[Bioperl-l] Problems installing bioperl (bioperl-live tarball from CVS)

Sendu Bala bix at sendu.me.uk
Fri Nov 30 03:45:57 EST 2007


alison waller wrote:
> I would like to install the CVS version of bioperl  as I know of some code
> changes that will be useful to me.  However, I am having problems installing
> it.  
> 
> I am trying to install bioperl in my home directly on a linux cluster.  
[...]
> Please check, if the URLs I found in your configuration file
> (ftp://ftp.nrc.ca/pub/CPAN/, ftp://cpan.sunsite.ualberta.ca/pub/CPAN/,
> ftp://cpan.mirror.cygnal.ca/pub/CPAN/, ftp://mirror.isurf.ca/pub/CPAN) are
> valid. The urllist can be edited. E.g. with 'o conf urllist push
> ftp://myurl/'

Either these urls are invalid as suggested (try setting the urllist to 
nothing), or your linux cluster doesn't have internet access. You can't 
do a 'proper' install of BioPerl and its dependencies without internet 
access.

However, for most purposes simply downloading the BioPerl modules (ie. 
from a different machine with internet access) and pointing your 
PERL5LIB to their location is sufficient. You can download CVS modules 
from the BioPerl website individually, or as a tarball or everything.


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