[Bioperl-l] BioPerl, CPAN Modules, and Linux Packages

Robert Buels rmb32 at cornell.edu
Fri Feb 19 16:33:10 EST 2010

I certainly understand this, but running short on time.

In my opinion, the short answer is:  do one or the other, Debian 
packages or CPAN, not both.  Also, I always recommend that people use 
local::lib to install the dependencies needed for whatever it is they 
are deploying or experimenting with, doing everything as a regular user 
account.  Within SGN, the policy is 'never run cpan as root for anything 

If somebody else starts the page I can come along and edit.


Dave Clements wrote:
> Hello all,
> One question that came up at last month's GMOD meeting was "What are the
> best practices for mixing and matching CPAN modules and Linux packages?"
> Users can sometimes find a Perl module at both CPAN and as a Linux package.
> Sometimes, a module is only available from CPAN.  Installing a Linux package
> is generally much easier for novice users, but then users run the risk of
> their packages and CPAN modules interacting badly (don't they?).
> I've scanned the BioPerl site for guidance on when to go with CPAN and when
> to use a Linux package, but I can't find anything.  Would someone who
> understands this be willing to create a BioPerl.org page about when to chose
> what, and what problems might arise from mixed installations (and maybe even
> how to address them)?  The page could just be pointers to external pages
> that address this.
> Thanks,
> Dave C.

Robert Buels
Bioinformatics Analyst, Sol Genomics Network
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

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