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

Mark Johnson johnsonm at gmail.com
Thu Jan 29 16:49:02 EST 2009


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 may be out of date, we've been getting license renewals, but I'm not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 Your gmhmmp package was out of date (the latest models I tested have the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.


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