[Bioperl-l] Fwd: Re: alignment by TCoffee as a subroutine

Chris Fields cjfields at uiuc.edu
Wed Apr 30 14:29:28 EDT 2008


Sorry, didn't catch that...

chris

On Apr 30, 2008, at 12:39 PM, Sergei Ryazansky wrote:

> On Wed, 30 Apr 2008 21:11:56 +0400, Sergei Ryazansky <dr.hogart at gmail.com 
> > wrote:
>
>> Oh, sorry, you right - I too fast read you message. I do it slight  
>> later.
>>
>>> Hmm, maybe you were confused?  From my last email:
>>>
>>> "The best way to handle this is to file a bug report, attaching  
>>> relevant data using the 'Create a new attachment' link (including  
>>> either the full script or a shortened one which demonstrates the  
>>> bug). Otherwise we're just shooting in the dark trying to diagnose  
>>> the problem."
>>>
>>> http://bugzilla.open-bio.org/
>>>
>>> Anyone can work on fixing the issue there (so it'll probably get  
>>> fixed faster).  The devs can also track progress on the problem  
>>> via the dev mail list (bioperl-guts).  Diagnosing the bug may also  
>>> reveal issues not just with Bio::Tools::Run::Alignment::TCoffee  
>>> but also with other related modules.
>>>
>>> If needed I can post it to bugzilla, but it helps to submit the  
>>> bug yourself (so you can receive posts on it's progress).
>>>
>>> chris
>>>
>>> On Apr 30, 2008, at 11:40 AM, Sergei Ryazansky wrote:
>>>
>>>> On Wed, 30 Apr 2008 20:25:06 +0400, Chris Fields  
>>>> <cjfields at uiuc.edu> wrote:
>>>>
>>>> Chris, I have already sent file to Sendu and also I am attaching  
>>>> it here. I have removed from it really unnecessary parts.
>>>>
>>>>> Sergei,
>>>>>
>>>>> I agree with Sendu; we can't diagnose this unless we either have  
>>>>> the entire script of a minimal version of it demonstrating the  
>>>>> bug.
>>>>>
>>>>> The best way to handle this is to file a bug report, attaching  
>>>>> relevant data using the 'Create a new attachment' link  
>>>>> (including either the full script or a shortened one which  
>>>>> demonstrates the bug). Otherwise we're just shooting in the dark  
>>>>> trying to diagnose the problem.
>>>>>
>>>>> http://bugzilla.open-bio.org/
>>>>>
>>>>> chris
>>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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