[Bioperl-l] installation bioperl

David Messina dmessina at wustl.edu
Mon Apr 2 12:19:51 EDT 2007

Hi Fahmi,

Please include the list on the reply so that others can comment, too.

Yes, it appears the machine you are installing on does not have an  
internet connection. You probably will want to resolve that problem  
before dealing with Bioperl. Alternatively, you could simply install  
and use Bioperl  on the machine which does have an internet connection.

If you really need to get Bioperl installed on that machine, however,  
probably the easiest way would be to find a machine that does have an  
internet connection, install CPAN::Mini, and use it to make a local  
mirror of CPAN. You could then copy that local mirror over to the  
machine without the internet connection and point that machine's cpan  
at the local mirror (read the CPAN documentation to find out how to  
do this). Also, the BioPerl install instructions list several  
external packages that you will need to use some parts of Bioperl  
(e.g. GD). Again, you can download those distributions using the  
machine with the internet connection and copy them over.


On Apr 2, 2007, at 9:22 AM, fahmi derbali wrote:

> thank you for answer. I will give you the maximum of informations  
> inorder to be able to diagnostic the problem:
> i use the linux mandriva 2006
> i'm traying to install bioperl-1.5.2_102.tar.gz which i obtained  
> from the url:
> http://www.bioperl.org/wiki/Release_1.5.2
> afetr that i made these commands which i found in the url
> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix (paragraph  
> >gunzip bioperl-1.5.2_102.tar.gz
> >tar xvf bioperl-1.5.2_102.tar
> >cd bioperl-1.5.2_102
> after that i made the command
> >perl Build.PL
> i obtained the text
> this package requires Module::Build v0.2805 or greater to install  
> itself
> install Module::Build now from CPAN?[y]
> i pushed enter and i obtained many lines such as
> System call"/usr/bin/wget -0-"ftp://.perl.org/pub/CPAN/modules/ 
> modlist.data.gz">home/fahmi/.cpan/sources/modules/03modlist.data
> Not connected
> cant access URL ftp://ftp.perl.org/CPAN/modules/modlist.data.gz
> ...
> i'm trying to install bioperl whithout having internet connection  
> beacause i don't know whay linux didn't detect my ethernet card.
> please tell me what should i do.
> tahnk you for your collaboration.

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