[Bioperl-l] Problems with Bioperl-ext package on WinVista?

[Chris Fields]

I say go for it if Yee Man is okay with the idea.  It gets the code  
out there that much faster.  This also doesn't depend on core being  
split up (only need a 'requires' bioperl 1.6.0).

chris

On Aug 17, 2009, at 10:48 AM, Robert Buels wrote:

> Also, I volunteer to make this branch and module machinery and such  
> if you want.  I just don't want to step on any ongoing development  
> you guys are going in the bioperl-ext trunk.
>
> If you want me to do it, just say the word, either here or in  
> #bioperl.
>
> Rob
>
> Robert Buels wrote:
>> Yee Man Chan wrote:
>>>    As to the release, my thinking is that I do understand that  
>>> your desire to maintain a high level of quality in BioPerl code  
>>> base. So if the HMM doesn't meet that standard, I am ok with it  
>>> being spinned off.
>> We're not pushing to spin it off because of code quality, we're  
>> pushing to spin it off because we're spinning everything off.  The  
>> plan is to break BioPerl up into many discrete distributions on  
>> CPAN with the dependencies between them well-known and codified.   
>> This will make maintenance of BioPerl *much* easier in the long run.
>> So this means that the plan of action should be
>>  1.) get the code so that it's working on all platforms,
>>  2.) create a CPAN distribution for it and put it on CPAN,
>>  3.) remove it from bioperl-ext
>> Also, doing a search for bioperl-ext on CPAN brings to light a  
>> couple of issues that probably need to be dealt with.  To wit:
>> 1.) there is an ancient version of bioperl-ext that probably needs  
>> to be removed, it's under ~birney's account.  Thoughts on this?
>> 2.) Bio::Tools::( dpAlign | HMM | pSW ) all state that they depend  
>> on bioperl-ext, which suggests that these really need to be split  
>> off, each with the Bio::Ext::Modules they depend on.   
>> Bio::Tools::HMM could be the first case of this:
>>   * make a dir in the repos called Bio-Tools-HMM alongside bioperl- 
>> live, having trunk/, and branches/ subdirs
>>   * move Bio::Tools::HMM out of bioperl-live into that
>>   * move Bio::Ext::HMM stuff out of bioperl-ext into that
>>   * repeat with Bio::Tools::dpAlign and pSW, which would probably
>>     go together into a Bio-Tools-Align distro, I think
>> Sounds like this is moving along nicely.
>> Rob
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>
>
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
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