[Bioperl-l] using BioPerl.ppd with ActiveState

[Jason Stajich]

We don't have anyone maintaining or dealing with PPM3, I'm not sure it
should even work with PPM3 as various people have reported bugs/problems
with this in the past.  AFAIK the ActiveState distro was really old and
the current distro on our site was only built for PPM and perl 5.6.1.

As I've posted before, we need a user/developer on windows to figure out
how things need to be setup for PPM3 and we'll be happy to give that
person an account on the server so that they can maintain the PPM3 bioperl
repository.

It would be a great service to the community since there are so many
windows users.

-jason

On Mon, 10 Mar 2003, Kevin Clancy wrote:

> Brian,
> Sorry ActiveState_Home was a shorthand for the path to the ActiveState
> folders. The path is actually correct. Thanks for the suggestion,
> though.
>
> What I have found is that some of the BioPerl builds in the various
> repositorues are usable and some are not. So the ppd distribution from
> the ActiveState repository is not usable in my hands, using either ppm
> or ppm3. For whatever reason, I cannot get it to be usable, despite
> giving fully qualified paths to the directory, pushing to the Perl5Lib
> variable, etc.
>
> The distribution from the bioperl site is usable. Using both ppm and
> ppm3 to install it was very smooth. So perhaps there is a problem with
> the various repository distributions of bioperl?
>
> kevin
>
> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: Sunday, March 09, 2003 4:06 PM
> To: Kevin Clancy; bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] using BioPerl.ppd with ActiveState
>
>
> Kevin,
>
> * The Bio folder is installed under ActiveState_Home\site\lib\Bio and
>
> So the actual name of the directory is "ActiveState_Home"? If so, then
> this location doesn't match @INC, and renaming it "ActiveState" should
> fix the problem.
>
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org
> [mailto:bioperl-l-bounces at bioperl.org]On
> Behalf Of Kevin Clancy
> Sent: Friday, March 07, 2003 6:44 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] using BioPerl.ppd with ActiveState
>
> Hi Folks
> I am using ActiveState Perl v5.6.1, binary build 633, built 21:33:05 Jun
> 17 2002 I have used ppm3 to load the latest bioperl distribution on the
> ActiveState repository site.
>
> >ppm3 describe bioperl
> ======================
> Name: bioperl
> Version: 1.2
> Author: Ewan Birney (birney at sanger.ac.uk)
> Title: bioperl
> Abstract: Bioinformatics Toolkit
> Location: Activestate PPM2 Repository
> Available Platforms:
>         1. i686-linux-thread-multi
>         2. MSWin32-x86-multi-thread
> ======================
>
> The Bio folder is installed under ActiveState_Home\site\lib\Bio and
> contains all the requirsite files. Everything appeared to have installed
> correctly.
>
> The @INC is set to $ACTIVESTATE_HOME/lib;$ACTIVESTATE_HOME/site/lib;.
>
> PERL5LIB is not set for the Windows box.
>
> I'm developing in Komodo and running the following script:
>
> #!/usr/bin/perl -w
> use strict;
> use Bio::SeqIO;
>
> my $in  = Bio::SeqIO->new('-file' => "inputfilename",
>                          '-format' => 'GenBank');
> my $out = Bio::SeqIO->new('-file' => ">outputfilename",
>                          '-format' => 'BSML');
> while ( my $seq = $in->next_seq() ) {
>     $out->write_seq($seq);
> }
>
> I get the following error message:
> Can't locate Bio/SeqIO.pm in @INC (@INC contains: E:\Program
> Files\Komodo-2.0 E:/Program Files/ActiveState/lib E:/Program
> Files/ActiveState/site/lib .) at
> E:\Projects\Perl\BioBus\DataConverter\DataConverter.pl line 4. BEGIN
> failed--compilation aborted at
> E:\Projects\Perl\BioBus\DataConverter\DataConverter.pl line 4.
>
> So I could always call the Bio::* distribution directly or copy the
> whole Bio:: distribution into my project folder, but I would prefer to
> fix the problem with Bio::* being recognised as being in the
> $ACTIVESTATE_HOME/site/lib path. Any suggestions on how to correct this?
> Thanks kevin
>
>
> Kevin Clancy, PhD
> Senior Bioinformatic Scientist
> InforMax, Inc.,
> 433 Park Point Drive,
> Suite 275,
> Golden, CO 80401
> Direct phone line: (720) 746 3707
> Cell Phone: (240) 417 8604
> Direct email: kclancy at informaxinc.com
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu