[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
me.

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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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com


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