[Bioperl-l] Packaging bioperl for Fedora

Chris Fields cjfields at uiuc.edu
Sat Mar 31 00:39:15 EDT 2007


On Mar 30, 2007, at 11:02 PM, Allen Day wrote:

> The majority of the Bioperl classes are file parsers, or manipulate
> data that comes from the file parsers.  Yes there are exceptions like
> the Eutils and Ensembl-intefacing classes, but they are the minority.
> The types of files that are worked with are generally either A)
> primary data sets such as genome data, or B) derivative data, such as
> sequence alignments that are derived from primary data using an
> algorithm.
>
> If we're in agreement that the primary data sets and
> libraries/applications for producing derivative data should not be
> present in Fedora Extras, then it follows that the Bioperl classes for
> manipulating these primary and derivative data  should also not be
> present in Fedora Extras as they are of little use without data to
> manipulate.
>
> -Allen

I respectfully disagree.  BioPerl, to me, is a toolkit which helps  
accomplish certain tasks.  As with any toolkit, not all parts are  
required to do what one needs.  A good number of end-users use  
BioPerl for remote database queries (Bio::DB::GenBank/Taxonomy/etc),  
remote BLAST, seq analysis, alignment analysis, phylogenetic tree  
manipulation, etc, none of which require outside apps be installed.   
For many a remote db is their primary source of data; not everybody  
sets up BioPerl for accessing local db records, running programs, etc  
(just the smart ones!).  As for outside apps, the docs are pretty  
explicit where certain outside resources (libxml2, expat, libgd) are  
needed for functionality.

When we package up a new release we generally have ActiveState PPM  
archives available for Win32 users who want an easy way to install  
BioPerl.  I wouldn't have a problem if ActiveState wanted to post  
these to their repository.  Why would allowing someone to do the same  
for fedora extras be any different?

chris

> On 3/30/07, Hilmar Lapp <hlapp at gmx.net> wrote:
>>
>> On Mar 30, 2007, at 8:30 PM, Allen Day wrote:
>>
>>> 2) academic packages, such as BLAT, NCBI Toolkit, CLUSTAL, genscan,
>>> etc. [...]
>>>
>>> 3) [...] Bioperl-live is not really that useful without type
>>> (2) packages.
>>
>> ?? Why's that?
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================



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