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

Chris Fields cjfields at illinois.edu
Tue Mar 15 11:45:20 EDT 2011

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, but
> maybe there is a new package that superseded it.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 getting 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 some changes:


Pjotr Prins is the lead on that, worth talking to.  The next big step is to interface with EMBOSS libraries, which is very promising.


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