scott Cain <cain.cshl at gmail.com>:
> > >
> > > > Stephan,
> > > >
> > > > Did you install Class::Base?  It was inadvertantly left out the
> > > > install
> > > > document, but is required.
> > > >
> > > > Scott
> > > >
> > > >
> > > > On Wed, 2006-12-20 at 21:40 +1300, Stephan Roessner wrote:
> > > > > Hi all,
> > > > >
> > > > > I did sudo ./Build install --uninst 1 and got the error
> > > > > * ERROR: Confiduration was initially created with MOdule::Build
> > > > version
> > > > > '0.2805', but we are now using '0.2806'. ...
> > > > >
> > > > > So I ran perl Build.PL and got the message
> > > > > Creating new 'Buid' script for 'bioperl' verion '1.0050021'.
> > > > >
> > > > > I did run sudo ./Build install --uninst 1 again.
> > > > > Seems to be fine with no error messages.
> > > > >
> > > > > When I run perl Makefile.PL for GBrowse 1.66-RC2 it results in
> > > > >
> > > > > Warning: prerequisite Bio::Perl 1.52 not found. We have
> > 1.0050021.
> > > > > Warning: prerequisite Class::Base 0 not found.
> > > > > Writing Makefile for Bio::Graphocs::Browser::CAlign
> > > > > Writing Makefile for Generic-Genome-Browser
> > > > >
> > > > > GBrowse is running but I have really troubles with aggregators
> > trying
> > > > to
> > > > > use xyplot. It does not plot anything. So I thought the bioperl
> > could
> > > > be
> > > > > the problem.
> > > > >
> > > > > Stephan
> > > > >
> > > > >
> > > > >
> > > > > Quoting Scott Cain <cain at cshl.edu>:
> > > > >
> > > > > > I really don't think the BioPerl version detection is wrong.
> > I
> > > > > > actually
> > > > > > don't check Bio::Root::Version::VERSION in Makefile.PL, I
> > check
> > > > > > Bio::Graphics::Panel->api_version.  When it doesn't find the
> > > > correct
> > > > > > api_version, it gives a warning the BioPerl 1.5.2 is not
> > installed.
> > > >  I
> > > > > > have seen this happen when more than one BioPerl instance is
> > > > installed
> > > > > > and `perl Makefile.PL` finds the wrong one first.  My
> > suggestion is
> > > > to
> > > > > > try reinstalling BioPerl and providing the --uninst 1 argument
> > to
> > > > > > remove
> > > > > > older versions of BioPerl:
> > > > > >
> > > > > >   sudo ./Build install --uninst 1
> > > > > >
> > > > > > Scott
> > > > > >
> > > > > >
> > > > > > On Tue, 2006-12-19 at 15:12 +0000, Sendu Bala wrote:
> > > > > > > Stephan Roessner wrote:
> > > > > > > > Dear support team,
> > > > > > > >
> > > > > > > > I installed bioperl 1.5.2_100 on a ferdora machine to be
> > able
> > > > to
> > > > > > use
> > > > > > > > gbrowse.
> > > > > > > > The installation seems to work (except of the test
> > failures)
> > > > but
> > > > > > the
> > > > > > > > gbrowse installation tells me that BIO::pERL 1.0050021 is
> > > > > > installed, but
> > > > > > > > of course it requires 1.52.
> > > > > > > >
> > > > > > > > Is there a chance to find out what went wrong?
> > > > > > >
> > > > > > > Nothing went wrong with the Bioperl installation (well,
> > expect
> > > > there
> > > > > > > shouldn't have been any test failures - can you post those
> > > > please?).
> > > > > > > gbrowse simply defined its Bioperl requirement incorrectly.
> > If
> > > > you
> > > > > > tell
> > > > > > > me exactly where you downloaded gbrowse from and how you
> > went
> > > > about
> > > > > > > installing it, and provide the exact, complete error message
> > you
> > > > got
> > > > > > > from it, I might be able help the authors fix the problem.
> > > > > > >
> > > > > > > Or I'm pretty sure they can figure it our for themselves :)
> > > > > > > _______________________________________________
> > > > > > > Bioperl-l mailing list
> > > > > > > Bioperl-l at lists.open-bio.org
> > > > > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > > > > > --
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > Scott Cain, Ph. D.
> > > > > > cain at cshl.edu
> > > > > > GMOD Coordinator (http://www.gmod.org/)
> > > > > > 216-392-3087
> > > > > > Cold Spring Harbor Laboratory
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > --
> > > >
> > ------------------------------------------------------------------------
> > > > Scott Cain, Ph. D.
> > > > cain.cshl at gmail.com
> > > > GMOD Coordinator (http://www.gmod.org/)
> > > > 216-392-3087
> > > > Cold Spring Harbor Laboratory
> > > >
> > > >
> > >
> > >
> > >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.
> > cain.cshl at gmail.com
> > GMOD Coordinator (http://www.gmod.org/)
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> >
> >
> 
> 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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