[Bioperl-l] Help installing BioPerl

Remo Sanges sanges at biogem.it
Mon Sep 13 14:04:01 EDT 2004

On Sep 13, 2004, at 7:47 PM, Michael Robeson wrote:

> Hmm, seems like I should just write things from scratch rather than 
> use BioPerl. Much less troubleshooting, ehh? Naa, I'd still rather try 
> installing/using BioPerl   :-)
> Sorry, about this but I am trying to learn. I am trying to follow 
> along with the "perl for bioinformatics" books but they are of no use 
> when it comes to trouble shooting bio::perl.

I' m not sure but it seems that you are triyng to install bioperl-run
before than bioperl, rigth?
They are two different packages and you should install them in
the rigth order...

if you perform a search in cpan you will find:

cpan> i /bioperl/
Bundle          Bundle::BioPerl 
Distribution    A/AL/ALLENDAY/bioperl-microarray-0.1.tar.gz
Distribution    B/BI/BIRNEY/bioperl-0.05.1.tar.gz
Distribution    B/BI/BIRNEY/bioperl-0.6.2.tar.gz
Distribution    B/BI/BIRNEY/bioperl-0.7.0.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.0.2.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.0.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.2.1.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.2.2.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.2.3.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.2.tar.gz
Distribution    B/BI/BIRNEY/bioperl-1.4.tar.gz
Distribution    B/BI/BIRNEY/bioperl-db-0.1.tar.gz
Distribution    B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
Distribution    B/BI/BIRNEY/bioperl-gui-0.7.tar.gz
Distribution    B/BI/BIRNEY/bioperl-run-1.2.2.tar.gz
Distribution    B/BI/BIRNEY/bioperl-run-1.4.tar.gz
Distribution    C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz
Module          Bio::LiveSeq::IO::BioPerl 

So you should install in this order:

- Bundle::BioPerl
- bioperl-1.4.tar.gz
and then
- bioperl-run-1.4.tar.gz

Consider always as a reference:

- the bioperl website http://bioperl.org/
- the bioperl tutorial 
- the bioperl how-to http://bioperl.org/HOWTOs/



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