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

Florent Angly florent.angly at gmail.com
Sun Feb 21 22:44:13 EST 2010

I tend to install the modules that are available in the repositories for 
my Linux distribution. When a module is the repository is not available 
or too old, the best thing to do is to make a suitable package for it. 
For systems that use the Debian package system, I have started using 
The nice thing is that, when building the package, dh-make-perl will 
look for dependencies. Also, it is suitable for Perl modules that are on 
CPAN, but not exclusively.

On 20/02/10 04:57, 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.

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