[Bioperl-l] trouble with pairwise_kaks.PLS on Cygwin/XP platform

Brian Osborne osborne1 at optonline.net
Fri Sep 1 13:50:38 EDT 2006


Caleb,

I'm no longer using Cygwin so I'm simply guessing here - how about compiling
clustalw within Cygwin rather than using the Windows executable? In this
case you'd reset TMPDIR to '/tmp'. By the way, I don't think your problem
has to do with the value of TMPDIR, but recompiling is easy and may help
you.

Brian O.


On 9/1/06 12:48 PM, "Caleb Davis" <cdavis at bcm.tmc.edu> wrote:

> Brian,
> 
> I tried changing the tmpdir environmental variable using the different
> path formats you suggested, and the only one that works for the clustalw
> wrappers is the c:/cygwin/tmp type.  None of them execute the script all
> the way through...?
> 
> --Caleb
> 
> Brian Osborne wrote:
>> Caleb,
>> 
>> In Cygwin there are 3 possible formats for a given path. Examples:
>> 
>> /cygdrive/c/cygwin/tmp
>> c:/cygwin/tmp
>> /tmp
>> 
>> What works will depend on the application and how it was compiled. Have you
>> tried all variations?
>> 
>> Brian O.
>> 
>> 
>> On 8/31/06 8:00 PM, "Caleb F. Davis" <cdavis at bcm.tmc.edu> wrote:
>> 
>>   
>>> out why.  I'm guessing it has something to do with the tmpdir
>>> environmental variable and the differences between windows and unix
>>>     
>> 
>> 
>>   
> 
> 
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