[Bioperl-l] issues with installation in home directory

Rutger Vos rvos at interchange.ubc.ca
Wed Feb 10 11:55:58 EST 2010

There must be something wrong elsewhere in the script, is it possible
there's a typo further down the line? What you have here looks ok to

On Mon, Feb 8, 2010 at 11:31 PM, Sheri Simmons <sherisim at gmail.com> wrote:
> 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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Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
United Kingdom
Tel: +44 (0) 118 378 7535

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