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

[Robert Buels]

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