[Bioperl-l] Packaging bioperl for Fedora

Sendu Bala bix at sendu.me.uk
Tue Apr 3 18:18:56 EDT 2007


Chris Fields wrote:
> 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.
>
> I respectfully disagree.

Likewise, but in a slightly different way: for myself and surely many 
others the primary data used either isn't publicly released or isn't in 
some major database and therefore won't be in any kind of repository. 
That doesn't mean I wouldn't want the parser for my files to be 
somewhere convenient.


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