[Bioperl-l] advice about bioperl-ext -- defunct?

Diego M. Vadell dvadell at clustering.com.ar
Tue Mar 15 16:01:22 UTC 2011

Hi Chris,

 Thank you! I will align with bioperl-run then, and keep an eye on biolib.

 -- Diego

----------------original message-----------------
From: "Chris Fields" cjfields at illinois.edu
To: "Diego M. Vadell" dvadell at clustering.com.ar
CC: bioperl-l at lists.open-bio.org
Date: Tue, 15 Mar 2011 10:45:20 -0500
> On Mar 15, 2011, at 9:59 AM, Diego M. Vadell wrote:
>> Hi,
>> I have just downloaded bioperl-ext from github, and it says "XS-based
>> BioPerl extensions to C libraries (defunct) — [Read more ->
>> https://github.com/bioperl/bioperl-ext#readme]" . I read the readme but 
>> it
>> looks alive ( i.e. no mention of an ending of the project ). 
>> I installed it ( adding "-fPIC" in the 3 Makefile.PLs ) and I'm about to
>> start using it. But, does is it still maintained? Is it still in use?
> Re: being maintained: No, except Bio::Tools::HMM 
> (https://github.com/bioperl/Bio-Tools-HMM)
> Re: in use: somewhat. I think some still use Bio::SeqIO::staden::read and 
> Bio::Ext::Align, but they haven't actively maintained in quite some time.
>> Recommended for a new project? I don't mind fixing compilation errors,
>> maybe there is a new package that superseded it. Maybe I'm downloading it
>> from the wrong place.
>> Regards,
>> -- Diego
> The code still works in some cases but is somewhat bit-rotted (I recall
> very inconsistent results from Bio::SearchUtils, not sure why). 
> We (Bio* projects) are starting to consolidate around using BioLib for 
> consistent bindings to C/C++ libraries, though that project is undergoing
> changes:
> http://biolib.open-bio.org/wiki/Main_Page
> Pjotr Prins is the lead on that, worth talking to. The next big step is to
> with EMBOSS libraries, which is very promising.
> chris

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