[Bioperl-l] Packaging bioperl for Fedora

Chris Fields cjfields at uiuc.edu
Tue Apr 17 10:35:10 EDT 2007

On Apr 17, 2007, at 8:54 AM, Alex Lancaster wrote:

> Hi all,
> Given that there seems to be a reasonable consensus (including list
> discussion here as well as in private e-mail) from bioperl folks that
> including bioperl in Fedora is OK, I'm going ahead and building
> bioperl for Fedora >= 6 (it's currently in the development branch).  I
> thought about the issue carefully and this seems to makes sense for
> several reasons:
> ...
> 2. Currently I've only run the the base bioperl (live) package through
>    the reviewing gauntlet, but I plan to add the bioperl-run package
>    as well.  Even though the bioperl-run package is intended to use
>    third party packages (e.g. Clustal etc.) which may not be
>    distributed with Fedora, it appears that the bioperl-run package
>    contains code that can download those packages directly (albeit
>    outside the RPM package system).  And some of the external tools
>    could be packaged in Fedora because they have open-source licenses
>    (e.g. Wise2, EMBOSS, NCBI toolkit etc.)

Do you mean the bioperl core modules instead of "bioperl-live"?  We  
use the term "bioperl-live" to designate code updated regularly via  
CVS, which can be buggy depending on when it's retrieved.

I'm not sure how others feel about this, but it's probably best to  
stick with either the latest official releases (v 1.5.2 at this time)  
or even GBrowse-sponsored interim releases (which fix GBrowse-related  
bugs and normally pass tests).


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