[Bioperl-l] issues with installation in home directory

Mark A. Jensen maj at fortinbras.us
Wed Feb 10 11:55:43 EST 2010

Hi Sheri-- better send the whole script; error is
reminiscent of a typo bug.
----- Original Message ----- 
From: "Sheri Simmons" <sherisim at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Monday, February 08, 2010 6:31 PM
Subject: [Bioperl-l] issues with installation in home directory

> hi,
> Apologies for the stupid question, but I think I am missing something basic. I 
> installed Bioperl 1.6.1 in my home directory on a shared system and wrote a 
> simple fastq converter script with headers as follows:
> #!/usr/bin/perl -w
> #use strict;
> # program to convert FASTQ files generated with Illumina pipeline 1.3+ to 
> Sanger format FASTQ files
> use lib "/home/perl_modules/";
> use Bio::Perl;
> use Bio::SeqIO;
> However, when I run the script I get this error:
> Can't locate object method "FASTQ" via package "parser" (perhaps you forgot to 
> load "parser"?)
> What is the parser package referred to here? I have written lots of Bioperl 
> scripts and never seen this before, but I always used to use a system 
> installation of Bioperl.
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> Bioperl-l at lists.open-bio.org
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