[Bioperl-l] where to document dependency? AND new SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene

Chris Dagdigian Chris at bioteam.net
Mon Mar 20 18:24:32 EST 2006


Sure!
Any other dependencies that should be added or removed?

-Chris


On Mar 20, 2006, at 6:07 PM, Cook, Malcolm wrote:

> Chris Dagdigian,
>
> Convert::Binary::C is now used by new Bio::SeqIO::strider module.   
> I've
> added this to bioperl's ./MakeFile.PL and ./INSTALL.  Methinks it  
> could
> be added to Bundle::BioPerl.  Would you like to do that?
>
> --Malcolm Cook
>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Friday, March 10, 2006 4:59 PM
>> To: Cook, Malcolm; 'Brian Osborne'; bioperl-l at lists.open-bio.org
>> Subject: RE: [Bioperl-l] where to document dependency? AND new
>> SeqIO formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene
>>
>>
>>> -----Original Message-----
>>> From: Cook, Malcolm [mailto:MEC at stowers-institute.org]
>>> Sent: Friday, March 10, 2006 4:38 PM
>>> To: Chris Fields; Brian Osborne; bioperl-l at lists.open-bio.org
>>> Subject: RE: [Bioperl-l] where to document dependency? AND new SeqIO
>>> formats: Bio::SeqIO::strider and Bio::SeqIO::lasergene
>>>
>>> Getting closer...
>>>
>>> So, I added it to the ./Makefile.PL and ./INSTALL with the
>> cvs comment
>>> 'added dependency on Convert::Binary::C needed by
>> Bio::SeqIO::strider'
>>>
>>> But, re the wiki, it looks to me like the contents of the
>> wiki page are
>>> (nearly) identical to the ./INSTALL.  Is one autogenerated from the
>>> other, or do the both get editted?
>>
>> No, at least not at the moment.  I suppose we could get it
>> into POD and use
>> pod2wiki.
>>
>>> Also, the only place I can think to add the dependency in the wiki
>>> content is to the list of modules installed by Bundle::CPAN.  Am I
>>> missing something, or should I be considering adding
>> Convert::Binary::C
>>> to Bundle::CPAN as well?
>>
>> That's the place, though I think you mean Bundle::Bioperl.
>>
>> I'm not sure what you should do about including it with
>> Bundle::Bioperl.
>> Looks like Chris Dagdigian is the maintainer for that; his
>> email listed on
>> CPAN is dag at sonsorol.org, though I wouldn't be surprised if
>> it's out of
>> date.
>>
>>>
>>> Thanks,
>>>
>>> Malcolm
>>>
>>
>>
>>
>> Christopher Fields
>> Postdoctoral Researcher - Switzer Lab
>> Dept. of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>



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