[Bioperl-l] Packaging Bio::Ext::HMM for CPAN, was Re: Problems with Bioperl-ext package on WinVista?

[Chris Fields]

On Aug 18, 2009, at 11:37 PM, Robert Buels wrote:

> Yee Man Chan wrote:
>> Is it going to be an arrangement similar to bioconductor? If so, I  
>> suppose then it makes sense. But you might want to develop scripts  
>> to automatically download and install new modules to make it user  
>> friendly.
> Yes, we are probably going to make a Task::BioPerl or something  
> similar.
>
>> What do you mean by Bio-Ext is going away? I notice quite many  
>> people using dpAlign. So if Bio-Ext is going away, then at least  
>> dpAlign should become another spin off.
> By going away, I meant that everything in there is going to be  
> spinned off.  Except modules that are no longer maintainable, if  
> there are any in there.
>
> Rob

dpAlign could become another spinoff, yes, if it's used (and works  
fine).  The problematic code dealt with pSW, alignment statistics, and  
staden io_lib support (the latter which is fairly bit rotted now):

http://bugzilla.open-bio.org/show_bug.cgi?id=2668
http://bugzilla.open-bio.org/show_bug.cgi?id=1857
http://bugzilla.open-bio.org/show_bug.cgi?id=2069
http://bugzilla.open-bio.org/show_bug.cgi?id=2074
http://bugzilla.open-bio.org/show_bug.cgi?id=2329

dpAlign has it's own bug:

http://bugzilla.open-bio.org/show_bug.cgi?id=2384

chris