[Bioperl-l] using BioPerl.ppd with ActiveState

[Kevin Clancy]

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

_______________________________________________
Bioperl-l mailing list
Bioperl-l at bioperl.org http://bioperl.org/mailman/listinfo/bioperl-l