[Bioperl-l] using BioPerl.ppd with ActiveState

[Brian Osborne]

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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