[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network

Chris Fields cjfields at illinois.edu
Thu Jan 29 12:36:50 EST 2009


On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote:

> On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields  
> <cjfields at illinois.edu> wrote:
>> I believe BioPerl-db (if configured correctly) and BioPerl-network  
>> should
>> pass tests w/o problems.  However, I would like to gather as many  
>> test
>> results as possible from BioPerl users prior to a final release on  
>> CPAN,
>> particularly with BioPerl-run (I would like to make sure that tests  
>> for
>> wrappers are bypassed if the executable isn't present or an  
>> environment
>> variable isn't set).
>
> I have one issue with Genemark.hmm.prokaryotic.t.  It's trying to use
> Helicobacter_pylori_26695.mod, which I don't have.  Our gmhmmp package
> may be out of date, we've been getting license renewals, but I'm not
> sure we're running the latest and greatest code / models.  This test
> *used* to use Helicobacter_pylori.mod.  If I change it, the tests
> pass.  It looks like you changed the model in revision 15319.\

Your gmhmmp package was out of date (the latest models I tested have  
the extra strain designation).  I have made the tests a little more  
flexible in bioperl-run trunk so it checks for both versions, running  
the newer one first.

chris


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