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

Chris Fields cjfields at illinois.edu
Thu Jan 29 20:13:31 EST 2009


On Jan 29, 2009, at 3:49 PM, Mark Johnson wrote:

> On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields  
> <cjfields at illinois.edu> wrote:
>> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote:
>>> 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 may be out of date, we've been getting license renewals, but I'm not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 Your gmhmmp package was out of date (the latest models I tested  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
>
> What version of gmhmmp do you have?  I'll have somebody on my end
> pester Gene Probe for an upgrade.


gmhmmp ver. 2.6p

Maybe my model is out-of-date; I got them from here:

http://exon.biology.gatech.edu/modelDownload.html

chris


More information about the Bioperl-l mailing list